diff options
| author |   Andrei Zavada <johnhommer@gmail.com> | 2015-06-17 02:31:45 +0300 |
|---|---|---|
| committer | Andrei Zavada <johnhommer@gmail.com> | 2015-06-17 02:31:45 +0300 |
| commit | fe50d2a782f3d44551fcbe34b9f91015916fc097 (patch) | |
| tree | ef955ab2a94cf5d4ed0eabc0eb490d70060cdfb3 | |
| parent | sci-biology/aghermann: new upstream version (diff) | |
| parent | Merge remote-tracking branch 'github/master' (diff) | |
| download | sci-fe50d2a782f3d44551fcbe34b9f91015916fc097.tar.gz sci-fe50d2a782f3d44551fcbe34b9f91015916fc097.tar.bz2 sci-fe50d2a782f3d44551fcbe34b9f91015916fc097.zip | |
Merge branch 'master' of github.com:gentoo-science/sci
1629 files changed, 21347 insertions, 22862 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog index 29de45c0d..79d1aacfc 100644 --- a/app-admin/eselect/ChangeLog +++ b/app-admin/eselect/ChangeLog @@ -2,6 +2,27 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $ +*eselect-1.4.4-r102 (06 Jun 2015) + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r102.ebuild, + -eselect-1.4.4-r100.ebuild, -eselect-1.4.4-r101.ebuild, + -files/eselect-1.4.2-alternatives.patch, + files/eselect-1.4.4-alternatives.patch: + app-admin/eselect: Add latest patch + +*eselect-1.4.4-r101 (24 May 2015) + + 24 May 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r101.ebuild, + +files/eselect-1.4.4-alternatives.patch: + app-admin/eselect: Latest patch + + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> -eselect-1.3.7-r100.ebuild, + -eselect-1.3.8-r100.ebuild, -eselect-1.4-r100.ebuild, + -eselect-1.4.1-r100.ebuild, -eselect-1.4.2-r100.ebuild, + -eselect-1.4.3-r100.ebuild, -files/eselect-1.3.8-alternatives.patch, + -files/eselect-alternatives.patch: + app-admin/eselect: Drop old + *eselect-1.4.4-r100 (26 Jan 2015) 26 Jan 2015; Justin Lecher <jlec@gentoo.org> +eselect-1.4.4-r100.ebuild: diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest index 316fc2686..c77de7fb1 100644 --- a/app-admin/eselect/Manifest +++ b/app-admin/eselect/Manifest @@ -1,7 +1 @@ -DIST eselect-1.3.7.tar.xz 166596 SHA256 68b3c9cf3f71633ca81c4d0edd64a77e02dc8d6b9a48641e59f0bf02378a0075 SHA512 909d79d76f144181895853ce132147daeee4ba6caf05bf08963aef147ef2d00be100d6181887d139614f1bebf15f0738ea58e755656b55b7d9d967d399ce72f0 WHIRLPOOL 82d7575e8bbcb2186ef1452e3edb07b7c242c4d14475da0c5867acc70d275e5fb9e166a2b0addb54fb3586eddabcf1eec1e208964db5489e4250bf1f8ad39468 -DIST eselect-1.3.8.tar.xz 168040 SHA256 d0c50bfe0faaddc54fc184f698ee74a6029a21f5155c4670a2bea3ead954c138 SHA512 159bf3ddb05b1966318eaf62d09e454a024f8be7ead2300392abbcbaa54ef748a1c4db1b2f96162994bcab43071396eb96a0b47268f04cb8557f8804818da18e WHIRLPOOL 9c4da0bde2ae2b53e8949d59b13498f55ef2c849dcc8cac503a7d0dda2511311d94dfc7aa27a97432f13aa0b430fec0ab280594dc165bbb40e573dce8c8a74b0 -DIST eselect-1.4.1.tar.xz 168616 SHA256 c60eb7e3b6eea36560ea16f8378de3c86926988a1eee3e6dd98c12f0340869c0 SHA512 c6754c3bb71efda36b807f2275aff0cc7bf5c3f58cbc7543b8255592940dae341e4b597ff1376b0997c37bcd0b736d813630b9fe4a4da2f85765217d8634deab WHIRLPOOL a9fb2dc6904c57878c744f70f0bd66a18b574eec04f042fa5ab60f608f31a0c90554153f3362c633742bb9918cb14f146269e0972cdf97998c60c236ae966f66 -DIST eselect-1.4.2.tar.xz 169036 SHA256 b3aef6a41c8f85f2f4b50204f0713b40586e8443965005c5fc2510218e359fc3 SHA512 d453ece6a06c6328dd3662520e7eba32ad8d10feeb6826d1f3e9c69c2f6b260e1872e0e9b5f1fc272b5d5a59145855a330454889306798808765f7530f4f4736 WHIRLPOOL 9322d5fe7085ffac7497d3f517860a5ba173edae86d4d058d0f4930ea1872712245ff094b777f0171d71d01ea38be3158614f358cf1923ceb6fbe0f735414503 -DIST eselect-1.4.3.tar.xz 169400 SHA256 eea297658235321727f174aca841fccd31ec1ec044519c6b74fd5f7f168a3faf SHA512 5c4468745cb3d8da731fcd9c0ad3897270b01b337fd33cb06f5523d71d5ceb03be01eb10dd624522700e23175462a87ebb9e84e58a250b1938981dc0d5b39595 WHIRLPOOL 3788f77082abb55bd4d07317fd08688522c059e95d7ae7c6958bc40e7ef9bbced996e909e4bb3fc367585b212d93bff950ca2072907e0a06ef8330cdbec53256 DIST eselect-1.4.4.tar.xz 177536 SHA256 120c123eae4a1d03515e94f9efd51af6ff2f09340daf1ada4dc21079df7a937f SHA512 1ed01cf00e3f13aad3e5f844c7086c3dd48398efd76e68cd91cf13b9939f4b48eef8915c5f3926954d158023115ad66ee67c0bc8fc4c9570900a37207674fc8f WHIRLPOOL e56c3ea3e54bdbcfffba3fbbe85b3c824cab796a0bae2680fac962356a2f707783571a9f73e0ea8299098838e593bea77b14edbeaadc372f186c2da2928e9ab5 -DIST eselect-1.4.tar.xz 168580 SHA256 38f457567ac6a400763e49c215a78d5a7efc3edad589dda37bbd70847e3e7260 SHA512 4c28df99d3a235ccda60cb576634cde6110d3b7bc2fb7b8e3e9a69f7e09377dd9a5c615d6bf0ab8d668c137e8f658484fd28c0fe45e6ad3b7915925a3384b999 WHIRLPOOL 6646c023283b111bf7a973993dfe8537bdd3fab4c6c738af1f37c1aed1bddefbf834562036386dce1359d1b04da89049e7c60e4498733ac56587e037ca0ea87f diff --git a/app-admin/eselect/eselect-1.3.7-r100.ebuild b/app-admin/eselect/eselect-1.3.7-r100.ebuild deleted file mode 100644 index 6be213339..000000000 --- a/app-admin/eselect/eselect-1.3.7-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="mirror://gentoo/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.3.8-r100.ebuild b/app-admin/eselect/eselect-1.3.8-r100.ebuild deleted file mode 100644 index 700374b30..000000000 --- a/app-admin/eselect/eselect-1.3.8-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="mirror://gentoo/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${P}-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4-r100.ebuild b/app-admin/eselect/eselect-1.4-r100.ebuild deleted file mode 100644 index e4d9a6f86..000000000 --- a/app-admin/eselect/eselect-1.4-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-1.3.8-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.1-r100.ebuild b/app-admin/eselect/eselect-1.4.1-r100.ebuild deleted file mode 100644 index e4d9a6f86..000000000 --- a/app-admin/eselect/eselect-1.4.1-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-1.3.8-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.2-r100.ebuild b/app-admin/eselect/eselect-1.4.2-r100.ebuild deleted file mode 100644 index 3fb583fee..000000000 --- a/app-admin/eselect/eselect-1.4.2-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${P}-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.3-r100.ebuild b/app-admin/eselect/eselect-1.4.3-r100.ebuild deleted file mode 100644 index 5af5f877b..000000000 --- a/app-admin/eselect/eselect-1.4.3-r100.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools eutils bash-completion-r1 - -DESCRIPTION="Gentoo's multi-purpose configuration and management tool" -HOMEPAGE="http://wiki.gentoo.org/wiki/Project:Eselect" -SRC_URI="http://dev.gentoo.org/~ulm/eselect/${P}.tar.xz" - -LICENSE="GPL-2+ || ( GPL-2+ CC-BY-SA-2.5 )" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~sparc-fbsd ~x86-fbsd ~x64-freebsd ~x86-freebsd ~hppa-hpux ~ia64-hpux ~x86-interix ~amd64-linux ~arm-linux ~ia64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~m68k-mint ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="doc emacs vim-syntax" - -RDEPEND="sys-apps/sed - || ( - sys-apps/coreutils - sys-freebsd/freebsd-bin - app-misc/realpath - )" -DEPEND="${RDEPEND} - app-arch/xz-utils - doc? ( dev-python/docutils )" -RDEPEND="!app-admin/eselect-news - ${RDEPEND} - sys-apps/file - sys-libs/ncurses" - -PDEPEND="emacs? ( app-emacs/eselect-mode ) - vim-syntax? ( app-vim/eselect-syntax )" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-1.4.2-alternatives.patch - AT_M4DIR="." eautoreconf -} - -src_compile() { - emake - use doc && emake html -} - -src_install() { - emake DESTDIR="${D}" install - newbashcomp misc/${PN}.bashcomp ${PN} - dodoc AUTHORS ChangeLog NEWS README TODO doc/*.txt - use doc && dohtml *.html doc/* - - # needed by news module - keepdir /var/lib/gentoo/news - if ! use prefix; then - fowners root:portage /var/lib/gentoo/news - fperms g+w /var/lib/gentoo/news - fi - - # band aid for prefix - if use prefix; then - cd "${ED}"/usr/share/eselect/libs - sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die - fi -} - -pkg_postinst() { - # fowners in src_install doesn't work for the portage group: - # merging changes the group back to root - if ! use prefix; then - chgrp portage "${EROOT}/var/lib/gentoo/news" \ - && chmod g+w "${EROOT}/var/lib/gentoo/news" - fi -} diff --git a/app-admin/eselect/eselect-1.4.4-r100.ebuild b/app-admin/eselect/eselect-1.4.4-r102.ebuild index 02730fa03..67b835c52 100644 --- a/app-admin/eselect/eselect-1.4.4-r100.ebuild +++ b/app-admin/eselect/eselect-1.4.4-r102.ebuild @@ -33,7 +33,7 @@ PDEPEND="emacs? ( app-emacs/eselect-mode ) vim-syntax? ( app-vim/eselect-syntax )" src_prepare() { - epatch "${FILESDIR}"/${PN}-1.4.2-alternatives.patch + epatch "${FILESDIR}"/${P}-alternatives.patch AT_M4DIR="." eautoreconf } @@ -57,7 +57,7 @@ src_install() { # band aid for prefix if use prefix; then - cd "${ED}"/usr/share/eselect/libs + cd "${ED}"/usr/share/eselect/libs || die sed -i "s:ALTERNATIVESDIR_ROOTLESS=\"${EPREFIX}:ALTERNATIVESDIR_ROOTLESS=\":" alternatives.bash || die fi } diff --git a/app-admin/eselect/files/eselect-1.3.8-alternatives.patch b/app-admin/eselect/files/eselect-1.3.8-alternatives.patch deleted file mode 100644 index 1e3b0ea77..000000000 --- a/app-admin/eselect/files/eselect-1.3.8-alternatives.patch +++ /dev/null @@ -1,616 +0,0 @@ -Index: bin/eselect.in -=================================================================== ---- bin/eselect.in (revision 863) -+++ bin/eselect.in (working copy) -@@ -22,10 +22,15 @@ - # Where are modules installed by default? - ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" - -+# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) -+ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" -+ - # Look in these places for modules --ESELECT_MODULES_PATH=( \ -- "${HOME}/.eselect/modules" \ -- "${ESELECT_DEFAULT_MODULES_PATH}" ) -+ESELECT_MODULES_PATH=( -+ "${HOME}/.eselect/modules" -+ "${ESELECT_DEFAULT_MODULES_PATH}" -+ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" -+) - - # Look in this place for libraries - ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" ---- bin/Makefile.am.orig 2013-09-02 14:35:05.328684465 +0400 -+++ bin/Makefile.am 2013-09-02 14:49:50.895842067 +0400 -@@ -4,6 +4,7 @@ - dosed = @SED@ -e 's,\@BASH\@,$(BASH),g' \ - -e 's,\@DATADIR\@,$(datadir),g' \ - -e 's,\@EPREFIX\@,$(EPREFIX),g' \ -+ -e 's,\@LIBEXECDIR\@,$(datadir),g' \ - -e 's,\@VERSION\@,$(VERSION)$(EXTRAVERSION),g' - - % : %.in -Index: libs/Makefile.am -=================================================================== ---- libs/Makefile.am (revision 863) -+++ libs/Makefile.am (working copy) -@@ -1,6 +1,7 @@ - eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ - - eselectlibs_DATA = \ -+ alternatives.bash \ - config.bash \ - core.bash \ - default.eselect \ -@@ -14,6 +15,7 @@ - tests.bash - - EXTRA_DIST = \ -+ alternatives.bash.in \ - config.bash.in \ - core.bash.in \ - default.eselect.in \ -@@ -30,7 +32,8 @@ - -e 's,\@SED\@,@SED@,g' \ - -e 's,\@PORTAGEQ\@,@PORTAGEQ@,g' \ - -e 's,\@ENV_UPDATE\@,@ENV_UPDATE@,g' \ -- -e 's,\@CANONICALISE\@,@CANONICALISE@,g' -+ -e 's,\@CANONICALISE\@,@CANONICALISE@,g' \ -+ -e 's,\@sysconfdir\@,@sysconfdir@,g' - - %.bash : %.bash.in - @$(dosed) $< > $@ ---- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 -+++ libs/alternatives.bash.in 2011-09-06 18:55:43.000000000 +0100 -@@ -0,0 +1,550 @@ -+# Copyright 2008 Mike Kelly -+# Copyright 2009 David Leverton -+# Copyright 2010 Bo Ørsted Andresen -+# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) -+# Distributed under the terms of the GNU General Public License v2 -+ -+inherit config output path-manipulation -+ -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" -+ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" -+ -+get_current_provider() { -+ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") -+ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" -+ -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || -+ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" -+ fi -+ -+ echo "${provider}" -+ -+ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" -+ fi -+} -+ -+compare_importance() { -+ local IFS=. -+ local a=( ${1} ) b=( ${2} ) -+ local -i i=0 -+ while (( i<${#a[@]} && i<${#b[@]} )); do -+ if (( a[i]<b[i] )); then -+ return 0 -+ elif (( a[i]>b[i] )); then -+ return 1 -+ fi -+ i+=1 -+ done -+ (( i<${#b[@]} )) -+} -+ -+sort_providers() { -+ local begin=${1:-0} -+ local count=${2:-${#providers[@]}} -+ [[ ${count} -le 1 ]] && return 0 -+ sort_providers ${begin} $((count/2)) -+ sort_providers $((begin+count/2)) $((count-count/2)) -+ local left=( "${providers[@]:begin:count/2}" ) -+ local right=( "${providers[@]:begin+count/2:count-count/2}" ) -+ local -i x i=0 j=0 -+ for (( x=begin; x<begin+count; ++x )); do -+ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then -+ providers[x]=${left[i++]} -+ else -+ providers[x]=${right[j++]} -+ fi -+ done -+} -+ -+get_providers() { -+ local p= importance providers=() -+ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do -+ [[ -d ${p} && ! -L ${p} ]] || continue -+ p=${p##*/} -+ -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") -+ importance=${importance:-0} -+ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" -+ -+ providers+=( "${importance}:${p}" ) -+ done -+ -+ sort_providers -+ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do -+ echo "${providers[p]#*:}" -+ done -+} -+ -+### show action ### -+describe_show() { -+ echo "Show the current provider in use for ${ALTERNATIVE}" -+} -+ -+do_show() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local current="$(get_current_provider)" -+ if [[ -z "${current}" ]] ; then -+ echo "(none)" -+ return 2 -+ fi -+ echo "${current}" -+} -+ -+options_show() { -+ : -+} -+ -+### list action ### -+describe_list() { -+ echo "Lists all available providers for ${ALTERNATIVE}" -+} -+ -+do_list() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local n cur= providers=( $(get_providers) ) -+ write_list_start "Available providers for ${ALTERNATIVE}:" -+ -+ cur="$(get_current_provider)" -+ -+ if [[ -n "${providers[@]}" ]] ; then -+ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do -+ [[ ${cur} == "${providers[${n}]}" ]] && \ -+ providers[${n}]="${providers[${n}]} $(highlight '*')" -+ done -+ write_numbered_list "${providers[@]}" -+ else -+ write_kv_list_entry "(none found)" "" -+ fi -+} -+ -+options_list() { -+ : -+} -+ -+### files action ### -+describe_files() { -+ echo "Lists symlinks provided by the currently selected provider" -+} -+ -+do_files() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" -+ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" -+ -+ local errors symlink rootsymlink -+ while read -r -d '' symlink; do -+ rootsymlink="${EROOT}${symlink}" -+ rootsymlink=${rootsymlink//+(\/)/\/} -+ echo "${rootsymlink}" -+ if [[ -L ${rootsymlink} ]]; then -+ if [[ ! -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is dangling symlink" -+ errors=yes -+ fi -+ elif [[ -d ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is a directory" -+ errors=yes -+ elif [[ -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} exists but is not a symlink" -+ errors=yes -+ else -+ write_error_msg "${rootsymlink} does not exist" -+ errors=yes -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+} -+ -+options_files() { -+ : -+} -+ -+### set action ### -+ -+describe_set() { -+ echo "Sets a provider for ${ALTERNATIVE}" -+} -+ -+describe_set_parameters() { -+ echo "[ --force ] <provider>" -+} -+ -+describe_set_options() { -+ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" -+ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" -+} -+ -+do_set() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force provider providers -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local symlink newsymlinks=() oldsymlinks=() -+ -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink#.} -+ nicesymlink=${nicesymlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" -+ -+ newsymlinks+=( "${nicesymlink}" ) -+ done < <( -+ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" -+ find . -type l -print0 | LC_ALL=C sort -r -u -z) -+ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" -+ -+ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ -+ oldsymlinks+=( "${nicesymlink}" ) -+ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") -+ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" -+ -+ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" -+ fi -+ -+ local pass errors= -+ for pass in check perform; do -+ local -i new_i=0 old_i=0 -+ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do -+ -+ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then -+ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ old_i+=1 -+ -+ else -+ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} -+ while [[ -n ${dir} ]]; do -+ target=../${target} -+ dir=${dir%/*} -+ done -+ -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then -+ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" -+ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 -+ new_i+=1 -+ fi -+ done -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ local oldcur="$(get_current_provider)" -+ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" -+ -+ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" -+ for symlink in "${newsymlinks[@]}"; do -+ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" -+ done -+ return 0 -+} -+ -+_options_parameters() { -+ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" -+ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS -+ if is_function ${describe_func}; then -+ IFS=$'\n' -+ options=( $(${describe_func}) ) -+ IFS=$oldifs -+ for opt in "${options[@]}"; do -+ [[ ${opt} == --* ]] || continue -+ if [[ -n ${descriptions} ]]; then -+ echo "${opt/ : /:}" -+ else -+ echo "${opt%% : *}" -+ fi -+ done -+ fi -+} -+ -+options_set() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### update action ### -+ -+describe_update() { -+ echo "Set a default provider if no valid one currently exists" -+} -+ -+describe_update_parameters() { -+ echo "[--ignore] <provider>" -+} -+ -+describe_update_options() { -+ echo "--ignore : update to any valid provider EXCEPT the specified provider" -+ echo "<provider> : the name of the provider to use" -+} -+ -+do_update() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore -+ if [[ "--ignore" == ${1} ]] ; then -+ # Try everything except setting the provider to the given -+ # one. So, if it isn't the given one, we end up doing -+ # nothing. Bug #128 -+ shift -+ ignore=${1} -+ fi -+ -+ if [[ ${cur} == ${1} && -z ${ignore} ]]; then -+ # if current provider was just updated, reselect it since it could have changed -+ do_set "${cur}" && return 0 -+ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then -+ # verify existing provider's symlinks -+ local p= bad=0 -+ while read -r -d '' p ; do -+ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) -+ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ "${bad}" -eq 0 ]] && return 0 -+ # fix existing provider if possible -+ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 -+ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then -+ # switch to new provider if none was set before or it can't be fixed -+ do_set "${1}" && return 0 -+ fi -+ -+ # if no valid provider has been selected switch to first available, valid -+ # provider, sorted according to importance -+ for p in "${providers[@]}"; do -+ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 -+ done -+ -+ # if a provider is set but no providers are available anymore cleanup -+ cur=$(get_current_provider) -+ if [[ -n ${cur} ]]; then -+ do_unset "${cur}" && return 2 -+ fi -+ # if no provider is set and none are available that are not ignored, return 2 for cleanup -+ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 -+ -+ # we tried everything to select a valid provider, but failed -+ return 1 -+} -+ -+options_update() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### unset action ### -+ -+describe_unset() { -+ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." -+} -+ -+describe_unset_parameters() { -+ echo "[ --force ]" -+} -+ -+describe_unset_options() { -+ echo "--force : remove existing non-symlink files (but not directories) if necessary" -+} -+ -+do_unset() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force= -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "Nothing to unset" -+ local dieprefix="Could not unset provider for ${ALTERNATIVE}" -+ -+ local one=false symlink pass errors= -+ for pass in check perform; do -+ while read -r -d '' symlink; do -+ one=true -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${symlink} ]]; then -+ : -+ elif [[ -d ${EROOT}${symlink} ]]; then -+ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${symlink} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ ${one} || die "${dieprefix}: does not provide any symlinks?" -+ -+ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" -+} -+ -+options_unset() { -+ _options_parameters $FUNCNAME "$@" -+ get_current_provider -+} -+ -+### script action ### -+ -+describe_script() { -+ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" -+} -+ -+describe_script_parameters() { -+ echo "[--sh | --csh] [<provider>]" -+} -+ -+describe_script_options() { -+ echo "--sh : use Bourne shell syntax (default)" -+ echo "--csh : use C shell syntax" -+ echo "<provider> : the provider to use or the index of the provider preceeded by a dash (if not specified, use the system default)" -+} -+ -+do_script() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local syntax=sh provider providers -+ if [[ ${1} == --sh ]]; then -+ shift -+ elif [[ ${1} == --csh ]]; then -+ syntax=csh -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local variables=( PATH LD_LIBRARY_PATH MANPATH ) -+ [[ -n ${!default_*} ]] && local ${!default_*} -+ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib -+ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) -+ -+ local var IFS=: -+ for var in "${variables[@]}"; do -+ local defvar=default_${var} path paths=( ) -+ for path in ${!var}; do -+ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue -+ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ paths+=( "${path}" ) -+ done -+ -+ [[ -n ${provider} ]] && for path in ${!defvar}; do -+ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ done -+ -+ local newval=${paths[*]} -+ if [[ ${newval} != ${!var} ]]; then -+ newval=${newval//\'/\'\\\'\'} -+ if [[ ${syntax} == sh ]]; then -+ echo "${var}='${newval}'; export ${var}" -+ else -+ echo "setenv ${var} '${newval}'" -+ fi -+ fi -+ done -+} -+ -+options_script() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch b/app-admin/eselect/files/eselect-1.4.2-alternatives.patch deleted file mode 100644 index 3f4a34bcf..000000000 --- a/app-admin/eselect/files/eselect-1.4.2-alternatives.patch +++ /dev/null @@ -1,616 +0,0 @@ -Index: bin/eselect.in -=================================================================== ---- bin/eselect.in (revision 863) -+++ bin/eselect.in (working copy) -@@ -22,10 +22,15 @@ - # Where are modules installed by default? - ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" - -+# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) -+ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" -+ - # Look in these places for modules --ESELECT_MODULES_PATH=( \ -- "${HOME}/.eselect/modules" \ -- "${ESELECT_DEFAULT_MODULES_PATH}" ) -+ESELECT_MODULES_PATH=( -+ "${HOME}/.eselect/modules" -+ "${ESELECT_DEFAULT_MODULES_PATH}" -+ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" -+) - - # Look in this place for libraries - ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" ---- bin/Makefile.am.orig 2013-09-02 14:35:05.328684465 +0400 -+++ bin/Makefile.am 2013-09-02 14:49:50.895842067 +0400 -@@ -4,6 +4,7 @@ - dosed = @SED@ -e 's%\@BASH\@%$(BASH)%g' \ - -e 's%\@DATADIR\@%$(datadir)%g' \ - -e 's%\@EPREFIX\@%$(EPREFIX)%g' \ -+ -e 's%\@LIBEXECDIR\@%$(datadir)%g' \ - -e 's%\@VERSION\@%$(VERSION)$(EXTRAVERSION)%g' - - % : %.in -Index: libs/Makefile.am -=================================================================== ---- libs/Makefile.am (revision 863) -+++ libs/Makefile.am (working copy) -@@ -1,6 +1,7 @@ - eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ - - eselectlibs_DATA = \ -+ alternatives.bash \ - config.bash \ - core.bash \ - default.eselect \ -@@ -14,6 +15,7 @@ - tests.bash - - EXTRA_DIST = \ -+ alternatives.bash.in \ - config.bash.in \ - core.bash.in \ - default.eselect.in \ -@@ -30,7 +32,8 @@ - -e 's%\@SED\@%@SED@%g' \ - -e 's%\@PORTAGEQ\@%@PORTAGEQ@%g' \ - -e 's%\@ENV_UPDATE\@%@ENV_UPDATE@%g' \ -- -e 's%\@CANONICALISE\@%@CANONICALISE@%g' -+ -e 's%\@CANONICALISE\@%@CANONICALISE@%g' \ -+ -e 's%\@sysconfdir\@%@sysconfdir@%g' - - %.bash : %.bash.in - @$(dosed) $< > $@ ---- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 -+++ libs/alternatives.bash.in 2011-09-06 18:55:43.000000000 +0100 -@@ -0,0 +1,550 @@ -+# Copyright 2008 Mike Kelly -+# Copyright 2009 David Leverton -+# Copyright 2010 Bo Ørsted Andresen -+# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) -+# Distributed under the terms of the GNU General Public License v2 -+ -+inherit config output path-manipulation -+ -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" -+ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" -+ -+get_current_provider() { -+ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") -+ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" -+ -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || -+ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" -+ fi -+ -+ echo "${provider}" -+ -+ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" -+ fi -+} -+ -+compare_importance() { -+ local IFS=. -+ local a=( ${1} ) b=( ${2} ) -+ local -i i=0 -+ while (( i<${#a[@]} && i<${#b[@]} )); do -+ if (( a[i]<b[i] )); then -+ return 0 -+ elif (( a[i]>b[i] )); then -+ return 1 -+ fi -+ i+=1 -+ done -+ (( i<${#b[@]} )) -+} -+ -+sort_providers() { -+ local begin=${1:-0} -+ local count=${2:-${#providers[@]}} -+ [[ ${count} -le 1 ]] && return 0 -+ sort_providers ${begin} $((count/2)) -+ sort_providers $((begin+count/2)) $((count-count/2)) -+ local left=( "${providers[@]:begin:count/2}" ) -+ local right=( "${providers[@]:begin+count/2:count-count/2}" ) -+ local -i x i=0 j=0 -+ for (( x=begin; x<begin+count; ++x )); do -+ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then -+ providers[x]=${left[i++]} -+ else -+ providers[x]=${right[j++]} -+ fi -+ done -+} -+ -+get_providers() { -+ local p= importance providers=() -+ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do -+ [[ -d ${p} && ! -L ${p} ]] || continue -+ p=${p##*/} -+ -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") -+ importance=${importance:-0} -+ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" -+ -+ providers+=( "${importance}:${p}" ) -+ done -+ -+ sort_providers -+ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do -+ echo "${providers[p]#*:}" -+ done -+} -+ -+### show action ### -+describe_show() { -+ echo "Show the current provider in use for ${ALTERNATIVE}" -+} -+ -+do_show() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local current="$(get_current_provider)" -+ if [[ -z "${current}" ]] ; then -+ echo "(none)" -+ return 2 -+ fi -+ echo "${current}" -+} -+ -+options_show() { -+ : -+} -+ -+### list action ### -+describe_list() { -+ echo "Lists all available providers for ${ALTERNATIVE}" -+} -+ -+do_list() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local n cur= providers=( $(get_providers) ) -+ write_list_start "Available providers for ${ALTERNATIVE}:" -+ -+ cur="$(get_current_provider)" -+ -+ if [[ -n "${providers[@]}" ]] ; then -+ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do -+ [[ ${cur} == "${providers[${n}]}" ]] && \ -+ providers[${n}]="${providers[${n}]} $(highlight '*')" -+ done -+ write_numbered_list "${providers[@]}" -+ else -+ write_kv_list_entry "(none found)" "" -+ fi -+} -+ -+options_list() { -+ : -+} -+ -+### files action ### -+describe_files() { -+ echo "Lists symlinks provided by the currently selected provider" -+} -+ -+do_files() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" -+ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" -+ -+ local errors symlink rootsymlink -+ while read -r -d '' symlink; do -+ rootsymlink="${EROOT}${symlink}" -+ rootsymlink=${rootsymlink//+(\/)/\/} -+ echo "${rootsymlink}" -+ if [[ -L ${rootsymlink} ]]; then -+ if [[ ! -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is dangling symlink" -+ errors=yes -+ fi -+ elif [[ -d ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is a directory" -+ errors=yes -+ elif [[ -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} exists but is not a symlink" -+ errors=yes -+ else -+ write_error_msg "${rootsymlink} does not exist" -+ errors=yes -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+} -+ -+options_files() { -+ : -+} -+ -+### set action ### -+ -+describe_set() { -+ echo "Sets a provider for ${ALTERNATIVE}" -+} -+ -+describe_set_parameters() { -+ echo "[ --force ] <provider>" -+} -+ -+describe_set_options() { -+ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" -+ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" -+} -+ -+do_set() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force provider providers -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local symlink newsymlinks=() oldsymlinks=() -+ -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink#.} -+ nicesymlink=${nicesymlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" -+ -+ newsymlinks+=( "${nicesymlink}" ) -+ done < <( -+ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" -+ find . -type l -print0 | LC_ALL=C sort -r -u -z) -+ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" -+ -+ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ -+ oldsymlinks+=( "${nicesymlink}" ) -+ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") -+ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" -+ -+ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" -+ fi -+ -+ local pass errors= -+ for pass in check perform; do -+ local -i new_i=0 old_i=0 -+ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do -+ -+ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then -+ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ old_i+=1 -+ -+ else -+ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} -+ while [[ -n ${dir} ]]; do -+ target=../${target} -+ dir=${dir%/*} -+ done -+ -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then -+ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" -+ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 -+ new_i+=1 -+ fi -+ done -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ local oldcur="$(get_current_provider)" -+ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" -+ -+ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" -+ for symlink in "${newsymlinks[@]}"; do -+ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" -+ done -+ return 0 -+} -+ -+_options_parameters() { -+ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" -+ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS -+ if is_function ${describe_func}; then -+ IFS=$'\n' -+ options=( $(${describe_func}) ) -+ IFS=$oldifs -+ for opt in "${options[@]}"; do -+ [[ ${opt} == --* ]] || continue -+ if [[ -n ${descriptions} ]]; then -+ echo "${opt/ : /:}" -+ else -+ echo "${opt%% : *}" -+ fi -+ done -+ fi -+} -+ -+options_set() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### update action ### -+ -+describe_update() { -+ echo "Set a default provider if no valid one currently exists" -+} -+ -+describe_update_parameters() { -+ echo "[--ignore] <provider>" -+} -+ -+describe_update_options() { -+ echo "--ignore : update to any valid provider EXCEPT the specified provider" -+ echo "<provider> : the name of the provider to use" -+} -+ -+do_update() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore -+ if [[ "--ignore" == ${1} ]] ; then -+ # Try everything except setting the provider to the given -+ # one. So, if it isn't the given one, we end up doing -+ # nothing. Bug #128 -+ shift -+ ignore=${1} -+ fi -+ -+ if [[ ${cur} == ${1} && -z ${ignore} ]]; then -+ # if current provider was just updated, reselect it since it could have changed -+ do_set "${cur}" && return 0 -+ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then -+ # verify existing provider's symlinks -+ local p= bad=0 -+ while read -r -d '' p ; do -+ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) -+ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ "${bad}" -eq 0 ]] && return 0 -+ # fix existing provider if possible -+ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 -+ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then -+ # switch to new provider if none was set before or it can't be fixed -+ do_set "${1}" && return 0 -+ fi -+ -+ # if no valid provider has been selected switch to first available, valid -+ # provider, sorted according to importance -+ for p in "${providers[@]}"; do -+ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 -+ done -+ -+ # if a provider is set but no providers are available anymore cleanup -+ cur=$(get_current_provider) -+ if [[ -n ${cur} ]]; then -+ do_unset "${cur}" && return 2 -+ fi -+ # if no provider is set and none are available that are not ignored, return 2 for cleanup -+ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 -+ -+ # we tried everything to select a valid provider, but failed -+ return 1 -+} -+ -+options_update() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### unset action ### -+ -+describe_unset() { -+ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." -+} -+ -+describe_unset_parameters() { -+ echo "[ --force ]" -+} -+ -+describe_unset_options() { -+ echo "--force : remove existing non-symlink files (but not directories) if necessary" -+} -+ -+do_unset() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force= -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "Nothing to unset" -+ local dieprefix="Could not unset provider for ${ALTERNATIVE}" -+ -+ local one=false symlink pass errors= -+ for pass in check perform; do -+ while read -r -d '' symlink; do -+ one=true -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${symlink} ]]; then -+ : -+ elif [[ -d ${EROOT}${symlink} ]]; then -+ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${symlink} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ ${one} || die "${dieprefix}: does not provide any symlinks?" -+ -+ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" -+} -+ -+options_unset() { -+ _options_parameters $FUNCNAME "$@" -+ get_current_provider -+} -+ -+### script action ### -+ -+describe_script() { -+ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" -+} -+ -+describe_script_parameters() { -+ echo "[--sh | --csh] [<provider>]" -+} -+ -+describe_script_options() { -+ echo "--sh : use Bourne shell syntax (default)" -+ echo "--csh : use C shell syntax" -+ echo "<provider> : the provider to use or the index of the provider preceeded by a dash (if not specified, use the system default)" -+} -+ -+do_script() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local syntax=sh provider providers -+ if [[ ${1} == --sh ]]; then -+ shift -+ elif [[ ${1} == --csh ]]; then -+ syntax=csh -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local variables=( PATH LD_LIBRARY_PATH MANPATH ) -+ [[ -n ${!default_*} ]] && local ${!default_*} -+ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib -+ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) -+ -+ local var IFS=: -+ for var in "${variables[@]}"; do -+ local defvar=default_${var} path paths=( ) -+ for path in ${!var}; do -+ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue -+ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ paths+=( "${path}" ) -+ done -+ -+ [[ -n ${provider} ]] && for path in ${!defvar}; do -+ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ done -+ -+ local newval=${paths[*]} -+ if [[ ${newval} != ${!var} ]]; then -+ newval=${newval//\'/\'\\\'\'} -+ if [[ ${syntax} == sh ]]; then -+ echo "${var}='${newval}'; export ${var}" -+ else -+ echo "setenv ${var} '${newval}'" -+ fi -+ fi -+ done -+} -+ -+options_script() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-admin/eselect/files/eselect-1.4.4-alternatives.patch b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch new file mode 100644 index 000000000..b2b943274 --- /dev/null +++ b/app-admin/eselect/files/eselect-1.4.4-alternatives.patch @@ -0,0 +1,1496 @@ +diff --git a/bin/eselect.in b/bin/eselect.in +index 934a10a..7c1c14b 100755 +--- a/bin/eselect.in ++++ b/bin/eselect.in +@@ -22,10 +22,15 @@ ESELECT_DATA_PATH="@DATADIR@/eselect" + # Where are modules installed by default? + ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" + ++# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) ++ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" ++ + # Look in these places for modules +-ESELECT_MODULES_PATH=( \ +- "${HOME}/.eselect/modules" \ +- "${ESELECT_DEFAULT_MODULES_PATH}" ) ++ESELECT_MODULES_PATH=( ++ "${HOME}/.eselect/modules" ++ "${ESELECT_DEFAULT_MODULES_PATH}" ++ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++) + + # Look in this place for libraries + ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" +@@ -64,12 +69,27 @@ fi + # Load core functions + source "${ESELECT_CORE_PATH}/core.bash" || exit 255 + # Load necessary functions for the main script +-inherit manip output path-manipulation tests ++inherit manip output path-manipulation tests config + + # Sneaky trick to make die in subshells work. If you don't get + # it, don't ask... + trap 'echo "exiting" >&2; exit 250' 15 + ++# es_find_module foo ++# Find and echo the filename of the foo module. If there's no foo module, ++# die. ++es_find_module() { ++ local modname="$1" modpath="" modfile="" ++ [[ -z ${modname} ]] && die "Usage: ${FUNCNAME} <module>" ++ for modpath in "${ESELECT_MODULES_PATH[@]}" ; do ++ [[ -f ${modpath}/${modname}.eselect ]] && break ++ done ++ ++ modfile="${modpath}/${modname}.eselect" ++ [[ -r ${modfile} ]] || die -q "Can't load module ${modname}" ++ echo ${modfile} ++} ++ + # es_do_usage + # Display eselect usage + es_do_usage() { +@@ -81,14 +101,10 @@ es_do_usage() { + es_do_help() { + es_do_usage + echo +- # display all recognized global options +- write_list_start "Global options:" +- write_kv_list_entry "--brief" "Make output shorter" +- write_kv_list_entry "--colour=<yes|no|auto>" \ +- "Enable or disable colour output (default 'auto')" ++ es_do_list-options + echo + # display all available eselect modules +- do_action modules list ++ es_do_list-modules + } + + # es_do_version +@@ -100,6 +116,114 @@ es_do_version() { + echo "Distributed under the terms of the GNU GPL version 2 or later." + } + ++# es_do_list-options ++# Display all recognized global options ++es_do_list-options() { ++ write_list_start "Global options:" ++ write_kv_list_entry "--brief" "Make output shorter" ++ write_kv_list_entry "--colour=<yes|no|auto>" "Enable or disable colour output (default 'auto')" ++ write_kv_list_entry "--debug" "Debug eselect (enable set -x)" ++} ++ ++# es_do_list-modules ++# Display all available eselect modules DEPRECATED ++es_do_list-modules() { ++ do_action modules list $@ ++} ++ ++### print-* actions, for use with bash_completion and zsh-completion ### ++ ++# es_do_print-modules ++# ++# Display all availble eselect modules in a way that's useful to bash ++# completion / zsh completion ++es_do_print-modules() { ++ local ret=1 path module group groupname want_descriptions ++ ++ while [[ -n $@ ]]; do ++ case "${1}" in ++ --descriptions) ++ want_descriptions='yes' ;; ++ --group) ++ groupname=${2} ++ [[ -z "$groupname" ]] && die -q "Required option (group name) missing." ++ shift ;; ++ esac ++ shift ++ done ++ ++ if [[ ${groupname} == Built-in || -z ${groupname} ]]; then ++ for module in help usage version print-{modules,actions,options}; do ++ echo "${module}" ++ done ++ [[ ${groupname} == Built-in ]] && return 0 ++ fi ++ ++ # TODO: factor this out in modules.eselect's do_list() ++ for path in "${ESELECT_MODULES_PATH[@]}" ; do ++ [[ -d "${path}" ]] || continue ++ for file in "${path}"/*.eselect ; do ++ [[ -f "${file}" ]] || continue ++ if [[ -n "${groupname}" ]]; then ++ group=$(load_config "${file}" ESELECT_MODULE_GROUP) ++ [[ "${groupname}" == "${group}" || ++ ( "${groupname}" == Extra && -z "${group}" ) ]] || continue ++ fi ++ module="${file##*/}" ++ module="${module%%.eselect}" ++ echo "${module}${want_descriptions:+:$(load_config "${file}" DESCRIPTION)}" ++ ret=0 ++ done ++ done ++ return $ret ++} ++ ++# es_do_print-actions ++# ++# Display all available actions for the given module. ++es_do_print-actions() { ++ local modfile="$(es_find_module "${1}")" actions action want_descriptions ++ [[ "${2}" == "--descriptions" ]] && want_descriptions='yes' ++ ( ++ source "${modfile}" 2>/dev/null \ ++ || die "Couldn't source ${modfile}" ++ actions=( $(declare -F \ ++ | sed -n -e 's/^declare\s\+-f\s\+do_//p' \ ++ | egrep -v '^(action|help|usage|version)$' \ ++ | sort ) ) ++ for action in "${actions[@]}" ; do ++ echo "${action}${want_descriptions:+:$(describe_${action})}" ++ done ++ ) ++} ++ ++# es_do_print-options ++# ++# Display all available options for the given module and action ++es_do_print-options() { ++ local modfile action want_descriptions ++ ++ [[ "${1}" == "--descriptions" ]] && want_descriptions='yes' && shift ++ ++ if [[ -z ${1} ]]; then ++ echo "--debug${want_descriptions:+:Debug eselect (enable set -x)}" ++ echo "--no-color${want_descriptions:+:Disable coloured output}" ++ echo "--no-colour${want_descriptions:+:Disable coloured output}" ++ elif [[ -n ${2} ]]; then ++ modfile="$(es_find_module "${1}")" ++ action=${2} ++ shift 2 ++ ( ++ source "${modfile}" 2>/dev/null \ ++ || die "Couldn't source ${modfile}" ++ is_function options_${action} || return 1 ++ options_${action} ${want_descriptions:+--descriptions} "$@" || return 2 ++ ) ++ else ++ die "Usage: ${FUNCNAME} [--descriptions] [<module> <action>]" ++ fi ++} ++ + ### main code ### + + # figure out what the action is. we need to know whether we're +@@ -141,6 +265,9 @@ while [[ ${1##--} != "$1" ]]; do + *) die -q "Invalid argument for ${1%%=*} option" ;; + esac + ;; ++ debug) ++ set -x ++ ;; + help|version) + [[ -z ${action} ]] || die -q "Too many parameters" + action=${1##--} +diff --git a/libs/Makefile.am b/libs/Makefile.am +index 027ef73..a5fe373 100644 +--- a/libs/Makefile.am ++++ b/libs/Makefile.am +@@ -1,6 +1,8 @@ + eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ + + eselectlibs_DATA = \ ++ alternatives.bash \ ++ alternatives-common.bash \ + config.bash \ + core.bash \ + default.eselect \ +@@ -14,6 +16,8 @@ eselectlibs_DATA = \ + tests.bash + + EXTRA_DIST = \ ++ alternatives.bash.in \ ++ alternatives-common.bash.in \ + config.bash.in \ + core.bash.in \ + default.eselect.in \ +@@ -30,7 +34,8 @@ dosed = @SED@ \ + -e 's%\@SED\@%@SED@%g' \ + -e 's%\@PORTAGEQ\@%@PORTAGEQ@%g' \ + -e 's%\@ENV_UPDATE\@%@ENV_UPDATE@%g' \ +- -e 's%\@CANONICALISE\@%@CANONICALISE@%g' ++ -e 's%\@CANONICALISE\@%@CANONICALISE@%g' \ ++ -e 's%\@sysconfdir\@%@sysconfdir@%g' + + %.bash : %.bash.in + @$(dosed) $< > $@ +diff --git a/libs/alternatives-common.bash.in b/libs/alternatives-common.bash.in +new file mode 100644 +index 0000000..64d74df +--- /dev/null ++++ b/libs/alternatives-common.bash.in +@@ -0,0 +1,488 @@ ++# Copyright 2015 Gentoo Foundation ++# Copyright 2008 Mike Kelly ++# Copyright 2009, 2013 David Leverton ++# Copyright 2010 Bo Ørsted Andresen ++# Distributed under the terms of the GNU General Public License v2 ++ ++inherit config output path-manipulation ++ ++: "${ALTERNATIVESDIR_ROOTLESS:=@sysconfdir@/env.d/alternatives}" ++ALTERNATIVESDIR="${EROOT%/}${ALTERNATIVESDIR_ROOTLESS}" ++ ++get_current_provider() { ++ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") ++ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" ++ ++ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || ++ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" ++ fi ++ ++ echo "${provider}" ++ ++ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" ++ fi ++} ++ ++compare_importance() { ++ local IFS=. ++ local a=( ${1} ) b=( ${2} ) ++ local -i i=0 ++ while (( i<${#a[@]} && i<${#b[@]} )); do ++ if (( a[i]<b[i] )); then ++ return 0 ++ elif (( a[i]>b[i] )); then ++ return 1 ++ fi ++ i+=1 ++ done ++ (( i<${#b[@]} )) ++} ++ ++sort_providers() { ++ local begin=${1:-0} ++ local count=${2:-${#providers[@]}} ++ [[ ${count} -le 1 ]] && return 0 ++ sort_providers ${begin} $((count/2)) ++ sort_providers $((begin+count/2)) $((count-count/2)) ++ local left=( "${providers[@]:begin:count/2}" ) ++ local right=( "${providers[@]:begin+count/2:count-count/2}" ) ++ local -i x i=0 j=0 ++ for (( x=begin; x<begin+count; ++x )); do ++ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then ++ providers[x]=${left[i++]} ++ else ++ providers[x]=${right[j++]} ++ fi ++ done ++} ++ ++get_providers() { ++ local p= importance providers=() ++ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do ++ [[ -d ${p} && ! -L ${p} ]] || continue ++ p=${p##*/} ++ ++ [[ -e "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance" ]] && ++ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") ++ importance=${importance:-0} ++ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" ++ ++ providers+=( "${importance}:${p}" ) ++ done ++ ++ sort_providers ++ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do ++ echo "${providers[p]#*:}" ++ done ++} ++ ++_options_parameters() { ++ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" ++ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS ++ if is_function ${describe_func}; then ++ IFS=$'\n' ++ options=( $(${describe_func}) ) ++ IFS=$oldifs ++ for opt in "${options[@]}"; do ++ [[ ${opt} == --* ]] || continue ++ if [[ -n ${descriptions} ]]; then ++ echo "${opt/ : /:}" ++ else ++ echo "${opt%% : *}" ++ fi ++ done ++ fi ++} ++ ++### set action stub ### ++ ++# not available in "eselect alternatives", but needed by do_update ++ ++alternatives_do_set() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force provider providers ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ local idx=${1} ++ if [[ ${1} == +(-|+|[[:digit:]]) ]]; then ++ idx=${1#+(-|+)} ++ providers=( $(get_providers) ) ++ (( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist" ++ provider=${providers[${idx}-1]} ++ else ++ provider="${1}" ++ fi ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" ++ ++ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then ++ if is_number ${provider} ; then ++ providers=( $(get_providers) ) ++ [[ -n ${providers[${idx}-1]} ]] && \ ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ ++ local symlink newsymlinks=() oldsymlinks=() ++ ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink#.} ++ nicesymlink=${nicesymlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" ++ ++ newsymlinks+=( "${nicesymlink}" ) ++ done < <( ++ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" ++ find . -type l -print0 | LC_ALL=C sort -r -u -z) ++ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" ++ ++ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ while read -r -d '' symlink; do ++ local nicesymlink=${symlink//+(\/)/\/} ++ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" ++ ++ oldsymlinks+=( "${nicesymlink}" ) ++ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") ++ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" ++ ++ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then ++ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" ++ fi ++ ++ local pass errors= ++ for pass in check perform; do ++ local -i new_i=0 old_i=0 ++ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do ++ ++ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT%/}${oldsymlinks[old_i]} ]]; then ++ : ++ elif [[ -d ${EROOT%/}${oldsymlinks[old_i]} ]]; then ++ write_error_msg "Can't remove ${EROOT%/}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT%/}${oldsymlinks[old_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT%/}${oldsymlinks[old_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT%/}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${EROOT%/}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ old_i+=1 ++ ++ else ++ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} ++ while [[ -n ${dir} ]]; do ++ target=../${target} ++ dir=${dir%/*} ++ done ++ ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT%/}${newsymlinks[new_i]} ]]; then ++ : ++ elif [[ -d ${EROOT%/}${newsymlinks[new_i]} ]]; then ++ write_error_msg "Can't overwrite ${EROOT%/}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT%/}${newsymlinks[new_i]} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Overwriting ${EROOT%/}${newsymlinks[new_i]} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to overwrite ${EROOT%/}${newsymlinks[new_i]}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ mkdir -p "${EROOT%/}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" ++ ln -snf "${target#/}" "${EROOT%/}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ ++ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 ++ new_i+=1 ++ fi ++ done ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ local oldcur="$(get_current_provider)" ++ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" ++ ++ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" ++ for symlink in "${newsymlinks[@]}"; do ++ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" ++ done ++ return 0 ++} ++ ++### add action ### ++alternatives_describe_add() { ++ echo "Add provider to selected alternative" ++} ++ ++alternatives_describe_add_parameters() { ++ echo "<provider> <importance> <source> <target> [<source> <target> [...]]" ++} ++ ++alternatives_describe_add_options() { ++ echo "<provider> : the name of the alternative provider" ++ echo "<importance> : interger value, representing the importance of the provider" ++ echo "<source> : source of the symlink" ++ echo "<target> : destination for the symlink" ++} ++ ++alternatives_do_add() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ (( $# >= 4 )) && (( ($#-2)%2 == 0)) || \ ++ die "exactly 3+N*2 arguments where N>=1 required" ++ local provider=${1} ++ local importance=${2} ++ shift 2 ++ local index src target ret=0 ++ local provider_dir="${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ++ ++ # Creating base dir ++ if [[ ! -e "${provider_dir}" ]]; then ++ mkdir -p "${provider_dir}" || die "Failed to create ${provider_dir}" ++ elif [[ ! -d "${provider_dir}" ]]; then ++ die "${provider_dir} exists but is a file" ++ else ++ die "${provider_dir} already present. You need ot remove it before adding it again" ++ fi ++ ++ # Make sure importance is a signed integer ++ if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then ++ die "Invalid importance (${importance}) detected" ++ else ++ # Setting importance ++ echo ${importance} > "${provider_dir}/_importance" ++ fi ++ ++ # Process source-target pairs ++ while (( $# >= 2 )); do ++ src=${1//+(\/)/\/}; target=${2//+(\/)/\/} ++ if [[ ${src} != /* ]]; then ++ die "Source path must be absolute, but got ${src}" ++ else ++ local reltarget= dir=${provider_dir}${src%/*} ++ while [[ -n ${dir} ]]; do ++ reltarget+=../ ++ dir=${dir%/*} ++ done ++ ++ reltarget=${reltarget%/} ++ [[ ${target} == /* ]] || reltarget+=${src%/*}/ ++ reltarget+=${target} ++ mkdir -p "${provider_dir}${src%/*}" || die "Failed to create ${provider_dir}${src%/*}" ++ ln -sf "${reltarget}" "${provider_dir}${src}" || die "Failed to create symlink" ++ # The -e test will fail if existing symlink points to non-existing target, ++ # so check for -L also. ++ # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). ++# if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then ++# local fulltarget=${target} ++# [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} ++# if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then ++# die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" ++# else ++# mv "${ED}${src}" "${ED}${fulltarget}" || die ++# fi ++# fi ++ fi ++ shift 2 ++ done ++} ++ ++alternatives_options_add() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ ++### remove action ### ++ ++alternatives_describe_remove() { ++ echo "Remove a provider for selected alternative" ++} ++ ++alternatives_describe_remove_parameters() { ++ echo "<provider>" ++} ++ ++alternatives_describe_remove_options() { ++ echo "<provider> : the name of the alternative provider to be removed" ++} ++ ++alternatives_do_remove() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ if [[ -d "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" ]]; then ++ rm -r "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || \ ++ die "Failed to remove '${provider}' for '${ALTERNATIVE}'" ++ else ++ einfo "'${provider}' is not a provider for '${ALTERNATIVE}'" ++ fi ++} ++ ++alternatives_options_remove() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++} ++ ++### update action ### ++ ++# available in both "eselect alternatives" and individual modules ++ ++alternatives_describe_update() { ++ echo "Set a default provider if no valid one currently exists" ++} ++ ++alternatives_describe_update_parameters() { ++ echo "[--best] [--ignore] <provider>" ++} ++ ++alternatives_describe_update_options() { ++ echo "--best : update to the best provider even if one is already selected" ++ echo "--ignore : update to any valid provider EXCEPT the specified provider" ++ echo "<provider> : the name of the provider to use" ++} ++ ++alternatives_do_update() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local p cur=$(get_current_provider) providers=( $(get_providers) ) best ignore ++ if [[ "--best" == ${1} ]] ; then ++ shift ++ best=1 ++ fi ++ if [[ "--ignore" == ${1} ]] ; then ++ # Try everything except setting the provider to the given ++ # one. So, if it isn't the given one, we end up doing ++ # nothing. Bug #128 ++ shift ++ ignore=${1} ++ fi ++ [[ -n ${best} && -n ${1} && -z ${ignore} ]] && die -q "Cannot specify both --best and a provider" ++ ++ if [[ -n ${best} ]] ; then ++ # set best provider ++ : # fall through to "switch to first available" loop below ++ elif [[ $# == "0" ]] && [[ -z ${cur} ]]; then ++ # if nothing is specified ++ : # fall through to "switch to first available" loop below ++ elif [[ ${cur} == ${1} && -z ${ignore} ]]; then ++ # if current provider was just updated, reselect it since it could have changed ++ alternatives_do_set "${cur}" && return 0 ++ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then ++ # verify existing provider's symlinks ++ local p= bad=0 ++ while read -r -d '' p ; do ++ [[ -L "${EROOT%/}${p}" && -e "${EROOT%/}${p}" ]] || (( bad++ )) ++ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ "${bad}" -eq 0 ]] && return 0 ++ # fix existing provider if possible ++ has "${cur}" "${providers[@]}" && alternatives_do_set "${cur}" && return 0 ++ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then ++ # switch to new provider if none was set before or it can't be fixed ++ alternatives_do_set "${1}" && return 0 ++ fi ++ ++ # if no valid provider has been selected switch to first available, valid ++ # provider, sorted according to importance ++ for p in "${providers[@]}"; do ++ [[ ${ignore} != ${p} ]] && alternatives_do_set "${p}" && return 0 ++ done ++ ++ # if a provider is set but no providers are available anymore cleanup ++ cur=$(get_current_provider) ++ if [[ -n ${cur} ]]; then ++ alternatives_do_unset "${cur}" && return 2 ++ fi ++ # if no provider is set and none are available that are not ignored, return 2 for cleanup ++ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 ++ ++ # we tried everything to select a valid provider, but failed ++ return 1 ++} ++ ++alternatives_options_update() { ++ _options_parameters ${FUNCNAME#alternatives_} "$@" ++ if [[ -n ${ALTERNATIVE} ]]; then ++ get_providers ++ else ++ for alt in ${ALTERNATIVESDIR_ROOTLESS}/_*/*/_importance; do ++ echo ${alt} | cut -d/ -f5 ++ done | sort -u ++ fi ++} ++ ++### unset action stub ### ++ ++# not available in "eselect alternatives", but needed by do_update ++ ++alternatives_do_unset() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local force= ++ if [[ ${1} == --force ]]; then ++ force=yes ++ shift ++ fi ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "Nothing to unset" ++ local dieprefix="Could not unset provider for ${ALTERNATIVE}" ++ ++ local one=false symlink pass errors= ++ for pass in check perform; do ++ while read -r -d '' symlink; do ++ one=true ++ if [[ ${pass} == check ]]; then ++ if [[ -L ${EROOT%/}${symlink} ]]; then ++ : ++ elif [[ -d ${EROOT%/}${symlink} ]]; then ++ write_error_msg "Can't remove ${EROOT%/}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" ++ errors=yes ++ elif [[ -e ${EROOT%/}${symlink} ]]; then ++ if [[ -n ${force} ]]; then ++ write_warning_msg "Removing ${EROOT%/}${symlink} due to --force: is not a symlink" ++ else ++ write_error_msg "Refusing to remove ${EROOT%/}${symlink}: is not a symlink (use --force to override)" ++ errors=yes ++ fi ++ fi ++ ++ elif [[ ${pass} == perform ]]; then ++ rm -f "${EROOT%/}${symlink}" || die "${dieprefix}: rm failed" ++ else ++ die "${dieprefix}: unknown \${pass} ${pass}???" ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++ ++ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" ++ done ++ ++ ${one} || die "${dieprefix}: does not provide any symlinks?" ++ ++ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" ++} ++ ++# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : +diff --git a/libs/alternatives.bash.in b/libs/alternatives.bash.in +new file mode 100644 +index 0000000..1b5a2b0 +--- /dev/null ++++ b/libs/alternatives.bash.in +@@ -0,0 +1,293 @@ ++# Copyright 2015 Gentoo Foundation ++# Copyright 2008 Mike Kelly ++# Copyright 2009, 2013 David Leverton ++# Copyright 2010 Bo Ørsted Andresen ++# Distributed under the terms of the GNU General Public License v2 ++ ++inherit alternatives-common ++ ++### show action ### ++describe_show() { ++ echo "Show the current provider in use for ${ALTERNATIVE}" ++} ++ ++do_show() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local current="$(get_current_provider)" ++ if [[ -z "${current}" ]] ; then ++ echo "(none)" ++ return 2 ++ fi ++ echo "${current}" ++} ++ ++options_show() { ++ : ++} ++ ++### list action ### ++describe_list() { ++ echo "Lists all available providers for ${ALTERNATIVE}" ++} ++ ++do_list() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local n cur= providers=( $(get_providers) ) ++ write_list_start "Available providers for ${ALTERNATIVE}:" ++ ++ cur="$(get_current_provider)" ++ ++ if [[ -n "${providers[@]}" ]] ; then ++ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do ++ [[ ${cur} == "${providers[${n}]}" ]] && \ ++ providers[${n}]="${providers[${n}]} $(highlight '*')" ++ done ++ write_numbered_list "${providers[@]}" ++ else ++ write_kv_list_entry "(none found)" "" ++ fi ++} ++ ++options_list() { ++ : ++} ++ ++### files action ### ++describe_files() { ++ echo "Lists symlinks provided by the currently selected provider" ++} ++ ++do_files() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ ++ local cur="$(get_current_provider)" p= ++ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" ++ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" ++ ++ local errors symlink rootsymlink ++ while read -r -d '' symlink; do ++ rootsymlink="${EROOT%/}${symlink}" ++ rootsymlink=${rootsymlink//+(\/)/\/} ++ echo "${rootsymlink}" ++ if [[ -L ${rootsymlink} ]]; then ++ if [[ ! -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is dangling symlink" ++ errors=yes ++ fi ++ elif [[ -d ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} is a directory" ++ errors=yes ++ elif [[ -e ${rootsymlink} ]]; then ++ write_error_msg "${rootsymlink} exists but is not a symlink" ++ errors=yes ++ else ++ write_error_msg "${rootsymlink} does not exist" ++ errors=yes ++ fi ++ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" ++} ++ ++options_files() { ++ : ++} ++ ++### set action ### ++ ++describe_set() { ++ echo "Sets a provider for ${ALTERNATIVE}" ++} ++ ++describe_set_parameters() { ++ echo "[ --force ] <provider>" ++} ++ ++describe_set_options() { ++ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" ++ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" ++} ++ ++do_set() { ++ # implementation defined in alternatives-common.bash as needed by do_update ++ alternatives_do_set "$@" ++} ++ ++options_set() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ alternatives_describe_add_parameters ++} ++ ++describe_add_options() { ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ alternatives_do_add ++ ++ # make sure we have something selected ++ eselect ${provider} show > /dev/null || eselect ${provider} update --best ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ alternatives_describe_remove_parameters ++} ++ ++describe_remove_options() { ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ alternatives_do_remove ++ ++# if no provider is present, remove whole Alternative ++ if ! eselect ${provider} update --best > /dev/null; then ++ eselect alternatives remove ${ALTERNATIVE} ++ fi ++} ++ ++### update action ### ++ ++# all functions implemented in alternatives-common.bash as defined for ++# both "eselect alternatives" and individual modules ++ ++describe_update() { ++ alternatives_describe_update ++} ++ ++describe_update_parameters() { ++ alternatives_describe_update_parameters ++} ++ ++describe_update_options() { ++ alternatives_describe_update_options ++} ++ ++do_update() { ++ alternatives_do_update "$@" ++} ++ ++options_update() { ++ alternatives_options_update ++} ++ ++### unset action ### ++ ++describe_unset() { ++ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." ++} ++ ++describe_unset_parameters() { ++ echo "[ --force ]" ++} ++ ++describe_unset_options() { ++ echo "--force : remove existing non-symlink files (but not directories) if necessary" ++} ++ ++do_unset() { ++ # implementation defined in alternatives-common.bash as needed by do_update ++ alternatives_do_unset "$@" ++} ++ ++options_unset() { ++ _options_parameters $FUNCNAME "$@" ++ get_current_provider ++} ++ ++### script action ### ++ ++describe_script() { ++ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" ++} ++ ++describe_script_parameters() { ++ echo "[--sh | --csh] [<provider>]" ++} ++ ++describe_script_options() { ++ echo "--sh : use Bourne shell syntax (default)" ++ echo "--csh : use C shell syntax" ++ echo "<provider> : the provider to use or the index of the provider (if not specified, use the system default)" ++} ++ ++do_script() { ++ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" ++ local syntax=sh provider providers ++ if [[ ${1} == --sh ]]; then ++ shift ++ elif [[ ${1} == --csh ]]; then ++ syntax=csh ++ shift ++ fi ++ ++ local idx=${!} ++ if [[ ${idx} == +(-|+|[[:digit:]]) ]]; then ++ idx=${1#+(-|+)} ++ providers=( $(get_providers) ) ++ (( ${idx} <= ${#providers[@]} )) || die -q "The given provider with index (${idx}) does not exist" ++ provider=${providers[${idx}-1]} ++ else ++ provider="${idx}" ++ fi ++ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" ++ ++ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then ++ if is_number ${provider} ; then ++ providers=( $(get_providers) ) ++ [[ -n ${providers[${idx}-1]} ]] && \ ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ die -q "The given provider (${provider}) does not exist" ++ fi ++ ++ local variables=( PATH LD_LIBRARY_PATH MANPATH ) ++ [[ -n ${!default_*} ]] && local ${!default_*} ++ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT%/}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib ++ local default_MANPATH=$(MANPATH= man -C"${EROOT%/}"/etc/man.conf -w) ++ ++ local var IFS=: ++ for var in "${variables[@]}"; do ++ local defvar=default_${var} path paths=( ) ++ for path in ${!var}; do ++ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue ++ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ paths+=( "${path}" ) ++ done ++ ++ [[ -n ${provider} ]] && for path in ${!defvar}; do ++ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) ++ done ++ ++ local newval=${paths[*]} ++ if [[ ${newval} != ${!var} ]]; then ++ newval=${newval//\'/\'\\\'\'} ++ if [[ ${syntax} == sh ]]; then ++ echo "${var}='${newval}'; export ${var}" ++ else ++ echo "setenv ${var} '${newval}'" ++ fi ++ fi ++ done ++} ++ ++options_script() { ++ _options_parameters $FUNCNAME "$@" ++ get_providers ++} ++ ++# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : +diff --git a/modules/Makefile.am b/modules/Makefile.am +index 73960c4..4da6465 100644 +--- a/modules/Makefile.am ++++ b/modules/Makefile.am +@@ -1,6 +1,7 @@ + modulesdir=$(datadir)/$(PACKAGE_NAME)/modules/ + + modules_DATA = \ ++ alternatives.eselect \ + binutils.eselect \ + editor.eselect \ + env.eselect \ +diff --git a/modules/alternatives.eselect b/modules/alternatives.eselect +new file mode 100644 +index 0000000..912bb3d +--- /dev/null ++++ b/modules/alternatives.eselect +@@ -0,0 +1,165 @@ ++# Copyright 2015 Gentoo Foundation ++# Copyright 2008 Mike Kelly ++# Copyright 2009, 2013 David Leverton ++# Copyright 2010 Bo Ørsted Andresen ++# Distributed under the terms of the GNU General Public License v2 ++ ++inherit alternatives-common ++ ++DESCRIPTION="Maintain Alternatives symlinks" ++VERSION="20150521" ++MAINTAINER="sci@gentoo.org" ++ ++show_extra_help_text() { ++ cat <<- ENDOFTEXT ++ This module is intended for internal use when a package is installed, ++ updated or removed. For alternatives for which it is likely that ++ users will need control over which provider is selected, there will be ++ a separate eselect module installed to do so. ++ ENDOFTEXT ++} ++ ++# all functions implemented in alternatives-common.bash as defined for ++# both "eselect alternatives" and individual modules ++ ++### update action ### ++ ++describe_update() { ++ alternatives_describe_update ++} ++ ++describe_update_parameters() { ++ echo "<alternative> $(alternatives_describe_update_parameters)" ++} ++ ++describe_update_options() { ++ echo "<alternative> : the name of the alternative to set a provider for" ++ alternatives_describe_update_options ++} ++ ++do_update() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_update "$@" ++} ++ ++options_update() { ++ alternatives_options_update ++} ++ ++### create action ### ++ ++describe_create() { ++ echo "Create a new alternative" ++} ++ ++describe_create_parameters() { ++ echo "<alternative>" ++} ++ ++describe_create_options() { ++ echo "<alternative> : the name of the alternative to create" ++} ++ ++do_create() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ ! -e "${auto_file}" ]]; then ++ if [[ ! -e "${auto_dir}" ]]; then ++ mkdir -p "${auto_dir}" || die "Failed to create ${auto_dir}" ++ elif [[ ! -d "${auto_dir}" ]]; then ++ die "${auto_dir} exists but is a file" ++ fi ++ cat >> ${auto_file} <<- ENDOFTEXT ++ DESCRIPTION="${DESCRIPTION} for ${1}" ++ VERSION="${VERSION}" ++ MAINTAINER="${MAINTAINER}" ++ ESELECT_MODULE_GROUP="Alternatives" ++ ++ ALTERNATIVE="${1}" ++ ++ inherit alternatives ++ ENDOFTEXT ++ fi ++} ++ ++### delete action ### ++ ++describe_delete() { ++ echo "Delete an existing alternative" ++} ++ ++describe_delete_parameters() { ++ echo "<alternative>" ++} ++ ++describe_delete_options() { ++ echo "<alternative> : the name of the alternative to delete" ++} ++ ++do_delete() { ++ [[ $# == 1 ]] || die "Need exactly one alternative name" ++ ++ local auto_dir="${ESELECT_AUTO_GENERATED_MODULES_PATH}" ++ local auto_file="${auto_dir}/${1}.eselect" ++ ++ if [[ -e "${auto_file}" ]]; then ++ rm "${auto_file}" || die "Failed to remove alternative: ${1}" ++ fi ++} ++ ++### add action ### ++ ++describe_add() { ++ alternatives_describe_add ++} ++ ++describe_add_parameters() { ++ echo "<alternative> $(alternatives_describe_add_parameters)" ++} ++ ++describe_add_options() { ++ echo "<alternative> : the name of the alternative to add a provider for" ++ alternatives_describe_add_options ++} ++ ++do_add() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_add "$@" ++} ++ ++options_add() { ++ alternatives_options_add ++} ++ ++### remove action ### ++ ++describe_remove() { ++ alternatives_describe_remove ++} ++ ++describe_remove_parameters() { ++ echo "<alternative> $(alternatives_describe_remove_parameters)" ++} ++ ++describe_remove_options() { ++ echo "<alternative> : the name of the alternative to remove a provider from" ++ alternatives_describe_remove_options ++} ++ ++do_remove() { ++ local ALTERNATIVE=$1 ++ shift ++ [[ -z "${ALTERNATIVE}" ]] && die -q "Missing required parameter 'alternative'" ++ alternatives_do_remove "$@" ++} ++ ++options_remove() { ++ alternatives_options_remove ++} +diff --git a/modules/modules.eselect b/modules/modules.eselect +index 038f630..eb73e16 100644 +--- a/modules/modules.eselect ++++ b/modules/modules.eselect +@@ -2,7 +2,7 @@ + # Copyright 2006-2015 Gentoo Foundation + # Distributed under the terms of the GNU GPL version 2 or later + +-inherit config ++inherit config output tests + + DESCRIPTION="Query eselect modules" + MAINTAINER="eselect@gentoo.org" +@@ -15,57 +15,94 @@ describe_list() { + echo "List all available modules" + } + +-describe_list_options() { +- echo "--only-names : Output names of modules only" +-} +- + # List all installed modules + do_list() { +- local only_names path file module name desc +- local -a extra_modules +- +- if [[ ${1#--} = only-names ]]; then +- only_names=1 +- shift +- fi +- [[ $# -gt 0 ]] && die -q "Too many parameters" +- +- for path in "${ESELECT_MODULES_PATH[@]}" ; do +- [[ -d ${path} ]] || continue +- for file in "${path}"/*.eselect ; do +- [[ -f ${file} ]] || continue +- extra_modules=( "${extra_modules[@]}" "${file}" ) +- done +- done +- +- if [[ -n ${only_names} ]]; then +- # This is mainly intended for bash completion +- echo "help" +- echo "usage" +- echo "version" +- for module in "${extra_modules[@]}" ; do +- name=${module##*/} +- echo "${name%%.eselect}" +- done +- else +- write_list_start "Built-in modules:" +- write_kv_list_entry "help" "Display a help message" +- write_kv_list_entry "usage" "Display a usage message" +- write_kv_list_entry "version" "Display version information" +- +- if [[ ${#extra_modules[@]} -gt 0 ]] ; then +- echo +- write_list_start "Extra modules:" +- for module in "${extra_modules[@]}" ; do +- name=${module##*/} +- name=${name%%.eselect} +- desc=$(ESELECT_MODULE_NAME=${name} \ +- load_config "${module}" DESCRIPTION) +- desc=${desc:-No description available} +- write_kv_list_entry "${name}" "${desc}" +- done +- fi +- fi ++ local path file module name desc group groups Extra_modules ++ ++ write_list_start "Built-in modules:" ++ write_kv_list_entry "help" "Display a help message" ++ write_kv_list_entry "usage" "Display a usage message" ++ write_kv_list_entry "version" "Display version information" ++ write_kv_list_entry "print-modules" "Print eselect modules" ++ write_kv_list_entry "print-actions" "Print actions for a given module" ++ write_kv_list_entry "print-options" "Print options for a given action" ++ ++ for path in "${ESELECT_MODULES_PATH[@]}" ; do ++ [[ -d ${path} ]] || continue ++ for file in ${path}/*.eselect ; do ++ [[ -f ${file} ]] || continue ++ group=$(load_config "${file}" ESELECT_MODULE_GROUP) ++ if [[ -n ${group} ]]; then ++ has ${group} ${groups} || groups+=" ${group}" ++ declare ${group}_modules+=" ${file}" ++ else ++ Extra_modules+=" ${file}" ++ fi ++ done ++ done ++ ++ for group in ${groups} Extra; do ++ local m ++ m="${group}_modules" ++ if [[ -n ${!m} ]] ; then ++ echo ++ write_list_start "${group} modules:" ++ for module in ${!m}; do ++ name=${module##*/} ++ name=${name%%.eselect} ++ desc=$(load_config "${module}" DESCRIPTION) ++ desc=${desc:-No description available} ++ write_kv_list_entry "${name}" "${desc}" ++ done ++ fi ++ done ++} ++ ++### group action ++ ++describe_group() { ++ echo "Lists all available modules belonging to a specified group." ++} ++ ++describe_group_parameters() { ++ echo "<group>" ++} ++ ++do_group() { ++ local path file groupname="$1" group module modules name desc ++ [[ -z "$groupname" ]] && die -q "Required option (group name) missing." ++ ++ if [[ ${groupname} == Built-in ]]; then ++ write_list_start "Built-in modules:" ++ write_kv_list_entry "help" "Display a help message" ++ write_kv_list_entry "usage" "Display a usage message" ++ write_kv_list_entry "version" "Display version information" ++ return 0 ++ fi ++ ++ for path in "${ESELECT_MODULES_PATH[@]}" ; do ++ [[ -d ${path} ]] || continue ++ for file in ${path}/*.eselect ; do ++ [[ -f ${file} ]] || continue ++ group=$(load_config "${file}" ESELECT_MODULE_GROUP) ++ [[ ${groupname} == ${group} || ++ ( ${groupname} == Extra && -z ${group} ) ]] || continue ++ modules+=" ${file}" ++ done ++ done ++ ++ if [[ -n ${modules} ]] ; then ++ write_list_start "${groupname} modules:" ++ for module in ${modules}; do ++ name=${module##*/} ++ name=${name%%.eselect} ++ desc=$(load_config "${module}" DESCRIPTION) ++ desc=${desc:-No description available} ++ write_kv_list_entry "${name}" "${desc}" ++ done ++ else ++ die -q "No modules belonging to ${groupname} was found" ++ fi + } + + ### has action +@@ -75,56 +112,89 @@ describe_has() { + } + + describe_has_parameters() { +- echo "<module>" ++ echo "<module>" + } + + do_has() { +- [[ -z $1 ]] && die -q "Required option (module name) missing" +- [[ $# -gt 1 ]] && die -q "Too many parameters" +- +- local modname=$1 modpath +- for modpath in "${ESELECT_MODULES_PATH[@]}" ; do +- [[ -f ${modpath}/${modname}.eselect ]] && return 0 +- done +- return 1 ++ [[ -z $1 ]] && die -q "Required option (module name) missing" ++ [[ $# -gt 1 ]] && die -q "Too many parameters" ++ local modname="$1" modpath ++ [[ -z "$modname" ]] && die -q "Required option (module name) missing." ++ for modpath in "${ESELECT_MODULES_PATH[@]}" ; do ++ [[ -f "${modpath}/${modname}.eselect" ]] && return 0 ++ done ++ return 1 + } + + ### add action +-# *** Commented out. Do we really want to have an eselect module that is +-# *** installing other modules in a system directory? Also, this should +-# *** go together with a "remove" action. +- +-# describe_add() { +-# echo "Install the given module file somewhere that eselect can find it." +-# echo "By default, install to \$HOME/.eselect/modules/, unless running as " +-# echo "root. Then, install to ${ESELECT_DATA_PATH}/modules/." +-# } +- +-# describe_add_parameters() { +-# echo "<module_file>" +-# } +- +-# do_add() { +-# local local_path="${ROOT}${HOME}/.eselect/modules/" module_file +-# local force_default=0 +-# +-# if [[ $1 = "--force-default-location" ]] ; then +-# force_default=1 +-# shift +-# fi +-# module_file=$1 +-# +-# [[ -z ${module_file} ]] && die -q "Required option (module file) missing" +-# +-# # TODO: Don't install the module "somewhere", depending on write access. +-# # Add an option to control if it goes to the user's or to the system dir. +-# if ! cp "${module_file}" "${ESELECT_DEFAULT_MODULES_PATH}" &> /dev/null ; then +-# [[ ${force_default} == 1 ]] \ +-# && die -q "Failed to install module file to default modules path" +-# +-# mkdir -p "${local_path}" \ +-# || die -q "Failed to create module install directory" +-# cp "${module_file}" "${local_path}" \ +-# || die -q "Failed to install module file" +-# fi +-# } ++ ++describe_add() { ++ echo "Install a module file to \$HOME/.eselect/modules/, or ${ESELECT_DEFAULT_MODULES_PATH//\/\///}/ when run as root" ++} ++ ++describe_add_parameters() { ++ echo "<module_file>" ++} ++ ++do_add() { ++ ++ local local_path="${ROOT}${HOME}/.eselect/modules/" module_file ++ local force_default=0 ++ ++ if [[ $1 = "--force-default-location" ]] ; then ++ force_default=1 ++ shift ++ fi ++ module_file=$1 ++ ++ [[ -z ${module_file} ]] && die -q "Required option (module file) missing" ++ ++ # TODO: Don't install the module "somewhere", depending on write access. ++ # Add an option to control if it goes to the user's or to the system dir. ++ if ! cp "${module_file}" "${ESELECT_DEFAULT_MODULES_PATH}" &> /dev/null ; then ++ [[ ${force_default} == 1 ]] \ ++ && die -q "Failed to install module file to default modules path" ++ ++ mkdir -p "${local_path}" \ ++ || die -q "Failed to create module install directory" ++ cp "${module_file}" "${local_path}" \ ++ || die -q "Failed to install module file" ++ fi ++} ++ ++### remove action ++ ++describe_remove() { ++ echo "Remove the given module name" ++ echo "By default, it will remove from \$HOME/.eselect/modules/, unless running as " ++ echo "root. Then, remove from ${ESELECT_DATA_PATH}/modules/." ++} ++ ++describe_remove_parameters() { ++ echo "<module>" ++} ++ ++do_remove() { ++ local local_path="${ROOT}${HOME}/.eselect/modules/" module_name ++ local force_default=0 ++ ++ if [[ $1 = "--force-default-location" ]] ; then ++ force_default=1 ++ shift ++ fi ++ module_name=$1 ++ ++ [[ -z ${module_name} ]] && die -q "Required option (module name) missing" ++ ++ # TODO: Don't install the module "somewhere", depending on write access. ++ # Add an option to control if it goes to the user's or to the system dir. ++ if ! rm "${ESELECT_DEFAULT_MODULES_PATH}"/${module_name}.eselect &> /dev/null ; then ++ [[ ${force_default} == 1 ]] \ ++ && die -q "Failed to remove module ${module_name} from default modules path" ++ ++ rm "${module_file}" "${local_path}"/${module_name}.eselect \ ++ || die -q "Failed to remove module ${module_name}" ++ fi ++} ++ ++# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-admin/eselect/files/eselect-alternatives.patch b/app-admin/eselect/files/eselect-alternatives.patch deleted file mode 100644 index 13f05935e..000000000 --- a/app-admin/eselect/files/eselect-alternatives.patch +++ /dev/null @@ -1,618 +0,0 @@ -Index: bin/eselect.in -=================================================================== ---- bin/eselect.in (revision 863) -+++ bin/eselect.in (working copy) -@@ -22,10 +22,15 @@ - # Where are modules installed by default? - ESELECT_DEFAULT_MODULES_PATH="${ESELECT_DATA_PATH}/modules" - -+# Where are auto-generated modules placed? (e.g. from alternatives-2.eclass) -+ESELECT_AUTO_GENERATED_MODULES_PATH="${ESELECT_DEFAULT_MODULES_PATH}/auto" -+ - # Look in these places for modules --ESELECT_MODULES_PATH=( \ -- "${HOME}/.eselect/modules" \ -- "${ESELECT_DEFAULT_MODULES_PATH}" ) -+ESELECT_MODULES_PATH=( -+ "${HOME}/.eselect/modules" -+ "${ESELECT_DEFAULT_MODULES_PATH}" -+ "${ESELECT_AUTO_GENERATED_MODULES_PATH}" -+) - - # Look in this place for libraries - ESELECT_CORE_PATH="${ESELECT_DATA_PATH}/libs" -Index: bin/Makefile.am -=================================================================== ---- bin/Makefile.am (revision 863) -+++ bin/Makefile.am (working copy) -@@ -4,6 +4,7 @@ - dosed = @SED@ -e 's,\@BASH\@,$(BASH),g' \ - -e 's,\@DATADIR\@,$(datadir),g' \ - -e 's,\@EPREFIX\@,$(EPREFIX),g' \ -+ -e 's,\@LIBEXECDIR\@,$(datadir),g' \ - -e 's,\@VERSION\@,$(VERSION),g' - - % : %.in -Index: libs/Makefile.am -=================================================================== ---- libs/Makefile.am (revision 863) -+++ libs/Makefile.am (working copy) -@@ -1,6 +1,7 @@ - eselectlibsdir = $(datadir)/$(PACKAGE_NAME)/libs/ - - eselectlibs_DATA = \ -+ alternatives.bash \ - config.bash \ - core.bash \ - default.eselect \ -@@ -14,6 +15,7 @@ - tests.bash - - EXTRA_DIST = \ -+ alternatives.bash.in \ - config.bash.in \ - core.bash.in \ - default.eselect.in \ -@@ -30,7 +32,8 @@ - -e 's,\@SED\@,@SED@,g' \ - -e 's,\@PORTAGEQ\@,@PORTAGEQ@,g' \ - -e 's,\@ENV_UPDATE\@,@ENV_UPDATE@,g' \ -- -e 's,\@CANONICALISE\@,@CANONICALISE@,g' -+ -e 's,\@CANONICALISE\@,@CANONICALISE@,g' \ -+ -e 's,\@sysconfdir\@,@sysconfdir@,g' - - %.bash : %.bash.in - @$(dosed) $< > $@ ---- libs/alternatives.bash.in.orig 1970-01-01 01:00:00.000000000 +0100 -+++ libs/alternatives.bash.in 2011-09-06 18:55:43.000000000 +0100 -@@ -0,0 +1,550 @@ -+# Copyright 2008 Mike Kelly -+# Copyright 2009 David Leverton -+# Copyright 2010 Bo Ørsted Andresen -+# 2010: Adapted to eselect Sebastien Fabbro (who doesn't like copyrights) -+# Distributed under the terms of the GNU General Public License v2 -+ -+inherit config output path-manipulation -+ -+ALTERNATIVESDIR_ROOTLESS="@sysconfdir@/env.d/alternatives" -+ALTERNATIVESDIR="${EROOT}${ALTERNATIVESDIR_ROOTLESS}" -+ -+get_current_provider() { -+ local dieprefix="Could not determine current provider for ${ALTERNATIVE}" -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ local provider=$(readlink "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: readlink ${symlink} failed") -+ [[ ${provider} == */* ]] && die "${dieprefix}: malformed target for ${symlink}" -+ -+ if [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} || -+ ( -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} && ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ) ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} is not a directory" -+ fi -+ -+ echo "${provider}" -+ -+ elif [[ -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current is not a symlink" -+ fi -+} -+ -+compare_importance() { -+ local IFS=. -+ local a=( ${1} ) b=( ${2} ) -+ local -i i=0 -+ while (( i<${#a[@]} && i<${#b[@]} )); do -+ if (( a[i]<b[i] )); then -+ return 0 -+ elif (( a[i]>b[i] )); then -+ return 1 -+ fi -+ i+=1 -+ done -+ (( i<${#b[@]} )) -+} -+ -+sort_providers() { -+ local begin=${1:-0} -+ local count=${2:-${#providers[@]}} -+ [[ ${count} -le 1 ]] && return 0 -+ sort_providers ${begin} $((count/2)) -+ sort_providers $((begin+count/2)) $((count-count/2)) -+ local left=( "${providers[@]:begin:count/2}" ) -+ local right=( "${providers[@]:begin+count/2:count-count/2}" ) -+ local -i x i=0 j=0 -+ for (( x=begin; x<begin+count; ++x )); do -+ if (( j>=${#right[@]} )) || { (( i<${#left[@]} )) && compare_importance "${left[i]%%:*}" "${right[j]%%:*}"; }; then -+ providers[x]=${left[i++]} -+ else -+ providers[x]=${right[j++]} -+ fi -+ done -+} -+ -+get_providers() { -+ local p= importance providers=() -+ for p in "${ALTERNATIVESDIR}/${ALTERNATIVE}"/* ; do -+ [[ -d ${p} && ! -L ${p} ]] || continue -+ p=${p##*/} -+ -+ importance=$(< "${ALTERNATIVESDIR}/${ALTERNATIVE}/${p}/_importance") -+ importance=${importance:-0} -+ [[ "${importance}" =~ ^[0123456789]+(\.[0123456789]+)*$ ]] || die "_importance (${importance}) for ${p} is not a dot-separated list of integers" -+ -+ providers+=( "${importance}:${p}" ) -+ done -+ -+ sort_providers -+ for (( p=${#providers[@]}-1 ; p>=0 ; --p )); do -+ echo "${providers[p]#*:}" -+ done -+} -+ -+### show action ### -+describe_show() { -+ echo "Show the current provider in use for ${ALTERNATIVE}" -+} -+ -+do_show() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local current="$(get_current_provider)" -+ if [[ -z "${current}" ]] ; then -+ echo "(none)" -+ return 2 -+ fi -+ echo "${current}" -+} -+ -+options_show() { -+ : -+} -+ -+### list action ### -+describe_list() { -+ echo "Lists all available providers for ${ALTERNATIVE}" -+} -+ -+do_list() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local n cur= providers=( $(get_providers) ) -+ write_list_start "Available providers for ${ALTERNATIVE}:" -+ -+ cur="$(get_current_provider)" -+ -+ if [[ -n "${providers[@]}" ]] ; then -+ for (( n = 0 ; n < ${#providers[@]} ; ++n )) ; do -+ [[ ${cur} == "${providers[${n}]}" ]] && \ -+ providers[${n}]="${providers[${n}]} $(highlight '*')" -+ done -+ write_numbered_list "${providers[@]}" -+ else -+ write_kv_list_entry "(none found)" "" -+ fi -+} -+ -+options_list() { -+ : -+} -+ -+### files action ### -+describe_files() { -+ echo "Lists symlinks provided by the currently selected provider" -+} -+ -+do_files() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "No selected provider, hence no symlinks provided" -+ local dieprefix="Could not list symlinks provided for ${ALTERNATIVE}" -+ -+ local errors symlink rootsymlink -+ while read -r -d '' symlink; do -+ rootsymlink="${EROOT}${symlink}" -+ rootsymlink=${rootsymlink//+(\/)/\/} -+ echo "${rootsymlink}" -+ if [[ -L ${rootsymlink} ]]; then -+ if [[ ! -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is dangling symlink" -+ errors=yes -+ fi -+ elif [[ -d ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} is a directory" -+ errors=yes -+ elif [[ -e ${rootsymlink} ]]; then -+ write_error_msg "${rootsymlink} exists but is not a symlink" -+ errors=yes -+ else -+ write_error_msg "${rootsymlink} does not exist" -+ errors=yes -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+} -+ -+options_files() { -+ : -+} -+ -+### set action ### -+ -+describe_set() { -+ echo "Sets a provider for ${ALTERNATIVE}" -+} -+ -+describe_set_parameters() { -+ echo "[ --force ] <provider>" -+} -+ -+describe_set_options() { -+ echo "--force : overwrite or remove existing non-symlink files (but not directories) if necessary" -+ echo "<provider> : the name of the provider to use or the index of the provider preceeded by a dash" -+} -+ -+do_set() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force provider providers -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ local dieprefix="Could not set provider ${provider} for alternative ${ALTERNATIVE}" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local symlink newsymlinks=() oldsymlinks=() -+ -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink#.} -+ nicesymlink=${nicesymlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: bad symlink ${symlink}?" -+ -+ newsymlinks+=( "${nicesymlink}" ) -+ done < <( -+ cd "${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}" || die "${dieprefix}: cd failed" -+ find . -type l -print0 | LC_ALL=C sort -r -u -z) -+ [[ ${#newsymlinks[@]} -gt 0 ]] || die "${dieprefix}: does not provide any symlinks?" -+ -+ if [[ -f ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ while read -r -d '' symlink; do -+ local nicesymlink=${symlink//+(\/)/\/} -+ [[ ${nicesymlink} == /* ]] || die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ [[ ${nicesymlink} == */ ]] && die "${dieprefix}: old provider ${oldcur} provides bad symlink ${symlink}?" -+ -+ oldsymlinks+=( "${nicesymlink}" ) -+ done < <(LC_ALL=C sort -r -u -z "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list") -+ [[ ${#oldsymlinks[@]} -gt 0 ]] || die "${dieprefix}: old provider ${oldcur} does not provide any symlinks?" -+ -+ elif [[ -L ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list || -e ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list ]]; then -+ die "${dieprefix}: ${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list is not a file" -+ fi -+ -+ local pass errors= -+ for pass in check perform; do -+ local -i new_i=0 old_i=0 -+ while [[ -n ${newsymlinks[new_i]} || -n ${oldsymlinks[old_i]} ]]; do -+ -+ if ( LC_ALL=C; [[ ${newsymlinks[new_i]} < ${oldsymlinks[old_i]} ]] ); then -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${oldsymlinks[old_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${oldsymlinks[old_i]} ]]; then -+ write_error_msg "Can't remove ${EROOT}${oldsymlinks[old_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${oldsymlinks[old_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${oldsymlinks[old_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${oldsymlinks[old_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${ROOT}${oldsymlinks[old_i]}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ old_i+=1 -+ -+ else -+ local target=${ALTERNATIVESDIR_ROOTLESS#/}/${ALTERNATIVE}/_current${newsymlinks[new_i]} dir=${newsymlinks[new_i]%/*} -+ while [[ -n ${dir} ]]; do -+ target=../${target} -+ dir=${dir%/*} -+ done -+ -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${newsymlinks[new_i]} ]]; then -+ : -+ elif [[ -d ${EROOT}${newsymlinks[new_i]} ]]; then -+ write_error_msg "Can't overwrite ${EROOT}${newsymlinks[new_i]}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${newsymlinks[new_i]} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Overwriting ${EROOT}${newsymlinks[new_i]} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to overwrite ${EROOT}${newsymlinks[new_i]}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ mkdir -p "${EROOT}${newsymlinks[new_i]%/*}" || die "${dieprefix}: mkdir -p failed" -+ ln -snf "${target#/}" "${EROOT}${newsymlinks[new_i]}" || die "${dieprefix}: ln -snf failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ -+ [[ ${newsymlinks[new_i]} == ${oldsymlinks[old_i]} ]] && old_i+=1 -+ new_i+=1 -+ fi -+ done -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ local oldcur="$(get_current_provider)" -+ ln -snf "${provider}" "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current" || die "${dieprefix}: ln -snf failed" -+ -+ : >"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: emptying/creating _current_list failed" -+ for symlink in "${newsymlinks[@]}"; do -+ echo -n -e "${symlink}\\0" >>"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" || die "${dieprefix}: appending ${symlink} to _current_list failed" -+ done -+ return 0 -+} -+ -+_options_parameters() { -+ [[ -n ${2} && ${2} != --descriptions ]] && die -q "Unrecognised option ${2}" -+ local describe_func=describe_${1#options_}_options descriptions=${2} opt options oldifs=$IFS -+ if is_function ${describe_func}; then -+ IFS=$'\n' -+ options=( $(${describe_func}) ) -+ IFS=$oldifs -+ for opt in "${options[@]}"; do -+ [[ ${opt} == --* ]] || continue -+ if [[ -n ${descriptions} ]]; then -+ echo "${opt/ : /:}" -+ else -+ echo "${opt%% : *}" -+ fi -+ done -+ fi -+} -+ -+options_set() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### update action ### -+ -+describe_update() { -+ echo "Set a default provider if no valid one currently exists" -+} -+ -+describe_update_parameters() { -+ echo "[--ignore] <provider>" -+} -+ -+describe_update_options() { -+ echo "--ignore : update to any valid provider EXCEPT the specified provider" -+ echo "<provider> : the name of the provider to use" -+} -+ -+do_update() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local p cur=$(get_current_provider) providers=( $(get_providers) ) ignore -+ if [[ "--ignore" == ${1} ]] ; then -+ # Try everything except setting the provider to the given -+ # one. So, if it isn't the given one, we end up doing -+ # nothing. Bug #128 -+ shift -+ ignore=${1} -+ fi -+ -+ if [[ ${cur} == ${1} && -z ${ignore} ]]; then -+ # if current provider was just updated, reselect it since it could have changed -+ do_set "${cur}" && return 0 -+ elif [[ -n ${cur} && ${cur} != ${ignore} ]] ; then -+ # verify existing provider's symlinks -+ local p= bad=0 -+ while read -r -d '' p ; do -+ [[ -L "${EROOT}${p}" && -e "${EROOT}${p}" ]] || (( bad++ )) -+ done < "${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ "${bad}" -eq 0 ]] && return 0 -+ # fix existing provider if possible -+ has "${cur}" "${providers[@]}" && do_set "${cur}" && return 0 -+ elif has "${1}" "${providers[@]}" && [[ -z ${ignore} ]] ; then -+ # switch to new provider if none was set before or it can't be fixed -+ do_set "${1}" && return 0 -+ fi -+ -+ # if no valid provider has been selected switch to first available, valid -+ # provider, sorted according to importance -+ for p in "${providers[@]}"; do -+ [[ ${ignore} != ${p} ]] && do_set "${p}" && return 0 -+ done -+ -+ # if a provider is set but no providers are available anymore cleanup -+ cur=$(get_current_provider) -+ if [[ -n ${cur} ]]; then -+ do_unset "${cur}" && return 2 -+ fi -+ # if no provider is set and none are available that are not ignored, return 2 for cleanup -+ [[ -z ${providers[@]} || ${providers[@]} == ${ignore} ]] && return 2 -+ -+ # we tried everything to select a valid provider, but failed -+ return 1 -+} -+ -+options_update() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+### unset action ### -+ -+describe_unset() { -+ echo "Unset any symlinks created for the current provider for ${ALTERNATIVE}." -+} -+ -+describe_unset_parameters() { -+ echo "[ --force ]" -+} -+ -+describe_unset_options() { -+ echo "--force : remove existing non-symlink files (but not directories) if necessary" -+} -+ -+do_unset() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ -+ local force= -+ if [[ ${1} == --force ]]; then -+ force=yes -+ shift -+ fi -+ -+ local cur="$(get_current_provider)" p= -+ [[ -n "${cur}" ]] || die -q "Nothing to unset" -+ local dieprefix="Could not unset provider for ${ALTERNATIVE}" -+ -+ local one=false symlink pass errors= -+ for pass in check perform; do -+ while read -r -d '' symlink; do -+ one=true -+ if [[ ${pass} == check ]]; then -+ if [[ -L ${EROOT}${symlink} ]]; then -+ : -+ elif [[ -d ${EROOT}${symlink} ]]; then -+ write_error_msg "Can't remove ${EROOT}${symlink}: is a directory${force:+ which is a fatal error that cannot be ignored by --force}" -+ errors=yes -+ elif [[ -e ${EROOT}${symlink} ]]; then -+ if [[ -n ${force} ]]; then -+ write_warning_msg "Removing ${EROOT}${symlink} due to --force: is not a symlink" -+ else -+ write_error_msg "Refusing to remove ${EROOT}${symlink}: is not a symlink (use --force to override)" -+ errors=yes -+ fi -+ fi -+ -+ elif [[ ${pass} == perform ]]; then -+ rm -f "${EROOT}${symlink}" || die "${dieprefix}: rm failed" -+ else -+ die "${dieprefix}: unknown \${pass} ${pass}???" -+ fi -+ done <"${ALTERNATIVESDIR}/${ALTERNATIVE}/_current_list" -+ -+ [[ -n ${errors} ]] && die "${dieprefix}: see previous errors" -+ done -+ -+ ${one} || die "${dieprefix}: does not provide any symlinks?" -+ -+ rm "${ALTERNATIVESDIR}/${ALTERNATIVE}"/{_current,_current_list} || die "${dieprefix}: rm failed" -+} -+ -+options_unset() { -+ _options_parameters $FUNCNAME "$@" -+ get_current_provider -+} -+ -+### script action ### -+ -+describe_script() { -+ echo "Output an evalable script fragment to set PATH, LD_LIBRARY_PATH and MANPATH to use the specified provider" -+} -+ -+describe_script_parameters() { -+ echo "[--sh | --csh] [<provider>]" -+} -+ -+describe_script_options() { -+ echo "--sh : use Bourne shell syntax (default)" -+ echo "--csh : use C shell syntax" -+ echo "<provider> : the provider to use or the index of the provider preceeded by a dash (if not specified, use the system default)" -+} -+ -+do_script() { -+ [[ -z "${ALTERNATIVE}" ]] && die "Need to set ALTERNATIVE in the eselect module" -+ local syntax=sh provider providers -+ if [[ ${1} == --sh ]]; then -+ shift -+ elif [[ ${1} == --csh ]]; then -+ syntax=csh -+ shift -+ fi -+ -+ if [[ ${1} == -+([[:digit:]]) ]]; then -+ providers=( $(get_providers) ) -+ (( ${1#-} <= ${#providers[@]} )) || die -q "The given provider with index (${1#-}) does not exist" -+ provider=${providers[${1#-}-1]} -+ else -+ provider="${1}" -+ fi -+ [[ -z "${provider}" ]] && die -q "Missing required parameter 'provider'" -+ -+ if [[ ! -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider} ]] ; then -+ if is_number ${provider} ; then -+ providers=( $(get_providers) ) -+ [[ -n ${providers[${1#-}-1]} ]] && -+ die -q "The given provider (${provider}) does not exist, did you mean -${provider} (${providers[${1#-}-1]})?" -+ fi -+ die -q "The given provider (${provider}) does not exist" -+ fi -+ -+ local variables=( PATH LD_LIBRARY_PATH MANPATH ) -+ [[ -n ${!default_*} ]] && local ${!default_*} -+ local default_LD_LIBRARY_PATH=$(grep '^[^#]' "${EROOT}"/etc/ld.so.conf | tr '\n' ':')/lib:/usr/lib -+ local default_MANPATH=$(MANPATH= man -C"${EROOT}"/etc/man.conf -w) -+ -+ local var IFS=: -+ for var in "${variables[@]}"; do -+ local defvar=default_${var} path paths=( ) -+ for path in ${!var}; do -+ [[ ${path} == ${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/* ]] && continue -+ [[ -n ${provider} && -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ paths+=( "${path}" ) -+ done -+ -+ [[ -n ${provider} ]] && for path in ${!defvar}; do -+ [[ -d ${ALTERNATIVESDIR}/${ALTERNATIVE}/${provider}/${path#/} ]] && paths+=( "${ALTERNATIVESDIR_ROOTLESS}/${ALTERNATIVE}/${provider}/${path#/}" ) -+ done -+ -+ local newval=${paths[*]} -+ if [[ ${newval} != ${!var} ]]; then -+ newval=${newval//\'/\'\\\'\'} -+ if [[ ${syntax} == sh ]]; then -+ echo "${var}='${newval}'; export ${var}" -+ else -+ echo "setenv ${var} '${newval}'" -+ fi -+ fi -+ done -+} -+ -+options_script() { -+ _options_parameters $FUNCNAME "$@" -+ get_providers -+} -+ -+# vim: set ft=eselect sw=4 sts=4 ts=4 et tw=80 : diff --git a/app-benchmarks/btl/ChangeLog b/app-benchmarks/btl/ChangeLog index ea8c75791..978091101 100644 --- a/app-benchmarks/btl/ChangeLog +++ b/app-benchmarks/btl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-benchmarks/btl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + app-benchmarks/btl: Add bitbucket to remote-id in metadata.xml + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> btl-9999.ebuild, metadata.xml: Bump to EAPI=5 and drop KEYWORDS of live ebuilds diff --git a/app-benchmarks/btl/metadata.xml b/app-benchmarks/btl/metadata.xml index 51688ab86..3a7222f06 100644 --- a/app-benchmarks/btl/metadata.xml +++ b/app-benchmarks/btl/metadata.xml @@ -8,4 +8,7 @@ <description>Bench Template Library</description> </maintainer> <longdescription>This package contains a modified copy of the BTL.</longdescription> + <upstream> + <remote-id type="bitbucket">spiros/btl</remote-id> + </upstream> </pkgmetadata> diff --git a/app-benchmarks/numbench/ChangeLog b/app-benchmarks/numbench/ChangeLog index 1c1a2bcbe..e18f1c920 100644 --- a/app-benchmarks/numbench/ChangeLog +++ b/app-benchmarks/numbench/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for app-benchmarks/numbench -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> numbench-0.2.ebuild, + numbench-9999.ebuild: + app-benchmarks/numbench: Move to new CAT + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> numbench-9999.ebuild: Switch from git-2 to git-r3 diff --git a/app-benchmarks/numbench/numbench-0.2.ebuild b/app-benchmarks/numbench/numbench-0.2.ebuild index 3239217be..aa16da7f3 100644 --- a/app-benchmarks/numbench/numbench-0.2.ebuild +++ b/app-benchmarks/numbench/numbench-0.2.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 vcs-snapshot @@ -20,9 +20,9 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=" - !app-admin/eselect-blas - !app-admin/eselect-cblas - !app-admin/eselect-lapack + !app-eselect/eselect-blas + !app-eselect/eselect-cblas + !app-eselect/eselect-lapack >=dev-python/matplotlib-1.0.0 >=app-admin/eselect-1.3.2-r100" diff --git a/app-benchmarks/numbench/numbench-9999.ebuild b/app-benchmarks/numbench/numbench-9999.ebuild index eb4e9267e..a16717983 100644 --- a/app-benchmarks/numbench/numbench-9999.ebuild +++ b/app-benchmarks/numbench/numbench-9999.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit git-r3 distutils-r1 @@ -20,9 +20,9 @@ KEYWORDS="" IUSE="" RDEPEND=" - !app-admin/eselect-blas - !app-admin/eselect-cblas - !app-admin/eselect-lapack + !app-eselect/eselect-blas + !app-eselect/eselect-cblas + !app-eselect/eselect-lapack >=dev-python/matplotlib-1.0.0 >=app-admin/eselect-1.3.2-r100" diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog index ca2ea86c5..9a184fc53 100644 --- a/app-doc/root-docs/ChangeLog +++ b/app-doc/root-docs/ChangeLog @@ -1,7 +1,41 @@ # ChangeLog for app-doc/root-docs -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/ChangeLog,v 1.42 2014/03/28 18:48:01 bicatali Exp $ + 12 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-docs-6.02.05.ebuild: + 6.02.05 is in the portage tree now + + 11 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> root-docs-6.02.05.ebuild: + Update deps: root and fonts are needed only for api docs. + +*root-docs-6.02.05 (08 Apr 2015) + + 08 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-docs-6.00.02.ebuild, + +root-docs-6.02.05.ebuild, root-docs-9999.ebuild, + -files/root-docs-6.00.01-fillpatterns.patch, + +files/root-docs-6.02.05-jsroot.patch: + Version bump for evaluation and testing. + Remove old. + + 03 Mar 2015; Andrew Savchenko <bircoph@gentoo.org> -root-docs-5.34.26.ebuild: + 5.34.26 is now in the portage tree + + 02 Mar 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml: + Update maintainer information. + + 24 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> root-docs-5.34.26.ebuild: + Install root banner from 5.x branch, not 6.x. + + 23 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> + -root-docs-5.34.18-r2.ebuild, -root-docs-6.00.01-r1.ebuild, + root-docs-9999.ebuild, -files/root-docs-5.34.01-makehtml.patch: + Remove old versions. + +*root-docs-5.34.26 (23 Feb 2015) + + 23 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> +root-docs-5.34.26.ebuild: + Version bump. + *root-docs-5.34.18-r2 (06 Jul 2014) 06 Jul 2014; Andrew Savchenko <bircoph@gmail.com> diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest index f5533c265..27710df7e 100644 --- a/app-doc/root-docs/Manifest +++ b/app-doc/root-docs/Manifest @@ -3,6 +3,3 @@ DIST TMVAUsersGuide-v4.2.0.pdf 4099493 SHA256 b61614d14289a20f5fa429f79e474e596c DIST info.png 2060 SHA256 51de6661250f3fb71c6c8250cbc4bdc4dc4283cc90240b4dc1ee6168e8d40279 SHA512 81a730eefbe7a7e15d5840491402c7644bf7ed5d5f8f3830ed9457b343cc7882480e993ea84aef93500742cd0fe8469859cd2c925e5582b91ef56406804ae276 WHIRLPOOL 02ea6daf9e3d21947ebf5dd01c455a13f2fcbf9981be34a150056a3510122ca49e3d137d4f242c7218d4d06ace09566d513a04f09071723ac244f5a38e982bac DIST roofit_quickstart_3.00.pdf 501576 SHA256 65aaf9e0c88352e265fd55b97a2503a9ee4a51d3219daff69c6f7f6427fe22cf SHA512 e8e1bd3bb3ead0ae3883512d7ff297651b99937fd5df0b61cf559ea5dd6cfbda35dfd8ebc953ed11a12f471849f6e95e05869b58a1e433ea6e5d1d1aa08bbb93 WHIRLPOOL a58b221272e3b2775639bf934f63cd06919105871ad736a84e18e6f3949a579301d1c6d69df39576dcc11867aa27274f5c78f36146a929698437b1a0c310aebe DIST root6-banner.jpg 32319 SHA256 9d6d226bbe61db257a1796a3ad04dfe97b3bb500a29349ff76bf6a929ed1e104 SHA512 f01dd253f24d59c374042efd239ce023e5ca82d3d617ca6763daf9720b169c4fb27a0f4573ea95d807f0e12095924606372df4940f65ce7d859164314d22b9af WHIRLPOOL 69976abe240235a4f4eb25d61a0ceb183dc5ad5f9e57e9130ae10615329dd23125848f45608e1ad2d65a286d1f191f95336316f7c8f1cc052d396c31433cbe4c -DIST root_v5.34.18.source.tar.gz 74218396 SHA256 9196dce7d76b31e5bcabd985bd31bc4d9b7c8c4d0c7ce84f730efa4ef82a3567 SHA512 7c659d1a92e6ad1b901956cf0a04aacc391c936eb2881528d105f61373128e5fd4caad6e76988050a8a8bc69a8ba0b53055974b4c618800345127ae2e6dd7a14 WHIRLPOOL 15221bbdabd5abd50dc87e3cc8fa3de24c5888e3ac0a75535983c8ec0718433c84c2400da59d27f3b83b687c7c5f5d60bf769c8a1eefce45dd7d39cbc002a6b7 -DIST root_v6.00.01.source.tar.gz 97783289 SHA256 245c75fd6b53b84cae6251f950e259311439da678b2cdebb9578d51561a6b61f SHA512 e5f56750a0637aa884ea2d9d2ebf7b677cd1fac1819042948ba3530a25366cb7d853dba6fa7127764e3ae7cec23f89ed60d8913c0ff10ce2664bcc87df1620cf WHIRLPOOL 92f34c13ee0161d556b54b1bdd971774b2637c5cd57916ee75f0572a30713df820df3bb07f276d16ca31d11fda7e762de673c943b8bffda9db501d2ee8848654 -DIST root_v6.00.02.source.tar.gz 97811067 SHA256 db92818781f842c33b8b583f1f9be02b51cedbf5f2943df986cbbd0c0006a06f SHA512 bd72eb43d2a4ace27738ba2dc509f6d81ec3555e59454426d28c2c5522b4b19d2678ed515b84efaf953146c1f50c65e304532456d76076d03598bda67c69e8a5 WHIRLPOOL 12b87e9b1612ea3625f7ea0970b733887051b5173b728b5f13a032eb103eeda22de8a4c18417e02a92fe02f29b9acd9114fa1420fac42bea31bde07c7a0ce697 diff --git a/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch b/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch deleted file mode 100644 index b339226c8..000000000 --- a/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch +++ /dev/null @@ -1,51 +0,0 @@ ---- root/Makefile.orig 2012-07-13 13:42:46.000000000 +0400 -+++ root/Makefile 2012-07-22 00:15:03.282994389 +0400 -@@ -1087,16 +1087,7 @@ - - ifeq ($(BUILDX11),yes) - ifeq ($(BUILDASIMAGE),yes) --html: rootexecs postbin changelog releasenotes --ifneq ($(USECONFIG),FALSE) -- @if [ "x`which root.exe`" != "x$(DESTDIR)$(BINDIR)/root.exe" ] \ -- || [ "`which root.exe`" -ot "bin/root.exe" ]; then \ -- echo 'ERROR: root.exe has not been installed by this build.'; \ -- echo ' Run "make install" before running "make html".'; \ -- exit 1; \ -- fi --endif -- @$(MAKELOGHTML) -+html: compiledata releasenotes - @$(MAKEHTML) - else - html: ---- root/build/unix/makehtml.sh.orig 2012-06-28 11:33:36.000000000 +0400 -+++ root/build/unix/makehtml.sh 2012-07-22 00:18:58.705804436 +0400 -@@ -1,16 +1,16 @@ - #! /bin/sh - - dir=`pwd` --ROOT=$dir/bin/root -+ROOT=root - cd tutorials - # we need tutorials/hsimple.root - if [ ! -f hsimple.root ]; then -- $ROOT -l -b -q hsimple.C -+ $ROOT -l -b -q hsimple.C && exit 1 - fi - cd tree - # we need tutorials/tree/cernstaff.root - if [ ! -f cernstaff.root ]; then -- $ROOT -l -b -q cernbuild.C -+ $ROOT -l -b -q cernbuild.C || exit 1 - fi - cd $dir - -@@ -20,7 +20,7 @@ - - # To generate the full documentation, we do need to - # use the graphics engine, so do not use '-b'. --$ROOT -l <<makedoc -+$ROOT -l <<makedoc || exit 1 - THtml h; - h.LoadAllLibs(); - h.MakeAll(); diff --git a/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch b/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch deleted file mode 100644 index e48a4f775..000000000 --- a/app-doc/root-docs/files/root-docs-6.00.01-fillpatterns.patch +++ /dev/null @@ -1,30 +0,0 @@ -diff --git a/core/base/doc/macros/fillpatterns.C b/core/base/doc/macros/fillpatterns.C -index b0a5132..fca81c8 100644 ---- a/core/base/doc/macros/fillpatterns.C -+++ b/core/base/doc/macros/fillpatterns.C -@@ -20,11 +20,11 @@ TCanvas * fillpatterns() - - // Fixed patterns. - for (i=1; i<=5; i++) { -- box(j++, 0.01, y-bh, 0.19, y); -- box(j++, 0.21, y-bh, 0.39, y); -- box(j++, 0.41, y-bh, 0.59, y); -- box(j++, 0.61, y-bh, 0.79, y); -- box(j++, 0.81, y-bh, 0.99, y); -+ box(j, 0.01, y-bh, 0.19, y); j++; -+ box(j, 0.21, y-bh, 0.39, y); j++; -+ box(j, 0.41, y-bh, 0.59, y); j++; -+ box(j, 0.61, y-bh, 0.79, y); j++; -+ box(j, 0.81, y-bh, 0.99, y); j++; - y = y-bh-db; - } - -@@ -55,7 +55,7 @@ TCanvas * fillpatterns() - return Pat; - } - --box(Int_t pat, Double_t x1, Double_t y1, Double_t x2, Double_t y2) -+void box(Int_t pat, Double_t x1, Double_t y1, Double_t x2, Double_t y2) - { - // Draw an box using the fill pattern "pat" with the "pat" value - // written on top. diff --git a/app-doc/root-docs/files/root-docs-6.02.05-jsroot.patch b/app-doc/root-docs/files/root-docs-6.02.05-jsroot.patch new file mode 100644 index 000000000..1ea170e84 --- /dev/null +++ b/app-doc/root-docs/files/root-docs-6.02.05-jsroot.patch @@ -0,0 +1,11 @@ +--- root-6.02.05/documentation/JSROOT/JSROOT.md.orig 2015-02-09 11:59:47.000000000 +0300 ++++ root-6.02.05/documentation/JSROOT/JSROOT.md 2015-04-05 19:13:24.010358387 +0300 +@@ -198,7 +198,7 @@ + <div id="drawing">loading...</div> + </body> + +-Internally, the JSROOT.loadScript(urllist, callback, debug) method is used. It can be useful when some other scripts should be loaded as well. __urllist__ is a string with scripts names, separated by ';' symbol. If a script name starts with __$$$__ (triple dollar sign), the script will be loaded from a location relative to the main JSROOT directory. ++Internally, the JSROOT.loadScript(urllist, callback, debug) method is used. It can be useful when some other scripts should be loaded as well. __urllist__ is a string with scripts names, separated by ';' symbol. If a script name starts with __\$\$\$__ (triple dollar sign), the script will be loaded from a location relative to the main JSROOT directory. + This location is automatically detected when JSRootCore.js script is loaded. + + diff --git a/app-doc/root-docs/metadata.xml b/app-doc/root-docs/metadata.xml index 3645ec784..10a4d1cf5 100644 --- a/app-doc/root-docs/metadata.xml +++ b/app-doc/root-docs/metadata.xml @@ -2,12 +2,10 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer> - <email>bircoph@gmail.com</email> + <email>bircoph@gentoo.org</email> <name>Andrew Savchenko</name> - <description>Maintainer. Assign bugs to him</description> </maintainer> <herd>sci-physics</herd> -<herd>proxy-maintainers</herd> <longdescription lang="en"> This package contains the automatically generated ROOT class documentation. diff --git a/app-doc/root-docs/root-docs-5.34.18-r2.ebuild b/app-doc/root-docs/root-docs-5.34.18-r2.ebuild deleted file mode 100644 index ac00ef207..000000000 --- a/app-doc/root-docs/root-docs-5.34.18-r2.ebuild +++ /dev/null @@ -1,132 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.18-r1.ebuild,v 1.2 2014/03/28 18:48:01 bicatali Exp $ - -EAPI=5 - -ROOT_PN="root" -ROOFIT_DOC_PV=2.91-33 -ROOFIT_QS_DOC_PV=3.00 -TMVA_DOC_PV=4.2.0 - -if [[ ${PV} == "9999" ]] ; then - inherit git-r3 - EVCS_OFFLINE=yes # we need exactly the same checkout as root itself - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - S="${WORKDIR}/${ROOT_PN}" -fi - -inherit eutils multilib virtualx - -DESCRIPTION="Documentation for ROOT Data Analysis Framework" -HOMEPAGE="http://root.cern.ch/drupal" -SRC_URI="${SRC_URI} - math? ( - http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf - http://root.cern.ch/download/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf - http://root.cern.ch/drupal/sites/default/files/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf ) - api? ( - ${HOMEPAGE}/sites/default/files/images/root6-banner.jpg - ${HOMEPAGE}/sites/all/themes/newsflash/images/info.png )" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="api +math +metric" - -VIRTUALX_REQUIRED="api" - -DEPEND=" - ~sci-physics/root-${PV}[X,graphviz,opengl] - app-text/pandoc - app-text/texlive - dev-haskell/pandoc-citeproc[bibutils] - media-fonts/dejavu - virtual/pkgconfig" -RDEPEND="" - -DOC_DIR="/usr/share/doc/${ROOT_PN}-${PV}" - -src_unpack() { - if [[ ${PV} == "9999" ]] ; then - # we need to force sci-physics/root checkout here - git-r3_checkout "${EGIT_REPO_URI}" "${WORKDIR}/${P}" "sci-physics/root/0" - else - default - fi -} - -src_prepare() { - use api && epatch \ - "${FILESDIR}/${PN}-5.34.01-makehtml.patch" \ - "${FILESDIR}/${PN}-6.00.01-fillpatterns.patch" - # prefixify the configure script - sed -i \ - -e "s:/usr:${EPREFIX}/usr:g" \ - configure || die "prefixify configure failed" -} - -src_configure() { - # we need only to setup paths here, html docs doesn't depend on USE flags - if use api; then - ./configure \ - --prefix="${EPREFIX}/usr" \ - --etcdir="${EPREFIX}/etc/root" \ - --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" \ - --docdir="${EPREFIX}/usr/share/doc/${PF}" \ - --tutdir="${EPREFIX}/usr/share/doc/${PF}/examples/tutorials" \ - --testdir="${EPREFIX}/usr/share/doc/${PF}/examples/tests" \ - --with-llvm-config="${EPREFIX}/usr/bin/llvm-config" \ - --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" \ - --nohowto - fi -} - -src_compile() { - pdf_target=( primer users-guide ) - local pdf_size=pdfa4 - use metric || pdf_size=pdfletter - use math && pdf_target+=( minuit2 spectrum ) - - for (( i=0; i<${#pdf_target[@]}; i++ )); do - emake -C documentation/"${pdf_target[i]}" "${pdf_size}" - done - - if use api; then - # video drivers may want to access hardware devices - cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g') - [[ -n "${cards}" ]] && addpredict "${cards}" - - ROOTSYS="${S}" Xemake html - # if root.exe crashes, return code will be 0 due to gdb attach, - # so we need to check if last html file was generated; - # this check is volatile and can't catch crash on the last file. - [[ -f htmldoc/tableDescriptor_st.html ]] || die "html doc generation crashed" - fi -} - -src_install() { - insinto "${DOC_DIR}" - - for (( i=0; i<${#pdf_target[@]}; i++ )); do - doins documentation/"${pdf_target[i]}"/*.pdf - done - unset pdf_target - - use math && doins \ - "${DISTDIR}/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf" \ - "${DISTDIR}/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf" \ - "${DISTDIR}/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf" - - if use api; then - # Install offline replacements for online messages - cp "${DISTDIR}"/{root6-banner.jpg,info.png} htmldoc/ || die "cp failed" - # too large data to copy - dodir "${DOC_DIR}/html" - mv htmldoc/* "${ED}${DOC_DIR}/html/" || die - docompress -x ${DOC_DIR}/html - fi -} diff --git a/app-doc/root-docs/root-docs-6.00.01-r1.ebuild b/app-doc/root-docs/root-docs-6.00.01-r1.ebuild deleted file mode 100644 index 096e0fe96..000000000 --- a/app-doc/root-docs/root-docs-6.00.01-r1.ebuild +++ /dev/null @@ -1,133 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.18-r1.ebuild,v 1.2 2014/03/28 18:48:01 bicatali Exp $ - -EAPI=5 - -ROOT_PN="root" -ROOFIT_DOC_PV=2.91-33 -ROOFIT_QS_DOC_PV=3.00 -TMVA_DOC_PV=4.2.0 - -if [[ ${PV} == "9999" ]] ; then - inherit git-r3 - EVCS_OFFLINE=yes # we need exactly the same checkout as root itself - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - S="${WORKDIR}/${ROOT_PN}" -fi - -inherit eutils multilib virtualx - -DESCRIPTION="Documentation for ROOT Data Analysis Framework" -HOMEPAGE="http://root.cern.ch/drupal" -SRC_URI="${SRC_URI} - math? ( - http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf - http://root.cern.ch/download/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf - http://root.cern.ch/drupal/sites/default/files/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf ) - api? ( - ${HOMEPAGE}/sites/default/files/images/root6-banner.jpg - ${HOMEPAGE}/sites/all/themes/newsflash/images/info.png )" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="api +math +metric http" - -VIRTUALX_REQUIRED="api" - -DEPEND=" - ~sci-physics/root-${PV}[X,graphviz,opengl] - app-text/pandoc - app-text/texlive - dev-haskell/pandoc-citeproc[bibutils] - media-fonts/dejavu - virtual/pkgconfig" -RDEPEND="" - -DOC_DIR="/usr/share/doc/${ROOT_PN}-${PV}" - -src_unpack() { - if [[ ${PV} == "9999" ]] ; then - # we need to force sci-physics/root checkout here - git-r3_checkout "${EGIT_REPO_URI}" "${WORKDIR}/${P}" "sci-physics/root/0" - else - default - fi -} - -src_prepare() { - use api && epatch \ - "${FILESDIR}/${PN}-6.00.01-makehtml.patch" \ - "${FILESDIR}/${PN}-6.00.01-fillpatterns.patch" - # prefixify the configure script - sed -i \ - -e "s:/usr:${EPREFIX}/usr:g" \ - configure || die "prefixify configure failed" -} - -src_configure() { - # we need only to setup paths here, html docs doesn't depend on USE flags - if use api; then - ./configure \ - --prefix="${EPREFIX}/usr" \ - --etcdir="${EPREFIX}/etc/root" \ - --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" \ - --docdir="${EPREFIX}/usr/share/doc/${PF}" \ - --tutdir="${EPREFIX}/usr/share/doc/${PF}/examples/tutorials" \ - --testdir="${EPREFIX}/usr/share/doc/${PF}/examples/tests" \ - --with-llvm-config="${EPREFIX}/usr/bin/llvm-config" \ - --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" \ - --nohowto - fi -} - -src_compile() { - pdf_target=( primer users-guide ) - local pdf_size=pdfa4 - use metric || pdf_size=pdfletter - use math && pdf_target+=( minuit2 spectrum ) - use http && pdf_target+=( HttpServer ) - - for (( i=0; i<${#pdf_target[@]}; i++ )); do - emake -C documentation/"${pdf_target[i]}" "${pdf_size}" - done - - if use api; then - # video drivers may want to access hardware devices - cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g') - [[ -n "${cards}" ]] && addpredict "${cards}" - - ROOTSYS="${S}" Xemake html - # if root.exe crashes, return code will be 0 due to gdb attach, - # so we need to check if last html file was generated; - # this check is volatile and can't catch crash on the last file. - [[ -f htmldoc/tableDescriptor_st.html ]] || die "html doc generation crashed" - fi -} - -src_install() { - insinto "${DOC_DIR}" - - for (( i=0; i<${#pdf_target[@]}; i++ )); do - doins documentation/"${pdf_target[i]}"/*.pdf - done - unset pdf_target - - use math && doins \ - "${DISTDIR}/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf" \ - "${DISTDIR}/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf" \ - "${DISTDIR}/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf" - - if use api; then - # Install offline replacements for online messages - cp "${DISTDIR}"/{root6-banner.jpg,info.png} htmldoc/ || die "cp failed" - # too large data to copy - dodir "${DOC_DIR}/html" - mv htmldoc/* "${ED}${DOC_DIR}/html/" || die - docompress -x ${DOC_DIR}/html - fi -} diff --git a/app-doc/root-docs/root-docs-6.00.02.ebuild b/app-doc/root-docs/root-docs-6.00.02.ebuild deleted file mode 120000 index 0ee27bf30..000000000 --- a/app-doc/root-docs/root-docs-6.00.02.ebuild +++ /dev/null @@ -1 +0,0 @@ -root-docs-6.00.01-r1.ebuild
\ No newline at end of file diff --git a/app-doc/root-docs/root-docs-9999.ebuild b/app-doc/root-docs/root-docs-9999.ebuild index 0ee27bf30..8999fb8cd 120000..100644 --- a/app-doc/root-docs/root-docs-9999.ebuild +++ b/app-doc/root-docs/root-docs-9999.ebuild @@ -1 +1,137 @@ -root-docs-6.00.01-r1.ebuild
\ No newline at end of file +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +ROOT_PN="root" +ROOFIT_DOC_PV=2.91-33 +ROOFIT_QS_DOC_PV=3.00 +TMVA_DOC_PV=4.2.0 + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + EVCS_OFFLINE=yes # we need exactly the same checkout as root itself + EGIT_REPO_URI="http://root.cern.ch/git/root.git" +else + SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + S="${WORKDIR}/${ROOT_PN}-${PV}" +fi + +inherit eutils multilib virtualx + +DESCRIPTION="Documentation for ROOT Data Analysis Framework" +HOMEPAGE="http://root.cern.ch/drupal" +SRC_URI="${SRC_URI} + math? ( + http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf + http://root.cern.ch/download/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf + http://root.cern.ch/drupal/sites/default/files/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf ) + api? ( + ${HOMEPAGE}/sites/default/files/images/root6-banner.jpg + ${HOMEPAGE}/sites/all/themes/newsflash/images/info.png )" + +SLOT="0" +LICENSE="LGPL-2.1" +IUSE="api +math +metric http" + +VIRTUALX_REQUIRED="api" + +DEPEND=" + app-text/pandoc + app-text/texlive + dev-haskell/pandoc-citeproc[bibutils] + virtual/pkgconfig + api? ( + media-fonts/dejavu + ~sci-physics/root-${PV}[X,graphviz,opengl] + )" +RDEPEND="" + +DOC_DIR="/usr/share/doc/${ROOT_PN}-${PV}" + +src_unpack() { + if [[ ${PV} == "9999" ]] ; then + # we need to force sci-physics/root checkout here + git-r3_checkout "${EGIT_REPO_URI}" "${WORKDIR}/${P}" "sci-physics/root/0" + else + default + fi +} + +src_prepare() { + epatch \ + "${FILESDIR}/${PN}-6.00.01-makehtml.patch" \ + "${FILESDIR}/${PN}-6.02.05-jsroot.patch" + + # prefixify the configure script + sed -i \ + -e "s:/usr:${EPREFIX}/usr:g" \ + configure || die "prefixify configure failed" +} + +src_configure() { + # we need only to setup paths here, html docs doesn't depend on USE flags + if use api; then + ./configure \ + --prefix="${EPREFIX}/usr" \ + --etcdir="${EPREFIX}/etc/root" \ + --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + --tutdir="${EPREFIX}/usr/share/doc/${PF}/examples/tutorials" \ + --testdir="${EPREFIX}/usr/share/doc/${PF}/examples/tests" \ + --with-llvm-config="${EPREFIX}/usr/bin/llvm-config" \ + --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" \ + --nohowto + fi +} + +src_compile() { + pdf_target=( primer users-guide ) + local pdf_size=pdfa4 + use metric || pdf_size=pdfletter + use math && pdf_target+=( minuit2 spectrum ) + use http && pdf_target+=( HttpServer JSROOT ) + + local i + for (( i=0; i<${#pdf_target[@]}; i++ )); do + emake -C documentation/"${pdf_target[i]}" "${pdf_size}" + done + + if use api; then + # video drivers may want to access hardware devices + cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g') + [[ -n "${cards}" ]] && addpredict "${cards}" + + ROOTSYS="${S}" Xemake html + # if root.exe crashes, return code will be 0 due to gdb attach, + # so we need to check if last html file was generated; + # this check is volatile and can't catch crash on the last file. + [[ -f htmldoc/WindowAttributes_t.html ]] || die "html doc generation crashed" + fi +} + +src_install() { + insinto "${DOC_DIR}" + + local i + for (( i=0; i<${#pdf_target[@]}; i++ )); do + doins documentation/"${pdf_target[i]}"/*.pdf + done + unset pdf_target + + use math && doins \ + "${DISTDIR}/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf" \ + "${DISTDIR}/roofit_quickstart_${ROOFIT_QS_DOC_PV}.pdf" \ + "${DISTDIR}/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf" + + if use api; then + # Install offline replacements for online messages + cp "${DISTDIR}"/{root6-banner.jpg,info.png} htmldoc/ || die "cp failed" + # too large data to copy + dodir "${DOC_DIR}/html" + mv htmldoc/* "${ED}${DOC_DIR}/html/" || die + docompress -x ${DOC_DIR}/html + fi +} diff --git a/app-editors/neovim/ChangeLog b/app-editors/neovim/ChangeLog deleted file mode 100644 index ef2a88db7..000000000 --- a/app-editors/neovim/ChangeLog +++ /dev/null @@ -1,19 +0,0 @@ -# ChangeLog for app-editors/neovim -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 19 Jan 2015; Justin Lecher <jlec@gentoo.org> neovim-9999.ebuild: - Fix deps, https://github.com/neovim/neovim/issues/1166 - - 14 Jun 2014; Jelte Fennema (JelteF) <github-tech@jeltef.nl> - neovim-9999.ebuild: - Use CFLAGS needed to get a working executable - - 10 May 2014; Jelte Fennema <github@jeltef.nl> neovim-9999.ebuild: - Add new cmsgpack and lpeg dependencies to neovim. - -*neovim-9999 (11 Mar 2014) - - 11 Mar 2014; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, - +neovim-9999.ebuild: - initial commit diff --git a/app-editors/neovim/neovim-9999.ebuild b/app-editors/neovim/neovim-9999.ebuild deleted file mode 100644 index 3871687e9..000000000 --- a/app-editors/neovim/neovim-9999.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit cmake-utils flag-o-matic - -if [ "${PV}" = "9999" ]; then - EGIT_REPO_URI="git://github.com/neovim/neovim.git" - inherit git-r3 - KEYWORDS="" -else - SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -DESCRIPTION="Vim's rebirth for the 21st century" -HOMEPAGE="https://github.com/neovim/neovim" - -LICENSE="vim" -SLOT="0" -KEYWORDS="" -IUSE="" - -src_configure() { - append-flags "-DNDEBUG -Wno-error -D_FORTIFY_SOURCE=1" - cmake-utils_src_configure -} - -RDEPEND="app-admin/eselect-vi - sys-libs/ncurses" -DEPEND="${RDEPEND} - dev-lang/luajit - >=dev-libs/libuv-0.11.19 - dev-lua/lpeg - >=dev-lua/cmsgpack-9999" diff --git a/app-forensics/vine/ChangeLog b/app-forensics/vine/ChangeLog index 69dd1edb2..79761a29c 100644 --- a/app-forensics/vine/ChangeLog +++ b/app-forensics/vine/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> vine-1.0.ebuild: + Drop keywords, since gmetadom is hardmasked + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> metadata.xml, vine-1.0.ebuild: app-forensics/vine: Drop unneeded @system deps diff --git a/app-forensics/vine/vine-1.0.ebuild b/app-forensics/vine/vine-1.0.ebuild index ffbb99544..3730551e1 100644 --- a/app-forensics/vine/vine-1.0.ebuild +++ b/app-forensics/vine/vine-1.0.ebuild @@ -12,7 +12,7 @@ SRC_URI="http://bitblaze.cs.berkeley.edu/release/${P}/${P}.tar.gz" LICENSE="GPL-2+" SLOT="0" -KEYWORDS="~amd64" +KEYWORDS="" IUSE="" DEPEND=" diff --git a/app-portage/g-octave/g-octave-9999.ebuild b/app-portage/g-octave/g-octave-9999.ebuild index 102947c82..efc119bd5 100644 --- a/app-portage/g-octave/g-octave-9999.ebuild +++ b/app-portage/g-octave/g-octave-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7,3_1,3_2} pypy{1_9,2_0} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/app-text/jabref/ChangeLog b/app-text/jabref/ChangeLog deleted file mode 100644 index 81f975de3..000000000 --- a/app-text/jabref/ChangeLog +++ /dev/null @@ -1,112 +0,0 @@ -# ChangeLog for app-text/jabref -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*jabref-2.10 (11 Mar 2014) - - 11 Mar 2014; Nicolas Bock <nicolasbock@gentoo.org> +jabref-2.10.ebuild: - app-text/jabref-2.10: Version bump to new stable version. - - 28 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> jabref-2.9.2-r1.ebuild: - app-text/jabref: Removed docs USE flag from jabref-2.9.2-r1 The documentation - build system in this version is broken. The current beta version (2.10_beta2) - fixes this issue. - - 28 Jan 2014; Justin Lecher <jlec@gentoo.org> -jabref-2.10_beta.ebuild, - -jabref-2.10_beta-r1.ebuild, -jabref-2.10_beta2.ebuild, - jabref-2.10_beta2-r1.ebuild: - Add missing dep - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> - jabref-2.10_beta2-r1.ebuild: - app-text/jabref: Remove another bundled library. - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> - jabref-2.10_beta2-r1.ebuild: - app-text/jabref: Remove another bundled lib. - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> jabref-2.10_beta-r1.ebuild, - jabref-2.10_beta2-r1.ebuild: - app-text/jabref: Do not remove unjarlib target yet. We need to first replace - all bundled libs with portage versions. - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> jabref-2.10_beta-r1.ebuild, - jabref-2.10_beta2-r1.ebuild: - app-text/jabref: Fix bug in java-pkg_getjars; use a '-' instead of ':' to - specify slot. - -*jabref-2.10_beta-r1 (03 Jan 2014) - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> - +jabref-2.10_beta-r1.ebuild: - app-text/jabref-2.10_beta-r1: Adding revised ebuild for first beta. - - 03 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> - jabref-2.10_beta2-r1.ebuild: - app-text/jabref-2.10_beta2-r1: Added back slotted fontbox package, but fixed - java-pkg_getjars. - - 03 Jan 2014; Justin Lecher <jlec@gentoo.org> jabref-2.10_beta2-r1.ebuild, - metadata.xml: - Fix fontbox SLOT - -*jabref-2.10_beta2-r1 (02 Jan 2014) - - 02 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> - +jabref-2.10_beta2-r1.ebuild: - app-text/jabref-2.10_beta2-r1: Started to remove bundled libraries. - -*jabref-2.10_beta2 (02 Jan 2014) - - 02 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> +jabref-2.10_beta2.ebuild: - app-text/jabref-2.10_beta2: Added new beta. - -*jabref-2.9.2-r1 (02 Jan 2014) - - 02 Jan 2014; Nicolas Bock <nicolasbock@gentoo.org> +jabref-2.9.2-r1.ebuild: - app-text/jabref-2.9.2-r1: Small cleanup. - - 20 Dec 2013; Nicolas Bock <nicolasbock@gentoo.org> -jabref-2.9.2-r1.ebuild, - -jabref-2.9.2.ebuild: - app-text/jabref: Moved jabref-2.9.2 to x86. - - 13 Dec 2013; Nicolas Bock <nicolasbock@gentoo.org> metadata.xml: - app-text/jabref: updated maintainter email to gentoo.org. - - 17 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.10_beta.ebuild: - Fixed bug in jabref ebuild. - -*jabref-2.10_beta (17 Jun 2013) - - 17 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.10_beta.ebuild, - -jabref-2.10b.ebuild: - Renamed ebuild to conform with Gentoo Ebuild Naming Convention (TM). - http://devmanual.gentoo.org/ebuild-writing/file-format/ - - 08 Apr 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.10b.ebuild: - Jabref-2.10b does not build anymore with Java 6. Bumping java requirement to - java 7. - -*jabref-2.10b (05 Apr 2013) - - 05 Apr 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.10b.ebuild: - Adding jabref-2.10b (beta) ebuild. - - 20 Feb 2013; Sébastien Fabbro <bicatali@gentoo.org> jabref-2.9.2-r1.ebuild: - app-text/jabref: Fixed doc generation, keyword amd64-linux and x86-linux - -*jabref-2.9.2-r1 (15 Feb 2013) - - 15 Feb 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.9.2-r1.ebuild, - jabref-2.9.2.ebuild: - Added ~x86 KEYWORD and API/README do docs. - - 14 Feb 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.9.2.ebuild, - metadata.xml: - Added changes suggested by Christoph Junghans <ottxor@gentoo.org>. - -*jabref-2.9.2 (14 Feb 2013) - - 14 Feb 2013; Nick <nbock@gentoo.org> +jabref-2.9.2.ebuild, +metadata.xml: - Adding first draft version of jabref-2.9.2 ebuild. This version is loosely - based on jabref-2.8.1.ebuild attached to bug 385751 on bugs.gentoo.org. diff --git a/app-text/jabref/Manifest b/app-text/jabref/Manifest deleted file mode 100644 index 1ee65b5a2..000000000 --- a/app-text/jabref/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST JabRef-2.10-src.tar.bz2 16769469 SHA256 09b57afcfeb1730b58a887dc28f0f4c803e9c00fade1f57245ab70e2a98ce6ad SHA512 72eee8fb08040fc7bfd395729d3c74f0a8841c90d5aa6e6e8d8e68ddcc1ffe1f6659a045aa951d51deffe266ee0b1ff844c4fdf36537d5463de6b361803bb942 WHIRLPOOL db0edafb63a6c37b001b071693278c2c0054ab20ae0744147fe8b1a828f1e575b7751d5aabca05a640fc7c099ce9402df835c6e81a0c3b21b7aa700110c426de -DIST JabRef-2.10b2-src.tar.bz2 16796962 SHA256 296a55bd480c252facfae25b6ee36b4d490ec6e1852d79609b01d6ad6d12d941 SHA512 611456d0fcc310987876b0210537ed5cc648bed43de543b465b93613bf6f2449ba4514e3086dc633005e630216ac776f716671b9085623940e380b5133cb4323 WHIRLPOOL 220548bf28ffef14e488838fbe7b2e130043518369de9bc95fc7ee7207f49a6995dd59f3e2857e2afabe3762739e6b0ecfc36ead5a46114bcf1932dfe08e25eb -DIST JabRef-2.9.2-src.tar.bz2 16664284 SHA256 12bc7e489709bc6f57327bf8e15c6bc9ceaa600369dca6452b7c13d792215e83 SHA512 40eb5d3f3528e92c4d5c62abce12d87ea63b84a58778a32151cd1af2a0198c49aa354ee295f8b3c9449d5b078f7119163babd3c29f358b0d56b3776980292463 WHIRLPOOL d2115e497066f31a3772085510f6820e46a55fbe36778471e6c81a4973f45607761cca80655cfefffb1308f65315ef72fb17791fe964d004826f345322ca0dcf diff --git a/app-text/jabref/jabref-2.10.ebuild b/app-text/jabref/jabref-2.10.ebuild deleted file mode 100644 index 47b2e1643..000000000 --- a/app-text/jabref/jabref-2.10.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-text/jabref/jabref-2.10_beta3.ebuild,v 1.1 2014/02/19 04:10:12 nicolasbock Exp $ - -EAPI=5 - -JAVA_ANT_REWRITE_CLASSPATH="true" - -inherit eutils java-pkg-2 java-ant-2 java-utils-2 - -MY_PV="${PV/_beta/b}" - -DESCRIPTION="Java GUI for managing BibTeX and other bibliographies" -HOMEPAGE="http://jabref.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/JabRef-${MY_PV}-src.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc" - -COMMON_DEP=" - dev-java/antlr:3 - dev-java/fontbox:1.7 - dev-java/jempbox:1.7 - dev-java/log4j:0 - dev-java/spin:0 - " - -DEPEND=" - >=virtual/jdk-1.6 - ${COMMON_DEP}" - -RDEPEND=" - >=virtual/jre-1.6 - ${COMMON_DEP}" - -S="${WORKDIR}/${PN}-${MY_PV}" - -java_prepare() { - # Remove bundled dependencies. - rm lib/antlr*.jar || die - rm lib/fontbox*.jar || die - rm lib/jempbox*.jar || die - rm lib/spin.jar || die - - # Remove unjarlib target (do this only once we have removed all - # bundled dependencies in lib). - #sed -i -e 's:depends="build, unjarlib":depends="build":' build.xml -} - -src_compile() { - local EXTERNAL_JARS="antlr-3,fontbox-1.7,jempbox-1.7,spin" - local CLASSPATH="$(java-pkg_getjars --with-dependencies ${EXTERNAL_JARS})" - eant \ - -Dgentoo.classpath=${CLASSPATH} \ - jars \ - $(usex doc docs "") -} - -src_install() { - java-pkg_newjar build/lib/JabRef-${MY_PV}.jar - - use doc && java-pkg_dojavadoc build/docs/API - dodoc src/txt/README - - java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef - newicon src/images/JabRef-icon-48.png JabRef-icon.png - make_desktop_entry ${PN} JabRef JabRef-icon Office -} diff --git a/app-text/jabref/jabref-2.10_beta2-r1.ebuild b/app-text/jabref/jabref-2.10_beta2-r1.ebuild deleted file mode 100644 index 7ac1db143..000000000 --- a/app-text/jabref/jabref-2.10_beta2-r1.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -JAVA_ANT_REWRITE_CLASSPATH="true" - -inherit eutils java-pkg-2 java-ant-2 java-utils-2 - -MY_PV="${PV/_beta/b}" - -DESCRIPTION="Java GUI for managing BibTeX and other bibliographies" -HOMEPAGE="http://jabref.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/JabRef-${MY_PV}-src.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc" - -COMMON_DEP=" - dev-java/antlr:3 - dev-java/fontbox:1.7 - dev-java/jempbox:1.7 - dev-java/log4j:0 - dev-java/spin:0 - " - -DEPEND=" - >=virtual/jdk-1.6 - ${COMMON_DEP}" - -RDEPEND=" - >=virtual/jre-1.6 - ${COMMON_DEP}" - -S="${WORKDIR}/${PN}-${MY_PV}" - -java_prepare() { - # Remove bundled dependencies. - rm lib/antlr*.jar || die - rm lib/fontbox*.jar || die - rm lib/jempbox*.jar || die - rm lib/spin.jar || die - - # Remove unjarlib target (do this only once we have removed all - # bundled dependencies in lib). - #sed -i -e 's:depends="build, unjarlib":depends="build":' build.xml -} - -src_compile() { - local EXTERNAL_JARS="antlr-3,fontbox-1.7,jempbox-1.7,spin" - local CLASSPATH="$(java-pkg_getjars --with-dependencies ${EXTERNAL_JARS})" - eant \ - -Dgentoo.classpath=${CLASSPATH} \ - jars \ - $(usex doc docs "") -} - -src_install() { - java-pkg_newjar build/lib/JabRef-${MY_PV}.jar - - use doc && java-pkg_dojavadoc build/docs/API - dodoc src/txt/README - - java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef - newicon src/images/JabRef-icon-48.png JabRef-icon.png - make_desktop_entry ${PN} JabRef JabRef-icon Office -} diff --git a/app-text/jabref/jabref-2.9.2-r1.ebuild b/app-text/jabref/jabref-2.9.2-r1.ebuild deleted file mode 100644 index 27395fad8..000000000 --- a/app-text/jabref/jabref-2.9.2-r1.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EANT_BUILD_TARGET="jars" - -inherit eutils java-pkg-2 java-ant-2 java-utils-2 - -DESCRIPTION="Java GUI for managing BibTeX and other bibliographies" -HOMEPAGE="http://jabref.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/JabRef-${PV}-src.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -DEPEND=">=virtual/jdk-1.6" -RDEPEND=">=virtual/jre-1.6" - -src_install() { - java-pkg_newjar build/lib/JabRef-${PV}.jar - java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef - newicon src/images/JabRef-icon-48.png JabRef-icon.png - make_desktop_entry ${PN} JabRef JabRef-icon Office -} diff --git a/app-vim/vim-gromacs/ChangeLog b/app-vim/vim-gromacs/ChangeLog index b9c719358..74853f725 100644 --- a/app-vim/vim-gromacs/ChangeLog +++ b/app-vim/vim-gromacs/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for app-vim/vim-gromacs -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + app-vim/vim-gromacs: Add github to remote-id in metadata.xml + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> vim-gromacs-9999.ebuild: removed empty line diff --git a/app-vim/vim-gromacs/metadata.xml b/app-vim/vim-gromacs/metadata.xml index 046c58b8a..de2225605 100644 --- a/app-vim/vim-gromacs/metadata.xml +++ b/app-vim/vim-gromacs/metadata.xml @@ -5,4 +5,7 @@ <longdescription lang="en"> VIM syntax plugin which provides syntax highlighting for the gromacs files. </longdescription> + <upstream> + <remote-id type="github">HubLot/vim-gromacs</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/eigen/ChangeLog b/dev-cpp/eigen/ChangeLog index 8c4143f8d..0f40946a6 100644 --- a/dev-cpp/eigen/ChangeLog +++ b/dev-cpp/eigen/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/dev-cpp/eigen/ChangeLog,v 1.44 2011/03/25 16:01:28 jlec Exp $ +*eigen-3.2.4 (16 Apr 2015) + + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> +eigen-3.2.4.ebuild, + -eigen-3.1.4.ebuild, -eigen-3.2.1-r2.ebuild: + dev-cpp/eigen: Drop old; Version Bump + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -eigen-3.2.0-r1.ebuild, eigen-9999.ebuild, metadata.xml: dev-cpp/eigen: Drop old; fix SLOT operators diff --git a/dev-cpp/eigen/Manifest b/dev-cpp/eigen/Manifest index 3380c85a0..c3cd8343e 100644 --- a/dev-cpp/eigen/Manifest +++ b/dev-cpp/eigen/Manifest @@ -1,6 +1,4 @@ -DIST eigen-3.1.4-cmake.patch 3294 SHA256 2be458affc18b833f31b767b823b1e490e6d0115d040a802eb334c5884c8ad88 SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6 WHIRLPOOL ae78de8cc7f3b58749dcfefc6ac4fd96cca84e048b0337b1590d5097b4838c751c237844b4aa996ce75d10e830d406fa52ef68f509d0ae8e21a75fc589a1a6d3 -DIST eigen-3.1.4.tar.bz2 1052745 SHA256 80ea2d76b649e9ea413090f96c32bd408f07872b50cc6844bc3136e635492414 SHA512 555aea79b5dcdb8a1c15f223bb64191d69012a9f895e15218a2e0478bc7dc3d8a61d257c072ca29cd9e5788541ac0540af45320cfdb4095360dce841dfaba692 WHIRLPOOL b0e52eb7f6a89a75e67a3f0f3ad73abd0e51bfc639960c9f5699ae48c628e6160f6b3059178f4fa5b5212357b7cd5fe31082f06e0bfe1557d4dad1332999d62f -DIST eigen-3.2.1-cmake.patch 3294 SHA256 2be458affc18b833f31b767b823b1e490e6d0115d040a802eb334c5884c8ad88 SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6 WHIRLPOOL ae78de8cc7f3b58749dcfefc6ac4fd96cca84e048b0337b1590d5097b4838c751c237844b4aa996ce75d10e830d406fa52ef68f509d0ae8e21a75fc589a1a6d3 -DIST eigen-3.2.1.tar.bz2 1138080 SHA256 66e6f2ede78d0ef650ae95aa570f548c095690b011000f9163c32618736c928a SHA512 0c60139d23c6e51883d06c92d4c089f1b3eb3b75738d7064cfa3bc79148dd23bb00c98a53636fe396d89a3734d950ef938993c5662181d5327a8ae930afeb4e5 WHIRLPOOL 85f25256732bf995b9431dfae6c44d2c42c7f610b351854f1c0e92ebe795578a9d0dac3d2444b535760bee0dc0c009808fcfe7e74a03737291777ff47a959b17 DIST eigen-3.2.2-cmake.patch 3294 SHA256 2be458affc18b833f31b767b823b1e490e6d0115d040a802eb334c5884c8ad88 SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6 WHIRLPOOL ae78de8cc7f3b58749dcfefc6ac4fd96cca84e048b0337b1590d5097b4838c751c237844b4aa996ce75d10e830d406fa52ef68f509d0ae8e21a75fc589a1a6d3 DIST eigen-3.2.2.tar.bz2 1142184 SHA256 929326dcf23a5b9125f898858f2b2b8e4685173c9a5963f86e593791abb621b1 SHA512 95e40a1abc88ec7790755f0156d9ab414fd61c2b476f38e71b91fe5135328109fa348473748a5440a163f0b5da101b380f34784533ad9326f1ccea3de0c11a99 WHIRLPOOL 013bf7b8489be191fd471216048eed0aa1ac3e108ff84f3ddeb91b91e0ecb9d53bb2dedf31ec8cfb92c3daf654b6980776f1d3c3b29eb8ae39321bc2e1b3f2bd +DIST eigen-3.2.4-cmake.patch 3294 SHA256 2be458affc18b833f31b767b823b1e490e6d0115d040a802eb334c5884c8ad88 SHA512 229c0c1f3d95ae505b5accd1aeba19f59a064218cf9b0d844dbc4c660a4cddb666f818268ba1899370877034a70a87317ca8bf14822e3b85d0bbe7f3bb5c7cf6 WHIRLPOOL ae78de8cc7f3b58749dcfefc6ac4fd96cca84e048b0337b1590d5097b4838c751c237844b4aa996ce75d10e830d406fa52ef68f509d0ae8e21a75fc589a1a6d3 +DIST eigen-3.2.4.tar.bz2 1147976 SHA256 d64332c92e31803d2c59f6646ed893965c666acfc7c284e4f5e9ffbb4d148922 SHA512 decf50a54011a8275d6d00194e98933b1184e665802892fe87515590ab92843d538d5170afc549730193dc93ae350674eb59d7d324e1f7d608867c7208c5509a WHIRLPOOL 8625bc0d4c171f7a80be070f72651ac8b58b7f4112980cb8c406d1e01f14a10efdf957c6c6fd170da8a595bc86c0016863f3815cb75db272ed789d18b97d8098 diff --git a/dev-cpp/eigen/eigen-3.2.1-r2.ebuild b/dev-cpp/eigen/eigen-3.2.1-r2.ebuild deleted file mode 120000 index eafd77401..000000000 --- a/dev-cpp/eigen/eigen-3.2.1-r2.ebuild +++ /dev/null @@ -1 +0,0 @@ -eigen-9999.ebuild
\ No newline at end of file diff --git a/dev-cpp/eigen/eigen-3.1.4.ebuild b/dev-cpp/eigen/eigen-3.2.4.ebuild index eafd77401..eafd77401 120000 --- a/dev-cpp/eigen/eigen-3.1.4.ebuild +++ b/dev-cpp/eigen/eigen-3.2.4.ebuild diff --git a/dev-cpp/icnc/ChangeLog b/dev-cpp/icnc/ChangeLog index 8de9e15ef..72d7f2105 100644 --- a/dev-cpp/icnc/ChangeLog +++ b/dev-cpp/icnc/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-cpp/icnc: Add github to remote-id in metadata.xml + 08 Feb 2015; Christoph Junghans <ottxor@gentoo.org> icnc-9999.ebuild: fix bug #539318 diff --git a/dev-cpp/icnc/metadata.xml b/dev-cpp/icnc/metadata.xml index 745b9e1ce..c3e80bdd7 100644 --- a/dev-cpp/icnc/metadata.xml +++ b/dev-cpp/icnc/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">icnc/icnc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/glazedlists/ChangeLog b/dev-java/glazedlists/ChangeLog deleted file mode 100644 index 92e286d3f..000000000 --- a/dev-java/glazedlists/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for dev-java/glazedlists -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*glazedlists-1.8.0 (20 Feb 2014) - - 20 Feb 2014; Nicolas Bock <nicolasbock@gentoo.org> - +files/glazedlists-1.8.0-build.xml.patch, +glazedlists-1.8.0.ebuild, - +metadata.xml: - dev-java/glazedlists-1.8.0: Version bump. Fixing bug 430062 [1]. These are - dmol's ebuild and patch. Thanks! [1] - https://bugs.gentoo.org/show_bug.cgi?id=430062 diff --git a/dev-java/glazedlists/Manifest b/dev-java/glazedlists/Manifest deleted file mode 100644 index 61623b304..000000000 --- a/dev-java/glazedlists/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST glazedlists-1.8.0-source_java15.zip 1169436 SHA256 1afbded7118d3026a666622c8a6aa46bc41ae09c9e832125fe3dc3a3dba5d42b SHA512 3fc3f339a248a8aad897409d752464d60b504474ae1e4d99fa7fbb41d767928137711d5d9979154b53d677e42746e2df2dfefdc71fa4a8017ec70ab23dc4b6a5 WHIRLPOOL b5d37cebde2be0a57032be29667763d97b54f3d1a5b48e40e09b5ce09e3ae654776c4d6817c09c018fad7fb0d9bdbdde6b6198e4405250fcc2451d008c90fb40 diff --git a/dev-java/glazedlists/files/glazedlists-1.8.0-build.xml.patch b/dev-java/glazedlists/files/glazedlists-1.8.0-build.xml.patch deleted file mode 100644 index 624df5ee9..000000000 --- a/dev-java/glazedlists/files/glazedlists-1.8.0-build.xml.patch +++ /dev/null @@ -1,57 +0,0 @@ ---- build.xml.orig 2009-01-25 18:14:28.000000000 -0700 -+++ build.xml 2014-02-20 11:22:45.000000000 -0700 -@@ -164,14 +164,18 @@ -
- <mkdir dir="tools"/>
- <!--download the BND library for creating entries in the manifest.mf file which make it a compliant OSGi bundle. See http://www.osgi.org/ -->
-+ <!--
- <java classname="ca.odell.glazedlists.impl.HttpClient">
- <classpath path="${classes.dir}"/>
- <arg value="https://glazedlists.dev.java.net/files/documents/1073/110958/bnd.jar"/>
- <arg value="tools/bnd.jar"/>
- </java>
-+ -->
-
- <!-- prepare the bnd task which generates OSGi bundle JARs -->
-+ <!--
- <taskdef resource="aQute/bnd/ant/taskdef.properties" classpath="tools/bnd.jar"/>
-+ -->
-
- <!-- create a normal jar file -->
- <jar destfile="${target.dir}/${jar.file}" update="true" index="true">
-@@ -184,13 +188,19 @@ - </jar>
-
- <!-- use the BND tool to generate an OSGi jar from scratch, using the original JAR file as input -->
-+ <!--
- <bnd classpath="${target.dir}/${jar.file}" output="${target.dir}/${jar.file}.osgi" exceptions="true" files="glazedlists.bnd"/>
-+ -->
-
- <!-- delete the original jar file -->
-+ <!--
- <delete file="${target.dir}/${jar.file}"/>
-+ -->
-
- <!-- rename the OSGi Bundle to the orignal jar file's name -->
-+ <!--
- <move file="${target.dir}/${jar.file}.osgi" toFile="${target.dir}/${jar.file}"/>
-+ -->
- </target>
-
- <!-- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-@@ -201,7 +211,7 @@ - description="Compile the default components of the source.">
- </target>
-
-- <target name="compileall" depends="core,migrationkit,swing,io,calculation,swt,ktable,issuesbrowser,swinglabs,hibernate,icu4j"
-+ <target name="compileall" depends="core,migrationkit,swing,io"
- description="Compile all components of the source.">
- </target>
-
-@@ -1032,4 +1042,4 @@ - </delete>
- </target>
-
--</project> -\ No newline at end of file -+</project>
diff --git a/dev-java/glazedlists/glazedlists-1.8.0.ebuild b/dev-java/glazedlists/glazedlists-1.8.0.ebuild deleted file mode 100644 index 16786dce8..000000000 --- a/dev-java/glazedlists/glazedlists-1.8.0.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="5" -JAVA_PKG_IUSE="doc source" - -inherit eutils java-pkg-2 java-ant-2 - -DESCRIPTION="A toolkit for list transformations" -HOMEPAGE="http://publicobject.com/glazedlists/" -SRC_URI="http://java.net/downloads/${PN}/${P}/${P}-source_java15.zip" -LICENSE="|| ( LGPL-2.1 MPL-1.1 )" -SLOT="0" -KEYWORDS="~amd64" -# TODO: there are extensions, some supported in the java-experimental ebuild -IUSE="" - -RDEPEND=">=virtual/jre-1.5" -DEPEND=">=virtual/jdk-1.5 - app-arch/unzip" - -S="${WORKDIR}" - -JAVA_PKG_BSFIX="off" - -# tests seem to be buggy -RESTRICT="test" - -java_prepare() { - # disable autodownloading of dependencies - # sort out test targets - epatch "${FILESDIR}/${P}-build.xml.patch" -} - -EANT_DOC_TARGET="docs" - -src_install() { - java-pkg_newjar "target/${PN}_java15.jar" - - if use doc; then - dohtml readme.html || die - java-pkg_dojavadoc "target/docs/api" - fi - if use source; then - # collect source folders for all the used extensions - local source_folders="source/ca extensions/treetable/source/*" - java-pkg_dosrc ${source_folders} - fi -} diff --git a/dev-java/gluegen/ChangeLog b/dev-java/gluegen/ChangeLog index df8ea936c..d23d7be03 100644 --- a/dev-java/gluegen/ChangeLog +++ b/dev-java/gluegen/ChangeLog @@ -1,7 +1,21 @@ # ChangeLog for dev-java/gluegen -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/gluegen: Add github to remote-id in metadata.xml + + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> + +files/2.2.4-dont-copy-jars.patch, +files/2.2.4-dont-strip.patch, + +files/2.2.4-dont-test-archive.patch, gluegen-2.2.4.ebuild: + dev-java/gluegen: rework ebuild starting from 2.1.4 + +*gluegen-2.2.4 (03 Apr 2015) + + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> + +gluegen-2.2.4.ebuild: + dev-java/gluegen: version bump + 03 Nov 2014; Justin Lecher <jlec@gentoo.org> gluegen-1_p20080421.ebuild, gluegen-2.0_rc8.ebuild, -gluegen-2.1.2.ebuild, gluegen-2.1.4.ebuild: Bump to EAPI=5; drop old diff --git a/dev-java/gluegen/Manifest b/dev-java/gluegen/Manifest index 9c3455f9f..763f377fd 100644 --- a/dev-java/gluegen/Manifest +++ b/dev-java/gluegen/Manifest @@ -1,3 +1,4 @@ DIST gluegen-2.1.4.tar.gz 42235490 SHA256 18826c58b136dc44089346791e6ed57c7e2828a1ee4d6279d15e26cb12c2b926 SHA512 196478de92686b168d6f35e2e7141a31f682d22a7f96b5bc84d46905c42eb5bf25bacd74ccc51975fc7894e2e0ba2e236a4a68c101bbabaaa5193e4bdc50f607 WHIRLPOOL c05e723d85021f464d49b48fc2a0f11e5979d42355e6ac0d7437c40407d34829d5a531bf2687d47fa29cd8affd14d400a333fe90624a7ecda832a1cf76696440 +DIST gluegen-2.2.4.tar.gz 43113191 SHA256 e931cf9924076a9cbf8ea040f8f5ab22edb9eed3c56f35806c8508fac0b70cc9 SHA512 53e973ca8478f4513f9662d1375406af95f2181dae3fb3e3247e4752960e60e741f7eae36981967dba10ac7bc3dc0e85c159c193323c177ce733a9eb0540b98b WHIRLPOOL 62aa65b0cea7eb9186e6aaf90b9c453656327b1a1562d0ec7ac91deaf91f4a3213bd52862ca792878cae9ea2e22ea94cf0b22dd117bac0535abe954fdc71318b DIST gluegen-20080421.tar.bz2 1044951 SHA256 15ef8f499afc2256615bf453b318fbc22fbe146293ca4c6ca87c98577bf5a026 SHA512 3bffb55ec8723ac452b38d41f1bc596ee3065b1f791b8c7aec06d8acffdfd83d81553d9090fc273b56fa748b501f3a25f8dc4736bad291bc77f15d211957470d WHIRLPOOL 6171345011955517e84c9b82d187e2fe0c96fc1733ee6427248159fd8456472ea15c9cd223bd784a33478a4cfc568ddcfd73ea0addd13daa1b483b7a8cfe66c1 DIST gluegen-v2.0-rc8.tar.7z 35196696 SHA256 8cae313dfe03d13cdd165aa7d9e698897affae290e7ce7c4a27479fe6522c0dc SHA512 9845246f9776139cd205f197203349eba28150d5018bd086e6f7484df765b4cd122d78fbf836780a10b0d6395c645eb8ec7a256b8f832453c0b20155a11b3a0f WHIRLPOOL 427d6ef990a0702b81a4f62a74dce628594144507392cb8d25b5af5cbeca186faef987c809eeb1faf5d99b8f867213c7786d43f4418f85d04ac68d96595b83b3 diff --git a/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch b/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch new file mode 100644 index 000000000..dca10dce8 --- /dev/null +++ b/dev-java/gluegen/files/2.2.4-dont-copy-jars.patch @@ -0,0 +1,17 @@ +diff --git a/gluegen-2.1.4_rc01/make/build.xml b/gluegen-2.1.4_rc01/make/build.xml +index 55ef270..bce6d12 100644 +--- a/gluegen-2.1.4_rc01/make/build.xml ++++ b/gluegen-2.1.4_rc01/make/build.xml +@@ -806,12 +806,6 @@ + </fileset> + </jar> + +- <!-- Copy antlr.jar into build directory for convenience so +- gluegen.jar can be run via "java -jar". antlr.jar is +- referenced via a Class-Path entry in the Manifest of +- gluegen.jar. --> +- <copy file="${antlr.jar}" todir="${build}" /> +- + <!-- copy a jnlp with empty codebase into build folder for local testing + overwrite property in gluegen.proerpties if desired --> + <property name="gluegen.jnlp.codebase" value=""/> diff --git a/dev-java/gluegen/files/2.2.4-dont-strip.patch b/dev-java/gluegen/files/2.2.4-dont-strip.patch new file mode 100644 index 000000000..02020d2ae --- /dev/null +++ b/dev-java/gluegen/files/2.2.4-dont-strip.patch @@ -0,0 +1,22 @@ +diff --git a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml +index 8b8b82e..ec39aeb 100755 +--- a/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml ++++ b/gluegen-2.1.4_rc01/make/gluegen-cpptasks-base.xml +@@ -1511,17 +1511,6 @@ + - Helper strip.libraries for stripping off debug information + --> + <target name="gluegen.cpptasks.striplibs" depends="gluegen.cpptasks.initialize" if="c.strip.libraries"> +- <echo message="Strip symbols from libs in ${libdir}" /> +- <apply dir="${libdir}" executable="${c.strip.tool}" parallel="false" +- failonerror="true"> +- <arg line="${c.strip.args}"/> +- <fileset dir="${libdir}"> +- <include name="**/*.so"/> <!-- unix --> +- <include name="**/*.dll"/> <!-- windows --> +- <include name="**/*.dylib"/> <!-- macosx --> +- <include name="**/*.jnilib"/> <!-- macosx --> +- </fileset> +- </apply> + </target> + + <!-- ================================================================== --> diff --git a/dev-java/gluegen/files/2.2.4-dont-test-archive.patch b/dev-java/gluegen/files/2.2.4-dont-test-archive.patch new file mode 100644 index 000000000..3eb061f27 --- /dev/null +++ b/dev-java/gluegen/files/2.2.4-dont-test-archive.patch @@ -0,0 +1,16 @@ +diff --git a/gluegen-2.1.4_rc01/make/build-test.xml b/gluegen-2.1.4_rc01/make/build-test.xml +index 31dc773..e872a0a 100644 +--- a/gluegen-2.1.4_rc01/make/build-test.xml ++++ b/gluegen-2.1.4_rc01/make/build-test.xml +@@ -614,9 +614,11 @@ chmod 644 ${results}/* \${line.separator} + + <!-- updates / create the test results zip file --> + <target name="test-zip-archive" depends="init"> ++ <!-- + <archive.7z destfile="${build}/${test.archive.name}.7z" + basedir="${project.root}" + includes="${rootrel.build}/test/results ${rootrel.build}/test/results-x64 ${rootrel.build}/test/results-x32" /> ++ --> + </target> + + diff --git a/dev-java/gluegen/gluegen-2.2.4.ebuild b/dev-java/gluegen/gluegen-2.2.4.ebuild new file mode 100644 index 000000000..e2f5a47d3 --- /dev/null +++ b/dev-java/gluegen/gluegen-2.2.4.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +JAVA_PKG_IUSE="doc source test" +WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Automatically generate the JNI code necessary to call C libraries" +HOMEPAGE="http://jogamp.org/gluegen/www/" +SRC_URI="https://github.com/sgothel/gluegen/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="2.2" +KEYWORDS="~amd64 ~x86" +IUSE="" + +COMMON_DEP=" + dev-java/ant-core:0 + dev-java/antlr:0" +RDEPEND="${COMMON_DEP} + >=virtual/jre-1.5" + +DEPEND="${COMMON_DEP} + >=virtual/jdk-1.5 + dev-java/cpptasks:0 + test? ( + dev-java/junit:4 + dev-java/ant-junit4 + )" + +JAVA_ANT_REWRITE_CLASSPATH="yes" +EANT_BUILD_XML="make/build.xml" +EANT_BUILD_TARGET="all.no_junit" +EANT_DOC_TARGET="" +EANT_GENTOO_CLASSPATH="antlr,ant-core" +EANT_NEEDS_TOOLS="yes" +EANT_TEST_TARGET="junit.run" +EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},junit-4" +EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}{,-rt}.jar" +EANT_EXTRA_ARGS="-Dc.strip.libraries=false" + +java_prepare() { + rm -rf make/lib + epatch "${FILESDIR}"/${PV}-*.patch + java-ant_bsfix_files "${S}/make/build-test.xml" +} + +src_test() { + EANT_TASKS="ant-junit4" java-pkg-2_src_test +} + +src_install() { + java-pkg_dojar build/${PN}{,-rt}.jar + java-pkg_doso build/obj/*.so + + use doc && dohtml -r doc/manual + use source && java-pkg_dosrc src/java/* + + # for building jogl + insinto /usr/share/${PN}-${SLOT}/make + doins -r make/* + insinto /usr/share/${PN}-${SLOT}/build + doins build/artifact.properties +} diff --git a/dev-java/gluegen/metadata.xml b/dev-java/gluegen/metadata.xml index d29f3a9fd..d6bbcc249 100644 --- a/dev-java/gluegen/metadata.xml +++ b/dev-java/gluegen/metadata.xml @@ -13,4 +13,7 @@ on the IR before glue code emission. GlueGen is currently powerful enough to bind even low-level APIs such as the Java Native Interface (JNI) and the AWT Native Interface (JAWT) back up to the Java programming language. </longdescription> + <upstream> + <remote-id type="github">sgothel/gluegen</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/hdf-java/hdf-java-2.9.ebuild b/dev-java/hdf-java/hdf-java-2.9.ebuild index 3bfe5610d..bcaad9716 100644 --- a/dev-java/hdf-java/hdf-java-2.9.ebuild +++ b/dev-java/hdf-java/hdf-java-2.9.ebuild @@ -10,7 +10,7 @@ inherit autotools eutils fdo-mime java-pkg-2 DESCRIPTION="Java interface to the HDF5 library" HOMEPAGE="http://www.hdfgroup.org/hdf-java-html/index.html" -SRC_URI="http://www.hdfgroup.org/ftp/HDF5/prev-releases/HDF-JAVA/hdf-java-2.9/src/${P}-src.tar" +SRC_URI="http://www.hdfgroup.org/ftp/HDF5/releases/HDF-JAVA/hdf-java-2.9/src/${P}-src.tar" LICENSE="NCSA-HDF" SLOT="0" diff --git a/dev-java/jcip-annotations/ChangeLog b/dev-java/jcip-annotations/ChangeLog deleted file mode 100644 index a5e7e0d53..000000000 --- a/dev-java/jcip-annotations/ChangeLog +++ /dev/null @@ -1,20 +0,0 @@ -# ChangeLog for dev-java/jcip-annotations -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 03 Nov 2014; Justin Lecher <jlec@gentoo.org> jcip-annotations-1.0-r1.ebuild: - Bump to EAPI=5 - - 02 Jun 2013; <calchan@gentoo.org> jcip-annotations-1.0-r1.ebuild: - Fixed SRC_URI. - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> jcip-annotations-1.0-r1.ebuild, - metadata.xml: - Correct license name - -*jcip-annotations-1.0-r1 (14 May 2012) - - 14 May 2012; Sébastien Fabbro <bicatali@gentoo.org> - +jcip-annotations-1.0-r1.ebuild, +metadata.xml: - import from the java overlay - diff --git a/dev-java/jcip-annotations/Manifest b/dev-java/jcip-annotations/Manifest deleted file mode 100644 index 38cc2891e..000000000 --- a/dev-java/jcip-annotations/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST jcip-annotations-1.0-src.jar 4998 SHA256 221f5cbe0b00a4c5f3c8870639de3573223fb9aa2636c631f901302fd4339efc SHA512 7c42b0669600fdca3cc5fdd6f1ea40ed79a0c448067474bf3cc60c9405565db793ea33ee816385314c5838bf807bdd229d0fe92d5392d7de08e9f8f760449b35 WHIRLPOOL 85f7c9722c96ccbcc8b73e51ca960d938c3f5e316873f46735e5f10d1cc858baa815e473a248f9bfea2502c6e92610ed9a0c03419ef258f947d6f4d752a530a8 diff --git a/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild b/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild deleted file mode 100644 index 133ff4a14..000000000 --- a/dev-java/jcip-annotations/jcip-annotations-1.0-r1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -JAVA_PKG_IUSE="source" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Annotations for Concurrency" -HOMEPAGE="http://www.jcip.net/" -SRC_URI="http://jcip.net.s3-website-us-east-1.amazonaws.com/${PN}-src.jar -> ${P}-src.jar" - -LICENSE="CC-BY-SA-2.5" -#Confirm license before entering tree. -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=">=virtual/jre-1.5" -DEPEND=" - >=virtual/jdk-1.5 - app-arch/unzip" - -S="${WORKDIR}" - -src_compile() { - mkdir -p build || die - ejavac -d build $(find net -name '*.java') - jar -cf "${PN}.jar" -C build net || die -} -src_install() { - java-pkg_dojar "${PN}.jar" - use source && java-pkg_dosrc net -} diff --git a/dev-java/jcip-annotations/metadata.xml b/dev-java/jcip-annotations/metadata.xml deleted file mode 100644 index 5ad381bdd..000000000 --- a/dev-java/jcip-annotations/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> - Annotations used within the Java Concurrency in Practice book by - Brain Goetz. - </longdescription> -</pkgmetadata> diff --git a/dev-java/jeuclid-core/ChangeLog b/dev-java/jeuclid-core/ChangeLog index b61221d1d..5c2ebdcc5 100644 --- a/dev-java/jeuclid-core/ChangeLog +++ b/dev-java/jeuclid-core/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jeuclid-core: Updating remote-id in metadata.xml + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> jeuclid-core-3.1.8.ebuild, jeuclid-core-3.1.9-r1.ebuild: Move to EAPI=5 diff --git a/dev-java/jeuclid-core/metadata.xml b/dev-java/jeuclid-core/metadata.xml index f80c0f1ba..d023325b1 100644 --- a/dev-java/jeuclid-core/metadata.xml +++ b/dev-java/jeuclid-core/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> JEuclid is a complete MathML rendering solution, consisting of: * A MathViewer application * Command line converters from MathML to other formats @@ -12,4 +12,7 @@ This package contains the basic JEuclid rendering and document handling classes. </longdescription> + <upstream> + <remote-id type="sourceforge">jeuclid</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jhealpix/ChangeLog b/dev-java/jhealpix/ChangeLog index b0d2ba520..a3c5e5de2 100644 --- a/dev-java/jhealpix/ChangeLog +++ b/dev-java/jhealpix/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-java/jhealpix -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jhealpix: Updating remote-id in metadata.xml + *jhealpix-3.11 (16 Jun 2013) 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +jhealpix-3.11.ebuild, diff --git a/dev-java/jhealpix/metadata.xml b/dev-java/jhealpix/metadata.xml index 9bb9481d8..debe4d929 100644 --- a/dev-java/jhealpix/metadata.xml +++ b/dev-java/jhealpix/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the Java framework. </longdescription> + <upstream> + <remote-id type="sourceforge">jhealpix</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jogl/ChangeLog b/dev-java/jogl/ChangeLog index 11ee69fdd..411673c12 100644 --- a/dev-java/jogl/ChangeLog +++ b/dev-java/jogl/ChangeLog @@ -1,7 +1,22 @@ # ChangeLog for dev-java/jogl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-java/jogl: Add github to remote-id in metadata.xml + + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> + -files/disable-applet.diff, -files/jogl-2.2.4-notests.patch, + jogl-2.2.4.ebuild: + dev-java/jogl: rework ebuild starting from 2.1.4 + +*jogl-2.2.4 (03 Apr 2015) + + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> + +files/disable-applet.diff, +files/jogl-2.2.4-notests.patch, + +jogl-2.2.4.ebuild: + dev-java/jogl: version bump + 03 Nov 2014; Justin Lecher <jlec@gentoo.org> jogl-2.0_rc8-r1.ebuild, -jogl-2.1.2.ebuild, jogl-2.1.4.ebuild: Bump to EAPI=5; drop old diff --git a/dev-java/jogl/Manifest b/dev-java/jogl/Manifest index 15f2d70ac..ba7492950 100644 --- a/dev-java/jogl/Manifest +++ b/dev-java/jogl/Manifest @@ -1,3 +1,4 @@ DIST jogl-1.1.1a-src.zip 3656870 SHA256 84fa71520fb186ce7a7b2818210a1a3667fcdfb1545e673b3cbe51bac6ba9113 SHA512 6de4273594c3bb4f17a629647a78619ba00d5998fa35cb25ee220e402059647b2c8fd111f1abdada9a78998d1b73052f1b432ed95220d1966e73cb50295b66bf WHIRLPOOL 077abf5829851aa40e5240c59f2f8dbc93fa7e67241109c2e7d435b1043013864788db88a1216ac950e0e80e1393fb8804505fda26a0af1c8ce079ce2644fa45 DIST jogl-2.1.4.tar.gz 32070918 SHA256 528c89643e532c6649f9243dd0cb0ee75800ab13e4f8d9a830163475dd1d5b0e SHA512 9d9f45676f671b1958352fcb7ddb4db539f19fb330db0146df6ce46167bcebf9c4fdc1a09bce72451a4bf2f4632a69cad2b4dd56df61c78f5e26e85a50918a0b WHIRLPOOL be0e9d4bc81b31a22050795b1b8e7f48c17e7c204c32ef0e47eca9175174f2f80a8ee3c0a024e744f692970b871dae0206ffd39e4f7db44a54a11720a54ed5a3 +DIST jogl-2.2.4.tar.gz 50214295 SHA256 48f2e11a8ee2dac3f9f34379b8729c0fa379d95bd1233d82a8260ccd81ef0e11 SHA512 79fb054d65e8aa532a75e8c8911f43987d877f7b71584ea24cc0f9152f8aaaddabd4afef7f7504b3df73c4d240bedc123bb8aeb8670d9ae2bd165bd0490e420e WHIRLPOOL d3cfcf38aafe3f0d8f5fe8d4c8b5b19cd4d4137e160575d825d0be1fe3f992608c13eb4bb43ffecd4836083d77afb97caa6725156ad9cfcdd662224aa9439445 DIST jogl-v2.0-rc8.tar.7z 18148821 SHA256 6d2338514b2e6c7ac61c59e0142d95d6b37434eefafecbbc2a8102f23f4f3e93 SHA512 ce335990dac4c868705f9cd041cab2e97050efcd9b6b0a8fa01e070aa7ee2f27162cb96ebbbd5e9f04a1aa9e7661dde6aa0ba1d02565f38fa76a39deeb48a500 WHIRLPOOL e38c1a7d6727f7dd8765d085ce2388afd7070c0625491038e84d26b8e14bb7fdaa5a89e75f742b5c30500cb02a198c5226d5ee743b1347acd31c6e555d281777 diff --git a/dev-java/jogl/jogl-2.2.4.ebuild b/dev-java/jogl/jogl-2.2.4.ebuild new file mode 100644 index 000000000..d034168c0 --- /dev/null +++ b/dev-java/jogl/jogl-2.2.4.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +JAVA_PKG_IUSE="doc source" +WANT_ANT_TASKS="ant-antlr ant-contrib dev-java/cpptasks:0" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java(TM) Binding fot the OpenGL(TM) API" +HOMEPAGE="http://jogamp.org/jogl/www/" +SRC_URI="https://github.com/sgothel/jogl/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="2.2" +KEYWORDS="~amd64 ~x86" +IUSE="cg" + +CDEPEND=" + =dev-java/gluegen-${PV}:${SLOT} + dev-java/antlr:0 + dev-java/ant-core:0 + x11-libs/libX11 + x11-libs/libXxf86vm + dev-java/swt:3.7 + virtual/opengl + cg? ( media-gfx/nvidia-cg-toolkit )" + +RDEPEND="${CDEPEND} + >=virtual/jre-1.5" +DEPEND="${CDEPEND} + >=virtual/jdk-1.5" + +# upstream has a crude way to call the junit tests, which cause a lot of trouble to pass +# our test classpath... +RESTRICT="test" + +JAVA_PKG_BSFIX_NAME+=" build-jogl.xml build-nativewindow.xml build-newt.xml" +JAVA_ANT_REWRITE_CLASSPATH="yes" +EANT_BUILD_XML="make/build.xml" +EANT_BUILD_TARGET="init build.nativewindow build.jogl build.newt build.oculusvr one.dir tag.build" +EANT_DOC_TARGET="" +EANT_GENTOO_CLASSPATH="gluegen-${SLOT},antlr,ant-core,swt-3.7" +EANT_GENTOO_CLASSPATH_EXTRA="${S}/build/${PN}/*.jar:${S}/build/nativewindow/*.jar" +EANT_NEEDS_TOOLS="yes" + +java_prepare() { + #we keep make/lib/plugin3/puglin3-public.jar + find -name 'make/lib/swt/*.jar' -delete -print || die + + # Empty filesets are never out of date! + sed -i -e 's/<outofdate>/<outofdate force="true">/' make/build*xml || die + + EANT_EXTRA_ARGS+=" -Dcommon.gluegen.build.done=true" + EANT_EXTRA_ARGS+=" -Dgluegen.root=/usr/share/gluegen-${SLOT}/" + EANT_EXTRA_ARGS+=" -Dgluegen.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen.jar)" + EANT_EXTRA_ARGS+=" -Dgluegen-rt.jar=$(java-pkg_getjar gluegen-${SLOT} gluegen-rt.jar)" + + use cg && EANT_EXTRA_ARGS+=" -Djogl.cg=1 -Dx11.cg.lib=/usr/lib" +} + +src_install() { + java-pkg_dojar build/jar/*.jar + java-pkg_doso build/lib/*.so + + use doc && dodoc -r doc + use source && java-pkg_dosrc src/jogl/classes/* +} diff --git a/dev-java/jogl/metadata.xml b/dev-java/jogl/metadata.xml index 975a649d1..cb3e7c1dd 100644 --- a/dev-java/jogl/metadata.xml +++ b/dev-java/jogl/metadata.xml @@ -9,4 +9,7 @@ to provide hardware-supported 3D graphics to applications written in Java. <use> <flag name="cg">Enable NVidia Cg binding.</flag> </use> + <upstream> + <remote-id type="github">sgothel/jogl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jrosetta/jrosetta-1.0.4.ebuild b/dev-java/jrosetta/jrosetta-1.0.4.ebuild index 040af6248..9b13d9142 100644 --- a/dev-java/jrosetta/jrosetta-1.0.4.ebuild +++ b/dev-java/jrosetta/jrosetta-1.0.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,9 @@ inherit java-pkg-2 java-ant-2 DESCRIPTION="Provides a common base for graphical component to build a graphical console." HOMEPAGE="http://dev.artenum.com/projects/jrosetta" -SRC_URI="http://maven.artenum.com/content/groups/public/com/artenum/${PN}/${PV}/${P}-sources.jar" +#currently down +#SRC_URI="http://maven.artenum.com/content/groups/public/com/artenum/${PN}/${PV}/${P}-sources.jar" +SRC_URI="http://pkgs.fedoraproject.org/repo/pkgs/${PN}/${P}-sources.jar/5c3589d4207f71bad6eeefd4857bce50/${P}-sources.jar" LICENSE="GPL-2" SLOT="0" diff --git a/dev-lang/berkeley_upc/ChangeLog b/dev-lang/berkeley_upc/ChangeLog index 4df972769..a00e96d35 100644 --- a/dev-lang/berkeley_upc/ChangeLog +++ b/dev-lang/berkeley_upc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-lang/berkeley_upc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*berkeley_upc-2.20.0 (03 Apr 2015) + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + +berkeley_upc-2.20.0.ebuild: + Version bump + *berkeley_upc-2.18.2 (01 Jun 2014) 01 Jun 2014; Jauhien Piatlicki <jauhien@gentoo.org> @@ -25,4 +31,3 @@ 17 Mar 2013; Jauhien Piatlicki (jauhien) <piatlicki@gmail.com> +berkeley_upc-2.16.0.ebuild, +metadata.xml: ebuild for bug#462026 - diff --git a/dev-lang/berkeley_upc/Manifest b/dev-lang/berkeley_upc/Manifest index 2c386b616..337180cd1 100644 --- a/dev-lang/berkeley_upc/Manifest +++ b/dev-lang/berkeley_upc/Manifest @@ -1,3 +1,4 @@ DIST berkeley_upc-2.16.2.tar.gz 6544935 SHA256 61b398417f3ceb86a73360122cad31feb77a9aa706c01bfba3a93231b1534c2d SHA512 fa7f7f6a36dd2a0c064daf301813f566fbd59a68c9186c81962384a98a2989c0ed26a816dd8196e388a714ca53dcbb34d27fffbdea33f1a29a70217d64cbe8f4 WHIRLPOOL 2b9284fe5c883f41e479536bf78badbc303fb33c487721234919f4980c82ab342c90c7304a5c419642320759584b45daa4def1f9768f4a7dc9b85e20c29458b9 DIST berkeley_upc-2.18.0.tar.gz 6175945 SHA256 238f3a220f63d9c53100589d6e971f521b27a6ef086a273ce88de272c8d6c05d SHA512 7d213af5f89fd9fda0a08dd8dabfb363227a138d64944dc95245a3f9a9bd0da5d091d1d0456c0a4d2bce16acdae09eaba7ee7c9be856267a135f7c77c98e2536 WHIRLPOOL df7d9402d7b9bd30d4b4c0fe24894d66efac3c7baa45cd75d609b3665994db6f1c8704f77c93dc6ea26a67e7198898f903eeb393d5fc22caf9e1db8b82882568 DIST berkeley_upc-2.18.2.tar.gz 6888644 SHA256 809ad3abc2ba0e33f4a72018511e7f0af73ffc3c7532b6f7acf24d0780185a0a SHA512 c7c362745003a1001600247654fe694922f397429ecdff7f798d29d4cb268eef709d03783bf082b0aa161586e0c680919631fae09835760b33b88171c717a47a WHIRLPOOL 0f75e880df97a59e2ec321032e49ba221c13237b1f7abd76ea6df00302ac86dc08683068b6061de94b8d17e91eeb64fad1193ff190e38da9f899c00a64465ef6 +DIST berkeley_upc-2.20.0.tar.gz 6914091 SHA256 6d531a69e9868879b7acd6a90f3786da0ab83de72b1c2069b33e54b185094979 SHA512 12e3a2b03b840daaaee90fbd03450517abbd61433c53169610719e7febc50353e682bbe85106b542c3405066d6c643d418ed9e35ed46f0162b47402ea5586b94 WHIRLPOOL 93553147247ea809a8fcae68faae8d6f8939788e24b217107bfc578920d8b1f5b138ed0bb74fb1a7944e26d72b98ef11405781cae824c18bb839c2165877d759 diff --git a/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild b/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild new file mode 100644 index 000000000..9fccbaac2 --- /dev/null +++ b/dev-lang/berkeley_upc/berkeley_upc-2.20.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="The Berkeley UPC Runtime/driver" +HOMEPAGE="http://upc.lbl.gov/" +SRC_URI="http://upc.lbl.gov/download/release/${P}.tar.gz" +LICENSE="BSD-4" + +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="mpi mpi-compat pshm +segment-fast segment-large +single +sptr-packed + sptr-struct sptr-symmetric threads +udp" + +REQUIRED_USE=" + ^^ ( segment-fast segment-large ) + ^^ ( sptr-packed sptr-struct sptr-symmetric )" + +DEPEND="mpi? ( virtual/mpi ) + mpi-compat? ( virtual/mpi )" + +pkg_setup() { + elog "There is a lot of options for this package," + elog "especially network conduits settings." + elog "You can set them using EXTRA_ECONF variable." + elog "To see full list of options visit ${HOMEPAGE}download/dist/INSTALL.TXT" +} + +src_configure() { + ./configure \ + --prefix="${EPREFIX}"/usr/libexec/${P} \ + --mandir="${EPREFIX}"/usr/share/man/ \ + --disable-aligned-segments \ + --disable-auto-conduit-detect \ + $(use_enable mpi) \ + $(use_enable mpi-compat) \ + $(use_enable pshm) \ + $(use_enable segment-fast) \ + $(use_enable segment-large) \ + $(use_enable single smp) \ + $(use_enable sptr-packed) \ + $(use_enable sptr-struct) \ + $(use_enable sptr-symmetric) \ + $(use_enable threads par) \ + $(use_enable udp) \ + ${EXTRA_ECONF} || die +} + +src_install() { + default + dodir /usr/bin + dosym ../libexec/${P}/bin/upc_trace /usr/bin/upc_trace + dosym ../libexec/${P}/bin/upcc /usr/bin/upcc + dosym ../libexec/${P}/bin/upcdecl /usr/bin/upcdecl + dosym ../libexec/${P}/bin/upcrun /usr/bin/upcrun +} diff --git a/dev-lang/conceptual/ChangeLog b/dev-lang/conceptual/ChangeLog index 429e81647..b1ab5942e 100644 --- a/dev-lang/conceptual/ChangeLog +++ b/dev-lang/conceptual/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/conceptual: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> conceptual-1.4.ebuild, metadata.xml: dev-lang/conceptual: fix SLOT operators diff --git a/dev-lang/conceptual/metadata.xml b/dev-lang/conceptual/metadata.xml index cdf1b6724..35143c2de 100644 --- a/dev-lang/conceptual/metadata.xml +++ b/dev-lang/conceptual/metadata.xml @@ -8,4 +8,7 @@ <use> <flag name="gui">Build the Java base graphical interface</flag> </use> + <upstream> + <remote-id type="sourceforge">conceptual</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/ispc/ChangeLog b/dev-lang/ispc/ChangeLog index 529d48d08..afec6c690 100644 --- a/dev-lang/ispc/ChangeLog +++ b/dev-lang/ispc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-lang/ispc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/ispc: Add github to remote-id in metadata.xml + 25 Oct 2014; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild: sync with gx86 diff --git a/dev-lang/ispc/ispc-9999.ebuild b/dev-lang/ispc/ispc-9999.ebuild index 793182dca..e7bdedd2a 100644 --- a/dev-lang/ispc/ispc-9999.ebuild +++ b/dev-lang/ispc/ispc-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit toolchain-funcs python-any-r1 diff --git a/dev-lang/ispc/metadata.xml b/dev-lang/ispc/metadata.xml index 06c3d15a6..4663d3aa7 100644 --- a/dev-lang/ispc/metadata.xml +++ b/dev-lang/ispc/metadata.xml @@ -5,4 +5,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">ispc/ispc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-lang/julia/ChangeLog b/dev-lang/julia/ChangeLog index 347e2fb03..a95ff5a0b 100644 --- a/dev-lang/julia/ChangeLog +++ b/dev-lang/julia/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-lang/julia -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Mar 2015; zcj <ustcscgy@163.com> julia-9999.ebuild: + dev-lang/julia: Add new dependency, fix build. + 13 Sep 2014; Mark Wright <gienah@gentoo.org> julia-9999.ebuild: Add int64 use flag to julia-9999.ebuild. Depend on >=virtual/blas-2.1-r2[int64?] and >=virtual/lapack-3.5-r2[int64?]. Fixes diff --git a/dev-lang/julia/julia-9999.ebuild b/dev-lang/julia/julia-9999.ebuild index b54ecfaed..fddb70c03 100644 --- a/dev-lang/julia/julia-9999.ebuild +++ b/dev-lang/julia/julia-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -21,6 +21,7 @@ RDEPEND=" dev-libs/double-conversion:0= dev-libs/gmp:0= dev-libs/libpcre:3= + >=dev-libs/libgit2-0.21 dev-libs/mpfr:0= dev-libs/utf8proc:0= sci-libs/arpack:0= @@ -32,7 +33,7 @@ RDEPEND=" sci-libs/spqr:0= sci-libs/umfpack:0= sci-mathematics/glpk:0= - =sys-devel/llvm-3.4* + >=sys-devel/llvm-3.4 >=sys-libs/libunwind-1.1:7= sys-libs/readline:0= sys-libs/zlib:0= @@ -120,6 +121,7 @@ src_configure() { USE_SYSTEM_GMP=1 USE_SYSTEM_GRISU=1 USE_SYSTEM_LAPACK=1 + USE_SYSTEM_LIBGIT2=1 USE_SYSTEM_LIBM=0 USE_SYSTEM_LIBUNWIND=1 USE_SYSTEM_LIBUV=0 diff --git a/dev-lang/terra/ChangeLog b/dev-lang/terra/ChangeLog new file mode 100644 index 000000000..817b66bb0 --- /dev/null +++ b/dev-lang/terra/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for dev-lang/terra +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-lang/terra: Add github to remote-id in metadata.xml + +*terra-2015.03.12 (24 Apr 2015) + + 24 Apr 2015; Christoph Junghans <ottxor@gentoo.org> +metadata.xml, + +terra-2015.03.12.ebuild: + initial commit thx to @zdevito for the nice intro to it diff --git a/dev-lang/terra/Manifest b/dev-lang/terra/Manifest new file mode 100644 index 000000000..ed9dc93ea --- /dev/null +++ b/dev-lang/terra/Manifest @@ -0,0 +1,2 @@ +DIST LuaJIT-2.0.3.tar.gz 844927 SHA256 55be6cb2d101ed38acca32c5b1f99ae345904b365b642203194c585d27bebd79 SHA512 7b3e3de22ac3602299b5918b60801e45a3278e547a15c16fdae7359538d4ada27ba664935d5f97c7409f330c2f8efeaae9ea03415f5e9d5a9d81e022cd5d36e0 WHIRLPOOL 1ba759b85048cfd57ebc02cfce477e9ddb327e7d27acd78f93fb2debfbf010a96e7b127324ebf6b81b1f35132f5a0a3a56ffca64fe0e66cba80c28b1cb49b433 +DIST terra-2015.03.12.tar.gz 303867 SHA256 4dfa9166ddee946ad24009ed2da0146be5d588cb2c964cae53116793e7227f34 SHA512 abda5cf8126e12ce199c3f8bde8a2fca0e7f7b5bf5f5048a97e3b3b827c83cd8140fb0fba803e116c55cb27a4cda1d13c8695a5cfe95f2383eb2f4515795aa09 WHIRLPOOL 58c9843d6a8f1dc35f0f9bcceea2d017b168bd85b0f743f144dbd825fd6eb46de67f7a5a5cd831fa031e884ce723c046d85f8ada8ba8102f313410c78aec5762 diff --git a/dev-lang/terra/metadata.xml b/dev-lang/terra/metadata.xml new file mode 100644 index 000000000..2e41c46b1 --- /dev/null +++ b/dev-lang/terra/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <upstream> + <remote-id type="github">zdevito/terra</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-lang/terra/terra-2015.03.12.ebuild b/dev-lang/terra/terra-2015.03.12.ebuild new file mode 100644 index 000000000..5faa4cc26 --- /dev/null +++ b/dev-lang/terra/terra-2015.03.12.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="A low-level counterpart to Lua" +HOMEPAGE="http://terralang.org/" +#cannot be unbundled easily, because needs to compiled with clang +LUAJIT="LuaJIT-2.0.3.tar.gz" +SRC_URI="https://github.com/zdevito/terra/archive/release-${PV//./-}.tar.gz -> ${P}.tar.gz + http://luajit.org/download/${LUAJIT}" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +DEPEND="sys-devel/clang + dev-lang/luajit:2" +RDEPEND="${DEPEND}" + +src_unpack() { + unpack "${P}.tar.gz" + mv "${PN}"-* "${S}" || die + ln -s "${DISTDIR}/${LUAJIT}" "${S}/build" || die +} + +src_install() { + cd release || die + dobin terra + dolib.so libterra.so + dodoc README.md + cd include || die + doheader terra.h *.t +} diff --git a/dev-lang/vtune/ChangeLog b/dev-lang/vtune/ChangeLog index 50fadc177..07871f91d 100644 --- a/dev-lang/vtune/ChangeLog +++ b/dev-lang/vtune/ChangeLog @@ -10,12 +10,12 @@ *vtune-15.1.380310 (02 Dec 2014) 02 Dec 2014; Justin Lecher <jlec@gentoo.org> +vtune-15.1.380310.ebuild: - Version BUmp + Version Bump *vtune-13.1.17.353306 (02 Jun 2014) 02 Jun 2014; Justin Lecher <jlec@gentoo.org> +vtune-13.1.17.353306.ebuild: - Version BUmp + Version Bump *vtune-13.1.13.313935 (21 Feb 2014) diff --git a/dev-libs/boost-compute/ChangeLog b/dev-libs/boost-compute/ChangeLog index eefb055eb..0b089ee71 100644 --- a/dev-libs/boost-compute/ChangeLog +++ b/dev-libs/boost-compute/ChangeLog @@ -1,10 +1,25 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> + boost-compute-9999.ebuild, metadata.xml: + dev-libs/boost-compute: Update HOMEPAGE, SRC_URI and github remote-id: project + was transfered on from kylelutz to boostorg + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/boost-compute: Add github to remote-id in metadata.xml + +*boost-compute-0.4-r1 (05 Jun 2015) + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> + +boost-compute-0.4-r1.ebuild, +files/boost-compute-0.4-CMakeLists.patch, + -boost-compute-0.4.ebuild, boost-compute-9999.ebuild: + Fix BoostComputeConfig.cmake location + *boost-compute-9999 (01 Feb 2015) *boost-compute-0.4 (01 Feb 2015) 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, +boost-compute-9999.ebuild, +boost-compute-0.4.ebuild: Add Boost.Compute to overlay -
\ No newline at end of file + diff --git a/dev-libs/boost-compute/boost-compute-0.4.ebuild b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild index 9782d2a2f..9782d2a2f 120000 --- a/dev-libs/boost-compute/boost-compute-0.4.ebuild +++ b/dev-libs/boost-compute/boost-compute-0.4-r1.ebuild diff --git a/dev-libs/boost-compute/boost-compute-9999.ebuild b/dev-libs/boost-compute/boost-compute-9999.ebuild index 320fa9d85..aebd86d14 100644 --- a/dev-libs/boost-compute/boost-compute-9999.ebuild +++ b/dev-libs/boost-compute/boost-compute-9999.ebuild @@ -7,16 +7,16 @@ EAPI=5 inherit eutils cmake-utils DESCRIPTION="A header-only C++ Computing Library for OpenCL" -HOMEPAGE="https://github.com/kylelutz/compute" +HOMEPAGE="https://github.com/boostorg/compute" LICENSE="Boost-1.0" SLOT="0" if [[ ${PV} == "9999" ]] ; then - EGIT_REPO_URI="https://github.com/kylelutz/compute.git git://github.com/kylelutz/compute.git" + EGIT_REPO_URI="https://github.com/boostorg/compute.git git://github.com/boostorg/compute.git" inherit git-r3 KEYWORDS="" else - SRC_URI="https://github.com/kylelutz/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz" + SRC_URI="https://github.com/boostorg/compute/archive/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64" S="${WORKDIR}/compute-${PV}" fi @@ -26,3 +26,7 @@ RDEPEND=" virtual/opencl " DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}"-0.4-CMakeLists.patch +) diff --git a/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch b/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch new file mode 100644 index 000000000..86d3a9e29 --- /dev/null +++ b/dev-libs/boost-compute/files/boost-compute-0.4-CMakeLists.patch @@ -0,0 +1,14 @@ +Install the BoostComputeConfig to /usr/lib/cmake instead of /usr/share/cmake. + +Patch by Marius Brehler. +--- CMakeLists.txt ++++ CMakeLists.txt +@@ -81,7 +81,7 @@ configure_file( + # install cmake config file + install( + FILES ${BoostCompute_BINARY_DIR}/BoostComputeConfig.cmake +- DESTINATION share/cmake/BoostCompute ++ DESTINATION lib/cmake/BoostCompute + ) + + # install header files diff --git a/dev-libs/boost-compute/metadata.xml b/dev-libs/boost-compute/metadata.xml index ae0b30066..b93ef2986 100644 --- a/dev-libs/boost-compute/metadata.xml +++ b/dev-libs/boost-compute/metadata.xml @@ -12,4 +12,7 @@ and provides access to compute devices, contexts, command queues and memory buffers. </longdescription> + <upstream> + <remote-id type="github">boostorg/compute</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/boost/ChangeLog b/dev-libs/boost/ChangeLog index 893df7618..3c5bc03b4 100644 --- a/dev-libs/boost/ChangeLog +++ b/dev-libs/boost/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/boost: Updating remote-id in metadata.xml + + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> boost-1.56.0-r2.ebuild, + metadata.xml: + dev-libs/boost: Move to new CAT + + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> boost-1.56.0-r2.ebuild: + dropped sparc + *boost-1.56.0-r2 (17 Feb 2015) 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +boost-1.56.0-r2.ebuild, diff --git a/dev-libs/boost/boost-1.56.0-r2.ebuild b/dev-libs/boost/boost-1.56.0-r2.ebuild index e03539937..e732f160f 100644 --- a/dev-libs/boost/boost-1.56.0-r2.ebuild +++ b/dev-libs/boost/boost-1.56.0-r2.ebuild @@ -1,9 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/dev-libs/boost/boost-1.56.0-r1.ebuild,v 1.3 2015/01/05 17:58:25 ottxor Exp $ +# $Header: $ EAPI="5" -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit eutils flag-o-matic multilib multiprocessing python-r1 toolchain-funcs versionator multilib-minimal @@ -16,7 +16,7 @@ SRC_URI="mirror://sourceforge/boost/${MY_P}.tar.bz2" LICENSE="Boost-1.0" SLOT="0/${PV}" # ${PV} instead ${MAJOR_V} due to bug 486122 -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~ppc-aix ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x86-solaris ~x86-winnt" +KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~x86 ~ppc-aix ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris ~x86-solaris ~x86-winnt" IUSE="context debug doc icu +nls mpi python static-libs +threads tools" @@ -27,7 +27,7 @@ RDEPEND="abi_x86_32? ( !app-emulation/emul-linux-x86-cpplibs[-abi_x86_32(-)] ) python? ( ${PYTHON_DEPS} ) app-arch/bzip2[${MULTILIB_USEDEP}] sys-libs/zlib[${MULTILIB_USEDEP}] - !app-admin/eselect-boost" + !app-eselect/eselect-boost" DEPEND="${RDEPEND} =dev-util/boost-build-${MAJOR_V}*" REQUIRED_USE=" diff --git a/dev-libs/boost/metadata.xml b/dev-libs/boost/metadata.xml index 03f221b7e..3fc1693b8 100644 --- a/dev-libs/boost/metadata.xml +++ b/dev-libs/boost/metadata.xml @@ -3,36 +3,39 @@ <pkgmetadata> <herd>cpp</herd> <use> - <flag name='context'> + <flag name="context"> Build and install the Boost.Context library and all other Boostlibraries that depends on it </flag> - <flag name='tools'> + <flag name="tools"> Build and install the boost tools (bcp, quickbook, inspect, wave) </flag> - <flag name='debug' restrict='<dev-libs/boost-1.50.0-r3'> + <flag name="debug" restrict="<dev-libs/boost-1.50.0-r3"> Build and install debug versions of the Boost libraries. These libraries are not used by default, and should not be used unless you're developing against Boost. </flag> - <flag name='debug' restrict='>dev-libs/boost-1.52.0-r2'> + <flag name="debug" restrict=">dev-libs/boost-1.52.0-r2"> Build and install only the debug version of the Boost libraries. Only enable this flag if you're developing against boost. </flag> - <flag name='threads'> + <flag name="threads"> Build multi-thread-compatible libraries instead of single-threaded only. </flag> - <flag name='nls'> + <flag name="nls"> Build libboost_locale. This library requires compatible C library interfaces, which might not be provided by uClibc or other embedded libraries. </flag> - <flag name='doc'> + <flag name="doc"> Install the full API documentation documentation. This takes over 200MB of extra disk space. </flag> </use> + <upstream> + <remote-id type="sourceforge">boost</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/libcuda/ChangeLog b/dev-libs/libcuda/ChangeLog index 74035e500..21a96bef5 100644 --- a/dev-libs/libcuda/ChangeLog +++ b/dev-libs/libcuda/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libcuda -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/libcuda: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> libcuda-9999.ebuild, metadata.xml: Punt base.eclass; add missing die; drop nneeded patches diff --git a/dev-libs/libcuda/metadata.xml b/dev-libs/libcuda/metadata.xml index f233055c0..f78356fd3 100644 --- a/dev-libs/libcuda/metadata.xml +++ b/dev-libs/libcuda/metadata.xml @@ -5,4 +5,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">shinpei0208/gdev</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/libflatarray/ChangeLog b/dev-libs/libflatarray/ChangeLog index 55bb692ec..bb1bdccd7 100644 --- a/dev-libs/libflatarray/ChangeLog +++ b/dev-libs/libflatarray/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libflatarray -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> -Manifest, + -libflatarray-0.1.1.ebuild: + dev-libs/libflatarray: In CVS + 22 Mar 2014; Justin Lecher <jlec@gentoo.org> metadata.xml: Add missing Manifest - diff --git a/dev-libs/libflatarray/Manifest b/dev-libs/libflatarray/Manifest deleted file mode 100644 index 9de59f0da..000000000 --- a/dev-libs/libflatarray/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libflatarray-0.1.1.tar.bz2 16866 SHA256 3287f0ab1e670f3a2c43dd42de6399a8f853453f228e45076339ec31ea68cb56 SHA512 feed796e3932fc0131634f2f83415372e8046ee137502614de5bfb5af88db2fc44afcdd995d9b2f245737d223b79fdae33ba772b154b4dac064eeed67d489542 WHIRLPOOL ab8089f8f6023c23db9edc5b3bd5b7a6b69f291d02268122bdd2b08e24285af2967ac237afa826a727b3a9cdfe1c59b34d8f77517cb7478ae343f28edc3792a4 diff --git a/dev-libs/libflatarray/libflatarray-0.1.1.ebuild b/dev-libs/libflatarray/libflatarray-0.1.1.ebuild deleted file mode 100644 index 3c7c0691c..000000000 --- a/dev-libs/libflatarray/libflatarray-0.1.1.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -if [ ${PV} == "9999" ] ; then - _SCM=mercurial - EHG_REPO_URI="http://bitbucket.org/gentryx/libflatarray" - SRC_URI="" - KEYWORDS="" - CMAKE_USE_DIR="${S}" -else - SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2" - KEYWORDS="~amd64 ~ppc ~x86" - S="${WORKDIR}/${P}" -fi - -inherit cmake-utils cuda ${_SCM} - -DESCRIPTION="Struct of arrays library with object oriented interface for C++" -HOMEPAGE="http://www.libgeodecomp.org/libflatarray.html" - -SLOT="0" -LICENSE="Boost-1.0" -IUSE="cuda doc" - -RDEPEND=" - >=dev-libs/boost-1.48 - cuda? ( dev-util/nvidia-cuda-toolkit )" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -src_configure() { - local mycmakeargs=( - $(cmake-utils_use_with cuda CUDA) - ) - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile -} - -src_install() { - DOCS=( README ) - cmake-utils_src_install -} - -src_test() { - cmake-utils_src_make test -} diff --git a/dev-libs/libgdev/ChangeLog b/dev-libs/libgdev/ChangeLog index bba9675f2..471e930e1 100644 --- a/dev-libs/libgdev/ChangeLog +++ b/dev-libs/libgdev/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libgdev -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/libgdev: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> libgdev-9999.ebuild, metadata.xml: Punt base.eclass; add missing die; drop nneeded patches diff --git a/dev-libs/libgdev/metadata.xml b/dev-libs/libgdev/metadata.xml index f233055c0..f78356fd3 100644 --- a/dev-libs/libgdev/metadata.xml +++ b/dev-libs/libgdev/metadata.xml @@ -5,4 +5,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">shinpei0208/gdev</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/libpfm/ChangeLog b/dev-libs/libpfm/ChangeLog deleted file mode 100644 index b3e75ce19..000000000 --- a/dev-libs/libpfm/ChangeLog +++ /dev/null @@ -1,18 +0,0 @@ -# ChangeLog for dev-libs/libpfm -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*libpfm-4.4.0 (16 Feb 2014) - - 16 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> +libpfm-4.4.0.ebuild, - metadata.xml: - dev-libs/libpfm: Version bump - - 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> libpfm-4.3.0.ebuild: - Add ~x86 - -*libpfm-4.3.0 (28 Feb 2013) - - 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> +libpfm-4.3.0.ebuild, - +metadata.xml: - Initial import diff --git a/dev-libs/libpfm/Manifest b/dev-libs/libpfm/Manifest deleted file mode 100644 index d7d9672db..000000000 --- a/dev-libs/libpfm/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST libpfm-4.3.0.tar.gz 581976 SHA256 a23eb9affbff279e13563a39317c0ad71c4de28908d4243c8bc109138430cc3b SHA512 556bc1e4e2bcd5672dbf083f2d726c3f94a2434791a8085da28137d763aa3c1fdd45e947b11d467ca6dc131c7f7141eaf3ca5397d8fd260f0c8c81359adf97c8 WHIRLPOOL 5cd0dd88f8068617025fa408798b9fe7db6cc0a2e5d2b5b0522839f7579b7304a93af1c7a24971f848e330e1ff216c7f9568275203156c262ab06b2191b878c2 -DIST libpfm-4.4.0.tar.gz 649910 SHA256 8351ff4bbab4e4cbf6f17f76dd18698ef3a7dff766ea0cfa1a6d60bce36f7c9c SHA512 e7f9b50d0c71c08697283d043231234b39695fda6796ad1e2c48fdd67e2936a3cf5d864b5e1b9c68a34f1d726f2b273eb1267adec3060085f3a51e9886f5704a WHIRLPOOL 9f1f1cbb2e56a3269b9f88c81273e69976d95e6557e1f1e08ade249cacbb6368e422e77c38d19603e28892683c37270e176f8854bfdfb6646b935c3e024d332f diff --git a/dev-libs/libpfm/libpfm-4.3.0.ebuild b/dev-libs/libpfm/libpfm-4.3.0.ebuild deleted file mode 100644 index afbd7c0c3..000000000 --- a/dev-libs/libpfm/libpfm-4.3.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit multilib toolchain-funcs - -DESCRIPTION="Hardware-based performance monitoring interface for Linux" -HOMEPAGE="http://perfmon2.sourceforge.net" -SRC_URI="mirror://sourceforge/perfmon2/${PN}4/${P}.tar.gz" - -LICENSE="GPL-2 MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_prepare() { - sed -e "s:SLDFLAGS=:SLDFLAGS=\$(LDFLAGS) :g" \ - -i lib/Makefile || die - sed -e "s:LIBDIR=\$(PREFIX)/lib:LIBDIR=\$(PREFIX)/$(get_libdir):g" \ - -i config.mk || die -} - -src_compile() { - emake CC=$(tc-getCC) -} - -src_install() { - emake DESTDIR="${D}" LDCONFIG=true PREFIX="${EPREFIX}/usr" install - use static-libs || find "${ED}" -name '*.a' -exec rm -f '{}' + -} diff --git a/dev-libs/libpfm/libpfm-4.4.0.ebuild b/dev-libs/libpfm/libpfm-4.4.0.ebuild deleted file mode 100644 index 848aca7a0..000000000 --- a/dev-libs/libpfm/libpfm-4.4.0.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit multilib toolchain-funcs - -DESCRIPTION="Hardware-based performance monitoring interface for Linux" -HOMEPAGE="http://perfmon2.sourceforge.net" -SRC_URI="mirror://sourceforge/perfmon2/${PN}4/${P}.tar.gz" - -LICENSE="GPL-2 MIT" -SLOT="0/4" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="static-libs" - -DEPEND="" -RDEPEND="${DEPEND}" - -src_prepare() { - sed -e "s:SLDFLAGS=:SLDFLAGS=\$(LDFLAGS) :g" \ - -i lib/Makefile || die - sed -e "s:LIBDIR=\$(PREFIX)/lib:LIBDIR=\$(PREFIX)/$(get_libdir):g" \ - -i config.mk || die -} - -src_compile() { - emake CC=$(tc-getCC) -} - -src_install() { - emake DESTDIR="${D}" LDCONFIG=true PREFIX="${EPREFIX}/usr" install - use static-libs || find "${ED}" -name '*.a' -exec rm -f '{}' + - dodoc README -} diff --git a/dev-libs/libpfm/metadata.xml b/dev-libs/libpfm/metadata.xml deleted file mode 100644 index 83f02cf0e..000000000 --- a/dev-libs/libpfm/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> -</maintainer> -<longdescription> - Libpfm4 helps convert from an event name, expressed as a string, to - the event encoding. The encoding can then be used with specific OS - interfaces. Libpfm4 also provides OS-specific interfaces to directly - setup OS-specific data structures to be passed to the kernel. The - current libpfm4, for instance, provides support for the perf_events - interface. -</longdescription> -</pkgmetadata> diff --git a/dev-libs/libunzip/ChangeLog b/dev-libs/libunzip/ChangeLog index 486ff991d..daed8c059 100644 --- a/dev-libs/libunzip/ChangeLog +++ b/dev-libs/libunzip/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-libs/libunzip -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> libunzip-5.52.ebuild: + Bump to EAPI=5 + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> libunzip-5.52.ebuild: Sort inherit and/or USE @@ -17,4 +20,3 @@ +files/libunzip-5.52-no-exec-stack.patch, +metadata.xml, +libunzip-5.52.ebuild: Initial checkin to sci - diff --git a/dev-libs/libunzip/libunzip-5.52.ebuild b/dev-libs/libunzip/libunzip-5.52.ebuild index 0a89ee6d6..a9140e24e 100644 --- a/dev-libs/libunzip/libunzip-5.52.ebuild +++ b/dev-libs/libunzip/libunzip-5.52.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 inherit eutils flag-o-matic toolchain-funcs @@ -41,14 +41,14 @@ src_prepare() { src_compile() { append-lfs-flags #104315 - emake -f unix/Makefile linux_shlib || die "emake failed" + emake -f unix/Makefile linux_shlib } src_install() { - dolib.so ${PN}.so.0.4 || die - dolib.so ${PN}.so.0 || die - dolib.so ${PN}.so || die - dolib.a ${PN}.a || die + dolib.so ${PN}.so.0.4 + dolib.so ${PN}.so.0 + dolib.so ${PN}.so + dolib.a ${PN}.a insinto /usr/include - doins unzip.h || die + doins unzip.h } diff --git a/dev-libs/papi/ChangeLog b/dev-libs/papi/ChangeLog deleted file mode 100644 index fe89460b0..000000000 --- a/dev-libs/papi/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for dev-libs/papi -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 16 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: - dev-libs/papi: Version bump - -*papi-5.1.0.2 (28 Feb 2013) - - 28 Feb 2013; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml, - +papi-5.1.0.2.ebuild: - Initial import diff --git a/dev-libs/papi/Manifest b/dev-libs/papi/Manifest deleted file mode 100644 index b4c96f201..000000000 --- a/dev-libs/papi/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST papi-5.1.0.2.tar.gz 3781062 SHA256 141fd3dbeb32120ba8ca5f6a64250c22167b5224457f8ea1c3f28c8774468a1c SHA512 c52a762ba5492c25fde284f86999fdbe38007da73ee09949d15c392935bd03004304a1194e331032961d370247c3b6c49c62504b0fce42985fd8fcf6cc97702f WHIRLPOOL 58642c1f49f5f554553245cca38d6f034dbe4981efffecf32fadff468e07670b98618c1a793980dfa6194a55dc7d9668efd9c0eb4bfed899504cadaa64968aad -DIST papi-5.3.0.tar.gz 3928589 SHA256 99f2f36398b370e75d100b4a189d5bc0ac4f5dd66df44d441f88fd32e1421524 SHA512 a88d28d895a1b44b0d05ac90c39406b7e9806a1d865b39df405e55b27d7f6bb191330ed7df52d4f3f04f46ff94ce867e6c1bdd9b38c314652cff1ee9d838b226 WHIRLPOOL cf1074f259831283292b57b636b6b0083a11ec6084bce2361eabe3ca706fd3d2420d3ab4074c8024296b06d11223a1dcc9782040ab08502481498b84bb2517e6 diff --git a/dev-libs/papi/metadata.xml b/dev-libs/papi/metadata.xml deleted file mode 100644 index 28feb32ae..000000000 --- a/dev-libs/papi/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>alexxy@gentoo.org</email> - <name>Alexey Shvetsov</name> -</maintainer> -<longdescription> - Performance Application Programming Interface provides the tool - designer and application engineer with a consistent interface and - methodology for use of the performance counter hardware found in - most major microprocessors. -</longdescription> -</pkgmetadata> diff --git a/dev-libs/papi/papi-5.1.0.2.ebuild b/dev-libs/papi/papi-5.1.0.2.ebuild deleted file mode 100644 index 47cf4c5eb..000000000 --- a/dev-libs/papi/papi-5.1.0.2.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit versionator - -DESCRIPTION="Performance Application Programming Interface" -HOMEPAGE="http://icl.cs.utk.edu/papi/index.html" -SRC_URI="http://icl.cs.utk.edu/projects/papi/downloads/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -DEPEND=" - dev-libs/libpfm[static-libs] - " -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}-$(get_version_component_range 1-3)/src" - -src_configure() { - econf \ - --with-perf-events \ - --with-pfm-prefix="${EPREFIX}/usr" \ - $(use_with static-libs) -} diff --git a/dev-libs/papi/papi-5.3.0.ebuild b/dev-libs/papi/papi-5.3.0.ebuild deleted file mode 100644 index 8bd3f8610..000000000 --- a/dev-libs/papi/papi-5.3.0.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -AUTOTOOLS_IN_SOURCE_BUILD=1 -inherit versionator autotools-utils - -DESCRIPTION="Performance Application Programming Interface" -HOMEPAGE="http://icl.cs.utk.edu/papi/" -SRC_URI="http://icl.cs.utk.edu/projects/${PN}/downloads/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="static-libs" - -DEPEND=" - dev-libs/libpfm[static-libs] - virtual/mpi -" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}-$(get_version_component_range 1-3)/src" - -src_configure() { - local myeconfargs=( - --with-shlib - --with-perf-events - --with-pfm-prefix="${EPREFIX}/usr" - ) - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - dodoc ../RE* -} diff --git a/dev-libs/utf8proc/ChangeLog b/dev-libs/utf8proc/ChangeLog index f5afbed53..758f69e9a 100644 --- a/dev-libs/utf8proc/ChangeLog +++ b/dev-libs/utf8proc/ChangeLog @@ -1,7 +1,23 @@ # ChangeLog for dev-libs/utf8proc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-libs/utf8proc: Add github to remote-id in metadata.xml + +*utf8proc-1.2-r1 (25 May 2015) + + 25 May 2015; Justin Lecher <jlec@gentoo.org> +utf8proc-1.2-r1.ebuild, + -utf8proc-1.2.ebuild, files/utf8proc-1.2-buildflags.patch, metadata.xml: + dev-libs/utf8proc: Fix build process, https://github.com/gentoo- + science/sci/issues/427 + +*utf8proc-1.2 (21 May 2015) + + 21 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/utf8proc-1.2-buildflags.patch, +utf8proc-1.2.ebuild: + Version bump + 02 Apr 2014; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml, utf8proc-1.1.6.ebuild: dev-libs/utf8proc: Keyworded for amd64-linux x86-linux diff --git a/dev-libs/utf8proc/Manifest b/dev-libs/utf8proc/Manifest index 4459cdb6a..7d19b7696 100644 --- a/dev-libs/utf8proc/Manifest +++ b/dev-libs/utf8proc/Manifest @@ -1 +1,2 @@ +DIST utf8proc-1.2.tar.gz 137294 SHA256 9b07ffe12e049974d120f1558459f6ba9b44681c182ac738ca96fb70aa842fd9 SHA512 066b77d599320e0f6d90e52f6ae482c3caf54276920ad4afacaf4d0c4969d94aa33401e63edee14b2887cdf60fdffd07f913d246212aac1a26b480f20cbc24d4 WHIRLPOOL 597f30c1f1b6d413d9ab7b81c203d01386a949bf33a99eb0bf90ffb7b2c560b78b55ad02d074bff57ecaccda46db991d0bbb9dcf113756c87914a488a2e44762 DIST utf8proc-v1.1.6.tar.gz 105825 SHA256 fedc8fa78022eb8f0584fbc85c9f9571bcd7fd510de0ce16955289c42f4199e7 SHA512 3bec2388298c201d9d6992cdd36330f1109d26a37b3411ba633f006f40da9e494ba0565051b763a7d3014e6113cd1e7754e6b95d5cbb2d7b50cee55193f0fdc1 WHIRLPOOL c211419407e80893b66fa7586a8148e9b2e45c89d2d31878658a4ae7f0b1ca72e269cef234ca8b30e27e4bac5a48715520dd546f6605af773d6e165ef76f81b0 diff --git a/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch new file mode 100644 index 000000000..de8847cdf --- /dev/null +++ b/dev-libs/utf8proc/files/utf8proc-1.2-buildflags.patch @@ -0,0 +1,40 @@ + Makefile | 9 +++++---- + 1 file changed, 5 insertions(+), 4 deletions(-) + +diff --git a/Makefile b/Makefile +index aba2453..5fab07d 100644 +--- a/Makefile ++++ b/Makefile +@@ -6,8 +6,8 @@ AR=ar + INSTALL=install + + # compiler settings +-cflags = -O2 -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS $(CFLAGS) +-cc = $(CC) $(cflags) ++CFLAGS ?= -O2 ++CFLAGS += -std=c99 -pedantic -Wall -fpic -DUTF8PROC_EXPORTS + + # shared-library version MAJOR.MINOR.PATCH ... this may be *different* + # from the utf8proc version number because it indicates ABI compatibility, +@@ -54,18 +54,19 @@ data/utf8proc_data.c.new: libutf8proc.$(SHLIB_EXT) data/data_generator.rb data/c + $(MAKE) -C data utf8proc_data.c.new + + utf8proc.o: utf8proc.h utf8proc.c utf8proc_data.c +- $(cc) -c -o utf8proc.o utf8proc.c ++ $(CC) $(CFLAGS) -c -o utf8proc.o utf8proc.c + + libutf8proc.a: utf8proc.o + rm -f libutf8proc.a + $(AR) rs libutf8proc.a utf8proc.o + + libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH): utf8proc.o +- $(cc) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o ++ $(CC) $(LDFLAGS) -shared -o $@ -Wl,-soname -Wl,libutf8proc.so.$(MAJOR) utf8proc.o + chmod a-x $@ + + libutf8proc.so: libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) + ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@ ++ ln -f -s libutf8proc.so.$(MAJOR).$(MINOR).$(PATCH) $@.$(MAJOR) + + libutf8proc.$(MAJOR).dylib: utf8proc.o + $(cc) -dynamiclib -o $@ $^ -install_name $(libdir)/$@ -Wl,-compatibility_version -Wl,$(MAJOR) -Wl,-current_version -Wl,$(MAJOR).$(MINOR).$(PATCH) diff --git a/dev-libs/utf8proc/metadata.xml b/dev-libs/utf8proc/metadata.xml index f8fff5b6f..4d104ac19 100644 --- a/dev-libs/utf8proc/metadata.xml +++ b/dev-libs/utf8proc/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription> + <herd>sci</herd> + <longdescription> utf8proc is a library for processing UTF-8 encoded Unicode strings. Some features are Unicode normalization, stripping of default ignorable characters, case folding and detection of grapheme @@ -11,4 +11,7 @@ (U+2212) and “Hyphen-Minus” (U+002D, ASCII Minus) all into the ASCII minus sign, to make them equal for comparisons. </longdescription> + <upstream> + <remote-id type="github">JuliaLang/utf8proc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild b/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild new file mode 100644 index 000000000..e00835dec --- /dev/null +++ b/dev-libs/utf8proc/utf8proc-1.2-r1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="library for processing UTF-8 encoded Unicode strings" +HOMEPAGE="http://www.public-software-group.org/utf8proc" +SRC_URI="https://github.com/JuliaLang/${PN}/archive/v1.2.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +src_prepare() { + epatch "${FILESDIR}"/"${P}"-buildflags.patch +} + +src_compile() { + emake \ + libutf8proc.so \ + $(usex static-libs libutf8proc.a "") \ + CC=$(tc-getCC) \ + AR=$(tc-getAR) +# CFLAGS="${CFLAGS}" +# LDFLAGS="${LDFLAGS} -Wl,--soname,lib${PN}.${PV}" +} + +src_install() { + doheader utf8proc.h + dolib.so libutf8proc.so* + use static-libs && dolib.a libutf8proc.a +} diff --git a/dev-lua/cmsgpack/ChangeLog b/dev-lua/cmsgpack/ChangeLog deleted file mode 100644 index 9c0a79df6..000000000 --- a/dev-lua/cmsgpack/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for dev-lua/cmsgpack -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> cmsgpack-9999.ebuild: - dev-lua/cmsgpack: fix SLOT operators; use symlink - -*cmsgpack-0.3.0 (10 May 2014) -*cmsgpack-9999 (10 May 2014) - - 10 May 2014; Jelte Fennema <github@jeltef.nl> +cmsgpack-0.3.0.ebuild, - +cmsgpack-9999.ebuild, +metadata.xml: - Initial commit for dev-lua/cmsgpack, this is a new dependency for neovim. diff --git a/dev-lua/cmsgpack/Manifest b/dev-lua/cmsgpack/Manifest deleted file mode 100644 index 35be53327..000000000 --- a/dev-lua/cmsgpack/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST cmsgpack-0.3.0.tar.gz 8931 SHA256 d0e819ddd67c317eae3506ae384b27d179aea1fb531cd06eb369636adfd6167a SHA512 0bae955df022d2f3998e6f84470ab9a8605f38c61bbdbe12e07bfe1aebb3e57b4671a960ded52ee642de60bab2e176863a7a92a17d7660c64d50c8a7363866e4 WHIRLPOOL cdb64970693aebd3ed875ab49e6c27ec5070c1469e927ca443483738c1974b6362c82e83f0c99e9e25e3f854a0ffa96e04a08ae4f23e1e5c8d3422e32033f0d4 diff --git a/dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild b/dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild deleted file mode 120000 index 8509204ab..000000000 --- a/dev-lua/cmsgpack/cmsgpack-0.3.0.ebuild +++ /dev/null @@ -1 +0,0 @@ -cmsgpack-9999.ebuild
\ No newline at end of file diff --git a/dev-lua/cmsgpack/cmsgpack-9999.ebuild b/dev-lua/cmsgpack/cmsgpack-9999.ebuild deleted file mode 100644 index 0d47408d8..000000000 --- a/dev-lua/cmsgpack/cmsgpack-9999.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -if [ "${PV}" = "9999" ]; then - EGIT_REPO_URI="git://github.com/antirez/lua-cmsgpack.git" - inherit git-r3 - KEYWORDS="" - DOCS=( README.md ) -else - SRC_URI="https://github.com/antirez/lua-${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - inherit vcs-snapshot - KEYWORDS="~amd64" - DOCS=( README ) - -fi - -inherit toolchain-funcs - -DESCRIPTION="A self contained Lua MessagePack C implementation" -HOMEPAGE="https://github.com/antirez/lua-cmsgpack" - -MY_PN="lua_${PN}" - -LICENSE="BSD-2" -SLOT="0" -IUSE="test" - -RDEPEND=">=dev-lang/lua-5.1:0" -DEPEND="${RDEPEND} - dev-libs/msgpack" - -src_compile() { - $(tc-getCC) -fPIC ${CFLAGS} -c -o ${MY_PN}.o ${MY_PN}.c || die - $(tc-getCC) ${LDFLAGS} -shared -o ${PN}.so ${MY_PN}.o || die -} - -src_test() { - lua test.lua || die -} - -src_install() { - default - insinto $($(tc-getPKG_CONFIG) --variable INSTALL_CMOD lua) - doins ${PN}.so -} diff --git a/dev-ml/gsl-ocaml/ChangeLog b/dev-ml/gsl-ocaml/ChangeLog index c724b6d0c..069753b13 100644 --- a/dev-ml/gsl-ocaml/ChangeLog +++ b/dev-ml/gsl-ocaml/ChangeLog @@ -1,10 +1,15 @@ # ChangeLog for dev-ml/gsl-ocaml -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> gsl-ocaml-1.10.2.ebuild: + dev-ml/gsl-ocaml: Bump EAPI=5 + + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-ml/gsl-ocaml: Add bitbucket to remote-id in metadata.xml + *gsl-ocaml-1.10.2 (11 Aug 2012) 11 Aug 2012; Guillaume Horel <guillaume.horel@gmail.com> +gsl-ocaml-1.10.2.ebuild, +metadata.xml: new package from #390583 - diff --git a/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild b/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild index 379d48fb7..c2568388d 100644 --- a/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild +++ b/dev-ml/gsl-ocaml/gsl-ocaml-1.10.2.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 OASIS_BUILD_DOCS=1 OASIS_BUILD_TESTS=1 @@ -21,7 +21,7 @@ IUSE="examples test" DEPEND=">=sci-libs/gsl-1.10" RDEPEND="${DEPEND}" -DOCS=( "CHANGES.txt" "README.md" "NOTES.md" "TODO.md" ) +DOCS=( CHANGES.txt README.md NOTES.md TODO.md ) src_prepare() { oasis_configure_opts="$(use_enable examples)" diff --git a/dev-ml/gsl-ocaml/metadata.xml b/dev-ml/gsl-ocaml/metadata.xml index f7b1637ca..8a2bb7bd7 100644 --- a/dev-ml/gsl-ocaml/metadata.xml +++ b/dev-ml/gsl-ocaml/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang='en'> + <herd>sci</herd> + <longdescription lang="en"> GSL interface for OCaml </longdescription> + <upstream> + <remote-id type="bitbucket">mmottl/gsl-ocaml</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-ml/ocamlgraph/ChangeLog b/dev-ml/ocamlgraph/ChangeLog deleted file mode 100644 index 5e0ac6b1b..000000000 --- a/dev-ml/ocamlgraph/ChangeLog +++ /dev/null @@ -1,40 +0,0 @@ -# ChangeLog for dev-ml/ocamlgraph -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 21 Jun 2014; Jonathan-Christofer Demay <jcdemay@gmail.com> - -ocamlgraph-1.8.3.ebuild, +ocamlgraph-1.8.5.ebuild: - version bump - - 10 Jan 2014; Jonathan-Christofer Demay <jcdemay@gmail.com> - -ocamlgraph-1.8.2.ebuild, +ocamlgraph-1.8.3.ebuild: - version bump - - 14 Jan 2013; Jonathan-Christofer Demay <jcdemay@gmail.com> - -ocamlgraph-1.8.1.ebuild, +ocamlgraph-1.8.2.ebuild: - version bump - - 21 Dec 2011; Jonathan-Christofer Demay <jcdemay@gmail.com> - -ocamlgraph-1.7.ebuild, +ocamlgraph-1.8.1.ebuild: - version bump - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> - ocamlgraph-1.7.ebuild: - Sort inherit and/or USE - - 06 May 2011; Jonathan-Christofer Demay <jcdemay@gmail.com> - -ocamlgraph-1.6.ebuild, +ocamlgraph-1.7.ebuild: - version bump - - 13 Jul 2010; Jonathan-Christofer Demay <jcdemay@gmail.com> - -files/ocamlgraph-1.5-makefile.patch, +files/ocamlgraph-makefile.patch, -ocamlgraph-1.5.ebuild, +ocamlgraph-1.6.ebuild: - version bump - - 04 Jul 2010; Jonathan-Christofer Demay <jcdemay@gmail.com> - -files/ocamlgraph-1.2-makefile.patch, +files/ocamlgraph-1.5-makefile.patch, -ocamlgraph-1.2.ebuild, +ocamlgraph-1.5.ebuild: - version bump - - 22 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - ocamlgraph-1.2.ebuild, +metadata.xml: - QA fixes - diff --git a/dev-ml/ocamlgraph/Manifest b/dev-ml/ocamlgraph/Manifest deleted file mode 100644 index 1b98a288d..000000000 --- a/dev-ml/ocamlgraph/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ocamlgraph-1.8.5.tar.gz 269438 SHA256 d167466435a155c779d5ec25b2db83ad851feb42ebc37dca8ffa345ddaefb82f SHA512 e3bf7f43f7b5167cbd23ea44a510d1a569d35771882ab7ae83bacc73822c5f4c944f62c95e0efa813b765e1e385a6b3ebff342cbf1c5589c73d022b8591a52dc WHIRLPOOL d25e124c2814e3196a441e706ca91a0429ab48669309c5dec2ae6697e48064ce54efc9d24440d9e52f3a1af8cfdd5c3ae04cd549fde4e9abc860a3506bd2de8d diff --git a/dev-ml/ocamlgraph/files/ocamlgraph-makefile.patch b/dev-ml/ocamlgraph/files/ocamlgraph-makefile.patch deleted file mode 100644 index 3e25630c5..000000000 --- a/dev-ml/ocamlgraph/files/ocamlgraph-makefile.patch +++ /dev/null @@ -1,37 +0,0 @@ -diff -Naurp ocamlgraph-1.5-orig/Makefile.in ocamlgraph-1.5-ptch/Makefile.in ---- ocamlgraph-1.5-orig/Makefile.in 2010-04-29 06:40:53.000000000 +0000 -+++ ocamlgraph-1.5-ptch/Makefile.in 2010-07-04 15:44:05.000000000 +0000 -@@ -16,7 +16,6 @@ - ########################################################################## - - # Where to install the binaries --DESTDIR = - prefix =@prefix@ - exec_prefix=@exec_prefix@ - datarootdir=@datarootdir@ -@@ -293,11 +292,13 @@ install: install-$(OCAMLBEST) install-by - mkdir -p $(BINDIR) - ifeq (@LABLGNOMECANVAS@,yes) - ifeq ($(OCAMLBEST),byte) -- cp -f $(BINDIR)/graph-editor.byte $(BINDIR)/graph-editor$(EXE) -- cp -f $(BINDIR)/graph-viewer.byte $(BINDIR)/graph-viewer$(EXE) -+ mv $(BINDIR)/graph-editor.byte $(BINDIR)/ocamlgraph-editor$(EXE) -+ mv $(BINDIR)/graph-viewer.byte $(BINDIR)/ocamlgraph-viewer$(EXE) - else -- cp -f $(BINDIR)/graph-editor.opt $(BINDIR)/graph-editor$(EXE) -- cp -f $(BINDIR)/graph-viewer.opt $(BINDIR)/graph-viewer$(EXE) -+ mv $(BINDIR)/graph-editor.opt $(BINDIR)/ocamlgraph-editor$(EXE) -+ mv $(BINDIR)/graph-viewer.opt $(BINDIR)/ocamlgraph-viewer$(EXE) -+ mv $(BINDIR)/graph-editor.byte $(BINDIR)/ocamlgraph-editor.byte -+ mv $(BINDIR)/graph-viewer.byte $(BINDIR)/ocamlgraph-viewer.byte - endif - endif - -@@ -305,6 +306,7 @@ install-byte: - mkdir -p $(INSTALL_LIBDIR) - cp -f graph.cmo graph.cmi $(CMA) $(INSTALL_LIBDIR) - cp -f $(SRCDIR)/*.mli $(INSTALL_LIBDIR) -+ cp -f META $(SRCDIR)/*.mli $(INSTALL_LIBDIR) - ifeq (@LABLGNOMECANVAS@,yes) - mkdir -p $(BINDIR) - cp -f $(ED_DIR)/editor.byte $(BINDIR)/graph-editor.byte diff --git a/dev-ml/ocamlgraph/metadata.xml b/dev-ml/ocamlgraph/metadata.xml deleted file mode 100644 index 87fc10d58..000000000 --- a/dev-ml/ocamlgraph/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription> - It provides an easy-to-use graph data structure together with several - operations and algorithms over graphs, in Graph.Pack. It is a reasonably - efficient imperative data structure for directed graphs with vertices - and edges labeled with integers. Several other graph implementations - are proposed for those not satisfied with the one above. Some are - persistent (imutable) and other imperative (mutable). Some are directed - and other are not. Some have labels for vertices, or labels for edges, - or both. Some have abstract types for vertices. etc. These - implementations are written as functors: you give the types of vertices - labels, edge labels, etc. and you get the data structure as a result. - it also provides several classic operations and algorithms over graphs. - They are also written as functors i.e. independently of the data - structure for graphs. One consequence is that you can define your own - data structure for graphs and yet re-use all the algorithms from this - library: you only need to provide a few operations such as iterating - over all vertices, over the successors of a vertex, etc. -</longdescription> -</pkgmetadata> diff --git a/dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild b/dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild deleted file mode 100644 index c28be862b..000000000 --- a/dev-ml/ocamlgraph/ocamlgraph-1.8.5.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="5" - -inherit eutils autotools - -DESCRIPTION="A graph library for Objective Caml" -HOMEPAGE="http://ocamlgraph.lri.fr" -SRC_URI="${HOMEPAGE}/download/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples gtk +ocamlopt" - -DEPEND=">=dev-lang/ocaml-3.10.2[ocamlopt?] - gtk? ( >=dev-ml/lablgtk-2.12[gnomecanvas,ocamlopt?] )" -RDEPEND="${DEPEND}" - -src_prepare() { - epatch "${FILESDIR}/${PN}-makefile.patch" - - #dirty fix for doc building - sed -i Makefile.in -e "s/-d doc -html \$(DGRAPH_INCLUDES) \$(DOC_SRC)/-d doc -html \$(DGRAPH_INCLUDES) \$(DOC_SRC:src\/merge.mli=)/g" - - eautoreconf -} - -src_compile() { - emake -j1 DESTDIR="/" || die "emake failed" - - if use doc; then - emake doc || die "emake doc failed" - fi -} - -src_install() { - emake install DESTDIR="${D}" || die "emake install failed" - dodoc CHANGES CREDITS FAQ README - - if use doc; then - dohtml doc/* - fi - - if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples - fi -} diff --git a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild index 5149f7a46..c9e5d206a 100644 --- a/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild +++ b/dev-perl/Bio-BigFile/Bio-BigFile-1.07.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -20,7 +20,7 @@ RDEPEND=" sci-biology/bioperl sci-biology/ucsc-genome-browser[static-libs]" DEPEND="${RDEPEND} - virtual/perl-Module-Build" + dev-perl/Module-Build" SRC_TEST="do" diff --git a/dev-perl/Bio-BigFile/ChangeLog b/dev-perl/Bio-BigFile/ChangeLog index df9646dfc..4d69032ac 100644 --- a/dev-perl/Bio-BigFile/ChangeLog +++ b/dev-perl/Bio-BigFile/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-perl/Bio-BigFile -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> Bio-BigFile-1.07.ebuild, + metadata.xml: + dev-perl/Bio-BigFile: Fix dependency problems due to recent mask of perl-core + packages + 18 Sep 2013; Justin Lecher <jlec@gentoo.org> -Bio-BigFile-1.06.ebuild, +Bio-BigFile-1.07.ebuild, metadata.xml: Version Bump, fix deps @@ -12,4 +17,3 @@ 09 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> Bio-BigFile-1.06.ebuild: initial ebuild, see bug #402835 - diff --git a/dev-perl/Bio-BigFile/metadata.xml b/dev-perl/Bio-BigFile/metadata.xml index 2bc893037..07b525505 100644 --- a/dev-perl/Bio-BigFile/metadata.xml +++ b/dev-perl/Bio-BigFile/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild index f18e1829f..e7e83d765 100644 --- a/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild +++ b/dev-perl/Bio-DB-Das-Chado/Bio-DB-Das-Chado-0.34.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -18,6 +18,6 @@ IUSE="" RDEPEND="" DEPEND="${RDEPEND} dev-perl/DBD-Pg - virtual/perl-Module-Build" + dev-perl/Module-Build" SRC_TEST="do" diff --git a/dev-perl/Bio-DB-Das-Chado/ChangeLog b/dev-perl/Bio-DB-Das-Chado/ChangeLog index d05b89e17..dd72b25b8 100644 --- a/dev-perl/Bio-DB-Das-Chado/ChangeLog +++ b/dev-perl/Bio-DB-Das-Chado/ChangeLog @@ -1,10 +1,15 @@ # ChangeLog for dev-perl/Bio-DB-Das-Chado -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> Bio-DB-Das-Chado-0.34.ebuild, + metadata.xml: + dev-perl/Bio-DB-Das-Chado: Fix dependency problems due to recent mask of perl- + core packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -Bio-DB-Das-Chado-0.32.ebuild, +Bio-DB-Das-Chado-0.34.ebuild, metadata.xml: - Version BUmp; Bump to EAPI=5 + Version Bump; Bump to EAPI=5 09 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> Bio-DB-Das-Chado-0.32.ebuild: @@ -16,4 +21,3 @@ 30 Jul 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +Bio-DB-Das-Chado-0.32.ebuild, +metadata.xml: dev-perl/Bio-DB-Das-Chado: new package required by sci-biology/gbrowse - diff --git a/dev-perl/Bio-DB-Das-Chado/metadata.xml b/dev-perl/Bio-DB-Das-Chado/metadata.xml index 2bc893037..07b525505 100644 --- a/dev-perl/Bio-DB-Das-Chado/metadata.xml +++ b/dev-perl/Bio-DB-Das-Chado/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/dev-perl/opal-client/ChangeLog b/dev-perl/opal-client/ChangeLog index 16c477298..ff44246c3 100644 --- a/dev-perl/opal-client/ChangeLog +++ b/dev-perl/opal-client/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-perl/opal-client -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-perl/opal-client: Updating remote-id in metadata.xml + 01 Nov 2014; Justin Lecher <jlec@gentoo.org> opal-client-1.9.2.ebuild, metadata.xml: Bump to EAPI=5 @@ -18,4 +21,3 @@ 21 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml, +opal-client-1.9.3.ebuild: Initial checkin to sci - diff --git a/dev-perl/opal-client/metadata.xml b/dev-perl/opal-client/metadata.xml index 897aa2e6b..46dbd9940 100644 --- a/dev-perl/opal-client/metadata.xml +++ b/dev-perl/opal-client/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">opaltoolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/Forthon/Forthon-0.8.13.ebuild b/dev-python/Forthon/Forthon-0.8.13.ebuild index 6f5f41de5..08a37772e 100644 --- a/dev-python/Forthon/Forthon-0.8.13.ebuild +++ b/dev-python/Forthon/Forthon-0.8.13.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit eutils distutils-r1 diff --git a/dev-python/GOGrapher/GOGrapher-9999.ebuild b/dev-python/GOGrapher/GOGrapher-9999.ebuild index e818807d1..5ad58a340 100644 --- a/dev-python/GOGrapher/GOGrapher-9999.ebuild +++ b/dev-python/GOGrapher/GOGrapher-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 subversion diff --git a/dev-python/RecSQL/ChangeLog b/dev-python/RecSQL/ChangeLog index ef054f357..e995523c0 100644 --- a/dev-python/RecSQL/ChangeLog +++ b/dev-python/RecSQL/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/RecSQL -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/RecSQL: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> RecSQL-9999.ebuild: Switch from git-2 to git-r3 diff --git a/dev-python/RecSQL/RecSQL-9999.ebuild b/dev-python/RecSQL/RecSQL-9999.ebuild index ac14fdb8c..929f3e971 100644 --- a/dev-python/RecSQL/RecSQL-9999.ebuild +++ b/dev-python/RecSQL/RecSQL-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="sqlite" if [[ $PV = *9999* ]]; then diff --git a/dev-python/RecSQL/metadata.xml b/dev-python/RecSQL/metadata.xml index 098ac091a..ba2081c24 100644 --- a/dev-python/RecSQL/metadata.xml +++ b/dev-python/RecSQL/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/RecSQL</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astlib/ChangeLog b/dev-python/astlib/ChangeLog index 992453036..2da13d24b 100644 --- a/dev-python/astlib/ChangeLog +++ b/dev-python/astlib/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/astlib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astlib: Updating remote-id in metadata.xml + *astlib-0.7.0 (29 Apr 2013) 29 Apr 2013; Sébastien Fabbro <bicatali@gentoo.org> +astlib-0.7.0.ebuild, diff --git a/dev-python/astlib/astlib-0.7.0.ebuild b/dev-python/astlib/astlib-0.7.0.ebuild index bb1214171..208a03fe6 100644 --- a/dev-python/astlib/astlib-0.7.0.ebuild +++ b/dev-python/astlib/astlib-0.7.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit distutils-r1 diff --git a/dev-python/astlib/metadata.xml b/dev-python/astlib/metadata.xml index 306677cbb..b4d862f31 100644 --- a/dev-python/astlib/metadata.xml +++ b/dev-python/astlib/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> astLib is a set of Python modules that provides some tools for research astronomers. It can be used for simple plots, statistics, common calculations, coordinate conversions, and manipulating FITS @@ -12,4 +12,7 @@ In Gentoo, PyWCSTools is using the stock library instead of the bundled one. </longdescription> + <upstream> + <remote-id type="sourceforge">astlib</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-helpers/ChangeLog b/dev-python/astropy-helpers/ChangeLog index 2c9ea827b..1e7733c0c 100644 --- a/dev-python/astropy-helpers/ChangeLog +++ b/dev-python/astropy-helpers/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astropy-helpers: Add github to remote-id in metadata.xml + + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> -Manifest, + -astropy-helpers-0.4.1.ebuild: + dev-python/astropy-helpers: In CVS + 14 Jan 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: Symlink diff --git a/dev-python/astropy-helpers/Manifest b/dev-python/astropy-helpers/Manifest deleted file mode 100644 index 2bae5556b..000000000 --- a/dev-python/astropy-helpers/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST astropy-helpers-0.4.1.tar.gz 98477 SHA256 0b4e47e535e7226d8795efb9e9453cac9343759058970a20734e66f443074577 SHA512 85975268372624bec4024dfbe560ef820bda308db898919c4d29643f10df11636f4996a8ff3f2fb7deece44f88963ddb0c8ca231e030713cf17db7503ceae42e WHIRLPOOL b37fa02ebe3e750052a9681e1e8a3a0aa9eede1909e69c70e2004ba738139707e1a0c21797681454ee782a6543bc8808b8de574d60aba601d228966c8659bb9f diff --git a/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild deleted file mode 120000 index 79b8b4c43..000000000 --- a/dev-python/astropy-helpers/astropy-helpers-0.4.1.ebuild +++ /dev/null @@ -1 +0,0 @@ -astropy-helpers-9999.ebuild
\ No newline at end of file diff --git a/dev-python/astropy-helpers/astropy-helpers-9999.ebuild b/dev-python/astropy-helpers/astropy-helpers-9999.ebuild index f23588953..5819aa799 100644 --- a/dev-python/astropy-helpers/astropy-helpers-9999.ebuild +++ b/dev-python/astropy-helpers/astropy-helpers-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 if [ ${PV} == "9999" ] ; then diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml index bacda05a5..e449320c9 100644 --- a/dev-python/astropy-helpers/metadata.xml +++ b/dev-python/astropy-helpers/metadata.xml @@ -6,4 +6,8 @@ astropy-helpers is a collection of build tools used by astropy that may be used by other projects. </longdescription> + <upstream> + <remote-id type="pypi">astropy-helpers</remote-id> + <remote-id type="github">astropy/astropy-helpers</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy/astropy-9999.ebuild b/dev-python/astropy/astropy-9999.ebuild index ebca5ef99..3304ff69a 100644 --- a/dev-python/astropy/astropy-9999.ebuild +++ b/dev-python/astropy/astropy-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 git-r3 diff --git a/dev-python/astropysics/ChangeLog b/dev-python/astropysics/ChangeLog index 8a75a59bc..4f1a5c93a 100644 --- a/dev-python/astropysics/ChangeLog +++ b/dev-python/astropysics/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for dev-python/astropysics -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> + astropysics-9999.ebuild: + dev-python/astropysics: Fix RDEPEND + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> astropysics-9999.ebuild: Switch from git-2 to git-r3 @@ -31,4 +35,3 @@ 28 Apr 2010; Kacper Kowalik <xarthisius.kk@gmail.com> +astropysics-9999.ebuild, +metadata.xml: Initial import wrt bug 317655. Ebuild was written by me - diff --git a/dev-python/astropysics/astropysics-9999.ebuild b/dev-python/astropysics/astropysics-9999.ebuild index 50d01a631..20b092141 100644 --- a/dev-python/astropysics/astropysics-9999.ebuild +++ b/dev-python/astropysics/astropysics-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -25,7 +25,7 @@ RDEPEND=" dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/networkx[${PYTHON_USEDEP}] dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/atpy[fits,votable,${PYTHON_USEDEP}] + dev-python/atpy[${PYTHON_USEDEP}] sci-astronomy/sextractor sci-visualization/mayavi[${PYTHON_USEDEP}] sci-libs/scipy[${PYTHON_USEDEP}]" diff --git a/dev-python/astroquery/ChangeLog b/dev-python/astroquery/ChangeLog index 4d7161d23..f5aadb9b9 100644 --- a/dev-python/astroquery/ChangeLog +++ b/dev-python/astroquery/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/astroquery -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/astroquery: Add github to remote-id in metadata.xml + *astroquery-0.2 (22 Aug 2014) *astroquery-9999 (22 Aug 2014) diff --git a/dev-python/astroquery/metadata.xml b/dev-python/astroquery/metadata.xml index 7fe0b4555..ba28af97d 100644 --- a/dev-python/astroquery/metadata.xml +++ b/dev-python/astroquery/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Astroquery is a package containing a collection of tools to use online astronomical databases. It integrates with Astropy and aims to support many services with a uniform API. </longdescription> + <upstream> + <remote-id type="pypi">astroquery</remote-id> + <remote-id type="github">astropy/astroquery</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/brewer2mpl/ChangeLog b/dev-python/brewer2mpl/ChangeLog index a79da6e04..a806cec23 100644 --- a/dev-python/brewer2mpl/ChangeLog +++ b/dev-python/brewer2mpl/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/brewer2mpl: Add github to remote-id in metadata.xml + *brewer2mpl-9999 (04 Feb 2015) *brewer2mpl-1.4.1 (04 Feb 2015) diff --git a/dev-python/brewer2mpl/metadata.xml b/dev-python/brewer2mpl/metadata.xml index a37a47ac0..42e39bdf4 100644 --- a/dev-python/brewer2mpl/metadata.xml +++ b/dev-python/brewer2mpl/metadata.xml @@ -12,4 +12,8 @@ colors of all 165 colorbrewer2.org color maps. The color map data ships with brewer2mpl so no internet connection is required. </longdescription> + <upstream> + <remote-id type="pypi">brewer2mpl</remote-id> + <remote-id type="github">jiffyclub/brewer2mpl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ccdproc/ChangeLog b/dev-python/ccdproc/ChangeLog index bb3af4dd1..2852131eb 100644 --- a/dev-python/ccdproc/ChangeLog +++ b/dev-python/ccdproc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ccdproc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ccdproc: Add github to remote-id in metadata.xml + *ccdproc-0.2.1 (18 Oct 2014) 18 Oct 2014; Joseph Jon Booker <joe@neoturbine.net> +ccdproc-0.2.1.ebuild, diff --git a/dev-python/ccdproc/ccdproc-0.2.1.ebuild b/dev-python/ccdproc/ccdproc-0.2.1.ebuild index 1fd337a3c..63a74b73c 100644 --- a/dev-python/ccdproc/ccdproc-0.2.1.ebuild +++ b/dev-python/ccdproc/ccdproc-0.2.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 if [ ${PV} == "9999" ] ; then diff --git a/dev-python/ccdproc/ccdproc-0.2.ebuild b/dev-python/ccdproc/ccdproc-0.2.ebuild index 1fd337a3c..63a74b73c 100644 --- a/dev-python/ccdproc/ccdproc-0.2.ebuild +++ b/dev-python/ccdproc/ccdproc-0.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 if [ ${PV} == "9999" ] ; then diff --git a/dev-python/ccdproc/ccdproc-9999.ebuild b/dev-python/ccdproc/ccdproc-9999.ebuild index 1fd337a3c..63a74b73c 100644 --- a/dev-python/ccdproc/ccdproc-9999.ebuild +++ b/dev-python/ccdproc/ccdproc-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 if [ ${PV} == "9999" ] ; then diff --git a/dev-python/ccdproc/metadata.xml b/dev-python/ccdproc/metadata.xml index 3cbb671a6..cdfbe201f 100644 --- a/dev-python/ccdproc/metadata.xml +++ b/dev-python/ccdproc/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> ccdproc is a AstroPy-affliated package for the basic reduction of CCD images. It provides a framework for accounting for error propagation and bad pixel tracking through the reduction steps. </longdescription> + <upstream> + <remote-id type="pypi">ccdproc</remote-id> + <remote-id type="github">astropy/ccdproc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/coards/coards-1.0.5.ebuild b/dev-python/coards/coards-1.0.5.ebuild index e4360153c..9fdb96ad5 100644 --- a/dev-python/coards/coards-1.0.5.ebuild +++ b/dev-python/coards/coards-1.0.5.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/coards/metadata.xml b/dev-python/coards/metadata.xml index c95dbb8d2..a94fb6cc1 100644 --- a/dev-python/coards/metadata.xml +++ b/dev-python/coards/metadata.xml @@ -9,4 +9,7 @@ This module converts between a given COARDS time specification and a Python datetime object, which is much more useful. </longdescription> + <upstream> + <remote-id type="pypi">coards</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/coords/coords-0.37.ebuild b/dev-python/coords/coords-0.37.ebuild index 878887b2b..6f7fc0344 100644 --- a/dev-python/coords/coords-0.37.ebuild +++ b/dev-python/coords/coords-0.37.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild b/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild index 8fe90afc2..c38f8e651 100644 --- a/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild +++ b/dev-python/cosmocalc/cosmocalc-0.1.2-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit distutils-r1 diff --git a/dev-python/dimensionful/ChangeLog b/dev-python/dimensionful/ChangeLog index e18714fad..647ffbeda 100644 --- a/dev-python/dimensionful/ChangeLog +++ b/dev-python/dimensionful/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/dimensionful -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/dimensionful: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> dimensionful-9999.ebuild: Switch from git-2 to git-r3 @@ -14,4 +17,3 @@ 19 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> +dimensionful-9999.ebuild, +metadata.xml: [dev-python/dimensionful] initial import, ebuild written by me - diff --git a/dev-python/dimensionful/dimensionful-9999.ebuild b/dev-python/dimensionful/dimensionful-9999.ebuild index 10325eeb0..a1a1a1a87 100644 --- a/dev-python/dimensionful/dimensionful-9999.ebuild +++ b/dev-python/dimensionful/dimensionful-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/dev-python/dimensionful/metadata.xml b/dev-python/dimensionful/metadata.xml index ef58ee263..ecf6df5d9 100644 --- a/dev-python/dimensionful/metadata.xml +++ b/dev-python/dimensionful/metadata.xml @@ -5,4 +5,7 @@ <email>xarthisius@gentoo.org</email> <name>Kacper Kowalik</name> </maintainer> + <upstream> + <remote-id type="github">caseywstark/dimensionful</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/emcee/emcee-1.2.0.ebuild b/dev-python/emcee/emcee-1.2.0.ebuild index 684742b64..21008c94b 100644 --- a/dev-python/emcee/emcee-1.2.0.ebuild +++ b/dev-python/emcee/emcee-1.2.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/emcee/emcee-2.0.0.ebuild b/dev-python/emcee/emcee-2.0.0.ebuild index 51b21257a..e956b17be 100644 --- a/dev-python/emcee/emcee-2.0.0.ebuild +++ b/dev-python/emcee/emcee-2.0.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit distutils-r1 diff --git a/dev-python/emcee/metadata.xml b/dev-python/emcee/metadata.xml index b4cb18f4a..726f85321 100644 --- a/dev-python/emcee/metadata.xml +++ b/dev-python/emcee/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> This provides a set of sparse matrix types for Python, with modules which implement: - Iterative methods for solving linear systems of equations @@ -13,4 +13,7 @@ standard sparse and dense matrix libraries (UMFPACK/AMD, SuperLU, BLAS/LAPACK) for maximum performance and robustness. </longdescription> + <upstream> + <remote-id type="pypi">emcee</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ffc/ChangeLog b/dev-python/ffc/ChangeLog index 37662b34f..07f0f2629 100644 --- a/dev-python/ffc/ChangeLog +++ b/dev-python/ffc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ffc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ffc: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> ffc-1.3.0.ebuild: fixed dependency issue diff --git a/dev-python/ffc/ffc-1.2.0.ebuild b/dev-python/ffc/ffc-1.2.0.ebuild index 81390468c..15342f77d 100644 --- a/dev-python/ffc/ffc-1.2.0.ebuild +++ b/dev-python/ffc/ffc-1.2.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ffc/ffc-1.3.0.ebuild b/dev-python/ffc/ffc-1.3.0.ebuild index d2a291810..6b17d6c11 100644 --- a/dev-python/ffc/ffc-1.3.0.ebuild +++ b/dev-python/ffc/ffc-1.3.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ffc/ffc-1.4.0.ebuild b/dev-python/ffc/ffc-1.4.0.ebuild index 9ec9a2057..a0701dd4b 100644 --- a/dev-python/ffc/ffc-1.4.0.ebuild +++ b/dev-python/ffc/ffc-1.4.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ffc/metadata.xml b/dev-python/ffc/metadata.xml index 34821f2af..893659eac 100644 --- a/dev-python/ffc/metadata.xml +++ b/dev-python/ffc/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> FFC works as a compiler for multilinear forms by generating code (C or C++) for the evaluation of a multilinear form given in mathematical notation. This new approach to form evaluation makes it possible to @@ -10,4 +10,7 @@ mathematical notation and the generated code is as efficient as hand-optimized code. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/ffc</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ffnet/ChangeLog b/dev-python/ffnet/ChangeLog index 53c9c2208..49cfe6fe9 100644 --- a/dev-python/ffnet/ChangeLog +++ b/dev-python/ffnet/ChangeLog @@ -1,10 +1,13 @@ # ChangeLog for dev-python/ffnet -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ffnet: Updating remote-id in metadata.xml + 09 Apr 2014; Justin Lecher <jlec@gentoo.org> -ffnet-0.6.2.ebuild, +ffnet-0.7.1.ebuild, metadata.xml: - Version BUmp; fix distutils-r1 eclass usage + Version Bump; fix distutils-r1 eclass usage 25 Oct 2012; Justin Lecher <jlec@gentoo.org> ffnet-0.6.2.ebuild, metadata.xml: @@ -28,4 +31,3 @@ 26 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +ffnet-0.6.2.ebuild, +metadata.xml: Import. Ebuild submitted by Marek Wojciechowski bug #158038 - diff --git a/dev-python/ffnet/ffnet-0.7.1.ebuild b/dev-python/ffnet/ffnet-0.7.1.ebuild index 8900c7b88..f656e5bdf 100644 --- a/dev-python/ffnet/ffnet-0.7.1.ebuild +++ b/dev-python/ffnet/ffnet-0.7.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python2_{6,7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 flag-o-matic fortran-2 toolchain-funcs diff --git a/dev-python/ffnet/metadata.xml b/dev-python/ffnet/metadata.xml index 56358e20c..d5cbb7029 100644 --- a/dev-python/ffnet/metadata.xml +++ b/dev-python/ffnet/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="matplotlib">Use matplotlib for drawing</flag> </use> + <upstream> + <remote-id type="sourceforge">ffnet</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/fiat/ChangeLog b/dev-python/fiat/ChangeLog index 26d00d366..2c71ff6ce 100644 --- a/dev-python/fiat/ChangeLog +++ b/dev-python/fiat/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/fiat -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/fiat: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> fiat-1.3.0.ebuild, fiat-1.4.0.ebuild: Added keyword diff --git a/dev-python/fiat/fiat-1.1.ebuild b/dev-python/fiat/fiat-1.1.ebuild index b699e74de..e6144b06e 100644 --- a/dev-python/fiat/fiat-1.1.ebuild +++ b/dev-python/fiat/fiat-1.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/fiat/fiat-1.3.0.ebuild b/dev-python/fiat/fiat-1.3.0.ebuild index 3db5363e6..c1431238f 100644 --- a/dev-python/fiat/fiat-1.3.0.ebuild +++ b/dev-python/fiat/fiat-1.3.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/fiat/fiat-1.4.0.ebuild b/dev-python/fiat/fiat-1.4.0.ebuild index 3db5363e6..c1431238f 100644 --- a/dev-python/fiat/fiat-1.4.0.ebuild +++ b/dev-python/fiat/fiat-1.4.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml index a67ae626b..b9c29fa54 100644 --- a/dev-python/fiat/metadata.xml +++ b/dev-python/fiat/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The FInite element Automatic Tabulator FIAT supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order @@ -12,4 +12,7 @@ supported on triangles and tetrahedra. Upcoming versions will also support Hermite and nonconforming elements. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/fiat</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/gammapy/ChangeLog b/dev-python/gammapy/ChangeLog index e94737626..bfb8bcf98 100644 --- a/dev-python/gammapy/ChangeLog +++ b/dev-python/gammapy/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/gammapy -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/gammapy: Add github to remote-id in metadata.xml + *gammapy-0.1 (28 Aug 2014) 28 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +gammapy-0.1.ebuild, diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml index 1370ffdb0..948014d9a 100644 --- a/dev-python/gammapy/metadata.xml +++ b/dev-python/gammapy/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Gammapy is a package for simulating and analysing gamma-ray sky data. It is currently designed to support users of telescopes such as Fermi, H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> + <upstream> + <remote-id type="pypi">gammapy</remote-id> + <remote-id type="github">gammapy/gammapy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/go-parser/go-parser-9999.ebuild b/dev-python/go-parser/go-parser-9999.ebuild index b4b019933..d4e02fb35 100644 --- a/dev-python/go-parser/go-parser-9999.ebuild +++ b/dev-python/go-parser/go-parser-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/healpy/ChangeLog b/dev-python/healpy/ChangeLog index 5251a637c..3ae21e5a2 100644 --- a/dev-python/healpy/ChangeLog +++ b/dev-python/healpy/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/healpy -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/healpy: Add github to remote-id in metadata.xml + *healpy-1.7.4 (03 Mar 2014) 03 Mar 2014; Sébastien Fabbro <bicatali@gentoo.org> +healpy-1.7.4.ebuild, diff --git a/dev-python/healpy/healpy-1.7.4.ebuild b/dev-python/healpy/healpy-1.7.4.ebuild index 3208f745e..857681da7 100644 --- a/dev-python/healpy/healpy-1.7.4.ebuild +++ b/dev-python/healpy/healpy-1.7.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/healpy/metadata.xml b/dev-python/healpy/metadata.xml index bd104d9d7..6157d9af6 100644 --- a/dev-python/healpy/metadata.xml +++ b/dev-python/healpy/metadata.xml @@ -1,13 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang='en'> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Healpy provides a python package to manipulate healpix maps. It is based on the standard numeric and visualisation tools for Python, Numpy and matplotlib. </longdescription> -<upstream> - <remote-id type="pypi">healpy</remote-id> -</upstream> + <upstream> + <remote-id type="pypi">healpy</remote-id> + <remote-id type="github">healpy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/imageutils/ChangeLog b/dev-python/imageutils/ChangeLog index 133e25091..4f637ac60 100644 --- a/dev-python/imageutils/ChangeLog +++ b/dev-python/imageutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/imageutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/imageutils: Add github to remote-id in metadata.xml + *imageutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +imageutils-9999.ebuild, diff --git a/dev-python/imageutils/metadata.xml b/dev-python/imageutils/metadata.xml index 281f12fe7..7eae1bb53 100644 --- a/dev-python/imageutils/metadata.xml +++ b/dev-python/imageutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> imageutils is a collection of image processing utilities that are generally useful to astronomers. These will likely become part of the core AstroPy package before the 1.0 release. </longdescription> + <upstream> + <remote-id type="pypi">imageutils</remote-id> + <remote-id type="github">astropy/imageutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/inference/inference-0.4.ebuild b/dev-python/inference/inference-0.4.ebuild index ee57fd7d3..c8dd08a00 100644 --- a/dev-python/inference/inference-0.4.ebuild +++ b/dev-python/inference/inference-0.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 flag-o-matic fortran-2 diff --git a/dev-python/instant/ChangeLog b/dev-python/instant/ChangeLog index af28b7f08..722f6f1b9 100644 --- a/dev-python/instant/ChangeLog +++ b/dev-python/instant/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/instant -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/instant: Add bitbucket to remote-id in metadata.xml + *instant-1.3.0 (16 Jul 2014) *instant-1.4.0 (16 Jul 2014) diff --git a/dev-python/instant/instant-1.2.0.ebuild b/dev-python/instant/instant-1.2.0.ebuild index bde5cc440..ab9398420 100644 --- a/dev-python/instant/instant-1.2.0.ebuild +++ b/dev-python/instant/instant-1.2.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit distutils-r1 diff --git a/dev-python/instant/instant-1.3.0.ebuild b/dev-python/instant/instant-1.3.0.ebuild index ffa211a96..b2ccc68fb 100644 --- a/dev-python/instant/instant-1.3.0.ebuild +++ b/dev-python/instant/instant-1.3.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/instant/instant-1.4.0.ebuild b/dev-python/instant/instant-1.4.0.ebuild index ffa211a96..b2ccc68fb 100644 --- a/dev-python/instant/instant-1.4.0.ebuild +++ b/dev-python/instant/instant-1.4.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/instant/metadata.xml b/dev-python/instant/metadata.xml index c446ffa73..37fa71c43 100644 --- a/dev-python/instant/metadata.xml +++ b/dev-python/instant/metadata.xml @@ -1,10 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Instant is a Python module that allows for instant inlining of C and C++ code in Python. It is a small Python module built on top of SWIG and Distutils. It is part of the FEniCS Project (http://www.fenics.org) </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/instant</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/jupyter-nbgrader/ChangeLog b/dev-python/jupyter-nbgrader/ChangeLog new file mode 100644 index 000000000..16875733c --- /dev/null +++ b/dev-python/jupyter-nbgrader/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-python/jupyter-nbgrader +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*jupyter-nbgrader-9999 (03 Mar 2015) + + 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +jupyter-nbgrader-9999.ebuild, +metadata.xml: + Initial ebuild diff --git a/dev-python/jupyter-nbgrader/jupyter-nbgrader-9999.ebuild b/dev-python/jupyter-nbgrader/jupyter-nbgrader-9999.ebuild new file mode 100644 index 000000000..b7f1f4a2a --- /dev/null +++ b/dev-python/jupyter-nbgrader/jupyter-nbgrader-9999.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="nbgrader" + +DESCRIPTION="A system for assigning and grading notebooks" +HOMEPAGE="http://jupyter.org" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/jupyter/${MY_PN}.git git://github.com/jupyter/${MY_PN}.git" +else + SRC_URI="" + KEYWORDS="~amd64" +fi + +LICENSE="BSD" +SLOT="0" + +RDEPEND=" + >=dev-python/ipython-3.0.0[notebook,${PYTHON_USEDEP}] + dev-python/sqlalchemy[${PYTHON_USEDEP}] + dev-python/flask[${PYTHON_USEDEP}] + dev-python/autopep8[${PYTHON_USEDEP}] + " +DEPEND="${RDEPEND}" diff --git a/sci-visualization/labplot/metadata.xml b/dev-python/jupyter-nbgrader/metadata.xml index 897aa2e6b..2c6fd84fa 100644 --- a/sci-visualization/labplot/metadata.xml +++ b/dev-python/jupyter-nbgrader/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <longdescription> + A system for assigning and grading notebooks. + </longdescription> </pkgmetadata> diff --git a/dev-python/jupyter-nbviewer/ChangeLog b/dev-python/jupyter-nbviewer/ChangeLog new file mode 100644 index 000000000..059df275d --- /dev/null +++ b/dev-python/jupyter-nbviewer/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-python/jupyter-nbviewer +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*jupyter-nbviewer-9999 (03 Mar 2015) + + 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +jupyter-nbviewer-9999.ebuild, +metadata.xml: + Initial ebuild diff --git a/dev-python/jupyter-nbviewer/jupyter-nbviewer-9999.ebuild b/dev-python/jupyter-nbviewer/jupyter-nbviewer-9999.ebuild new file mode 100644 index 000000000..941c5caae --- /dev/null +++ b/dev-python/jupyter-nbviewer/jupyter-nbviewer-9999.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="nbviewer" + +DESCRIPTION="Nbconvert as a webservice (rendering ipynb to static HTML)" +HOMEPAGE="http://jupyter.org" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/jupyter/${MY_PN}.git git://github.com/jupyter/${MY_PN}.git" +else + SRC_URI="" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-4" +SLOT="0" + +RDEPEND=" + >=dev-python/ipython-3.0.0[notebook,${PYTHON_USEDEP}] + >=www-servers/tornado-3.1.1[${PYTHON_USEDEP}] + dev-python/pycurl[${PYTHON_USEDEP}] + dev-python/pylibmc[${PYTHON_USEDEP}] + dev-python/newrelic[${PYTHON_USEDEP}] + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/elasticsearch-py[${PYTHON_USEDEP}] + " +DEPEND="${RDEPEND}" diff --git a/dev-python/jupyter-nbviewer/metadata.xml b/dev-python/jupyter-nbviewer/metadata.xml new file mode 100644 index 000000000..5ac942bc2 --- /dev/null +++ b/dev-python/jupyter-nbviewer/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + Jupyter nbviewer is the web application behind The Jupyter Notebook + Viewer, which is graciously hosted by Rackspace. Run this locally + to get most of the features of nbviewer on your own network. + </longdescription> +</pkgmetadata> diff --git a/dev-python/matlab_wrapper/ChangeLog b/dev-python/matlab_wrapper/ChangeLog index 478753411..f396c02ff 100644 --- a/dev-python/matlab_wrapper/ChangeLog +++ b/dev-python/matlab_wrapper/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/matlab_wrapper: Add github to remote-id in metadata.xml + *matlab_wrapper-9999 (20 Jan 2015) *matlab_wrapper-0.9.6 (20 Jan 2015) diff --git a/dev-python/matlab_wrapper/metadata.xml b/dev-python/matlab_wrapper/metadata.xml index f24eccb56..4bdcc4c27 100644 --- a/dev-python/matlab_wrapper/metadata.xml +++ b/dev-python/matlab_wrapper/metadata.xml @@ -13,4 +13,8 @@ shell. MATLAB session is started in the background and appears as a regular Python module. </longdescription> + <upstream> + <remote-id type="pypi">matlab_wrapper</remote-id> + <remote-id type="github">mrkrd/matlab_wrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/matplotlib2tikz/ChangeLog b/dev-python/matplotlib2tikz/ChangeLog new file mode 100644 index 000000000..0ee8f934f --- /dev/null +++ b/dev-python/matplotlib2tikz/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for dev-python/matplotlib2tikz +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/matplotlib2tikz: Add github to remote-id in metadata.xml + +*matplotlib2tikz-0.1.0 (31 May 2015) +*matplotlib2tikz-9999 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +matplotlib2tikz-0.1.0.ebuild, +matplotlib2tikz-9999.ebuild, +metadata.xml: + New ebuild written by me diff --git a/dev-python/matplotlib2tikz/Manifest b/dev-python/matplotlib2tikz/Manifest new file mode 100644 index 000000000..b3bc18006 --- /dev/null +++ b/dev-python/matplotlib2tikz/Manifest @@ -0,0 +1 @@ +DIST matplotlib2tikz-0.1.0.tar.gz 16369 SHA256 d1c07d8a7d5fcdba77509769f2a477a75562d6b87d1de9d50ea78ea0f1285acd SHA512 0ed25659afeeec279c0d97033b37357fa9c91d49f3547a789b1add9faa7285e73a4eec94c3cd70d1edfa7186cbad1d452256586ceb7066a8908ad2d3e73a274e WHIRLPOOL eabe83d14b1d0c362bc325e0a9b5612cd787098440df634fa4bbf828e6c5b7085ec78d00545ab9d2463e9251a3c1978b8edd866ea74ef4b1d58da251e82be0b3 diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild new file mode 120000 index 000000000..49bc235a9 --- /dev/null +++ b/dev-python/matplotlib2tikz/matplotlib2tikz-0.1.0.ebuild @@ -0,0 +1 @@ +matplotlib2tikz-9999.ebuild
\ No newline at end of file diff --git a/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild b/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild new file mode 100644 index 000000000..6af9d49d6 --- /dev/null +++ b/dev-python/matplotlib2tikz/matplotlib2tikz-9999.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit distutils-r1 + +DESCRIPTION="Python script for converting matplotlib figures into native Pgfplots (TikZ) figures" +HOMEPAGE="https://github.com/nschloe/matplotlib2tikz" + +if [ ${PV} = "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/nschloe/${PN}.git git://github.com/nschloe/${PN}.git" + KEYWORDS="" +else + SRC_URI="https://github.com/nschloe/matplotlib2tikz/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" +fi + +LICENSE="LGPL-3" +SLOT="0" +IUSE="" + +RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}] + dev-texlive/texlive-pictures" +DEPEND="${RDEPEND}" + #test? ( dev-python/pytest[${PYTHON_USEDEP}] )" diff --git a/dev-python/matplotlib2tikz/metadata.xml b/dev-python/matplotlib2tikz/metadata.xml new file mode 100644 index 000000000..112456f47 --- /dev/null +++ b/dev-python/matplotlib2tikz/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <maintainer> + <email>marbre@linux.sungazer.de</email> + <name>Marius Brehler</name> + </maintainer> + <upstream> + <remote-id type="github">nschloe/matplotlib2tikz</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/meshpy/ChangeLog b/dev-python/meshpy/ChangeLog index 1f223ae38..084d36c0a 100644 --- a/dev-python/meshpy/ChangeLog +++ b/dev-python/meshpy/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-python/meshpy -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*meshpy-2014.1 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +meshpy-2014.1.ebuild: + Version bump; Implement python_test() + *meshpy-2013.1.2 (14 Jun 2013) 14 Jun 2013; Justin Lecher <jlec@gentoo.org> -meshpy-0.91.2.ebuild, diff --git a/dev-python/meshpy/Manifest b/dev-python/meshpy/Manifest index 62fc27c21..607e920e1 100644 --- a/dev-python/meshpy/Manifest +++ b/dev-python/meshpy/Manifest @@ -1 +1,2 @@ DIST MeshPy-2013.1.2.tar.gz 1885753 SHA256 425ffa0f5a7dacfc1301bbb165ff78fbe6beacb0ab6c0a8dd581f565896c6762 SHA512 6004a609fc62ff44e5770a0d041da42eea1e185def5b1efca357d4cac3dcd34a7ccb5b0ca2d2f7fb4ba81bbc0251b8c998eb64bcff828f05cfc1a0a49385b9ae WHIRLPOOL 48266e5838c6a416622fc0cc804112af1331b9d74952030e225500f8f6426c4a9679088e8f3b06dbf26169128e33e2173bae73d198e20b5ffabd02c9e7762660 +DIST MeshPy-2014.1.tar.gz 1851120 SHA256 a090729c9b99360b2741099906361b2e9ba6373b97707817c9b81f66531380b6 SHA512 d8d7823df60250382577f67bb5ffd3b6523c84729c013220eaddccfa4b227839c2e0ffb285f87e752cf0dc5292eb1e5c693d04139d2fb33a05877e0b2b1bcecc WHIRLPOOL b84442d92933c5b5745c8a91ba4f65df80a1c94fd08668d8575c154de61ce0b67605f87b638341adb3f2b43ab8d2f6c82989e9d2bfcab177dabdf0119f07ab9b diff --git a/dev-python/meshpy/meshpy-2013.1.2.ebuild b/dev-python/meshpy/meshpy-2013.1.2.ebuild index c0d2032cf..ea9cd6d2e 100644 --- a/dev-python/meshpy/meshpy-2013.1.2.ebuild +++ b/dev-python/meshpy/meshpy-2013.1.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/meshpy/meshpy-2014.1.ebuild b/dev-python/meshpy/meshpy-2014.1.ebuild new file mode 100644 index 000000000..9727775af --- /dev/null +++ b/dev-python/meshpy/meshpy-2014.1.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python{3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="MeshPy" + +DESCRIPTION="Quality triangular and tetrahedral mesh generation for Python" +HOMEPAGE="http://mathema.tician.de/software/meshpy http://pypi.python.org/pypi/MeshPy" +SRC_URI="mirror://pypi/M/${MY_PN}/${MY_PN}-${PV}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-libs/boost[python,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pytools[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/setuptools[${PYTHON_USEDEP}] + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +S="${WORKDIR}/${MY_PN}-${PV}" + +python_prepare_all() { + sed 's: delay = 10: delay = 1:g' -i aksetup_helper.py || die + distutils-r1_python_prepare_all +} + +python_compile() { + mkdir "${BUILD_DIR}" || die + echo "BOOST_PYTHON_LIBNAME = [\'boost_${EPYTHON}-mt\']">> "${BUILD_DIR}"/siteconf.py + distutils-r1_python_compile +} + +python_test() { + py.test || die +} diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml index 0c0b3caa3..5bd8e24f7 100644 --- a/dev-python/meshpy/metadata.xml +++ b/dev-python/meshpy/metadata.xml @@ -10,4 +10,7 @@ In order to generate these 2D and 3D meshes, MeshPy provides Python interfaces to two well-regarded mesh generators, Triangle by J. Shewchuk and TetGen by Hang Si. Both are included in the package in slightly modified versions. </longdescription> + <upstream> + <remote-id type="pypi">MeshPy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/montage-wrapper/metadata.xml b/dev-python/montage-wrapper/metadata.xml index 101fb4b35..5cfc153a9 100644 --- a/dev-python/montage-wrapper/metadata.xml +++ b/dev-python/montage-wrapper/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription> + <herd>sci-astronomy</herd> + <longdescription> This Astropy-affiliated package provides a python wrapper to the Montage Astronomical Image Mosaic Engine, including both functions to access individual Montage commands, and high-level functions to facilitate mosaicking and re-projecting. </longdescription> + <upstream> + <remote-id type="pypi">montage-wrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/newrelic/ChangeLog b/dev-python/newrelic/ChangeLog new file mode 100644 index 000000000..f904df843 --- /dev/null +++ b/dev-python/newrelic/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for dev-python/newrelic +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*newrelic-2.50.0.39 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +newrelic-2.50.0.39.ebuild: + Version bump + +*newrelic-2.44.0.36 (03 Mar 2015) + + 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +newrelic-2.44.0.36.ebuild: + Initial ebuild diff --git a/dev-python/newrelic/Manifest b/dev-python/newrelic/Manifest new file mode 100644 index 000000000..d32de2b4f --- /dev/null +++ b/dev-python/newrelic/Manifest @@ -0,0 +1,2 @@ +DIST newrelic-2.44.0.36.tar.gz 656605 SHA256 373d3af3e9f0c233932ddcf024f978eed3bd6ceaee9563aedb65c029f7f9b2b7 SHA512 2e9b7b6afd74c562c82813d0245822a194e151abf1e32827915b83677db811032711418ae2bd0c26b3ea4727323ca53d538862957d8cd07f7f6a2ce26630a682 WHIRLPOOL a36537b56d9e18c5143149821120296e3aae53094d9038bc0f2e4ac175820f7d6600c84d8cf17199d7a53e6dc93ef2e41885f17f2ace7de87c97a3100200149d +DIST newrelic-2.50.0.39.tar.gz 662564 SHA256 fddd47a8d048e0c5f42eee511a8aaf35891c996d6c959553c7bec8b3ac74b3cb SHA512 935973b7897348113ab40ac4f1ea173cf31886057569a0384e4a26d96463220a43768a4dd88ac4e4a8a7db01ab4fe6fde7825860a7fbd62911ead5fc2e3f0774 WHIRLPOOL e2044913e7274703fe76368db84f2f670810653b08855e5ac067e8f009b42cb222bd8958c92a12401ac5a1630d2797f0ae77f832d85288941d56eb181efe1693 diff --git a/dev-python/newrelic/metadata.xml b/dev-python/newrelic/metadata.xml new file mode 100644 index 000000000..d5e4ca843 --- /dev/null +++ b/dev-python/newrelic/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + Python agent for the New Relic web application performance + monitoring service. + </longdescription> + <upstream> + <remote-id type="pypi">newrelic</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/newrelic/newrelic-2.44.0.36.ebuild b/dev-python/newrelic/newrelic-2.44.0.36.ebuild new file mode 100644 index 000000000..b34576f02 --- /dev/null +++ b/dev-python/newrelic/newrelic-2.44.0.36.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="newrelic" + +DESCRIPTION="New Relic Python Agent" +HOMEPAGE="http://newrelic.com/docs/python/new-relic-for-python" + +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="newrelic" +SLOT="0" + +RDEPEND=" + || ( + dev-python/bottle[${PYTHON_USEDEP}] + dev-python/cherrypy[${PYTHON_USEDEP}] + dev-python/django[${PYTHON_USEDEP}] + dev-python/flask[${PYTHON_USEDEP}] + dev-python/pylons[${PYTHON_USEDEP}] + dev-python/pyramid[${PYTHON_USEDEP}] + )" + #|| ( + # dev-python/cython[${PYTHON_USEDEP}] + # virtual/pypy + # virtual/pypy3 + #)" +DEPEND="${RDEPEND}" diff --git a/dev-python/newrelic/newrelic-2.50.0.39.ebuild b/dev-python/newrelic/newrelic-2.50.0.39.ebuild new file mode 100644 index 000000000..92fd5f79a --- /dev/null +++ b/dev-python/newrelic/newrelic-2.50.0.39.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit distutils-r1 + +MY_PN="newrelic" + +DESCRIPTION="New Relic Python Agent" +HOMEPAGE="http://newrelic.com/docs/python/new-relic-for-python" + +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="newrelic" +SLOT="0" + +RDEPEND=" + || ( + dev-python/bottle[${PYTHON_USEDEP}] + dev-python/cherrypy[${PYTHON_USEDEP}] + dev-python/django[${PYTHON_USEDEP}] + dev-python/flask[${PYTHON_USEDEP}] + dev-python/pylons[${PYTHON_USEDEP}] + dev-python/pyramid[${PYTHON_USEDEP}] + )" + #|| ( + # dev-python/cython[${PYTHON_USEDEP}] + # virtual/pypy + # virtual/pypy3 + #)" +DEPEND="${RDEPEND}" + +src_install() { + default + dobin scripts/newrelic-admin +} diff --git a/dev-python/nvidia-ml-py/ChangeLog b/dev-python/nvidia-ml-py/ChangeLog index 8933fc9b0..4ac601d84 100644 --- a/dev-python/nvidia-ml-py/ChangeLog +++ b/dev-python/nvidia-ml-py/ChangeLog @@ -1,6 +1,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nvidia-ml-py-7.346.0 (13 May 2015) + + 13 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +nvidia-ml-py-7.346.0.ebuild: + Version bump + *nvidia-ml-py-6.340.0 (26 Jan 2015) 26 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, diff --git a/dev-python/nvidia-ml-py/Manifest b/dev-python/nvidia-ml-py/Manifest index 837ed163f..691824114 100644 --- a/dev-python/nvidia-ml-py/Manifest +++ b/dev-python/nvidia-ml-py/Manifest @@ -1 +1,2 @@ DIST nvidia-ml-py-6.340.0.tar.gz 19787 SHA256 74c7bc63858f074c758a3f7b21ede47d2db24c23539b05ee7d6dfc2b0820bae1 SHA512 31ab48b090970f53b49074b9059bd972d3943468a8dd481ce70397fc6509bc0fb6c2de20aa4cdd4624501ae6036bf5d657f5a186ea26441f54867d160938fda4 WHIRLPOOL a82fe44af35bf216bdc41d4e67e5bd888a07e88f06ba64d8d9bf03ea960438b4ff34163ed95c16777e0dd47a229132b1a095f0d92ba915c98ffd71d74bc7af6a +DIST nvidia-ml-py-7.346.0.tar.gz 19186 SHA256 7a04fff2252202dc6f3d6ab50840372959cf498d0ba59c93e0361513b50a24d6 SHA512 01bd80b99682a5d33f007acbd886efe5f427290534a2f20a8d34a075cb1a722ea29c56ad187372ccb74192dc0af16a94da238b7068190b758176cfdd7698d4ff WHIRLPOOL 1adf1cf456883ca0db75d9e4c64a77593b53919fdd4a7b7f5947310fea63845ac39a38782a07ea2d8cefc5f49d02cb0ad927ee16520e12487b5450a899eab1c3 diff --git a/dev-python/nvidia-ml-py/metadata.xml b/dev-python/nvidia-ml-py/metadata.xml index 75b9f4d16..07ccaa0d1 100644 --- a/dev-python/nvidia-ml-py/metadata.xml +++ b/dev-python/nvidia-ml-py/metadata.xml @@ -10,4 +10,7 @@ Provides a Python interface to GPU management and monitoring functions. This is a wrapper around the NVML library. </longdescription> + <upstream> + <remote-id type="pypi">nvidia-ml-py</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/nvidia-ml-py/nvidia-ml-py-7.346.0.ebuild b/dev-python/nvidia-ml-py/nvidia-ml-py-7.346.0.ebuild new file mode 100644 index 000000000..20abe15a9 --- /dev/null +++ b/dev-python/nvidia-ml-py/nvidia-ml-py-7.346.0.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit distutils-r1 + +DESCRIPTION="Python Bindings for the NVIDIA Management Library" +HOMEPAGE="https://developer.nvidia.com/ganglia-monitoring-system" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="BSD" +SLOT="0" + +RDEPEND="=dev-util/nvidia-cuda-gdk-340.29[nvml]" +DEPEND="${RDEPEND}" diff --git a/dev-python/omniorbpy/ChangeLog b/dev-python/omniorbpy/ChangeLog index 5cc37e99b..97660aa5b 100644 --- a/dev-python/omniorbpy/ChangeLog +++ b/dev-python/omniorbpy/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/omniorbpy: Updating remote-id in metadata.xml + + 08 Apr 2015; Justin Lecher <jlec@gentoo.org> omniorbpy-3.4.ebuild: + dev-python/omniorbpy: Fix python dependency + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> omniorbpy-3.4.ebuild: dev-python/omniorbpy: fix SLOT operators diff --git a/dev-python/omniorbpy/metadata.xml b/dev-python/omniorbpy/metadata.xml index 897aa2e6b..50d473bb3 100644 --- a/dev-python/omniorbpy/metadata.xml +++ b/dev-python/omniorbpy/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">omniorb</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/omniorbpy/omniorbpy-3.4.ebuild b/dev-python/omniorbpy/omniorbpy-3.4.ebuild index 0f4236f4a..4ec65acee 100644 --- a/dev-python/omniorbpy/omniorbpy-3.4.ebuild +++ b/dev-python/omniorbpy/omniorbpy-3.4.ebuild @@ -22,8 +22,8 @@ IUSE="ssl" REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} - >=net-misc/omniORB-4.1.3 - ssl? ( dev-libs/openssl:0 )" + >=net-misc/omniORB-4.1.3[${PYTHON_USEDEP}] + ssl? ( dev-libs/openssl:0= )" RDEPEND=${DEPEND} S=${WORKDIR}/${MY_P} diff --git a/dev-python/opal-client/ChangeLog b/dev-python/opal-client/ChangeLog index c75fb455c..9b6b8d455 100644 --- a/dev-python/opal-client/ChangeLog +++ b/dev-python/opal-client/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/opal-client -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/opal-client: Updating remote-id in metadata.xml + 15 Oct 2013; Justin Lecher <jlec@gentoo.org> opal-client-2.4.1.ebuild, metadata.xml: Add missing PYTHON_DEPS and PYTHON_REQUIRED_USE @@ -33,4 +36,3 @@ 21 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml, +opal-client-1.9.3.ebuild: Initial checkin to sci - diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml index f17a827e3..a32846566 100644 --- a/dev-python/opal-client/metadata.xml +++ b/dev-python/opal-client/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">opaltoolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/opal-client/opal-client-2.4.1.ebuild b/dev-python/opal-client/opal-client-2.4.1.ebuild index 455e0203c..a037a071a 100644 --- a/dev-python/opal-client/opal-client-2.4.1.ebuild +++ b/dev-python/opal-client/opal-client-2.4.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-r1 versionator diff --git a/dev-python/photutils/ChangeLog b/dev-python/photutils/ChangeLog index fe8069d96..2c0ec070b 100644 --- a/dev-python/photutils/ChangeLog +++ b/dev-python/photutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/photutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/photutils: Add github to remote-id in metadata.xml + *photutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +metadata.xml, diff --git a/dev-python/photutils/metadata.xml b/dev-python/photutils/metadata.xml index 9f819f64b..7cb319709 100644 --- a/dev-python/photutils/metadata.xml +++ b/dev-python/photutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> photutils is a python package for determining photometric properties of sources in astronomical images. This includes source detection, centroid and shape parameters, and performing photometry. </longdescription> + <upstream> + <remote-id type="pypi">photutils</remote-id> + <remote-id type="github">astropy/photutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pickleshare/ChangeLog b/dev-python/pickleshare/ChangeLog new file mode 100644 index 000000000..bf4233eb4 --- /dev/null +++ b/dev-python/pickleshare/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for dev-python/pickleshare +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pickleshare: Add github to remote-id in metadata.xml + +*pickleshare-0.5 (31 May 2015) +*pickleshare-9999 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +pickleshare-0.5.ebuild, +pickleshare-9999.ebuild: + Initial ebuild (required for >dev-python/ipython-3.1.0) diff --git a/dev-python/pickleshare/Manifest b/dev-python/pickleshare/Manifest new file mode 100644 index 000000000..79e862d1c --- /dev/null +++ b/dev-python/pickleshare/Manifest @@ -0,0 +1 @@ +DIST pickleshare-0.5.tar.gz 4441 SHA256 c0be5745035d437dbf55a96f60b7712345b12423f7d0951bd7d8dc2141ca9286 SHA512 1021b76591b5b1d6c777e03c9544fea63602f719b786a2a2e73590f8e8275156fa69b336adf81a6e8abcaad2263eacd76ce4abf2ceff04126ff6b1ffd96cb4e3 WHIRLPOOL 07907feb8dab2dfbfc74e43d17cc076027ab450091a8dd4af197019c6c46e268eda1d5761ab22fc774e37090ab7d51212d82ba284d89018fbc0f52c38f235c62 diff --git a/dev-python/pickleshare/metadata.xml b/dev-python/pickleshare/metadata.xml new file mode 100644 index 000000000..ea703f9fd --- /dev/null +++ b/dev-python/pickleshare/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + Like shelve, a PickleShareDB object acts like a normal dictionary. + Unlike shelve, many processes can access the database + simultaneously. Changing a value in database is immediately visible + to other processes accessing the same database. + Concurrency is possible because the values are stored in separate + files. Hence the "database" is a directory where all files are + governed by PickleShare. + </longdescription> + <upstream> + <remote-id type="pypi">pickleshare</remote-id> + <remote-id type="github">pickleshare/pickleshare</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pickleshare/pickleshare-0.5.ebuild b/dev-python/pickleshare/pickleshare-0.5.ebuild new file mode 120000 index 000000000..16ddbe44b --- /dev/null +++ b/dev-python/pickleshare/pickleshare-0.5.ebuild @@ -0,0 +1 @@ +pickleshare-9999.ebuild
\ No newline at end of file diff --git a/dev-python/pickleshare/pickleshare-9999.ebuild b/dev-python/pickleshare/pickleshare-9999.ebuild new file mode 100644 index 000000000..5c56ccb9c --- /dev/null +++ b/dev-python/pickleshare/pickleshare-9999.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python{3_3,3_4} ) + +inherit distutils-r1 + +DESCRIPTION="A small 'shelve' like datastore with concurrency support" +HOMEPAGE="https://github.com/pickleshare/pickleshare" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git" +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64" + # test_pickleshare.py is not included in the pickleshare-0.5 source + # we fetched from pipy + RESTRICT="test" +fi + +LICENSE="MIT" +SLOT="0" +IUSE="test" + +RDEPEND=" + dev-python/path-py[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}"/lib || die + cp "${S}"/test_pickleshare.py "${TEST_DIR}"/lib/ || die + py.test || die +} diff --git a/dev-python/prettyplotlib/metadata.xml b/dev-python/prettyplotlib/metadata.xml index 123422a50..621e56cd1 100644 --- a/dev-python/prettyplotlib/metadata.xml +++ b/dev-python/prettyplotlib/metadata.xml @@ -9,4 +9,7 @@ Python matplotlib-enhancer library which painlessly creates beautiful default matplotlib plots. </longdescription> + <upstream> + <remote-id type="pypi">prettyplotlib</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/psubprocess/psubprocess-0.1.2.ebuild b/dev-python/psubprocess/psubprocess-0.1.2.ebuild index ec26a026d..9856336ec 100644 --- a/dev-python/psubprocess/psubprocess-0.1.2.ebuild +++ b/dev-python/psubprocess/psubprocess-0.1.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ptyprocess/ChangeLog b/dev-python/ptyprocess/ChangeLog new file mode 100644 index 000000000..d67ba2736 --- /dev/null +++ b/dev-python/ptyprocess/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for dev-python/ptyprocess +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ptyprocess: Add github to remote-id in metadata.xml + + 30 May 2015; Justin Lecher <jlec@gentoo.org> -Manifest, + -ptyprocess-0.5.ebuild, ptyprocess-9999.ebuild: + dev-python/ptyprocess: Add missing test funcion and drop ebuild which was + moved to tree + +*ptyprocess-0.5 (29 May 2015) +*ptyprocess-9999 (29 May 2015) + + 29 May 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +ptyprocess-0.5.ebuild, +ptyprocess-9999.ebuild: + Initial ebuild diff --git a/app-text/jabref/metadata.xml b/dev-python/ptyprocess/metadata.xml index c25a2567c..217a66929 100644 --- a/app-text/jabref/metadata.xml +++ b/dev-python/ptyprocess/metadata.xml @@ -2,7 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> - <maintainer> - <email>nicolasbock@gentoo.org</email> - </maintainer> + <upstream> + <remote-id type="github">pexpect/ptyprocess</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ptyprocess/ptyprocess-9999.ebuild b/dev-python/ptyprocess/ptyprocess-9999.ebuild new file mode 100644 index 000000000..6d24550a5 --- /dev/null +++ b/dev-python/ptyprocess/ptyprocess-9999.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="Run a subprocess in a pseudo terminal" +HOMEPAGE="https://github.com/pexpect/ptyprocess" +SRC_URI="" +EGIT_REPO_URI="https://github.com/pexpect/${PN}.git git://github.com/pexpect/${PN}.git" + +LICENSE="ISC" +SLOT="0" +KEYWORDS="" +IUSE="test" + +DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + py.test --verbose --verbose || die +} diff --git a/dev-python/pyfftw/ChangeLog b/dev-python/pyfftw/ChangeLog index 3c19f1ea4..abebe1952 100644 --- a/dev-python/pyfftw/ChangeLog +++ b/dev-python/pyfftw/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 May 2015; Marius Brehler <marbre@linux.sungazer.de> pyfftw-9999.ebuild: + Implement python_test() + *pyfftw-9999 (04 Feb 2015) *pyfftw-0.9.2 (04 Feb 2015) diff --git a/dev-python/pyfftw/metadata.xml b/dev-python/pyfftw/metadata.xml index 07e8f0384..707eaf20d 100644 --- a/dev-python/pyfftw/metadata.xml +++ b/dev-python/pyfftw/metadata.xml @@ -10,4 +10,7 @@ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. </longdescription> + <upstream> + <remote-id type="pypi">pyFFTW</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyfftw/pyfftw-9999.ebuild b/dev-python/pyfftw/pyfftw-9999.ebuild index 962cf05fc..1d34389ff 100644 --- a/dev-python/pyfftw/pyfftw-9999.ebuild +++ b/dev-python/pyfftw/pyfftw-9999.ebuild @@ -23,6 +23,7 @@ fi LICENSE="BSD" SLOT="0" +IUSE="test" RDEPEND=" >=dev-python/numpy-1.8.0[${PYTHON_USEDEP}] @@ -30,3 +31,11 @@ RDEPEND=" >=dev-python/cython-0.19.1[${PYTHON_USEDEP}] " DEPEND="${RDEPEND}" + +python_test() { + distutils_install_for_testing + cd "${TEST_DIR}"/lib || die + cp "${S}"/setup.py "${TEST_DIR}"/lib/ || die + cp -r "${S}"/test "${TEST_DIR}"/lib/ || die + esetup.py test || die +} diff --git a/dev-python/pyhdf/ChangeLog b/dev-python/pyhdf/ChangeLog index 9a3683c2c..08370d422 100644 --- a/dev-python/pyhdf/ChangeLog +++ b/dev-python/pyhdf/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for dev-python/pyhdf -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pyhdf: Updating remote-id in metadata.xml + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> pyhdf-0.8.3.ebuild, metadata.xml: Bump to EAPI=5 and distutils-r1.eclass - diff --git a/dev-python/pyhdf/metadata.xml b/dev-python/pyhdf/metadata.xml index 194e251e3..87469d49e 100644 --- a/dev-python/pyhdf/metadata.xml +++ b/dev-python/pyhdf/metadata.xml @@ -9,4 +9,7 @@ <use> <flag name="szip">Allow to use <pkg>sci-libs/szip</pkg> for SZIP compression method in SDsetcompress()</flag> </use> + <upstream> + <remote-id type="sourceforge">pysclint</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyhdf/pyhdf-0.8.3.ebuild b/dev-python/pyhdf/pyhdf-0.8.3.ebuild index 53c810f10..eeef22b02 100644 --- a/dev-python/pyhdf/pyhdf-0.8.3.ebuild +++ b/dev-python/pyhdf/pyhdf-0.8.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/pymvpa/pymvpa-0.4.4.ebuild b/dev-python/pymvpa/pymvpa-0.4.4.ebuild index b1a149d03..a150aefe3 100644 --- a/dev-python/pymvpa/pymvpa-0.4.4.ebuild +++ b/dev-python/pymvpa/pymvpa-0.4.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/pynomo/ChangeLog b/dev-python/pynomo/ChangeLog index 5fc5c8b85..2116da469 100644 --- a/dev-python/pynomo/ChangeLog +++ b/dev-python/pynomo/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pynomo -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pynomo: Updating remote-id in metadata.xml + *pynomo-0.2.2 (01 Jul 2014) 01 Jul 2014; Witold Pilat (fau) <witold.pilat@gmail.com> +metadata.xml, diff --git a/dev-python/pynomo/metadata.xml b/dev-python/pynomo/metadata.xml index f293a3afc..42183519d 100644 --- a/dev-python/pynomo/metadata.xml +++ b/dev-python/pynomo/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<maintainer> - <email>witold.pilat@gmail.com</email> -</maintainer> -<longdescription> + <maintainer> + <email>witold.pilat@gmail.com</email> + </maintainer> + <longdescription> Pynomo is a program to create (pdf) nomographs (nomograms) using Python interpreter. A nomograph (nomogram) is a graphical solution to an equation. </longdescription> + <upstream> + <remote-id type="sourceforge">pynomo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyqtgraph/ChangeLog b/dev-python/pyqtgraph/ChangeLog deleted file mode 100644 index 417792d55..000000000 --- a/dev-python/pyqtgraph/ChangeLog +++ /dev/null @@ -1,23 +0,0 @@ -# ChangeLog for dev-python/pyqtgraph -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*pyqtgraph-0.9.8 (25 Nov 2013) - - 25 Nov 2013; Guillaume Poulin <poulin.guillaume@gmail.com> - +pyqtgraph-0.9.8.ebuild, -pyqtgraph-0.9.7.ebuild: - Update PyQtGraph to 0.9.8. Support of python 3.3 - - 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> - pyqtgraph-0.9.7.ebuild: - remove untested keywords - - 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> - pyqtgraph-0.9.7.ebuild: - add [${PYTHON_USEDEP}] to depencies to sastify python-r1 - -*pyqtgraph-0.9.7 (07 Sep 2013) - - 07 Sep 2013; Guillaume Poulin <poulin.guillaume@gmail.com> +metadata.xml, - +pyqtgraph-0.9.7.ebuild: - Add dev-python/pyqtgraph diff --git a/dev-python/pyqtgraph/Manifest b/dev-python/pyqtgraph/Manifest deleted file mode 100644 index 9343219cb..000000000 --- a/dev-python/pyqtgraph/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pyqtgraph-0.9.8.tar.gz 958092 SHA256 257e7de9053c325ea2cce7a93d54ac035276350e5524d065c538e3d48c90d0ba SHA512 66c578fec00bb3fef791bcdaedfc420b7049d1346a5132b7a016d0d016e886381f4e38fe1c39ab4499df50d1cf4f19ef8bfc52ddf20bba8a928a7bf3b5f21e10 WHIRLPOOL 54098f47711fbfed6ce6b429c554effdc1ceed85d86f7da76a04c5583d8b68af26fe1b06e5bafabc064c7e241078e8fd13c452c901a59d77c114f3d4b7c128e7 diff --git a/dev-python/pyqtgraph/metadata.xml b/dev-python/pyqtgraph/metadata.xml deleted file mode 100644 index b05689e41..000000000 --- a/dev-python/pyqtgraph/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <longdescription> - PyQtGraph is a pure-python graphics and GUI library built on - PyQt4/PySide and numpy. It is intended for use in mathematics / - scientific / engineering applications. Despite being written entirely - in python, the library is very fast due to its heavy leverage of numpy - for number crunching and Qt's GraphicsView framework for fast display. - PyQtGraph is distributed under the MIT open-source license. - </longdescription> - <use><flag name="example">Install example of code</flag></use> -</pkgmetadata> diff --git a/dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild b/dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild deleted file mode 100644 index 821248b16..000000000 --- a/dev-python/pyqtgraph/pyqtgraph-0.9.8.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) - -inherit distutils-r1 - -DESCRIPTION="Pure-python graphics and GUI library built on PyQt4/PySide and numpy." -HOMEPAGE="http://www.pyqtgraph.org/" -SRC_URI="http://www.pyqtgraph.org/downloads/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="opengl example" - -DEPEND="" -RDEPEND="${DEPEND} - dev-python/numpy[${PYTHON_USEDEP}] - sci-libs/scipy[${PYTHON_USEDEP}] - opengl? ( dev-python/pyopengl[${PYTHON_USEDEP}] ) - || ( >=dev-python/PyQt4-4.7.0[${PYTHON_USEDEP}] dev-python/pyside[${PYTHON_USEDEP}] )" - -src_prepare() { - use opengl || rm -r pyqtgraph/opengl - if ! use example; then - sed -i -e '/package_dir/d' setup.py || die "Unable to remove example" - sed -i -e "s/+ \['pyqtgraph\.examples'\]//" setup.py || die "Unable to remove example" - fi -} diff --git a/dev-python/pysolar/ChangeLog b/dev-python/pysolar/ChangeLog index a103d4a14..1c538ff17 100644 --- a/dev-python/pysolar/ChangeLog +++ b/dev-python/pysolar/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pysolar -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pysolar: Add github to remote-id in metadata.xml + 23 Jul 2013; Sébastien Fabbro <bicatali@gentoo.org> -pysolar-0.4.4.ebuild, metadata.xml, pysolar-0.5.ebuild: dev-python/pysolar: Fixed syntax, removed old, keyword for prefix diff --git a/dev-python/pysolar/metadata.xml b/dev-python/pysolar/metadata.xml index 96827aac9..072ad7c77 100644 --- a/dev-python/pysolar/metadata.xml +++ b/dev-python/pysolar/metadata.xml @@ -1,15 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun. It includes code for extremely precise ephemeris calculations, and more. Pysolar can calculate the location of the sun or the shading percentage as a function of time for a row of 2-axis tracked panels. </longdescription> -<upstream> - <remote-id type="pypi">Pysolar</remote-id> -</upstream> + <upstream> + <remote-id type="pypi">Pysolar</remote-id> + <remote-id type="github">pingswept/pysolar</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pysolar/pysolar-0.5.ebuild b/dev-python/pysolar/pysolar-0.5.ebuild index 6608076c8..71b25de2c 100644 --- a/dev-python/pysolar/pysolar-0.5.ebuild +++ b/dev-python/pysolar/pysolar-0.5.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) AUTHOR=pingswept diff --git a/dev-python/pysparse/ChangeLog b/dev-python/pysparse/ChangeLog index 189c671d9..ee022f590 100644 --- a/dev-python/pysparse/ChangeLog +++ b/dev-python/pysparse/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/pysparse -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/pysparse: Updating remote-id in metadata.xml + 06 May 2013; Justin Lecher <jlec@gentoo.org> pysparse-1.1.1-r1.ebuild: USe internal umfpack due to incompatibility with latest umfpack from tree @@ -28,4 +31,3 @@ +files/pysparse-1.1-setup.patch, +files/pysparse-1.1-superlu3.patch, +metadata.xml: Initial import - diff --git a/dev-python/pysparse/metadata.xml b/dev-python/pysparse/metadata.xml index 84d83504b..f5da15e04 100644 --- a/dev-python/pysparse/metadata.xml +++ b/dev-python/pysparse/metadata.xml @@ -13,4 +13,7 @@ standard sparse and dense matrix libraries (UMFPACK/AMD, SuperLU, BLAS/LAPACK) for maximum performance and robustness. </longdescription> + <upstream> + <remote-id type="sourceforge">pysparse</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pysparse/pysparse-1.1.1-r1.ebuild b/dev-python/pysparse/pysparse-1.1.1-r1.ebuild index 7253b95a2..941708008 100644 --- a/dev-python/pysparse/pysparse-1.1.1-r1.ebuild +++ b/dev-python/pysparse/pysparse-1.1.1-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 multilib diff --git a/dev-python/python-ivi/ChangeLog b/dev-python/python-ivi/ChangeLog index f299a0285..f0498551c 100644 --- a/dev-python/python-ivi/ChangeLog +++ b/dev-python/python-ivi/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/python-ivi: Add github to remote-id in metadata.xml + *python-ivi-9999 (23 Jan 2015) *python-ivi-0.14.9 (23 Jan 2015) diff --git a/dev-python/python-ivi/metadata.xml b/dev-python/python-ivi/metadata.xml index b4235335b..6c3444c18 100644 --- a/dev-python/python-ivi/metadata.xml +++ b/dev-python/python-ivi/metadata.xml @@ -12,4 +12,7 @@ use Python VXI-11, Python USBTMC, PyVISA, pySerial and linux-gpib to connect to instruments. </longdescription> -</pkgmetadata>
\ No newline at end of file + <upstream> + <remote-id type="github">python-ivi/python-ivi</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/python-vxi11/ChangeLog b/dev-python/python-vxi11/ChangeLog index e3ba7e6ef..8cbe4a547 100644 --- a/dev-python/python-vxi11/ChangeLog +++ b/dev-python/python-vxi11/ChangeLog @@ -1,6 +1,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/python-vxi11: Add github to remote-id in metadata.xml + *python-vxi11-9999 (23 Jan 2015) *python-vxi11-0.7 (23 Jan 2015) diff --git a/dev-python/python-vxi11/metadata.xml b/dev-python/python-vxi11/metadata.xml index 05deeb066..d9174e52f 100644 --- a/dev-python/python-vxi11/metadata.xml +++ b/dev-python/python-vxi11/metadata.xml @@ -11,4 +11,7 @@ instrument control protocol. It is compatible with VXI-11, LXI instruments and VXI-11 to GPIB bridges (HP E2050A, etc.). </longdescription> -</pkgmetadata>
\ No newline at end of file + <upstream> + <remote-id type="github">python-ivi/python-vxi11</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pythoncgns/metadata.xml b/dev-python/pythoncgns/metadata.xml index 897aa2e6b..83eff763e 100644 --- a/dev-python/pythoncgns/metadata.xml +++ b/dev-python/pythoncgns/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="pypi">CGNS</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild b/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild index 7851237be..a28a3bf73 100644 --- a/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild +++ b/dev-python/pythoncgns/pythoncgns-2009.10.30.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/pythonqt/pythonqt-2.1.ebuild b/dev-python/pythonqt/pythonqt-2.1.ebuild index a7a876504..e231179fc 100644 --- a/dev-python/pythonqt/pythonqt-2.1.ebuild +++ b/dev-python/pythonqt/pythonqt-2.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils python-single-r1 diff --git a/dev-python/pythonqt/pythonqt-9999.ebuild b/dev-python/pythonqt/pythonqt-9999.ebuild index 69151905c..346a657db 100644 --- a/dev-python/pythonqt/pythonqt-9999.ebuild +++ b/dev-python/pythonqt/pythonqt-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils python-single-r1 subversion diff --git a/dev-python/simplepam/ChangeLog b/dev-python/simplepam/ChangeLog new file mode 100644 index 000000000..c9e8f09cf --- /dev/null +++ b/dev-python/simplepam/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for dev-python/simplepam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/simplepam: Add github to remote-id in metadata.xml + +*simplepam-0.1.5 (03 Mar 2015) +*simplepam-9999 (03 Mar 2015) + + 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, + +simplepam-0.1.5.ebuild, +simplepam-9999.ebuild: + Initial ebuild diff --git a/dev-python/simplepam/Manifest b/dev-python/simplepam/Manifest new file mode 100644 index 000000000..8d60e73c5 --- /dev/null +++ b/dev-python/simplepam/Manifest @@ -0,0 +1 @@ +DIST simplepam-0.1.5.tar.gz 2442 SHA256 9b4dd50da41a04dd6afff932b8b7e33c015af05beb3b3e5bcd323b64c2390a5f SHA512 489c7be29fc7cc16e29dc587c53c2fb94aeca3f08bc647772e3512e65c20a182f8244ca5127d5c04fd8aab57484ce79c2f0e214370f872f67734970da5acd414 WHIRLPOOL 70861a82fd10dc3a679ede5a2151c3597c8a07cbcc497ec030f99a74dec3826bbde4036870282080f61a91f2fce7736ab1308916192e21265e347a6243043354 diff --git a/dev-python/simplepam/metadata.xml b/dev-python/simplepam/metadata.xml new file mode 100644 index 000000000..04613906b --- /dev/null +++ b/dev-python/simplepam/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + An interface to the Pluggable Authentication Modules (PAM) library, + written in pure python (using ctypes). This module provides an + authenticate function that allows the caller to authenticate a + given username / password against the PAM system. + </longdescription> + <upstream> + <remote-id type="pypi">simplepam</remote-id> + <remote-id type="github">leonnnn/python3-simplepam</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/simplepam/simplepam-0.1.5.ebuild b/dev-python/simplepam/simplepam-0.1.5.ebuild new file mode 120000 index 000000000..58783615d --- /dev/null +++ b/dev-python/simplepam/simplepam-0.1.5.ebuild @@ -0,0 +1 @@ +simplepam-9999.ebuild
\ No newline at end of file diff --git a/dev-python/simplepam/simplepam-9999.ebuild b/dev-python/simplepam/simplepam-9999.ebuild new file mode 100644 index 000000000..3694e0d0a --- /dev/null +++ b/dev-python/simplepam/simplepam-9999.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) + +inherit distutils-r1 + +DESCRIPTION="A pure python interface to the PAM library" +HOMEPAGE="https://github.com/leonnnn/python3-simplepam" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/leonnnn/python3-${PN}.git git://github.com/leonnnn/python3-${PN}.git" +else + SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + KEYWORDS="~amd64" +fi + +LICENSE="MIT" +SLOT="0" diff --git a/dev-python/specutils/ChangeLog b/dev-python/specutils/ChangeLog index 6447cd6a1..53a0b768e 100644 --- a/dev-python/specutils/ChangeLog +++ b/dev-python/specutils/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/specutils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/specutils: Add github to remote-id in metadata.xml + *specutils-9999 (08 Aug 2014) 08 Aug 2014; Joseph Jon Booker <joe@neoturbine.net> +metadata.xml, diff --git a/dev-python/specutils/metadata.xml b/dev-python/specutils/metadata.xml index 91594d03b..e0d374f5d 100644 --- a/dev-python/specutils/metadata.xml +++ b/dev-python/specutils/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> specutils is a package to implement utilities and data structures to analyse astronomical spectra within python. It extends NDData from Astropy into a class with special handling of 1D spectra. </longdescription> + <upstream> + <remote-id type="pypi">specutils</remote-id> + <remote-id type="github">astropy/specutils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/specutils/specutils-9999.ebuild b/dev-python/specutils/specutils-9999.ebuild index df3386b42..76236e642 100644 --- a/dev-python/specutils/specutils-9999.ebuild +++ b/dev-python/specutils/specutils-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit distutils-r1 if [ ${PV} == "9999" ] ; then diff --git a/dev-python/ufl/ChangeLog b/dev-python/ufl/ChangeLog index 135766527..1685c46b3 100644 --- a/dev-python/ufl/ChangeLog +++ b/dev-python/ufl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/ufl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/ufl: Add bitbucket to remote-id in metadata.xml + *ufl-1.3.0 (16 Jul 2014) *ufl-1.4.0 (16 Jul 2014) diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml index c1c80201a..ddf216c08 100644 --- a/dev-python/ufl/metadata.xml +++ b/dev-python/ufl/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element @@ -12,4 +12,7 @@ <use> <flag name="scipy">Adds support for evaluating Bessel functions using <pkg>dev-python/scipy</pkg></flag> </use> + <upstream> + <remote-id type="bitbucket">fenics-project/ufl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ufl/ufl-0.5.4.ebuild b/dev-python/ufl/ufl-0.5.4.ebuild index 423c6729d..c75edc09e 100644 --- a/dev-python/ufl/ufl-0.5.4.ebuild +++ b/dev-python/ufl/ufl-0.5.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ufl/ufl-1.3.0.ebuild b/dev-python/ufl/ufl-1.3.0.ebuild index 622187c56..1cd23678e 100644 --- a/dev-python/ufl/ufl-1.3.0.ebuild +++ b/dev-python/ufl/ufl-1.3.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/ufl/ufl-1.4.0.ebuild b/dev-python/ufl/ufl-1.4.0.ebuild index 622187c56..1cd23678e 100644 --- a/dev-python/ufl/ufl-1.4.0.ebuild +++ b/dev-python/ufl/ufl-1.4.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-python/viper/ChangeLog b/dev-python/viper/ChangeLog index 036f6367f..85d81efb6 100644 --- a/dev-python/viper/ChangeLog +++ b/dev-python/viper/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for dev-python/viper -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-python/viper: Updating remote-id in metadata.xml + *viper-1.0.1 (14 Jun 2013) 14 Jun 2013; Justin Lecher <jlec@gentoo.org> -viper-0.4.6.ebuild, @@ -13,4 +16,3 @@ 14 Dec 2010; Nico Schlömer <nico.schloemer@gmail.com> +viper-0.4.6.ebuild, +metadata.xml: Initial import. - diff --git a/dev-python/viper/metadata.xml b/dev-python/viper/metadata.xml index c1ca1a083..39623d309 100644 --- a/dev-python/viper/metadata.xml +++ b/dev-python/viper/metadata.xml @@ -1,10 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Viper is a minimalistic scientific plotter and run-time visualization module. Viper has support for visualizing meshes and solutions in DOLFIN. </longdescription> + <upstream> + <remote-id type="launchpad">fenics-viper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/viper/viper-1.0.1.ebuild b/dev-python/viper/viper-1.0.1.ebuild index 8a14ee6e7..4ccaf1fb3 100644 --- a/dev-python/viper/viper-1.0.1.ebuild +++ b/dev-python/viper/viper-1.0.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/dev-tcltk/togl/ChangeLog b/dev-tcltk/togl/ChangeLog index 89ad729d2..f66fddd99 100644 --- a/dev-tcltk/togl/ChangeLog +++ b/dev-tcltk/togl/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-tcltk/togl -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> togl-1.7-r1.ebuild: + dev-tcltk/togl: Add SLOT operator + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> togl-1.7-r1.ebuild: + Bump to EAPI=5; Cleanup + 01 Oct 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: Fixed install paths for togl-1.7; removed 2.0 as this is now in portage @@ -22,4 +28,3 @@ 20 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +metadata.xml, +togl-2.0.ebuild: Initial checkin - diff --git a/dev-tcltk/togl/metadata.xml b/dev-tcltk/togl/metadata.xml index b229aec85..987e72a0d 100644 --- a/dev-tcltk/togl/metadata.xml +++ b/dev-tcltk/togl/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">togl</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-tcltk/togl/togl-1.7-r1.ebuild b/dev-tcltk/togl/togl-1.7-r1.ebuild index dae6ddbfa..891128af1 100644 --- a/dev-tcltk/togl/togl-1.7-r1.ebuild +++ b/dev-tcltk/togl/togl-1.7-r1.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 MY_P="Togl-${PV}" @@ -15,7 +15,8 @@ SLOT="1.7" KEYWORDS="~amd64 ~x86" IUSE="debug +threads" -RDEPEND="dev-lang/tk +RDEPEND=" + dev-lang/tk:0 virtual/opengl" DEPEND="${RDEPEND}" @@ -32,8 +33,8 @@ src_configure() { } src_install() { - emake DESTDIR="${D}" install || die "failed to install" - rm "${D}"/usr/include/* + default + rm "${D}"/usr/include/* || die insinto /usr/include/${PN}-${SLOT} doins togl*.h } diff --git a/dev-tex/pythontex/ChangeLog b/dev-tex/pythontex/ChangeLog index c0fb531e3..7f6f08cce 100644 --- a/dev-tex/pythontex/ChangeLog +++ b/dev-tex/pythontex/ChangeLog @@ -1,8 +1,22 @@ # ChangeLog for dev-tex/pythontex -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + dev-tex/pythontex: Add github to remote-id in metadata.xml + +*pythontex-0.14-r1 (12 May 2015) + + 12 May 2015; Justin Lecher <jlec@gentoo.org> +pythontex-0.14-r1.ebuild, + -pythontex-0.14.ebuild, pythontex-9999.ebuild: + dev-tex/pythontex: Fix installation of latex files, bug #548534 + +*pythontex-0.14 (09 Mar 2015) + + 09 Mar 2015; Justin Lecher <jlec@gentoo.org> +pythontex-0.14.ebuild, + -pythontex-0.12.ebuild, pythontex-9999.ebuild: + dev-tex/pythontex: Version Bump + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> pythontex-0.12.ebuild, pythontex-9999.ebuild, +metadata.xml: Switch from git-2 to git-r3 - diff --git a/dev-tex/pythontex/Manifest b/dev-tex/pythontex/Manifest index 1bc092444..f169302cd 100644 --- a/dev-tex/pythontex/Manifest +++ b/dev-tex/pythontex/Manifest @@ -1 +1 @@ -DIST pythontex_0.12.zip 1537341 SHA256 5d37f59200fd4d41180dac7ebdf1d4c1ce276b25cb66483a8d64c6a285220579 SHA512 1e2fc36100be20b16fa25d987a6e4568724e6ab3edff3e9544dd90a14428b471e98ac29413aa9ef60e144aa963e6ef260932cad1903bb762d55421c35a0b69ff WHIRLPOOL 957a43e31f17f91386df739840cb0cb30d84db330c0b0e76e5602eb28ea24836569f72790d9dd6a8bdb26a6c073992a876db47102e46107467c349c0771f03bf +DIST pythontex-0.14.tar.gz 9704671 SHA256 d26501386d313cc7a0375e4ea3bec61aed38abb059f09042c8e0e015e980bce4 SHA512 dc37e3ac112ace95d4ac253f51fe08074cf465537fa8e686637dd2342edb397e89a1e9ee1111fd6b93bcf4194b8bbbcb5cbcc5256d4c451809bf96bb28ae3db6 WHIRLPOOL 9a5106446b61f514b3575170abcba0b9cd6eb2c896c6a12174cd4ae1c01e442e7625cde2cab06b2828e3fc07f4fac9edca4388253c49e8952fb4ad7829355366 diff --git a/dev-tex/pythontex/metadata.xml b/dev-tex/pythontex/metadata.xml index 1087ec907..f94d2c754 100644 --- a/dev-tex/pythontex/metadata.xml +++ b/dev-tex/pythontex/metadata.xml @@ -5,4 +5,7 @@ <use> <flag name="highlighting">PLEASE FIX MY DESCRIPTION</flag> </use> + <upstream> + <remote-id type="github">gpoore/pythontex</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-tex/pythontex/pythontex-0.12.ebuild b/dev-tex/pythontex/pythontex-0.12.ebuild deleted file mode 100644 index 9cd7cac32..000000000 --- a/dev-tex/pythontex/pythontex-0.12.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_7,3_2,3_3} ) - -inherit latex-package python-single-r1 - -DESCRIPTION="Fast Access to Python from within LaTeX" -HOMEPAGE="https://github.com/gpoore/pythontex" -SRC_URI="https://github.com/gpoore/pythontex/raw/master/package_downloads/${PN}_${PV}.zip https://github.com/gpoore/pythontex/raw/master/package_downloads/old_versions/${PN}_${PV}.zip" - -SLOT="0" -LICENSE="LPPL-1.3 BSD" -KEYWORDS="~amd64" -IUSE="highlighting" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS} - app-text/texlive" -RDEPEND="${DEPEND} - dev-texlive/texlive-xetex - >=dev-python/matplotlib-1.2.0[${PYTHON_USEDEP}] - highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )" - -TEXMF=/usr/share/texmf-site - -S="${WORKDIR}"/${PN} -src_prepare() { - rm pythontex.sty || die "Could not remove pythontex.sty!" -} - -src_compile() { - ebegin "Compiling ${PN}" - latex ${PN}.ins extra > "${T}"/build-latex.log || die "Building style from ${PN}.ins failed" - eend - sed -i -e '1i#!/usr/bin/env python' depythontex2.py || die "adding shebang failed!" - sed -i -e '1i#!/usr/bin/env python' depythontex3.py || die "adding shebang failed!" -} - -src_install() { - python_optimize . - if python_is_python3; then - python_newscript pythontex3.py pythontex.py - python_newscript depythontex3.py depythontex.py - else - python_newscript pythontex2.py pythontex.py - python_doscript pythontex_2to3.py - python_newscript depythontex2.py depythontex.py - fi - - python_export PYTHON_SCRIPTDIR - - python_moduleinto ${PYTHON_SCRIPTDIR} - python_domodule "${S}"/pythontex_engines.py "${S}"/pythontex_utils.py - - insinto /usr/share/texmf-site/tex/latex/pythontex/ - doins "${S}"/pythontex.sty - - insinto /usr/share/texmf-site/source/latex/pythontex/ - doins "${S}"/pythontex.dtx "${S}"/pythontex.ins - - latex-package_src_install - - dodoc README - mktexlsr -} diff --git a/dev-tex/pythontex/pythontex-0.14-r1.ebuild b/dev-tex/pythontex/pythontex-0.14-r1.ebuild new file mode 100644 index 000000000..d49ef7f23 --- /dev/null +++ b/dev-tex/pythontex/pythontex-0.14-r1.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_{3,4} ) + +inherit latex-package python-r1 + +DESCRIPTION="Fast Access to Python from within LaTeX" +HOMEPAGE="https://github.com/gpoore/pythontex" +SRC_URI="https://github.com/gpoore/pythontex/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="LPPL-1.3 BSD" +KEYWORDS="~amd64" +IUSE="highlighting" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS} + dev-texlive/texlive-latex" +RDEPEND="${DEPEND} + dev-texlive/texlive-xetex + >=dev-python/matplotlib-1.2.0[${PYTHON_USEDEP}] + highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )" + +TEXMF=/usr/share/texmf-site + +src_compile() { + cd ${PN} || die + ebegin "Compiling ${PN}" + rm ${PN}.sty || die + latex ${PN}.ins extra || die + eend +} + +src_install() { + dodoc ${PN}/README "${S}"/*rst ${PN}_quickstart/* + + cd ${PN} || die + + installation() { + if python_is_python3; then + python_domodule {de,}${PN}3.py + else + python_domodule {de,}${PN}2.py + fi + python_domodule ${PN}_{engines,utils}.py + python_doscript {de,}${PN}.py syncpdb.py + python_optimize + } + python_foreach_impl installation + + latex-package_src_doinstall dtx ins sty +} diff --git a/dev-tex/pythontex/pythontex-9999.ebuild b/dev-tex/pythontex/pythontex-9999.ebuild index 5e7ac367a..c9c538824 100644 --- a/dev-tex/pythontex/pythontex-9999.ebuild +++ b/dev-tex/pythontex/pythontex-9999.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3} ) +PYTHON_COMPAT=( python2_7 python3_{3,4} ) -inherit latex-package python-single-r1 git-r3 +inherit latex-package python-r1 git-r3 DESCRIPTION="Fast Access to Python from within LaTeX" HOMEPAGE="https://github.com/gpoore/pythontex" @@ -21,46 +21,38 @@ IUSE="highlighting" REQUIRED_USE="${PYTHON_REQUIRED_USE}" DEPEND="${PYTHON_DEPS} - app-text/texlive" + dev-texlive/texlive-latex" RDEPEND="${DEPEND} dev-texlive/texlive-xetex >=dev-python/matplotlib-1.2.0[${PYTHON_USEDEP}] highlighting? ( dev-python/pygments[${PYTHON_USEDEP}] )" -src_prepare() { - S="${WORKDIR}/${P}/${PN}" - cd "${S}" || die - rm pythontex.sty || die "Could not remove pre-compiled pythontex.sty!" -} +TEXMF=/usr/share/texmf-site src_compile() { + cd ${PN} || die ebegin "Compiling ${PN}" - latex ${PN}.ins extra > "${T}"/build-latex.log || die "Building style from ${PN}.ins failed" + rm ${PN}.sty || die + latex ${PN}.ins extra || die eend } src_install() { - python_optimize . - if python_is_python3; then - #python_scriptinto /usr/share/texmf-site/scripts/${PN}/ - python_newscript pythontex3.py pythontex.py - python_newscript depythontex3.py depythontex.py - else - python_newscript pythontex2.py pythontex.py - python_doscript pythontex_2to3.py - python_newscript depythontex2.py depythontex.py - fi - - python_domodule "${S}"/pythontex_engines.py "${S}"/pythontex_utils.py - - insinto /usr/share/texmf-site/tex/latex/pythontex/ - doins "${S}"/pythontex.sty - - insinto /usr/share/texmf-site/source/latex/pythontex/ - doins "${S}"/pythontex.dtx "${S}"/pythontex.ins - - latex-package_src_install - - dodoc README - mktexlsr || die + dodoc ${PN}/README "${S}"/*rst ${PN}_quickstart/* + + cd ${PN} || die + + installation() { + if python_is_python3; then + python_domodule {de,}${PN}3.py + else + python_domodule {de,}${PN}2.py + fi + python_domodule ${PN}_{engines,utils}.py + python_doscript {de,}${PN}.py syncpdb.py + python_optimize + } + python_foreach_impl installation + + latex-package_src_doinstall dtx ins sty } diff --git a/dev-util/VampirTrace/ChangeLog b/dev-util/VampirTrace/ChangeLog new file mode 100644 index 000000000..e2713a40c --- /dev/null +++ b/dev-util/VampirTrace/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-util/VampirTrace +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*VampirTrace-5.14.4 (04 Mar 2015) + + 04 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +VampirTrace-5.14.4.ebuild: + Version bump diff --git a/dev-util/VampirTrace/Manifest b/dev-util/VampirTrace/Manifest index 55591bfc9..ac3ec2fa3 100644 --- a/dev-util/VampirTrace/Manifest +++ b/dev-util/VampirTrace/Manifest @@ -1 +1,2 @@ +DIST dcount.php?package=gputrace&get=VampirTrace-5.14.4-gpu2.tar.gz 5930789 SHA256 3906a5e56495cb597e87d17e9726c2e3f53eb39b980001d6a507aee26b4c657b SHA512 ea76ccf3bcd21a395a3fa233d16804f1e287449b3fef2a71c0e16d8df45dab9b62434dae3fa644479ac58784e5b198cd89ab2975dc9813163a4849f332aeb47d WHIRLPOOL 33297cfebc2297ce4311d8bc6ec727f5b47b5387fad11743deedae3013cf811516a5424d42a35718de5f5533885d19481f3c75a222830fe6e913320f65a9cf11 DIST dcount.php?package=vampirtrace&get=VampirTrace-5.14.3.tar.gz 5956627 SHA256 d3bc18662ee48c9c02de0b5933c52213849cbb79b21a3b4ec786bc21e3126209 SHA512 2b1faa707d12b672ba12b399f6b1c14c8d3cff0b3f961f70b81adb1e5ba69960a217ae228cbacd1ffd3f54aab1b30697ef66748a4fd604e8684910d98041d458 WHIRLPOOL 2bcf401f25f4ed500e92739e36265979cab1c5c0caebb53555caf6f293411b4ac8c542254bc95cad5a81f3458ccb74126580450873ff53a9df3e944f67cb9d48 diff --git a/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild b/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild new file mode 100644 index 000000000..5ff44d14f --- /dev/null +++ b/dev-util/VampirTrace/VampirTrace-5.14.4.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils cuda + +MY_PV="${PV}-gpu2" +MY_P="${PN}-${MY_PV}" + +DESCRIPTION="An open source library that allows detailed logging of program execution for parallel applications" +HOMEPAGE="http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/forschung/projekte/vampirtrace/accelerator" +SRC_URI="http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=gputrace&get=${MY_P}.tar.gz" + +SLOT="0" +LICENSE="vampir" +KEYWORDS="~amd64" +IUSE="cuda" + +S="${WORKDIR}/${MY_P}" + +DEPEND=" + virtual/mpi + cuda? ( >=dev-util/nvidia-cuda-toolkit-4.0.0 )" + +src_prepare() { + use cuda && cuda_src_prepare +} + +src_configure() { + econf $(use_with cuda cuda-dir "${EPREFIX}"/opt/cuda) +} + +src_install() { + default + # avoid collisions with app-text/lcdf-typetools: + mv "${D}/usr/bin/otfinfo" "${D}/usr/bin/otfinfo.vampir" || die + if [ -e "${D}/usr/lib/debug/usr/bin/otfinfo.debug" ]; then + mv "${D}/usr/lib/debug/usr/bin/otfinfo.debug" "${D}/usr/lib/debug/usr/bin/otfinfo.vampir.debug" || die + fi + # libtool is already installed: + rm "${D}/usr/share/libtool" || die +} diff --git a/dev-util/amdapp/ChangeLog b/dev-util/amdapp/ChangeLog index 8cf85ee02..22843d182 100644 --- a/dev-util/amdapp/ChangeLog +++ b/dev-util/amdapp/ChangeLog @@ -2,6 +2,22 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> amdapp-2.9.1.ebuild, + amdapp-2.9.ebuild, amdapp-3.0_beta.ebuild: + dev-util/amdapp: Move to new CAT + +*amdapp-3.0_beta (23 Mar 2015) + + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +amdapp-3.0_beta.ebuild: + Add 3.0_beta + +*amdapp-2.9.1 (03 Mar 2015) + + 03 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +amdapp-2.9.1.ebuild: + Version bump + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -amdapp-2.8.ebuild, amdapp-2.9.ebuild, metadata.xml: dev-util/amdapp: fix SLOT operators; restrict fetch; drop old diff --git a/dev-util/amdapp/Manifest b/dev-util/amdapp/Manifest index d26fd78d0..cfd020605 100644 --- a/dev-util/amdapp/Manifest +++ b/dev-util/amdapp/Manifest @@ -1,2 +1,6 @@ +DIST AMD-APP-SDK-linux-v2.9-1.599.381-GA-x64.tar.bz2 126276109 SHA256 05337de10a4731a4f6b602849e8f0d2d0eec7bdd3637e94a8ea04aa332d26036 SHA512 41267cc5f020c6ddb6e60e6ed7141584aba4728c7f471d1b1244747fadfa175c811f7a0a273d95ddc07ac1b4fde8b64ad514a5eeee771e375b2d68f86eefcb50 WHIRLPOOL 172f3c9081569cbf5781a460b3a4ffcd9a2851cc0f47554fc9a1da5dcfd970fb774de46e8846c08331a166cac56687f13a661c2b74912e092b36d3b1d8829bc5 +DIST AMD-APP-SDK-linux-v2.9-1.599.381-GA-x86.tar.bz2 100512787 SHA256 a66bd935dfe871ecb0e940a4b5bc3bde310fca59a61bf9669f6b580d845c2db5 SHA512 59b3a12b51b22437fe0e743e7e0429455853f11c2a1b65fc91a63d6250dce1230460702287b1dc16a4672114d097a9e002ec93ed8c5063be2b070c242299aa5e WHIRLPOOL 56442f1a6bf03757b3a637f69c4083391540d523a74091318686da9ac8e342ff876285ce05ed3b6d21ce6e50072cdd6f0c239bee3550adafaff0cf2ae2065c6f DIST AMD-APP-SDK-v2.9-lnx32.tgz 100284370 SHA256 86c0ebfd6a9037385d83d43237d986614f05ba035f50fd8d45e27c0d3c465646 SHA512 c0490223e5d8880bedf076fc6d7518507d59827caa29507cb0962b3ca4670f2a3a1d083019600ce838385d3116574887739f505cfdc01f5077a00ae584854bd0 WHIRLPOOL e6655eeeb47588d999585249f335571e427528d1a25878d6f16e47d37e1b30db5e1a1e13603f934ee20d76e5a3d16445c348169c3b6b6cbb81e5dfd543a43674 DIST AMD-APP-SDK-v2.9-lnx64.tgz 149825628 SHA256 6287d3d0700e563f2086188b1b2143a0e988a12c1dc22709b9a23d28b8ae83bb SHA512 b00d92b9e2ead559aa66120697a1dc15ecbc1c880eed99c2a7ed030f6cccce7434245a94aa6149e2ce2dc287cb9443700d7dbc8b3756c7420c0f54cc008065bb WHIRLPOOL b839c042a73251c0b774d1c2f6b968c166f4b74b4828a4f12709220e2c79783833979140127ec98a19b0883d7bf49d031088aeaeeb150855907f18378d5de0a9 +DIST AMD-APP-SDK-v3.0-0.113.50-Beta-linux32-1.tar.bz2 137488316 SHA256 0520a2fac0e945195419ec560e7d340cbcb2da3a3412cb2f38584263a7198d35 SHA512 004d8f26a91e9489953895a9cdb8411701403aa89d8c593eb60c7ebb8eee0bc13f5ffad31a44641b8ac2c25abcc728ed34b78d61b246aa4055806b9ac8715e2c WHIRLPOOL fd1f2f1f4a019c4265eac6c5a3a0098d785878aef7d3f24a81073b188895ade582a44d6c5937c88ec0554141db991ede9f5f3a067ffe60e615bda4d8904b0afc +DIST AMD-APP-SDK-v3.0-0.113.50-Beta-linux64.tar.bz2 138207347 SHA256 0d806087e5fef7fdfb9372388afe2ff7b382041ba5a23160d58143166005f2d4 SHA512 2b30d7dbaf7004c319c85f272a33d9eb15810839cae1cb70c8097e3c89e488d44efc63059b0e467493b3a7ea8a2336af53c5e99ab862676c35bb9288faa7074c WHIRLPOOL f8b78898d1acb8625512bf0b303aecb8e3bea9c0011c2394494e724af7ed0253e554b791e80cdfdfd8454b8b7516b7f0898879a3912eb08704d9ad38a6905b22 diff --git a/dev-util/amdapp/amdapp-2.9.1.ebuild b/dev-util/amdapp/amdapp-2.9.1.ebuild new file mode 100644 index 000000000..1f54be1f0 --- /dev/null +++ b/dev-util/amdapp/amdapp-2.9.1.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit multilib unpacker versionator + +MY_V=$(get_version_component_range 1).$(get_version_component_range 2) + +X86_AT="AMD-APP-SDK-linux-v${MY_V}-1.599.381-GA-x86.tar.bz2" +AMD64_AT="AMD-APP-SDK-linux-v${MY_V}-1.599.381-GA-x64.tar.bz2" + +MY_P_AMD64="AMD-APP-SDK-v${MY_V}-1.599.381-GA-linux64.sh" +MY_P_AMD32="AMD-APP-SDK-v${MY_V}-1.599.381-GA-linux32.sh" + +DESCRIPTION="AMD Accelerated Parallel Processing (APP) SDK" +HOMEPAGE="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk" +SRC_URI=" + amd64? ( ${AMD64_AT} ) + x86? ( ${X86_AT} )" +LICENSE="AMD-APPSDK" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +RDEPEND=" + app-eselect/eselect-opengl + !<dev-util/amdstream-2.6 + sys-devel/llvm + sys-devel/gcc:* + media-libs/mesa + media-libs/freeglut + virtual/opencl + examples? ( media-libs/glew ) + app-eselect/eselect-opencl" +DEPEND=" + ${RDEPEND} + dev-lang/perl + dev-util/patchelf + sys-apps/fakeroot" + +RESTRICT="mirror strip" + +S="${WORKDIR}" + +pkg_nofetch() { + einfo "AMD doesn't provide direct download links. Please download" + einfo "${ARCHIVE} from ${HOMEPAGE}" +} + +src_unpack() { + default + + cd "${WORKDIR}" || die + + if use amd64 || use amd64-linux ; then + unpacker ./${MY_P_AMD64} + else + unpacker ./${MY_P_X86} + fi +} + +src_prepare() { + AMD_CL=usr/$(get_libdir)/OpenCL/vendors/amd/ +} + +src_compile() { + MAKEOPTS+=" -j1" + use examples && cd samples/opencl && emake +} + +src_install() { + dodir /opt/AMDAPP + cp -R "${S}/"* "${ED}/opt/AMDAPP" || die "Install failed!" + + dodir "${AMD_CL}" + dosym "/opt/AMDAPP/lib/`arch`/libOpenCL.so" "${AMD_CL}" + dosym "/opt/AMDAPP/lib/`arch`/libOpenCL.so.1" "${AMD_CL}" + + #insinto /etc/OpenCL/vendors/ + #doins ../etc/OpenCL/vendors/* +} diff --git a/dev-util/amdapp/amdapp-2.9.ebuild b/dev-util/amdapp/amdapp-2.9.ebuild index d5880832f..1228f5d5e 100644 --- a/dev-util/amdapp/amdapp-2.9.ebuild +++ b/dev-util/amdapp/amdapp-2.9.ebuild @@ -25,7 +25,7 @@ KEYWORDS="~x86 ~amd64" IUSE="examples" RDEPEND=" - app-admin/eselect-opengl + app-eselect/eselect-opengl !<dev-util/amdstream-2.6 sys-devel/llvm sys-devel/gcc:* @@ -33,7 +33,7 @@ RDEPEND=" media-libs/freeglut virtual/opencl examples? ( media-libs/glew ) - app-admin/eselect-opencl" + app-eselect/eselect-opencl" DEPEND=" ${RDEPEND} dev-lang/perl diff --git a/dev-util/amdapp/amdapp-3.0_beta.ebuild b/dev-util/amdapp/amdapp-3.0_beta.ebuild new file mode 100644 index 000000000..858a469b0 --- /dev/null +++ b/dev-util/amdapp/amdapp-3.0_beta.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit multilib unpacker versionator + +MY_V="$(get_version_component_range 1).$(get_version_component_range 2)-0.113.50-Beta" + +X86_AT="AMD-APP-SDK-v${MY_V}-linux32-1.tar.bz2" +AMD64_AT="AMD-APP-SDK-v${MY_V}-linux64.tar.bz2" + +MY_P_AMD64="AMD-APP-SDK-v${MY_V}-linux64.sh" +MY_P_AMD32="AMD-APP-SDK-v${MY_V}-linux32.sh" + +DESCRIPTION="AMD Accelerated Parallel Processing (APP) SDK" +HOMEPAGE="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk" +SRC_URI=" + amd64? ( ${AMD64_AT} ) + x86? ( ${X86_AT} )" +LICENSE="AMD-APPSDK" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +RDEPEND=" + app-eselect/eselect-opengl + !<dev-util/amdstream-2.6 + sys-devel/llvm + sys-devel/gcc:* + media-libs/mesa + media-libs/freeglut + virtual/opencl + examples? ( media-libs/glew ) + app-eselect/eselect-opencl" +DEPEND=" + ${RDEPEND} + dev-lang/perl + dev-util/patchelf + sys-apps/fakeroot" + +RESTRICT="mirror strip" + +S="${WORKDIR}" + +pkg_nofetch() { + einfo "AMD doesn't provide direct download links. Please download" + einfo "${ARCHIVE} from ${HOMEPAGE}" +} + +src_unpack() { + default + + cd "${WORKDIR}" || die + + if use amd64 || use amd64-linux ; then + unpacker ./${MY_P_AMD64} + else + unpacker ./${MY_P_X86} + fi +} + +src_prepare() { + AMD_CL=usr/$(get_libdir)/OpenCL/vendors/amd/ +} + +src_compile() { + MAKEOPTS+=" -j1" + use examples && cd samples/opencl && emake +} + +src_install() { + dodir /opt/AMDAPP + cp -R "${S}/"* "${ED}/opt/AMDAPP" || die "Install failed!" + + dodir "${AMD_CL}" + dosym "/opt/AMDAPP/lib/`arch`/libOpenCL.so" "${AMD_CL}" + dosym "/opt/AMDAPP/lib/`arch`/libOpenCL.so.1" "${AMD_CL}" + + #insinto /etc/OpenCL/vendors/ + #doins ../etc/OpenCL/vendors/* +} diff --git a/dev-util/f90cache/ChangeLog b/dev-util/f90cache/ChangeLog index 4b14c0a2f..69945470b 100644 --- a/dev-util/f90cache/ChangeLog +++ b/dev-util/f90cache/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for dev-util/f90cache -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*f90cache-0.95 (19 May 2015) + + 19 May 2015; Marius Brehler <marbre@linux.sungazer.de> +f90cache-0.95.ebuild: + Version bump + *f90cache-0.94 (24 Dec 2012) 24 Dec 2012; Christoph Junghans <ottxor@gentoo.org> +f90cache-0.94.ebuild, diff --git a/dev-util/f90cache/Manifest b/dev-util/f90cache/Manifest index 73afa26e3..61e613037 100644 --- a/dev-util/f90cache/Manifest +++ b/dev-util/f90cache/Manifest @@ -1 +1,2 @@ DIST f90cache-0.94.tar.bz2 64670 SHA256 0ddc06ad98dcfb2b4b2a45561eabdd9c31e872eaef83d0719d5546e5a1dd775b SHA512 bd36a20614e82a8728fbb5ba7897c13d6e59243a4fbb8878cfb8019ca4ee976280cfe8ba5a00c19b620756910f257cd7fe72de6bdfc06f4ee2f7f17c5f9b892d WHIRLPOOL c2509d420228eb839dc1a4e92c2de27a45a74ff45c660e3379f2b3ad8f12ffd9be5e13331cf898e66be9dd72833856aa2de46129c80b410b9e10dc168f7409d1 +DIST f90cache-0.95.tar.bz2 74843 SHA256 3976a15d99442f96d8a4d5f1d468339167a1e7538079b647f6ed2ef9e970a5b8 SHA512 21b19a1bc3b5b329eab3669cf5396085a454b6745d7c6f02ad73472be59346388953e62daaccd414df5b183eef580b6f5673ba16a012942bef160e1d6848f331 WHIRLPOOL 2cb69ff47125edf1d77049a3b466aba484ed2a9f0ad4c32a8b68596d93b7c62b70f77a142431c9a97066b5f7397b3432f8851edd45814bd9b00c447f79116bfe diff --git a/dev-util/f90cache/f90cache-0.95.ebuild b/dev-util/f90cache/f90cache-0.95.ebuild new file mode 100644 index 000000000..43e04c269 --- /dev/null +++ b/dev-util/f90cache/f90cache-0.95.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit fortran-2 multilib toolchain-funcs + +DESCRIPTION="a compiler cache for fortran" +HOMEPAGE="http://people.irisa.fr/Edouard.Canot/f90cache/" +SRC_URI="http://people.irisa.fr/Edouard.Canot/${PN}/${P}.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="" + +DEPEND="" +RDEPEND="dev-util/ccache" + +src_prepare() { + sed -i -e '/OBJS/s/CFLAGS/LDFLAGS/' -e '/strip/d' Makefile.in || die +} + +src_install() { + default + dohtml web/* + + #we depend on ccache, put links in there so that portage fined it + #TODO improve this + dosym "/usr/bin/f90cache" "${ROOT}/usr/$(get_libdir)/ccache/bin/gfortran" +} + +pkg_postinst() { + elog "Please add F90CACHE_DIR=\"${ROOT%/}/var/tmp/f90cache\"" + elog "to your make.conf otherwise f90cache files end up in" + elog "home of the user executing portage" +} diff --git a/dev-util/intel-ocl-sdk/ChangeLog b/dev-util/intel-ocl-sdk/ChangeLog deleted file mode 100644 index 6375e9cdd..000000000 --- a/dev-util/intel-ocl-sdk/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for dev-util/intel-ocl-sdk -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*intel-ocl-sdk-3.2.1.16712 (03 Mar 2014) - - 03 Mar 2014; <xhochy@gentoo.org> +intel-ocl-sdk-3.2.1.16712.ebuild: - Bump to 3.2.1.16712 - -*intel-ocl-sdk-3.1.1.11385 (02 Dec 2013) - - 02 Dec 2013; <xhochy@gentoo.org> +intel-ocl-sdk-3.1.1.11385.ebuild: - [dev-util/intel-ocl-sdk] Bump version to 3.1.1.11385 diff --git a/dev-util/intel-ocl-sdk/Manifest b/dev-util/intel-ocl-sdk/Manifest deleted file mode 100644 index 391880361..000000000 --- a/dev-util/intel-ocl-sdk/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST intel_sdk_for_ocl_applications_2013_xe_sdk_3.0.67279_x64.tgz 46570772 SHA256 72c84a29b36f55b0cf356b70d3530830360c1e49206ecec62aee665f8d4954f5 SHA512 5e569c16e23e21818549f87247a3de88f65c077e40113dd0e6eda445a56a7fa8e4bf08a2bb32e1087b9bb09af4b04f9fe63e383571b97e4ea50f2b1b165299ea WHIRLPOOL 4207135dfd83d0a2ab0a38f4eb133319ca7b9361722102ea0b2bf9e0650aeef86eb803b4cc841161a403d34babb1807d670f97d7f6b826a1a6be7c7c705665c3 -DIST intel_sdk_for_ocl_applications_xe_2013_r2_sdk_3.1.1.11385_x64.tgz 58725851 SHA256 317748cab4cff42163d6efa15f36865eb3fe4112f57a69a0185a43c2b244ead0 SHA512 52ac2f70965ca8fb19aa85d52262605718a6db04a071190893c0cad75be74980df120f8e1ee22597fcb3f0d5bedad672315be365ba5a0542892fea83b947b281 WHIRLPOOL 3b43d5dd80fa7eb956dc3691cf84ec5072eb805d2bf8f5f36a507ab04125abef504147bd36a6dce58d6cc169456c804ffa8f2628c1f9b2ae1871b7ec545b69eb -DIST intel_sdk_for_ocl_applications_xe_2013_r3_sdk_3.2.1.16712_x64.tgz 58713222 SHA256 3691c322a10f977e2c377b13d03cdc38d5d9acaeabc477b0fa2fbaac1b2236c3 SHA512 71857df8976b4b984ce7fa613b50b368095fd9f5ee8f9a65bf0ef65f17b439de7c3362c6ac78e47f67c4dd59453fbcb55438cd91c3b7d8903e713a8510f82004 WHIRLPOOL bf3271888462bd1616bb31de39d4a25f60d194428d3128542ab593bafb1fc92659552f6ca579d69c31a24b887fed3dcd508aabe5fa5197e1b7e45a94f90514c8 diff --git a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild b/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild deleted file mode 100644 index d43b6a9ca..000000000 --- a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.0.67279.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit rpm multilib - -DESCRIPTION="Intel's implementation of the OpenCL standard" -HOMEPAGE="http://software.intel.com/en-us/articles/opencl-sdk/" -SRC_URI="http://registrationcenter.intel.com/irc_nas/3142/\ -intel_sdk_for_ocl_applications_2013_xe_sdk_${PV}_x64.tgz" - -LICENSE="Intel-SDP" -SLOT="0" -IUSE="mic" -KEYWORDS="~amd64" - -RDEPEND="app-admin/eselect-opencl - sys-process/numactl" - -RESTRICT="mirror strip" - -QA_EXECSTACK=" - /opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64.bin -" -QA_PREBUILT=" - /opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64.bin - /opt/intel/opencl-1.2-${PV}/bin/ioc64.bin - /opt/intel/opencl-1.2-${PV}/lib64/libcl_logger.so - /opt/intel/opencl-1.2-${PV}/lib64/libclang_compiler.so - /opt/intel/opencl-1.2-${PV}/lib64/libintelocl.so - /opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1.2 - /opt/intel/opencl-1.2-${PV}/lib64/libtask_executor.so - /opt/intel/opencl-1.2-${PV}/lib64/libcpu_device.so -" - -S="${WORKDIR}/intel_sdk_for_ocl_applications_2013_xe_sdk_${PV}_x64" - -src_unpack() { - default - cd "${S}" - rpm_unpack "./opencl-1.2-base-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-devel-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-cpu-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-devel-${PV}-1.x86_64.rpm" - use mic && rpm_unpack "./opencl-1.2-intel-mic-${PV}-1.x86_64.rpm" -} - -src_prepare() { - INTEL_CL=usr/$(get_libdir)/OpenCL/vendors/intel/ -} - -src_install() { - doins -r etc - doins -r opt - - dodir "${INTEL_CL}" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so" "${INTEL_CL}" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1" "${INTEL_CL}" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1.2" "${INTEL_CL}" - - dodir "/etc/OpenCL/vendors" - dosym "/opt/intel/opencl-1.2-${PV}/etc/intel64.icd" /etc/OpenCL/vendors -} diff --git a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.1.1.11385.ebuild b/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.1.1.11385.ebuild deleted file mode 100644 index 53c26dab2..000000000 --- a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.1.1.11385.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit rpm multilib - -DESCRIPTION="Intel's implementation of the OpenCL standard" -HOMEPAGE="http://software.intel.com/en-us/articles/opencl-sdk/" -SRC_URI="http://registrationcenter.intel.com/irc_nas/3555/\ -intel_sdk_for_ocl_applications_xe_2013_r2_sdk_${PV}_x64.tgz" - -LICENSE="Intel-SDP" -SLOT="0" -IUSE="mic" -KEYWORDS="~amd64" - -RDEPEND="app-admin/eselect-opencl - sys-process/numactl" - -RESTRICT="mirror strip" - -QA_PREBUILT="opt/*" - -S="${WORKDIR}/intel_sdk_for_ocl_applications_xe_2013_r2_sdk_${PV}_x64" - -src_unpack() { - default - cd "${S}" || die - rpm_unpack "./opencl-1.2-base-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-devel-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-cpu-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-devel-${PV}-1.x86_64.rpm" - use mic && rpm_unpack "./opencl-1.2-intel-mic-${PV}-1.x86_64.rpm" -} - -src_prepare() { - INTEL_CL=usr/$(get_libdir)/OpenCL/vendors/intel/ -} - -src_install() { - insinto / - doins -r etc - doins -r opt - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/ioc64" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/ioc64.bin" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64.bin" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/lib64/llc" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/lib64/llvm-dis" - - dodir "${INTEL_CL}" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so" "${INTEL_CL}/libOpenCL.so" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1" "${INTEL_CL}/libOpenCL.so.1" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1.2" "${INTEL_CL}libOpenCL.so.1.2" - - dodir "/etc/OpenCL/vendors" - dosym "/opt/intel/opencl-1.2-${PV}/etc/intel64.icd" "/etc/OpenCL/vendors/intel64.icd" -} diff --git a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.2.1.16712.ebuild b/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.2.1.16712.ebuild deleted file mode 100644 index 7fd0f0ce9..000000000 --- a/dev-util/intel-ocl-sdk/intel-ocl-sdk-3.2.1.16712.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit rpm multilib - -DESCRIPTION="Intel's implementation of the OpenCL standard" -HOMEPAGE="http://software.intel.com/en-us/articles/opencl-sdk/" -SRC_URI="http://registrationcenter.intel.com/irc_nas/3809/\ -intel_sdk_for_ocl_applications_xe_2013_r3_sdk_${PV}_x64.tgz" - -LICENSE="Intel-SDP" -SLOT="0" -IUSE="mic" -KEYWORDS="~amd64" - -RDEPEND="app-admin/eselect-opencl - sys-process/numactl" - -RESTRICT="mirror strip" - -QA_PREBUILT="opt/*" - -S="${WORKDIR}/intel_sdk_for_ocl_applications_xe_2013_r3_sdk_${PV}_x64" - -src_unpack() { - default - cd "${S}" || die - rpm_unpack "./opencl-1.2-base-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-devel-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-cpu-${PV}-1.x86_64.rpm" - rpm_unpack "./opencl-1.2-intel-devel-${PV}-1.x86_64.rpm" - use mic && rpm_unpack "./opencl-1.2-intel-mic-${PV}-1.x86_64.rpm" -} - -src_prepare() { - INTEL_CL=usr/$(get_libdir)/OpenCL/vendors/intel/ -} - -src_install() { - insinto / - doins -r etc - doins -r opt - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/ioc64" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/ioc64.bin" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/bin/KernelBuilder64.bin" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/lib64/llc" - fperms 0755 "/opt/intel/opencl-1.2-${PV}/lib64/llvm-dis" - - dodir "${INTEL_CL}" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so" "${INTEL_CL}/libOpenCL.so" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1" "${INTEL_CL}/libOpenCL.so.1" - dosym "/opt/intel/opencl-1.2-${PV}/lib64/libOpenCL.so.1.2" "${INTEL_CL}libOpenCL.so.1.2" - - dodir "/etc/OpenCL/vendors" - dosym "/opt/intel/opencl-1.2-${PV}/etc/intel64.icd" "/etc/OpenCL/vendors/intel64.icd" -} diff --git a/dev-util/intel-ocl-sdk/metadata.xml b/dev-util/intel-ocl-sdk/metadata.xml deleted file mode 100644 index 4597a1206..000000000 --- a/dev-util/intel-ocl-sdk/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>cluster</herd> - <longdescription> - Intel SDKs for OpenCL applications provide development environments - including code samples, build and debug tools, and optimization tools - for OpenCL on Intel architecture. Supports both Intel processors and - Intel Xeon Phi coprocessors. - </longdescription> - <maintainer> - <email>gentryx@gmx.de</email> - </maintainer> - <use> - <flag name='mic'>Installs the OpenCL libraries for Xeon Phi (a.k.a. MIC)</flag> - </use> -</pkgmetadata> diff --git a/dev-util/nvidia-cuda-gdk/ChangeLog b/dev-util/nvidia-cuda-gdk/ChangeLog index be83b871f..a338fa49a 100644 --- a/dev-util/nvidia-cuda-gdk/ChangeLog +++ b/dev-util/nvidia-cuda-gdk/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nvidia-cuda-gdk-346.46 (19 Mar 2015) + + 19 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +nvidia-cuda-gdk-346.46.ebuild: + Version bump + 19 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> nvidia-cuda-gdk-340.29.ebuild: Fix /opt/bin/nvidia-healthmon diff --git a/dev-util/nvidia-cuda-gdk/Manifest b/dev-util/nvidia-cuda-gdk/Manifest index c2264b195..385b6b9de 100644 --- a/dev-util/nvidia-cuda-gdk/Manifest +++ b/dev-util/nvidia-cuda-gdk/Manifest @@ -1,2 +1,3 @@ DIST cuda_340_29_gdk_linux_32.run 2736726 SHA256 69dd21a556c04982ad720d8eed5ef90cd7c00d3ff4f1ac7087c9a98433a5795e SHA512 30e659fd337c455fd23a3120650565340d7963c77c6b5f46d5549b8f9b1d080659ae3dd6d12cfc4eaa7f9862fe4b2b511b19b023be5180e5e9937cd5d74938d7 WHIRLPOOL 569972d4281f71d450c88794e1b7efef4c6c24ce5a4717b203e0c961fb42a44e6b89d0be167c145705632de63da3d14c63335ba0eec24c34f99bf67b60a6a011 DIST cuda_340_29_gdk_linux_64.run 2752832 SHA256 c4dcc5294731bc7f01cd0eafe42a6784f897760e2ed44224db9865db6f7cd6fa SHA512 3310600ccddf0f79087aa48c61cf7c10bde2543f041571f1bf7c9721a5e41a993e6b231f6b01e37b22062e0b978da7135d89382b9a3a996b82b04283676469ff WHIRLPOOL 91b5c104140b9beb28fec6733f7fd71478993497bff7e9814777e3a8f2e4242c26bd383fcd3e3fbed94e221cdbecaecc53e98a4779d9f17ca4ee20362f36463d +DIST cuda_346.46_gdk_linux.run 1888773 SHA256 cae9dde44631ac927bad8237e1380c12977202e1186803db70e8afde0479b6a3 SHA512 ef37196bd97c3c2b4644505dcc28990e6264613d018398251287bf0332709ac1419dcc310197b3426162174703c4a07e5a8c11d4d40035c6df19da741862e8d2 WHIRLPOOL 1a93d876f624c2e83ceea78978a7db50fd31e9120c1f412b7b0bdea47c6e3ea5bf5d291dde1ed4e2363a06ce7f7851c79eb7120aca308d8e05c6363c9935948f diff --git a/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild new file mode 100644 index 000000000..0fa56caff --- /dev/null +++ b/dev-util/nvidia-cuda-gdk/nvidia-cuda-gdk-346.46.ebuild @@ -0,0 +1,121 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils portability toolchain-funcs unpacker versionator + +HEALTMON_PV="346.45" + +DESCRIPTION="NVIDIA GPU Deployment Kit" +HOMEPAGE="https://developer.nvidia.com/gpu-deployment-kit" +SRC_URI="http://developer.download.nvidia.com/compute/cuda/7_0/Prod/local_installers/cuda_${PV}_gdk_linux.run" + +LICENSE="NVIDIA-gdk" +SLOT="0" +KEYWORDS="-* ~amd64" +IUSE="+healthmon +nvml +doc examples" + +RDEPEND=" + >=dev-util/nvidia-cuda-toolkit-7.0 + media-libs/freeglut + examples? ( >=x11-drivers/nvidia-drivers-346.47[uvm] ) + " +DEPEND="${RDEPEND}" + +S="${WORKDIR}/payload" + +QA_PREBUILT="/opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon + /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/gpu_rdma_bw + /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/ibv_rdma_bw + /opt/cuda/gdk/nvml/lib/libnvidia-ml.so.1" + +src_unpack() { + unpacker +} + +src_compile() { + use examples || return + cd "${S}"/nvml/example || die + emake +} + +src_install() { + local i j f t + + if use doc; then + if use healthmon ; then + ebegin "Installing healthmon docs..." + doman nvidia-healthmon/docs/man/man8/nvidia-healthmon.8 + cd "${S}/nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}" || die + treecopy \ + $(find -type f \( -name README.txt -name COPYING.txt -o -name "*.pdf" \)) \ + "${ED}"/usr/share/doc/${PF}/nvidia-healthmon/ + docompress -x \ + $(find "${ED}"/usr/share/doc/${PF}/nvidia-healthmon/ -type f -name readme.txt | sed -e "s:${ED}::") + cd "${S}/" || die + eend + fi + + if use nvml ; then + ebegin "Installing nvml docs..." + doman nvml/doc/man/man3/*.3 + cd "${S}/nvml/" || die + treecopy \ + $(find -type f \( -name README.txt -name COPYRIGHT.txt -o -name "*.pdf" \)) \ + "${ED}"/usr/share/doc/${PF}/nvml/ + docompress -x \ + $(find "${ED}"/usr/share/doc/${PF}/nvml/ -type f -name readme.txt | sed -e "s:${ED}::") + cd "${S}/" || die + eend + fi + fi + + ebegin "Cleaning before installation..." + find -type f \ + \( -name "*.o" -o -name "*.pdf" -o -name "*.txt" -o -name "*.3" \) -delete \ + || die + rm -f "${S}"/nvml/lib/libnvidia-ml.so + eend + + if use healthmon; then + ebegin "Installing nvidia-healthmon" + exeinto /opt/cuda/gdk/nvidia-healthmon/nvidia-healthmon-tests/ + doexe "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}/bin"/{*,*.*} + exeinto /opt/cuda/gdk/nvidia-healthmon/ + doexe "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}"/nvidia-healthmon + insinto /etc/nvidia-healthmon/ + doins "nvidia-healthmon/nvidia-healthmon-amd64-${HEALTMON_PV}"/nvidia-healthmon.conf + + # install launch script + exeinto /opt/bin + doexe "${FILESDIR}"/nvidia-healthmon + eend + fi + + if use nvml; then + ebegin "Installing nvml" + cd "${S}/nvml" || die + for f in $(find .); do + local t="$(dirname ${f})" + if [[ "${t/obj\/}" != "${t}" || "${t##*.}" == "a" ]]; then + continue + fi + + if [[ ! -d "${f}" ]]; then + if [[ -x "${f}" ]]; then + exeinto "/opt/cuda/gdk/nvml/${t}" + doexe "${f}" + else + insinto "/opt/cuda/gdk/nvml/${t}" + doins "${f}" + fi + fi + done + + dosym libnvidia-ml.so.1 /opt/cuda/gdk/nvml/lib/libnvidia-ml.so + cd "${S}/" || die + eend + fi +} diff --git a/dev-util/nvidia-cuda-sdk/ChangeLog b/dev-util/nvidia-cuda-sdk/ChangeLog deleted file mode 100644 index 37753b1df..000000000 --- a/dev-util/nvidia-cuda-sdk/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*nvidia-cuda-sdk-7.0.18 (14 Jan 2015) - - 14 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> +metadata.xml, - +nvidia-cuda-sdk-7.0.18.ebuild: - Add version 7.0.18 (release candidate) diff --git a/dev-util/nvidia-cuda-sdk/Manifest b/dev-util/nvidia-cuda-sdk/Manifest deleted file mode 100644 index 53f62a62f..000000000 --- a/dev-util/nvidia-cuda-sdk/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST cuda_7.0.18_rc_linux.run 1037536115 SHA256 e81164baa1f344c3f26ebe8345ce9f38448d9a82a8cf79bae28b5df3b3e4f44c SHA512 7f1c86585ed33be4714a3c9b067cf3858b44a391ae2e2e16af0d3eaf9e7097605380bed79f97463982bf05f616f9573f83b957f080a41ac33d848e597f7d2985 WHIRLPOOL cb5c36275d9a819385f1e6ee225b47b977656c971b038001d093356aefda0afc00a289801e32935b5dec0f95b83118122118ecf150936afa8dc5958e164df82d diff --git a/dev-util/nvidia-cuda-sdk/metadata.xml b/dev-util/nvidia-cuda-sdk/metadata.xml deleted file mode 100644 index 288e4957a..000000000 --- a/dev-util/nvidia-cuda-sdk/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> - <use> - <flag name="opencl"> - Build OpenCL binaries. - </flag> - <flag name="cuda"> - Build CUDA binaries. - </flag> - </use> -</pkgmetadata> diff --git a/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild b/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild deleted file mode 100644 index cfc9f99b2..000000000 --- a/dev-util/nvidia-cuda-sdk/nvidia-cuda-sdk-7.0.18.ebuild +++ /dev/null @@ -1,151 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit cuda eutils flag-o-matic portability toolchain-funcs unpacker versionator - -MYD=$(get_version_component_range 1)_$(get_version_component_range 2) - -DESCRIPTION="NVIDIA CUDA Software Development Kit" -HOMEPAGE="http://developer.nvidia.com/cuda" -CURI="https://developer.nvidia.com/rdp/cuda-70-rc-downloads" -SRC_URI="cuda_${PV}_rc_linux.run" - -LICENSE="CUDPP" -SLOT="0" -KEYWORDS="~amd64 ~amd64-linux" -IUSE="debug +doc +examples opencl +cuda" - -RDEPEND=" - ~dev-util/nvidia-cuda-toolkit-${PV} - media-libs/freeglut - examples? ( - media-libs/freeimage - media-libs/glew - virtual/mpi - >=x11-drivers/nvidia-drivers-346.35[uvm] - )" -DEPEND="${RDEPEND}" - -RESTRICT="test fetch" - -pkg_nofetch() { - einfo "Please download the Fedora 21 \"Runfile Installer\"" - einfo " - cuda_${P}_rc_linux.run" - einfo "from ${CURI} and place it in ${DISTDIR}" -} - -S=${WORKDIR}/cuda-samples - -QA_EXECSTACK=( - opt/cuda/sdk/0_Simple/cdpSimplePrint/cdpSimplePrint - opt/cuda/sdk/0_Simple/cdpSimpleQuicksort/cdpSimpleQuicksort - opt/cuda/sdk/bin/x86_64/linux/release/cdpSimplePrint - opt/cuda/sdk/bin/x86_64/linux/release/cdpSimpleQuicksort - ) - -src_unpack() { - unpacker - unpacker run_files/cuda-samples*run -} - -pkg_setup() { - if use cuda || use opencl; then - cuda_pkg_setup - fi -} - -src_prepare() { - export RAWLDFLAGS="$(raw-ldflags)" -# epatch "${FILESDIR}"/${P}-asneeded.patch - - sed \ - -e 's:-O2::g' \ - -e 's:-O3::g' \ - -e "/LINK/s:gcc:$(tc-getCC) ${LDFLAGS}:g" \ - -e "/LINK/s:g++:$(tc-getCXX) ${LDFLAGS}:g" \ - -e "/CC/s:gcc:$(tc-getCC):g" \ - -e "/GCC/s:g++:$(tc-getCXX):g" \ - -e "/NVCC /s|\(:=\).*|:= ${EPREFIX}/opt/cuda/bin/nvcc|g" \ - -e "/ CFLAGS/s|\(:=\)|\1 ${CFLAGS}|g" \ - -e "/ CXXFLAGS/s|\(:=\)|\1 ${CXXFLAGS}|g" \ - -e "/NVCCFLAGS/s|\(:=\)|\1 ${NVCCFLAGS} |g" \ - -e 's:-Wimplicit::g' \ - -e "s|../../common/lib/linux/\$(OS_ARCH)/libGLEW.a|$(pkg-config --libs glew)|g" \ - -e "s|../../common/lib/\$(OSLOWER)/libGLEW.a|$(pkg-config --libs glew)|g" \ - -e "s|../../common/lib/\$(OSLOWER)/\$(OS_ARCH)/libGLEW.a|$(pkg-config --libs glew)|g" \ - -i $(find . -type f -name "Makefile") || die - -# -e "/ALL_LDFLAGS/s|:=|:= ${RAWLDFLAGS} |g" \ - find common/inc/GL -delete || die - find . -type f -name "*\.a" -delete || die -} - -src_compile() { - use examples || return - local myopts verbose="verbose=1" - use debug && myopts+=" dbg=1" - export FAKEROOTKEY=1 # Workaround sandbox issue in #462602 - emake \ - cuda-install="${EPREFIX}/opt/cuda" \ - CUDA_PATH="${EPREFIX}/opt/cuda/" \ - MPI_GCC=10 \ - ${myopts} ${verbose} -} - -src_test() { - local _dir _subdir - - addwrite /dev/nvidiactl - addwrite /dev/nvidia0 - - for _dir in {0..9}*; do - pushd ${_dir} > /dev/null - for _subdir in *; do - emake -C ${_subdir} run - done - popd > /dev/null - done -} - -src_install() { - local i j f t crap="" - - if use doc; then - ebegin "Installing docs ..." - treecopy $(find -type f \( -name readme.txt -o -name "*.pdf" \)) "${ED}"/usr/share/doc/${PF}/ - docompress -x $(find "${ED}"/usr/share/doc/${PF}/ -type f -name readme.txt | sed -e "s:${ED}::") - eend - fi - - crap+=" *.txt Samples.htm*" - - ebegin "Cleaning before installation..." - for i in ${crap}; do - if [[ -e ${i} ]]; then - find ${i} -delete || die - fi - done - find -type f \( -name "*.o" -o -name "*.pdf" -o -name "readme.txt" \) -delete || die - eend - - ebegin "Moving files..." - for f in $(find .); do - local t="$(dirname ${f})" - if [[ ${t/obj\/} != ${t} || ${t##*.} == a ]]; then - continue - fi - if [[ ! -d ${f} ]]; then - if [[ -x ${f} ]]; then - exeinto /opt/cuda/sdk/${t} - doexe ${f} - else - insinto /opt/cuda/sdk/${t} - doins ${f} - fi - fi - done - eend -} diff --git a/dev-util/nvidia-cuda-toolkit/ChangeLog b/dev-util/nvidia-cuda-toolkit/ChangeLog deleted file mode 100644 index 07be9bc43..000000000 --- a/dev-util/nvidia-cuda-toolkit/ChangeLog +++ /dev/null @@ -1,15 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*nvidia-cuda-toolkit-7.0.18-r1 (19 Feb 2015) - - 19 Feb 2015; Justin Lecher <jlec@gentoo.org> - +nvidia-cuda-toolkit-7.0.18-r1.ebuild, -nvidia-cuda-toolkit-7.0.18.ebuild: - dev-util/nvidia-cuda-toolkit: Create convinience symlink lib32 -> lib - -*nvidia-cuda-sdk-7.0.18 (14 Jan 2015) - - 14 Jan 2014; Marius Brehler <marbre@linux.sungazer.de> +files/cuda-config.in, - +metadata.xml, +nvidia-cuda-toolkit-7.0.18.ebuild: - Add version 7.0.18 (release candidate) -
\ No newline at end of file diff --git a/dev-util/nvidia-cuda-toolkit/Manifest b/dev-util/nvidia-cuda-toolkit/Manifest deleted file mode 100644 index 53f62a62f..000000000 --- a/dev-util/nvidia-cuda-toolkit/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST cuda_7.0.18_rc_linux.run 1037536115 SHA256 e81164baa1f344c3f26ebe8345ce9f38448d9a82a8cf79bae28b5df3b3e4f44c SHA512 7f1c86585ed33be4714a3c9b067cf3858b44a391ae2e2e16af0d3eaf9e7097605380bed79f97463982bf05f616f9573f83b957f080a41ac33d848e597f7d2985 WHIRLPOOL cb5c36275d9a819385f1e6ee225b47b977656c971b038001d093356aefda0afc00a289801e32935b5dec0f95b83118122118ecf150936afa8dc5958e164df82d diff --git a/dev-util/nvidia-cuda-toolkit/files/cuda-config.in b/dev-util/nvidia-cuda-toolkit/files/cuda-config.in deleted file mode 100644 index ca0d1d77e..000000000 --- a/dev-util/nvidia-cuda-toolkit/files/cuda-config.in +++ /dev/null @@ -1,28 +0,0 @@ -#!/bin/bash - -SUPPORT_GCC_VERSIONS_BY_CUDA="CUDA_SUPPORTED_GCC" - -_print_help() { - cat <<- EOF - Usage: - $(basename $0) [options] - - -s | --supported Returns by current CUDA supported gcc versions - -h | --help Shows this help - EOF -} - -case ${1} in - -s|--supported) - echo "${SUPPORT_GCC_VERSIONS_BY_CUDA}" - exit 0 - ;; - -h|--help) - _print_help - exit -1 - ;; - *) - _print_help - exit 1 - ;; -esac diff --git a/dev-util/nvidia-cuda-toolkit/metadata.xml b/dev-util/nvidia-cuda-toolkit/metadata.xml deleted file mode 100644 index 5e09419f5..000000000 --- a/dev-util/nvidia-cuda-toolkit/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> - <use> - <flag name="profiler"> - Installs the NVIDIA CUDA visual profiler. - </flag> - <flag name="debugger"> - Installs the CUDA debugger. - </flag> - <flag name="eclipse">Install the <pkg>dev-util/eclipse-sdk</pkg> plugins</flag> - </use> -</pkgmetadata> diff --git a/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-7.0.18-r1.ebuild b/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-7.0.18-r1.ebuild deleted file mode 100644 index 69df15f06..000000000 --- a/dev-util/nvidia-cuda-toolkit/nvidia-cuda-toolkit-7.0.18-r1.ebuild +++ /dev/null @@ -1,154 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit check-reqs cuda unpacker versionator - -MYD=$(get_version_component_range 1)_$(get_version_component_range 2) - -DESCRIPTION="NVIDIA CUDA Toolkit (compiler and friends)" -HOMEPAGE="http://developer.nvidia.com/cuda" -CURI="https://developer.nvidia.com/rdp/cuda-70-rc-downloads" -SRC_URI="cuda_${PV}_rc_linux.run" - -SLOT="0/${PV}" -LICENSE="NVIDIA-CUDA" -KEYWORDS="-* ~amd64 ~amd64-linux" -IUSE="debugger doc eclipse profiler" - -DEPEND="" -RDEPEND="${DEPEND} - >=sys-devel/gcc-4.7[cxx] - >=x11-drivers/nvidia-drivers-346.35[uvm] - debugger? ( - sys-libs/libtermcap-compat - sys-libs/ncurses[tinfo] - ) - eclipse? ( >=virtual/jre-1.6 ) - profiler? ( >=virtual/jre-1.6 )" - -RESTRICT="fetch" - -pkg_nofetch() { - einfo "Please download the Fedora 21 \"Runfile Installer\"" - einfo " - cuda_${P}_rc_linux.run" - einfo "from ${CURI} and place it in ${DISTDIR}" -} - -S="${WORKDIR}" - -QA_PREBUILT="opt/cuda/*" - -CHECKREQS_DISK_BUILD="1500M" - -pkg_setup() { - # We don't like to run cuda_pkg_setup as it depends on us - check-reqs_pkg_setup -} - -src_unpack() { - unpacker - unpacker run_files/cuda-linux*.run -} - -src_prepare() { - local cuda_supported_gcc - - cuda_supported_gcc="4.7 4.8 4.9" - - sed \ - -e "s:CUDA_SUPPORTED_GCC:${cuda_supported_gcc}:g" \ - "${FILESDIR}"/cuda-config.in > "${T}"/cuda-config || die -} - -src_install() { - local i j - local remove="doc jre run_files install-linux.pl " - local cudadir=/opt/cuda - local ecudadir="${EPREFIX}"${cudadir} - - # dodoc doc/*txt - if use doc; then - dodoc doc/pdf/* - dohtml -r doc/html/* - fi - - if use amd64; then - mv doc/man/man3/{,cuda-}deprecated.3 || die - doman doc/man/man*/* - fi - - use debugger || remove+=" bin/cuda-gdb extras/Debugger" - ( use profiler || use eclipse ) || remove+=" libnsight" - use amd64 || remove+=" cuda-installer.pl" - - if use profiler; then - # hack found in install-linux.pl - for j in nvvp nsight; do - cat > bin/${j} <<- EOF - #!${EPREFIX}/bin/sh - LD_LIBRARY_PATH=\${LD_LIBRARY_PATH}:${ecudadir}/lib:${ecudadir}/lib64 \ - UBUNTU_MENUPROXY=0 LIBOVERLAY_SCROLLBAR=0 \ - ${ecudadir}/lib${j}/${j} -vm ${EPREFIX}/usr/bin/java - EOF - chmod a+x bin/${j} - done - else - use eclipse || remove+=" libnvvp" - remove+=" extras/CUPTI" - fi - - for i in ${remove}; do - ebegin "Cleaning ${i}..." - if [[ -e ${i} ]]; then - find ${i} -delete || die - eend - else - eend $1 - fi - done - - ln -sf lib lib32 || die - - dodir ${cudadir} - mv * "${ED}"${cudadir} || die - - cat > "${T}"/99cuda <<- EOF - PATH=${ecudadir}/bin$(use profiler && echo ":${ecudadir}/libnvvp") - ROOTPATH=${ecudadir}/bin - LDPATH=${ecudadir}/lib$(use amd64 && echo "64:${ecudadir}/lib") - EOF - doenvd "${T}"/99cuda - - use profiler && \ - make_wrapper nvprof "${EPREFIX}"${cudadir}/bin/nvprof "." ${ecudadir}/lib$(use amd64 && echo "64:${ecudadir}/lib") - - dobin "${T}"/cuda-config -} - -pkg_postinst_check() { - local a b - a="$(version_sort $(cuda-config -s))"; a=( $a ) - # greatest supported version - b=${a[${#a[@]}-1]} - - # if gcc and if not gcc-version is at least greatesst supported - if [[ $(tc-getCC) == *gcc* ]] && \ - ! version_is_at_least $(gcc-version) ${b}; then - echo - ewarn "gcc >= ${b} will not work with CUDA" - ewarn "Make sure you set an earlier version of gcc with gcc-config" - ewarn "or append --compiler-bindir= pointing to a gcc bindir like" - ewarn "--compiler-bindir=${EPREFIX}/usr/*pc-linux-gnu/gcc-bin/gcc${b}" - ewarn "to the nvcc compiler flags" - echo - fi -} - -pkg_postinst() { - if [[ ${MERGE_TYPE} != binary ]]; then - pkg_postinst_check - fi -} diff --git a/dev-util/smartgit/ChangeLog b/dev-util/smartgit/ChangeLog index 722b9c19e..0b252ff9c 100644 --- a/dev-util/smartgit/ChangeLog +++ b/dev-util/smartgit/ChangeLog @@ -27,7 +27,7 @@ 28 Sep 2014; Justin Lecher <jlec@gentoo.org> -smartgit-1.0.2.ebuild, +smartgit-6.0.6.ebuild, metadata.xml: - Version BUmp + Version Bump 25 Oct 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: Removed no-herd from herd tag in metadata.xml diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass index 53d1881f8..4fcf67295 100644 --- a/eclass/alternatives-2.eclass +++ b/eclass/alternatives-2.eclass @@ -1,4 +1,4 @@ -# Copyright 2010-2014 Gentoo Foundation +# Copyright 2010-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -21,24 +21,22 @@ # sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate. case "${EAPI:-0}" in - 0|1|2|3) + 0|1|2|3|4) die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}" ;; - 4|5) + 5) ;; *) die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}" ;; esac -DEPEND=">=app-admin/eselect-1.4.4-r100" +DEPEND=">=app-admin/eselect-1.4.4-r102" RDEPEND="${DEPEND} !app-admin/eselect-blas !app-admin/eselect-cblas !app-admin/eselect-lapack" -EXPORT_FUNCTIONS pkg_postinst pkg_prerm - # @ECLASS-VARIABLE: ALTERNATIVES_DIR # @INTERNAL # @DESCRIPTION: @@ -46,106 +44,39 @@ EXPORT_FUNCTIONS pkg_postinst pkg_prerm ALTERNATIVES_DIR="/etc/env.d/alternatives" # @FUNCTION: alternatives_for -# @USAGE: alternative provider importance source target [source target [...]] +# @USAGE: <alternative> <provider> <importance> <source> <target> [<source> <target> [...]] # @DESCRIPTION: # Set up alternative provider. # # EXAMPLE: # @CODE -# alternatives_for cblas atlas 0 \ -# /usr/$(get_libdir)/pkgconfig/cblas.pc atlas-cblas.pc \ -# /usr/include/cblas.h atlas/cblas.h +# alternatives_for sh bash 0 \ +# /usr/bin/sh bash # @CODE alternatives_for() { - (( $# >= 5 )) && (( ($#-3)%2 == 0)) || die "${FUNCNAME} requires exactly 3+N*2 arguments where N>=1" - local alternative=${1} provider=${2} importance=${3} index src target ret=0 - shift 3 - - # Make sure importance is a signed integer - if [[ -n ${importance} ]] && ! [[ ${importance} =~ ^[0-9]+(\.[0-9]+)*$ ]]; then - eerror "Invalid importance (${importance}) detected" - ((ret++)) - fi + debug-print-function ${FUNCNAME} "${@}" - # Create alternative provider subdirectories under ALTERNATIVES_DIR if needed - [[ -d "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}" ]] || dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}" - - # Keep track of provided alternatives for use in pkg_{postinst,prerm}. - # Keep a mapping between importance and provided alternatives - # and make sure the former is set to only one value. - if ! has "${alternative}:${provider}" "${ALTERNATIVES_PROVIDED[@]}"; then - # Add new provider and set its importance - index=${#ALTERNATIVES_PROVIDED[@]} - ALTERNATIVES_PROVIDED+=( "${alternative}:${provider}" ) - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - else - # Set importance for existing provider - for((index=0;index<${#ALTERNATIVES_PROVIDED[@]};index++)); do - if [[ ${alternative}:${provider} == ${ALTERNATIVES_PROVIDED[index]} ]]; then - if [[ -n ${ALTERNATIVES_IMPORTANCE[index]} ]]; then - if [[ -n ${importance} && ${ALTERNATIVES_IMPORTANCE[index]} != ${importance} ]]; then - eerror "Differing importance (${ALTERNATIVES_IMPORTANCE[index]} != ${importance}) detected" - ((ret++)) - fi - else - ALTERNATIVES_IMPORTANCE[index]=${importance} - [[ -n ${importance} ]] && echo "${importance}" > "${ED}${ALTERNATIVES_DIR}/${alternative}/${provider}/_importance" - fi - fi - done - fi + dodir /etc/env.d/alternatives - # Process source-target pairs - while (( $# >= 2 )); do - src=${1//+(\/)/\/}; target=${2//+(\/)/\/} - if [[ ${src} != /* ]]; then - eerror "Source path must be absolute, but got ${src}" - ((ret++)) - - else - local reltarget= dir=${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*} - while [[ -n ${dir} ]]; do - reltarget+=../ - dir=${dir%/*} - done - - reltarget=${reltarget%/} - [[ ${target} == /* ]] || reltarget+=${src%/*}/ - reltarget+=${target} - dodir "${ALTERNATIVES_DIR}/${alternative}/${provider}${src%/*}" - dosym "${reltarget}" "${ALTERNATIVES_DIR}/${alternative}/${provider}${src}" - - # The -e test will fail if existing symlink points to non-existing target, - # so check for -L also. - # Say ${ED}/sbin/init exists and links to /bin/systemd (which doesn't exist yet). - if [[ -e ${ED}${src} || -L ${ED}${src} ]]; then - local fulltarget=${target} - [[ ${fulltarget} != /* ]] && fulltarget=${src%/*}/${fulltarget} - if [[ -e ${ED}${fulltarget} || -L ${ED}${fulltarget} ]]; then - die "${src} defined as provider for ${fulltarget}, but both already exist in \${ED}" - else - mv "${ED}${src}" "${ED}${fulltarget}" || die - fi - fi - fi - shift 2 - done + ALTERNATIVESDIR_ROOTLESS="${ED}/etc/env.d/alternatives" \ + eselect alternatives add ${@} || die - # Stop if there were any errors - [[ ${ret} -eq 0 ]] || die "Errors detected for ${provider}, provided for ${alternative}" + ALTERNATIVES_CREATED+=( ${1} ) } # @FUNCTION: cleanup_old_alternatives_module -# @USAGE: alternative +# @USAGE: <alternative> # @DESCRIPTION: # Remove old alternatives module. cleanup_old_alternatives_module() { + debug-print-function ${FUNCNAME} "${@}" + local alt=${1} old_module="${EROOT%/}/usr/share/eselect/modules/${alt}.eselect" + if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')" if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then - echo "rm ${old_module}" + einfo "rm ${old_module}" rm "${old_module}" || eerror "rm ${old_module} failed" fi fi @@ -160,29 +91,14 @@ cleanup_old_alternatives_module() { # # Provided alternatives are set up using alternatives_for(). alternatives-2_pkg_postinst() { - local a alt provider module_version="20090908" - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" - if [[ ! -f "${EAUTO}/${alt}.eselect" \ - || "$(grep '^VERSION=' "${EAUTO}/${alt}.eselect" | grep -o '[0-9]\+')" \ - -ne "${module_version}" ]]; then - if [[ ! -d ${EAUTO} ]]; then - install -d "${EAUTO}" || eerror "Could not create eselect modules dir" - fi - einfo "Creating alternatives eselect module for ${alt}" - cat > "${EAUTO}/${alt}.eselect" <<-EOF - # This module was automatically generated by alternatives-2.eclass - DESCRIPTION="Alternatives for ${alt}" - VERSION="${module_version}" - MAINTAINER="eselect@gentoo.org" - ESELECT_MODULE_GROUP="Alternatives" - - ALTERNATIVE="${alt}" - - inherit alternatives - EOF + debug-print-function ${FUNCNAME} "${@}" + + local alt + + for alt in ${ALTERNATIVES_CREATED[@]}; do + if ! eselect ${alt} show > /dev/null; then + einfo "Creating Alternative for ${alt}" + eselect alternatives create ${alt} fi # Set alternative provider if there is no valid provider selected @@ -195,29 +111,27 @@ alternatives-2_pkg_postinst() { # @FUNCTION: alternatives-2_pkg_prerm # @DESCRIPTION: # Ensure a valid provider is set in case the package is unmerged and -# remove autogenerated eselect modules for all alternatives when last +# remove autogenerated eselect modules for alternative when last # provider is unmerged. # # Provided alternatives are set up using alternatives_for(). alternatives-2_pkg_prerm() { - local a alt provider ignore ret - local EAUTO="${EROOT%/}/usr/share/eselect/modules/auto" + debug-print-function ${FUNCNAME} "${@}" + + local alt ret + # If we are uninstalling, update alternatives to valid provider [[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore" - for a in "${ALTERNATIVES_PROVIDED[@]}"; do - alt="${a%:*}" - provider="${a#*:}" + + for alt in ${ALTERNATIVES_CREATED[@]}; do eselect "${alt}" update ${ignore} "${provider}" - ret=$? - [[ -n ${REPLACED_BY_VERSION} ]] || \ - einfo "Removing ${provider} alternative module for ${alt}, current is $(eselect ${alt} show)" + case ${ret} in 0) : ;; 2) # This was last provider for the alternative, remove eselect module einfo "Cleaning up unused alternatives module for ${alt}" - rm "${EAUTO}/${alt}.eselect" || \ - eerror "rm ${EAUTO}/${alt}.eselect failed" + eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}" ;; *) eerror "eselect ${alt} update ${provider} returned ${ret}" @@ -225,3 +139,5 @@ alternatives-2_pkg_prerm() { esac done } + +EXPORT_FUNCTIONS pkg_postinst pkg_prerm diff --git a/eclass/emboss-r1.eclass b/eclass/emboss-r1.eclass deleted file mode 100644 index 90b9a8c02..000000000 --- a/eclass/emboss-r1.eclass +++ /dev/null @@ -1,144 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -# @ECLASS: emboss-r1.eclass -# @MAINTAINER: -# sci-biology@gentoo.org -# jlec@gentoo.org -# ted.tanberry@gmail.com -# @AUTHOR: -# Original author: Author Olivier Fisette <ofisette@gmail.com> -# Next gen author: Justin Lecher <jlec@gentoo.org> -# Next gen author: Ted Tanberry <ted.tanberry@gmail.com> -# @BLURB: Use this to easy install EMBOSS and EMBASSY programs (EMBOSS add-ons). -# @DESCRIPTION: -# The inheriting ebuild must set at least EAPI=5 and provide EBO_DESCRIPTION before the inherit line. -# KEYWORDS should be set. Additionally "(R|P)DEPEND"encies and other standard -# ebuild variables can be extended (FOO+=" bar"). -# -# Example: -# -# EAPI="5" -# -# EBO_DESCRIPTION="applications from the CBS group" -# -# inherit emboss - -# @ECLASS-VARIABLE: EBO_DESCRIPTION -# @DESCRIPTION: -# Should be set. Completes the generic description of the embassy module as follows: -# -# EMBOSS integrated version of ${EBO_DESCRIPTION}, -# e.g. -# "EMBOSS integrated version of applications from the CBS group" -# -# Defaults to the upstream name of the module. - -# @ECLASS-VARIABLE: EBO_EXTRA_ECONF -# @DEFAULT_UNSET -# @DESCRIPTION: -# Extra config options passed to econf, similar to EXTRA_ECONF. - -case ${EAPI:-0} in - 5) ;; - *) die "this eclass doesn't support < EAPI 5" ;; -esac - -if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then - AUTOTOOLS_AUTORECONF=1 -fi - -inherit autotools-utils eutils flag-o-matic - -HOMEPAGE="http://emboss.sourceforge.net/" -LICENSE="LGPL-2 GPL-2" - -SLOT="0" -IUSE="mysql pdf png postgres static-libs X" - -DEPEND=" - dev-libs/expat - dev-libs/libpcre:3 - sci-libs/plplot - sys-libs/zlib - mysql? ( virtual/mysql ) - pdf? ( media-libs/libharu ) - png? ( media-libs/gd[png] ) - postgres? ( dev-db/postgresql:= ) - X? ( x11-libs/libXt )" -RDEPEND="${DEPEND}" - -if [[ ${PN} == embassy-* ]]; then - EMBASSY_PACKAGE=yes - # The EMBASSY package name, retrieved from the inheriting ebuild's name - EN=${PN:8} - # The full name and version of the EMBASSY package (excluding the Gentoo - # revision number) - EF=$(echo ${EN} | tr "[:lower:]" "[:upper:]")-${PV} - : ${EBO_DESCRIPTION:=${EN}} - DESCRIPTION="EMBOSS integrated version of ${EBO_DESCRIPTION}" - SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/${EF}.tar.gz -> embassy-${EN}-${PVR}.tar.gz" - DEPEND+=" >=sci-biology/emboss-6.3.1_p4[mysql=,pdf=,png=,postgres=,static-libs=,X=]" - - S="${WORKDIR}"/${EF} -fi - -# @FUNCTION: emboss_src_prepare -# @DESCRIPTION: -# Does the following things -# -# 1. Patches with "${FILESDIR}"/${P}_fix-build-system.patch, if present, -# and eventually runs eautoreconf in autotools-utils -# 2. Patches with "${FILESDIR}"/${PF}.patch, if present -# 3. Applies ${PATCHES[@]} via autotools-utils.eclass -# - -emboss-r1_src_prepare() { - if [[ -f "${FILESDIR}"/${P}_fix-build-system.patch ]]; then - mv configure.{in,ac} || die - epatch "${FILESDIR}"/${P}_fix-build-system.patch - fi - - [[ -f "${FILESDIR}"/${PF}.patch ]] && epatch "${FILESDIR}"/${PF}.patch - - autotools-utils_src_prepare -} - -# @FUNCTION: emboss_src_configure -# @DESCRIPTION: -# runs econf with following options. -# -# $(use_with X x) -# $(use_with png pngdriver) -# $(use_with pdf hpdf) -# $(use_with mysql mysql) -# $(use_with postgres postgresql) -# $(use_enable static-libs static) -# --enable-large -# --without-java -# --enable-systemlibs -# --docdir="${EPREFIX}/usr/share/doc/${PF}" -# ${EBO_EXTRA_ECONF} - -emboss-r1_src_configure() { - local myeconfargs=( - $(use_with X x) - $(use_with png pngdriver "${EPREFIX}/usr") - $(use_with pdf hpdf "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr/bin/mysql_config") - $(use_with postgres postgresql "${EPREFIX}/usr/bin/pg_config") - --enable-large - --without-java - --enable-systemlibs - --docdir="${EPREFIX}/usr/share/doc/${PF}" - ${EBO_EXTRA_ECONF} - ) - - [[ ${EMBASSY_PACKAGE} == yes ]] && \ - append-cppflags "-I${EPREFIX}/usr/include/emboss" - - autotools-utils_src_configure -} - -EXPORT_FUNCTIONS src_prepare src_configure diff --git a/licenses/AMD-APPSDK b/licenses/AMD-APPSDK new file mode 100644 index 000000000..fece351dd --- /dev/null +++ b/licenses/AMD-APPSDK @@ -0,0 +1,267 @@ + + SOFTWARE DEVELOPMENT KIT LICENSE AGREEMENT + (Linux APP SDK Installer) + +IMPORTANT-READ CAREFULLY: This is a legal agreement +("Agreement") between you and Advanced Micro Devices, Inc. +("AMD"). Your use of this AMD Software Development Kit, (the +"SDK") including software, tools, utilities, +Documentation, and to the extent provided hereunder, Libraries, +Sample Code, header files, any related AMD materials, and +updates thereto (collectively, "Licensed Materials"), are +subject to the following terms and conditions. +Do not use these Licensed Materials until you have carefully +read the following terms and conditions. By downloading or +using the Licensed Materials obtained herewith, you are +expressly agreeing to all of the following +terms: +WARRANTIES, SUPPORT, RIGHTS, AND DAMAGES ARE DISCLAIMED AND/OR +LIMITED BELOW, PLEASE READ ENTIRELY AND CAREFULLY. IF YOU DO +NOT AGREE TO THE TERMS OF THIS AGREEMENT, DO NOT DOWNLOAD OR +USE THE LICENSED MATERIALS OR ANY PORTION THEREOF. DOWNLOADING +OR USING THE LICENSED MATERIALS OR ANY PORTION THEREOF +CONSTITUTES YOUR ACCEPTANCE OF THIS AGREEMENT. + +1. Definitions. + + 1.1. "Documentation" means install scripts and online or +electronic documentation included with the Licensed +Materials, or portions thereof. + + 1.2. "Free Software License" means an open source or other +license that requires, as a condition of use, modification or +distribution, that any resulting software must be (a) disclosed +or distributed in source code form; (b) licensed for the +purpose of making derivative works; or (c) re-distributable at +no charge. + + 1.3. "Licensee Software" means any software developed or +modified by you using the Licensed Materials, and which may +include any Libraries, Sample Code and/or derivative works of +Sample Code. + + 1.4. "Intellectual Property Rights" means all copyrights, +trademarks, trade secrets, patents, mask works, and all +related, similar, or other intellectual property rights +recognized in any jurisdiction worldwide, including all +applications and registrations with respect thereto. + + 1.5. "Libraries" means any run-times or other functionality +provided in Object Code including but not limited to codecs and +video processing libraries. + + 1.6. "Object Code" means machine readable computer +programming code files, which is not in a human readable form. + + 1.7. "Sample Code" means the Source Code identified within +the SDK as sample code. + + 1.8. "Source Code" means computer programming code in human +readable form and related system level documentation, including +all comments, symbols and any procedural code such as job +control language. + +2 License Grants. + + 2.1 Internal Use. Subject to the terms and conditions of +this Agreement, AMD hereby grants to you a non-exclusive, non- +transferable, royalty-free copyright license solely for your +internal use in developing Licensee Software for use with +products based on or incorporating AMD products (a) to use the +Licensed Materials, (b) to download, use, copy, and create +derivative works of Sample Code in Source Code and to create +compilations of same in Object Code form, and (c) to download, +use and copy the Libraries. + + 2.2 Restrictions. This Agreement does not grant you any +rights, by license, implication or otherwise, in or to any +associated materials or technology, except as is expressly +provided herein. Furthermore, you acknowledge that except as +expressly provided herein, the Licensed Materials provided by +AMD hereunder are for your internal use only and you may not +sell, transfer, assign, sublicense or distribute the Licensed +Materials, in whole or in part, in any manner. Except as +expressly specified in Section 2.1, you will have no right to +make or have made derivatives of the Licensed Materials, to +reverse engineer, modify, disassemble or to decompile the +Licensed Materials, or otherwise reduce any part of the +Licensed Materials to any human readable form. You will not +use the Licensed Materials in applications intended to support +or sustain life, or in which the failure of your product could +create a situation where personal injury, death, or severe +property or environmental damage may occur. You will not use or +distribute with any Licensee Software any code that is licensed +under a Free Software License. No portion of the Licensed +Materials may in any event be distributed on a stand-alone +basis or other than in the form of Licensee Software. You must +not alter or remove any copyright, trademark or patent notice +in the Licensed Materials. You must reproduce all AMD +trademark and/or copyright notices on any derivative work that +incorporates Sample Code or Libraries. You may not use AMD's +trademarks in the Licensee Software name or advertising in a +way that suggests the Licensee Software comes from or is +endorsed by AMD. + + 2.3 Third Party Materials. Together with the Licensed +Materials, AMD may include third party technologies (e.g. third +party libraries) for which you must obtain licenses from +parties other than AMD. You agree that AMD has not obtained or +conveyed to you, and that you shall be responsible for +obtaining, Intellectual Property Rights to use and/or +distribute the applicable, underlying Intellectual Property +Rights related to the third party technologies. These third +party technologies are not licensed as part of the Licensed +Materials and are not licensed under this Agreement. + + 2.4 Other AMD Software Components. The Licensed +Materials may be accompanied by AMD software components (e.g. +libraries, sample code) which are licensed to you under the +terms and conditions of their respective licenses located in +the directory with the software component. + + 2.5 Feedback. You have no obligation to give AMD any +suggestions, comments or other feedback ("Feedback") relating +to the Licensed Materials. However, AMD may use and include +any Feedback that you voluntarily provide to improve the +Licensed Materials or other AMD products and technologies. +Accordingly, if you provide Feedback, you grant AMD and its +affiliates and subsidiaries a worldwide, non-exclusive, +irrevocable, royalty-free, perpetual license to use, reproduce, +license, sublicense, distribute, make, have made, sell and +otherwise commercialize the Feedback in the Licensed Materials +or other AMD technologies. You further agree not to provide +any Feedback that (a) you know is subject to any patent, +copyright or other intellectual property claim or right of any +third party; or (b) is subject to a Free Software License. + +3 Ownership and Copyright Notices. The Licensed Materials are +owned or licensed by AMD and are protected by United States and +foreign intellectual property laws and international treaty +provisions. All title and copyrights in and to the Licensed +Materials, all copies thereof (in whole or in part, and in any +form), and all rights therein will remain vested in AMD. +Except as expressly provided herein, AMD does not grant any +express or implied right to you under AMD patents, copyrights, +trademarks, or trade secrets. You agree the Licensed Materials +are licensed, not sold by AMD. + +4 Support. You will not be entitled to any support of any kind +from AMD or AMD's licensors. Furthermore, you will be solely +responsible for providing support to your end users for the +Licensee Software distributed by you or your +products. AMD may, in its sole discretion, provide to you +updates to the Licensed Materials. + +5 Warranty, Limitations of Liability and Indemnification. + + 5.1 THE LICENSED MATERIALS ARE PROVIDED "AS IS," WITH ALL +FAULTS, AND WITHOUT WARRANTY OF ANY KIND. AMD DISCLAIMS ALL +WARRANTIES, EXPRESS, IMPLIED, OR STATUTORY, INCLUDING BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS +FOR A PARTICULAR PURPOSE, TITLE, AND NON-INFRINGEMENT. AMD +DOES NOT WARRANT THAT THE LICENSED MATERIALS ARE ERROR FREE OR +THAT THE LICENSED MATERIALS WILL RUN CONTINUOUSLY. + + 5.2 AMD WILL NOT, UNDER ANY CIRCUMSTANCES, BE LIABLE TO +YOU FOR CONSEQUENTIAL, INCIDENTAL, PUNITIVE OR SPECIAL DAMAGES, +INCLUDING BUT NOT LIMITED TO, LOSS OF USE, DATA OR PROFITS, +ARISING FROM THIS AGREEMENT, EVEN IF AMD HAS BEEN APPRISED OF +THE LIKELIHOOD OF SUCH DAMAGES. In no event will AMD's total +liability to you for all damages, losses, and causes of action +(whether in contract, tort (including negligence) or otherwise) +exceed the amount of $100 USD. + + 5.3 You agree to defend, indemnify and hold harmless AMD +and its licensors, and any of their directors, officers, +employees, affiliates or agents, from and against any and all +loss, damage, liability and other expenses (including +reasonable attorneys' fees), resulting from (a) your improper +use of the Licensed Materials or (b) use of Licensee Software. + +6 Termination. Either party may terminate this Agreement upon +thirty (30) days prior written notice to the other party. This +Agreement will terminate immediately without notice from AMD or +judicial resolution if you fail to comply +with any provisions of this Agreement or upon AMD's written +request for return of the Licensed Materials. Upon termination +of this Agreement, you will cease using the Licensed Materials. +Termination of this Agreement will have no effect on any sub- +licenses properly granted by you to end users under Section 2, +which sub-licenses will survive in accordance with their terms. + +7 Survival. Notwithstanding the foregoing, Sections 2.2, 2.3, +2.4, 2.5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 and 13 will survive +any expiration or termination of this Agreement, until by their +own terms they are fulfilled. + +8 Export Restrictions. You shall adhere to all applicable +U.S., European, and other export laws, including but not +limited to the U.S. Export Administration Regulations ("EAR"), +(15 C.F.R. Sections 730 through 774), and E.U. Council +Regulation (EC) No 428/2009 of 5 May 2009. Further, pursuant +to Section 740.6 of the EAR, you hereby certify that, except +pursuant to a license granted by the United States Department +of Commerce Bureau of Industry and Security or as otherwise +permitted pursuant to a License Exception under the EAR, you +will not (1) export, re-export or release to a national of a +country in Country Groups D:1, E:1 or E:2 any restricted +technology, software, or source code you receive from AMD, or +(2) export to Country Groups D:1, E:1 or E:2 the direct product +of such technology or software, if such foreign produced direct +product is subject to national security controls as identified +on the Commerce Control List (currently found in Supplement 1 +to Part 774 of EAR). For the most current Country Group +listings, or for additional information about the EAR or your +obligations under those regulations, please refer to the U.S. +Bureau of Industry and Security's website at +http://www.bis.doc.gov/. + +9. U.S. Government Restricted Rights. The Licensed Materials +are provided with "RESTRICTED RIGHTS." Use, duplication or +disclosure by the Government is subject to restrictions as set +forth in FAR 52.227-14 and DFAR 252.227-7013, et seq., or its +successor. Use of the Licensed Materials by the Government +constitutes acknowledgement of AMD's proprietary rights in +them. + +10. Governing Law. This Agreement will be governed under the +laws of Texas, excluding the conflicts of law rules, and is +deemed to have been executed and performed in Austin, Texas. + +11. Equitable Remedies. You acknowledge that your breach of +this Agreement may cause irreparable damage to AMD and agree +that AMD shall be entitled to seek injunctive relief under this +Agreement, as well as such further relief as may be granted by +a court of competent jurisdiction. + +12. General. You may not assign this Agreement. Any attempted +assignment by you will be null and void. The parties do not +intend that any agency or partnership relationship be created +between them by this Agreement. Each +provision of this Agreement shall be interpreted in such a +manner as to be effective and valid under applicable law. +However, in the event that any provision of this Agreement +becomes or is declared unenforceable by any court of +competent jurisdiction, such provision shall be deemed deleted +and the remainder of this Agreement shall remain in full force +and effect + +13. Entire Agreement. This Agreement sets forth the entire +agreement and understanding between the parties and supersedes +and merges all prior and contemporaneous oral and/or written +agreements, discussions and +understandings concerning the subject matter hereof. This +Agreement may not be modified except by a written instrument +executed by the parties. No waiver or modification of any +provision of this Agreement shall be binding unless made in +writing and signed by an authorized representative of each +party. + +If you agree to abide by the terms and conditions of this +Agreement, please press "Accept." If you do not agree to abide +by the terms and conditions of this Agreement, press "Decline" +and you may not use or access the Licensed +Materials. + +By clicking accept, you confirm that you are neither a resident +nor a national of Cuba, Iran, North Korea, the Sudan or Syria. diff --git a/licenses/FSL b/licenses/FSL new file mode 100644 index 000000000..566feecda --- /dev/null +++ b/licenses/FSL @@ -0,0 +1,94 @@ + +FMRIB Software Library, Release 5.0 (c) 2012, The University of Oxford +(the "Software") + +The Software remains the property of the University of Oxford ("the +University"). + +The Software is distributed "AS IS" under this Licence solely for +non-commercial use in the hope that it will be useful, but in order +that the University as a charitable foundation protects its assets for +the benefit of its educational and research purposes, the University +makes clear that no condition is made or to be implied, nor is any +warranty given or to be implied, as to the accuracy of the Software, +or that it will be suitable for any particular purpose or for use +under any specific conditions. Furthermore, the University disclaims +all responsibility for the use which is made of the Software. It +further disclaims any liability for the outcomes arising from using +the Software. + +The Licensee agrees to indemnify the University and hold the +University harmless from and against any and all claims, damages and +liabilities asserted by third parties (including claims for +negligence) which arise directly or indirectly from the use of the +Software or the sale of any products based on the Software. + +No part of the Software may be reproduced, modified, transmitted or +transferred in any form or by any means, electronic or mechanical, +without the express permission of the University. The permission of +the University is not required if the said reproduction, modification, +transmission or transference is done without financial return, the +conditions of this Licence are imposed upon the receiver of the +product, and all original and amended source code is included in any +transmitted product. You may be held legally responsible for any +copyright infringement that is caused or encouraged by your failure to +abide by these terms and conditions. + +You are not permitted under this Licence to use this Software +commercially. Use for which any financial return is received shall be +defined as commercial use, and includes (1) integration of all or part +of the source code or the Software into a product for sale or license +by or on behalf of Licensee to third parties or (2) use of the +Software or any derivative of it for research with the final aim of +developing software products for sale or license to a third party or +(3) use of the Software or any derivative of it for research with the +final aim of developing non-software products for sale or license to a +third party, or (4) use of the Software to provide any service to an +external organisation for which payment is received. If you are +interested in using the Software commercially, please contact Isis +Innovation Limited ("Isis"), the technology transfer company of the +University, to negotiate a licence. Contact details are: +innovation@isis.ox.ac.uk quoting reference BS/9564. + + +------------------------------------------------------------------- + +The Standard Space Atlases + +The Cerebellum, Harvard-Oxford, JHU, Juelich, Striatum and Thalamus atlases, +whilst not being the property of Oxford, are released under the terms of the +main FSL licence above, at the request of their owners. These atlases +should therefore not be used for commercial purposes; for such +purposes please contact the primary co-ordinator for the relevant +atlas: + +Harvard-Oxford: steve@fmrib.ox.ac.uk +JHU: susumu@mri.jhu.edu +Juelich: S.Eickhoff@fz-juelich.de +Thalamus: behrens@fmrib.ox.ac.uk +Cerebellum: j.diedrichsen@bangor.ac.uk +Striatum: andri.tziortzi@gmail.com + +------------------------------------------------------------------- + +FSLView + +FSLView sources are released under the terms of the GPLv2 +(http://www.gnu.org/licenses/old-licenses/gpl-2.0.html). FSLView +binaries use Qt (http://qt.nokia.com) which is released under LGPLv2.1. +The FSLView binaries are released under the GPL, with the added +exception that we also give permission to link this program with the Qt +non-commercial edition, and distribute the resulting executable, +without including the source code for the Qt non-commercial edition in +the source distribution. + +FSLView is distributed "AS IS" under this Licence in the hope that it +will be useful, but in order that the University as a charitable +foundation protects its assets for the benefit of its educational and +research purposes, the University makes clear that no condition is +made or to be implied, nor is any warranty given or to be implied, as +to the accuracy of the Software, or that it will be suitable for any +particular purpose or for use under any specific conditions. +Furthermore, the University disclaims all responsibility for the use +which is made of the Software. It further disclaims any liability for +the outcomes arising from using the Software. diff --git a/licenses/NVIDIA-CUDA b/licenses/NVIDIA-CUDA deleted file mode 100644 index 44b570503..000000000 --- a/licenses/NVIDIA-CUDA +++ /dev/null @@ -1,2262 +0,0 @@ -End User License Agreement --------------------------- - - -Preface -------- - -The following contains specific license terms and conditions -for four separate NVIDIA products. By accepting this -agreement, you agree to comply with all the terms and -conditions applicable to the specific product(s) included -herein. - - -NVIDIA CUDA Toolkit - - -Description - -The NVIDIA CUDA Toolkit provides command-line and graphical -tools for building, debugging and optimizing the performance -of applications accelerated by NVIDIA GPUs, runtime and math -libraries, and documentation including programming guides, -user manuals, and API references. The NVIDIA CUDA Toolkit -License Agreement is available in Chapter 1. - - -Default Install Location of CUDA Toolkit - -Windows platform: - -%ProgramFiles%\NVIDIA GPU Computing Toolkit\CUDA\v#.# - -Linux platform: - -/usr/local/cuda-#.# - -Mac platform: - -/Developer/NVIDIA/CUDA-#.# - - -NVIDIA CUDA Samples - - -Description - -This package includes over 100+ CUDA examples that demonstrate -various CUDA programming principles, and efficient CUDA -implementation of algorithms in specific application domains. -The NVIDIA CUDA Samples License Agreement is available in -Chapter 2. - - -Default Install Location of CUDA Samples - -Windows platform: - -%ProgramData%\NVIDIA Corporation\CUDA Samples\v#.# - -Linux platform: - -/usr/local/cuda-#.#/samples - -and - -$HOME/NVIDIA_CUDA-#.#_Samples - -Mac platform: - -/Developer/NVIDIA/CUDA-#.#/samples - - -NVIDIA Driver - - -Description - -This package contains the operating system driver and -fundamental system software components for NVIDIA GPUs. The -NVIDIA Driver License for the Windows platform is available in -Chapter 3, and the NVIDIA Driver License for the Linux and Mac -OSX platforms is available in Chapter 4. - - -NVIDIA Nsight Visual Studio Edition (Windows only) - - -Description - -NVIDIA Nsight Development Platform, Visual Studio Edition is a -development environment integrated into Microsoft Visual -Studio that provides tools for debugging, profiling, analyzing -and optimizing your GPU computing and graphics applications. -The NVIDIA Nsight Visual Studio Edition License Agreement is -available in Chapter 5. - - -Default Install Location of Nsight Visual Studio Edition - -Windows platform: - -%ProgramFiles%\NVIDIA Corporation\Nsight Visual Studio Edition #.# - - -NVIDIA CUDA General Terms - - -Description - -General terms that apply to all of the software components are -available in Chapter 6. - - -1. NVIDIA CUDA Toolkit License Agreement ----------------------------------------- - - -Important Notice ----------------- - -READ CAREFULLY: This Software License Agreement ("Agreement") -for NVIDIA CUDA Toolkit, including computer software and -associated documentation ("Software"), is the Agreement which -governs use of the SOFTWARE of NVIDIA Corporation and its -subsidiaries ("NVIDIA") downloadable herefrom. By downloading, -installing, copying, or otherwise using the SOFTWARE, You (as -defined below) agree to be bound by the terms of this -Agreement. If You do not agree to the terms of this Agreement, -do not download the SOFTWARE. - - -Recitals --------- - -Use of NVIDIA's SOFTWARE requires three elements: the -SOFTWARE, an NVIDIA GPU or application processor ("NVIDIA -Hardware"), and a computer system. The SOFTWARE is protected -by copyright laws and international copyright treaties, as -well as other intellectual property laws and treaties. The -SOFTWARE is not sold, and instead is only licensed for Your -use, strictly in accordance with this Agreement. The NVIDIA -Hardware is protected by various patents, and is sold, but -this Agreement does not cover the sale or use of such -hardware, since it may not necessarily be sold as a package -with the SOFTWARE. This Agreement sets forth the terms and -conditions of the SOFTWARE only. - - -1.1. Definitions - - -1.1.1. Licensee - -"You", or "Your" shall mean the entity or individual that -downloads and uses the SOFTWARE. - - -1.1.2. Redistributable Software - -"Redistributable Software" shall mean the redistributable -libraries referenced in Attachment A of this Agreement. - - -1.1.3. Software - -"SOFTWARE" shall mean the deliverables provided pursuant to -this Agreement. SOFTWARE may be provided in either source or -binary form, at NVIDIA's discretion. - - -1.2. Grant of License - - -1.2.1. Rights and Limitations of Grant - -Provided that Licensee complies with the terms of this -Agreement, NVIDIA hereby grants Licensee the following -limited, non-exclusive, non-transferable, non-sublicensable -(except as expressly permitted otherwise for Redistributable -Software in Section 1.2.1.1 and Section 1.2.1.3 of this -Agreement) right to use the SOFTWARE -- and, if the SOFTWARE -is provided in source form, to compile the SOFTWARE -- with -the following limitations: - - -1.2.1.1. Redistribution Rights - -Licensee may transfer, redistribute, and sublicense certain -files of the Redistributable SOFTWARE, as defined in -Attachment A of this Agreement, provided, however, that (a) -the Redistributable SOFTWARE shall be distributed solely in -binary form to Licensee's licensees ("Customers") only as a -component of Licensee's own software products (each, a -"Licensee Application"); (b) Licensee shall design the -Licensee Application such that the Redistributable SOFTWARE -files are installed only in a private (non-shared) directory -location that is used only by the Licensee Application; (c) -Licensee shall obtain each Customer's written or clickwrap -agreement to the license terms under a written, legally -enforceable agreement that has the effect of protecting the -SOFTWARE and the rights of NVIDIA under terms no less -restrictive than this Agreement. - - -1.2.1.2. Usage Rights - -Licensee may install and use multiple copies of the SOFTWARE -on a shared computer or concurrently on different computers, -and make multiple back-up copies of the SOFTWARE, solely for -Licensee's use within Licensee's Enterprise. "Enterprise" -shall mean individual use by Licensee or any legal entity -(such as a corporation or university) and the subsidiaries it -owns by more than 50 percent. - - -1.2.1.3. Further Redistribution Rights - -Subject to the terms and conditions of the Agreement, Licensee -may authorize Customers to further redistribute the -Redistributable SOFTWARE that such Customers receive as part -of the Licensee Application, solely in binary form, provided, -however, that Licensee shall require in their standard -software license agreements with Customers that all such -redistributions must be made pursuant to a license agreement -that has the effect of protecting the SOFTWARE and the rights -of NVIDIA whose terms and conditions are at least as -restrictive as those in the applicable Licensee software -license agreement covering the Licensee Application. For -avoidance of doubt, termination of this Agreement shall not -affect rights previously granted by Licensee to its Customers -under this Agreement to the extent validly granted to -Customers under Section 1.2.1.1. - - -1.2.1.4. Linux/FreeBSD Exception - -Notwithstanding the foregoing terms of Section 1.2.1.2, -Section 1.2.1.1 and Section 1.2.1.3, SOFTWARE designed -exclusively for use on the Linux or FreeBSD operating systems, -or other operating systems derived from the source code to -these operating systems, may be copied and redistributed, -provided that the binary files thereof are not modified in any -way (except for unzipping of compressed files). - - -1.2.1.5. Additional Licensing Obligations - -Licensee acknowledges and agrees that its use of certain third -party components included with the SOFTWARE may be subject to -additional licensing terms and conditions as set forth or -referenced in Attachment B of this Agreement. - - -1.2.1.6. Limitations - -No Reverse Engineering - -If the SOFTWARE is provided in binary form, Licensee may not -reverse engineer, decompile, or disassemble the SOFTWARE, nor -attempt in any other manner to obtain the source code. - -No Separation of Components - -The SOFTWARE is licensed as a single product. Except as -authorized in this Agreement, Software component parts of the -Software may not be separated for use on more than one -computer, nor otherwise used separately from the other parts. - -No Rental - -Licensee may not rent or lease the SOFTWARE to someone else. - -No Modifications - -If the SOFTWARE is provided in source form, Licensee may not -modify or create derivative works of the SOFTWARE. - - -1.3. Term and Termination - -This Agreement will continue in effect for two (2) years -("Initial Term") after Your initial download and use of the -SOFTWARE, subject to the exclusive right of NVIDIA to -terminate as provided herein. The term of this Agreement will -automatically renew for successive one (1) year renewal terms -after the Initial Term, unless either party provides to the -other party at least three (3) months prior written notice of -termination before the end of the applicable renewal term. - -This Agreement will automatically terminate if Licensee fails -to comply with any of the terms and conditions hereof. In such -event, Licensee must destroy all copies of the SOFTWARE and -all of its component parts. - - -Defensive Suspension - -If Licensee commences or participates in any legal proceeding -against NVIDIA, then NVIDIA may, in its sole discretion, -suspend or terminate all license grants and any other rights -provided under this Agreement during the pendency of such -legal proceedings. - - -1.4. Copyright - -All rights, title, interest and copyrights in and to the -SOFTWARE (including but not limited to all images, -photographs, animations, video, audio, music, text, and other -information incorporated into the SOFTWARE), the accompanying -printed materials, and any copies of the SOFTWARE, are owned -by NVIDIA, or its suppliers. The SOFTWARE is protected by -copyright laws and international treaty provisions. -Accordingly, Licensee is required to treat the SOFTWARE like -any other copyrighted material, except as otherwise allowed -pursuant to this Agreement and that it may make one copy of -the SOFTWARE solely for backup or archive purposes. - -RESTRICTED RIGHTS NOTICE. Software has been developed entirely -at private expense and is commercial computer software -provided with RESTRICTED RIGHTS. Use, duplication or -disclosure by the U.S. Government or a U.S. Government -subcontractor is subject to the restrictions set forth in the -Agreement under which Software was obtained pursuant to DFARS -227.7202-3(a) or as set forth in subparagraphs (c)(1) and (2) -of the Commercial Computer Software - Restricted Rights clause -at FAR 52.227-19, as applicable. Contractor/manufacturer is -NVIDIA, 2701 San Tomas Expressway, Santa Clara, CA 95050. - - -1.5. Applicable Law - -This Agreement shall be deemed to have been made in, and shall -be construed pursuant to, the laws of the State of Delaware. -The United Nations Convention on Contracts for the -International Sale of Goods is specifically disclaimed. The -courts of Santa Clara County, California shall have exclusive -jurisdiction and venue over any dispute arising out of or -relating to this Agreement. - - -1.6. Disclaimer of Warranties and Limitations on Liability - - -1.6.1. No Warranties - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE -SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS -DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, -BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT. - - -1.6.2. No Liability for Consequential Damages - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT -SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, -INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER -(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS -PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, -OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR -INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED -OF THE POSSIBILITY OF SUCH DAMAGES. - - -1.6.3. No Support - -NVIDIA has no obligation to support or to provide any updates -of the Software. - - -1.7. Miscellaneous - - -1.7.1. Feedback - -Notwithstanding any Non-Disclosure Agreement executed by and -between the parties, the parties agree that in the event -Licensee or NVIDIA provides Feedback (as defined below) to the -other party on how to design, implement, or improve the -SOFTWARE or Licensee's product(s) for use with the SOFTWARE, -the following terms and conditions apply the Feedback: - - -1.7.1.1. Exchange of Feedback - -Both parties agree that neither party has an obligation to -give the other party any suggestions, comments or other -feedback, whether verbally or in written or source code form, -relating to (i) the SOFTWARE; (ii) Licensee's products; (iii) -Licensee's use of the SOFTWARE; or (iv) -optimization/interoperability of Licensee's product with the -SOFTWARE (collectively defined as "Feedback"). In the event -either party provides Feedback to the other party, the party -receiving the Feedback may use any Feedback that the other -party voluntarily provides to improve the (i) SOFTWARE or -other related NVIDIA technologies, respectively for the -benefit of NVIDIA; or (ii) Licensee's product or other related -Licensee technologies, respectively for the benefit of -Licensee. Accordingly, if either party provides Feedback to -the other party, both parties agree that the other party and -its respective licensees may freely use, reproduce, license, -distribute, and otherwise commercialize the Feedback in the -(i) SOFTWARE or other related technologies; or (ii) Licensee's -products or other related technologies, respectively, without -the payment of any royalties or fees. - - -1.7.1.2. Residual Rights - -Licensee agrees that NVIDIA shall be free to use any general -knowledge, skills and experience, (including, but not limited -to, ideas, concepts, know-how, or techniques) ("Residuals"), -contained in the (i) Feedback provided by Licensee to NVIDIA; -(ii) Licensee's products shared or disclosed to NVIDIA in -connection with the Feedback; or (c) Licensee's confidential -information voluntarily provided to NVIDIA in connection with -the Feedback, which are retained in the memories of NVIDIA's -employees, agents, or contractors who have had access to such -Residuals. Subject to the terms and conditions of this -Agreement, NVIDIA's employees, agents, or contractors shall -not be prevented from using Residuals as part of such -employee's, agent's or contractor's general knowledge, skills, -experience, talent, and/or expertise. NVIDIA shall not have -any obligation to limit or restrict the assignment of such -employees, agents or contractors or to pay royalties for any -work resulting from the use of Residuals. - - -1.7.1.3. Disclaimer of Warranty - -FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S -USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS, -IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE -IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A -PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT -REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER -PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION -OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE. - - -1.7.1.4. No Liability for Consequential Damages - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT -SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, -INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER -(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS -PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, -OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR -INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS -BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - - -1.7.2. Freedom of Action - -Licensee agrees that this Agreement is nonexclusive and NVIDIA -may currently or in the future be developing software, other -technology or confidential information internally, or -receiving confidential information from other parties that -maybe similar to the Feedback and Licensee's confidential -information (as provided in Section 1.7.1.2 above), which may -be provided to NVIDIA in connection with Feedback by Licensee. -Accordingly, Licensee agrees that nothing in this Agreement -will be construed as a representation or inference that NVIDIA -will not develop, design, manufacture, acquire, market -products, or have products developed, designed, manufactured, -acquired, or marketed for NVIDIA, that compete with the -Licensee's products or confidential information. - - -1.7.3. No Implied Licenses - -Under no circumstances should anything in this Agreement be -construed as NVIDIA granting by implication, estoppel or -otherwise, (i) a license to any NVIDIA product or technology -other than the SOFTWARE; or (ii) any additional license rights -for the SOFTWARE other than the licenses expressly granted in -this Agreement. - - -1.7.4. - -If any provision of this Agreement is inconsistent with, or -cannot be fully enforced under, the law, such provision will -be construed as limited to the extent necessary to be -consistent with and fully enforceable under the law. This -Agreement is the final, complete and exclusive agreement -between the parties relating to the subject matter hereof, and -supersedes all prior or contemporaneous understandings and -agreements relating to such subject matter, whether oral or -written. This Agreement may only be modified in writing signed -by an authorized officer of NVIDIA. Licensee agrees that it -will not ship, transfer or export the SOFTWARE into any -country, or use the SOFTWARE in any manner, prohibited by the -United States Bureau of Industry and Security or any export -laws, restrictions or regulations. - - -1.7.5. - -The parties agree that the following sections of the Agreement -will survive the termination of the License: Section 1.2.1.4, -Section 1.4, Section 1.5, Section 1.6, and Section 1.7. - - -1.8. Attachment A - - -Redistributable Software - -In connection with Section 1.2.1.1 of this Agreement, the -following files may be redistributed with software -applications developed by Licensee, including certain -variations of these files that have version number or -architecture specific information embedded in the file name - -as an example only, for release version 6.0 of the 64-bit -Windows software, the file cudart64_60.dll is redistributable. - -Component : CUDA Runtime - Windows : cudart.dll, cudart_static.lib, cudadevrt.lib - Mac OSX : libcudart.dylib, libcudart_static.a, libcudadevrt.a - Linux : libcudart.so, libcudart_static.a, libcudadevrt.a - Android : libcudart.so, libcudart_static.a, libcudadevrt.a - -Component : CUDA FFT Library - Windows : cufft.dll, cufftw.dll - Mac OSX : libcufft.dylib, libcufft_static.a, libcufftw.dylib, libcufftw_static.a - Linux : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a - Android : libcufft.so, libcufft_static.a, libcufftw.so, libcufftw_static.a - -Component : CUDA BLAS Library - Windows : cublas.dll, cublas_device.lib - Mac OSX : libcublas.dylib, libcublas_static.a, libcublas_device.a - Linux : libcublas.so, libcublas_static.a, libcublas_device.a - Android : libcublas.so, libcublas_static.a, libcublas_device.a - -Component : NVIDIA "Drop-in" BLAS Library - Windows : nvblas.dll - Mac OSX : libnvblas.dylib - Linux : libnvblas.so - -Component : CUDA Sparse Matrix Library - Windows : cusparse.dll - Mac OSX : libcusparse.dylib, libcusparse_static.a - Linux : libcusparse.so, libcusparse_static.a - Android : libcusparse.so, libcusparse_static.a - -Component : CUDA Random Number Generation Library - Windows : curand.dll - Mac OSX : libcurand.dylib, libcurand_static.a - Linux : libcurand.so, libcurand_static.a - Android : libcurand.so, libcurand_static.a - -Component : NVIDIA Performance Primitives Library - Windows : nppc.dll, nppi.dll, npps.dll - Mac OSX : libnppc.dylib, libnppi.dylib, libnpps.dylib, libnppc_static.a, libnpps_static.a, libnppi_static.a - Linux : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a - Android : libnppc.so, libnppi.so, libnpps.so, libnppc_static.a, libnpps_static.a, libnppi_static.a - -Component : Internal common library required for statically linking to cuBLAS, cuSPARSE, cuFFT, cuRAND and NPP - Mac OSX : libculibos.a - Linux : libculibos.a - -Component : NVIDIA Runtime Compilation Library - Windows : nvrtc.dll, nvrtc-builtins.dll - Mac OSX : libnvrtc.dylib, libnvrtc-builtins.dylib - Linux : libnvrtc.so, libnvrtc-builtins.so - -Component : NVIDIA Optimizing Compiler Library - Windows : nvvm.dll - Mac OSX : libnvvm.dylib - Linux : libnvvm.so - -Component : NVIDIA Common Device Math Functions Library - Windows : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc - Mac OSX : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc - Linux : libdevice.compute_20.bc, libdevice.compute_30.bc, libdevice.compute_35.bc - -Component : CUDA Occupancy Calculation Header Library - All : cuda_occupancy.h - -Component : Profiling Tools Interface Library - Windows : cupti.dll - Mac OSX : libcupti.dylib - Linux : libcupti.so - - - -1.9. Attachment B - - -Additional Licensing Obligations - -The following third party components included in the SOFTWARE -are licensed to Licensee pursuant to the following terms and -conditions: - - 1. Licensee's use of the following third party components is - subject to the terms and conditions of GNU GPL v3.0: - - a. gdb - - This product includes copyrighted third-party software - licensed under the terms of the GNU General Public License - v3.0 ("GPL v3.0). All third-party software packages are - copyright by their respective authors. GPL v2.0 terms and - conditions are hereby incorporated into the Agreement by - this reference. http://www.gnu.org/licenses/gpl.txt - - 2. Licensee represents and warrants that any and all third - party licensing and/or royalty payment obligations in - connection with Licensee's use of the H.264 video codecs - are solely the responsibility of Licensee. - - 3. Licensee's use of the Thrust library is subject to the - terms and conditions of the Apache License Version 2.0. - All third-party software packages are copyright by their - respective authors. Apache License Version 2.0 terms and - conditions are hereby incorporated into the Agreement by - this reference. - http://www.apache.org/licenses/LICENSE-2.0.html - - In addition, Licensee acknowledges the following notice: - Thrust includes source code from the Boost Iterator, - Tuple, System, and Random Number libraries. - - Boost Software License - Version 1.0 - August 17th, 2003 - . . . . - - Permission is hereby granted, free of charge, to any person or - organization obtaining a copy of the software and accompanying - documentation covered by this license (the "Software") to use, - reproduce, display, distribute, execute, and transmit the Software, - and to prepare derivative works of the Software, and to permit - third-parties to whom the Software is furnished to do so, all - subject to the following: - - The copyright notices in the Software and this entire statement, - including the above license grant, this restriction and the following - disclaimer, must be included in all copies of the Software, in whole - or in part, and all derivative works of the Software, unless such - copies or derivative works are solely in the form of machine-executable - object code generated by a source language processor. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND - NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR - ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR - OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING - FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - OTHER DEALINGS IN THE SOFTWARE. - - 4. Licensee's use of the LLVM third party component is - subject to the following terms and conditions: - - ====================================================== - LLVM Release License - ====================================================== - University of Illinois/NCSA - Open Source License - - Copyright (c) 2003-2010 University of Illinois at Urbana-Champaign. - All rights reserved. - - Developed by: - - LLVM Team - - University of Illinois at Urbana-Champaign - - http://llvm.org - - Permission is hereby granted, free of charge, to any person obtaining a copy - of this software and associated documentation files (the "Software"), to - deal with the Software without restriction, including without limitation the - rights to use, copy, modify, merge, publish, distribute, sublicense, and/or - sell copies of the Software, and to permit persons to whom the Software is - furnished to do so, subject to the following conditions: - - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimers. - - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimers in the - documentation and/or other materials provided with the distribution. - - * Neither the names of the LLVM Team, University of Illinois at Urbana- - Champaign, nor the names of its contributors may be used to endorse or - promote products derived from this Software without specific prior - written permission. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR - IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, - FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL - THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR - OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, - ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER - DEALINGS WITH THE SOFTWARE. - - 5. Licensee's use of the PCRE third party component is - subject to the following terms and conditions: - - ------------ - PCRE LICENCE - ------------ - PCRE is a library of functions to support regular expressions whose syntax - and semantics are as close as possible to those of the Perl 5 language. - Release 8 of PCRE is distributed under the terms of the "BSD" licence, as - specified below. The documentation for PCRE, supplied in the "doc" - directory, is distributed under the same terms as the software itself. The - basic library functions are written in C and are freestanding. Also - included in the distribution is a set of C++ wrapper functions, and a just- - in-time compiler that can be used to optimize pattern matching. These are - both optional features that can be omitted when the library is built. - - THE BASIC LIBRARY FUNCTIONS - --------------------------- - Written by: Philip Hazel - Email local part: ph10 - Email domain: cam.ac.uk - University of Cambridge Computing Service, - Cambridge, England. - Copyright (c) 1997-2012 University of Cambridge - All rights reserved. - - PCRE JUST-IN-TIME COMPILATION SUPPORT - ------------------------------------- - Written by: Zoltan Herczeg - Email local part: hzmester - Emain domain: freemail.hu - Copyright(c) 2010-2012 Zoltan Herczeg - All rights reserved. - - STACK-LESS JUST-IN-TIME COMPILER - -------------------------------- - Written by: Zoltan Herczeg - Email local part: hzmester - Emain domain: freemail.hu - Copyright(c) 2009-2012 Zoltan Herczeg - All rights reserved. - - THE C++ WRAPPER FUNCTIONS - ------------------------- - Contributed by: Google Inc. - Copyright (c) 2007-2012, Google Inc. - All rights reserved. - - THE "BSD" LICENCE - ----------------- - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - - * Neither the name of the University of Cambridge nor the name of Google - Inc. nor the names of their contributors may be used to endorse or - promote products derived from this software without specific prior - written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" - AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE - IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE - ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE - LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR - CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF - SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS - INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN - CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) - ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE - POSSIBILITY OF SUCH DAMAGE. - - 6. Some of the cuBLAS library routines were written by or - derived from code written by Vasily Volkov and are subject - to the Modified Berkeley Software Distribution License as - follows: - - Copyright (c) 2007-2009, Regents of the University of California - - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - * Neither the name of the University of California, Berkeley nor - the names of its contributors may be used to endorse or promote - products derived from this software without specific prior - written permission. - - THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR - IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED - WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, - INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR - SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) - HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, - STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING - IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE - POSSIBILITY OF SUCH DAMAGE. - - 7. Some of the cuBLAS library routines were written by or - derived from code written by Davide Barbieri and are - subject to the Modified Berkeley Software Distribution - License as follows: - - Copyright (c) 2008-2009 Davide Barbieri @ University of Rome Tor Vergata. - - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - * The name of the author may not be used to endorse or promote - products derived from this software without specific prior - written permission. - - THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR - IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED - WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE - DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, - INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES - (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR - SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) - HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, - STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING - IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE - POSSIBILITY OF SUCH DAMAGE. - - 8. Some of the cuBLAS library routines were derived from - code developed by the University of Tennessee and are - subject to the Modified Berkeley Software Distribution - License as follows: - - Copyright (c) 2010 The University of Tennessee. - - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer listed in this license in the documentation and/or - other materials provided with the distribution. - * Neither the name of the copyright holders nor the names of its - contributors may be used to endorse or promote products derived - from this software without specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - 9. Some of the cuBLAS library routines were written by or - derived from code written by Jonathan Hogg and are subject - to the Modified Berkeley Software Distribution License as - follows: - - Copyright (c) 2012, The Science and Technology Facilities Council (STFC). - - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - * Neither the name of the STFC nor the names of its contributors - may be used to endorse or promote products derived from this - software without specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE STFC BE - LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR - CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF - SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR - BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, - WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE - OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN - IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - 10. Some of the cuBLAS library routines were written by or - derived from code written by Ahmad M. Abdelfattah, David - Keyes, and Hatem Ltaief, and are subject to the Apache - License, Version 2.0, as follows: - - -- (C) Copyright 2013 King Abdullah University of Science and Technology - Authors: - Ahmad Abdelfattah (ahmad.ahmad@kaust.edu.sa) - David Keyes (david.keyes@kaust.edu.sa) - Hatem Ltaief (hatem.ltaief@kaust.edu.sa) - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions - are met: - - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright - notice, this list of conditions and the following disclaimer in the - documentation and/or other materials provided with the distribution. - * Neither the name of the King Abdullah University of Science and - Technology nor the names of its contributors may be used to endorse - or promote products derived from this software without specific prior - written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE - - 11. Some of the cuSPARSE library routines were written by or - derived from code written by Li-Wen Chang and are subject - to the NCSA Open Source License as follows: - - Copyright (c) 2012, University of Illinois. - - All rights reserved. - - Developed by: IMPACT Group, University of Illinois, http://impact.crhc.illinois.edu - - Permission is hereby granted, free of charge, to any person obtaining - a copy of this software and associated documentation files (the - "Software"), to deal with the Software without restriction, including - without limitation the rights to use, copy, modify, merge, publish, - distribute, sublicense, and/or sell copies of the Software, and to - permit persons to whom the Software is furnished to do so, subject to - the following conditions: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimers in the documentation and/or other materials provided - with the distribution. - * Neither the names of IMPACT Group, University of Illinois, nor - the names of its contributors may be used to endorse or promote - products derived from this Software without specific prior - written permission. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND - NONINFRINGEMENT. IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT - HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER - IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR - IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE - SOFTWARE. - - 12. Some of the cuRAND library routines were written by or - derived from code written by Mutsuo Saito and Makoto - Matsumoto and are subject to the following license: - - Copyright (c) 2009, 2010 Mutsuo Saito, Makoto Matsumoto and Hiroshima - University. All rights reserved. - - Copyright (c) 2011 Mutsuo Saito, Makoto Matsumoto, Hiroshima - University and University of Tokyo. All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - * Neither the name of the Hiroshima University nor the names of - its contributors may be used to endorse or promote products - derived from this software without specific prior written - permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - 13. Some of the cuRAND library routines were derived from - code developed by D. E. Shaw Research and are subject to - the following license: - - Copyright 2010-2011, D. E. Shaw Research. - - All rights reserved. - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - * Redistributions of source code must retain the above copyright - notice, this list of conditions, and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions, and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - * Neither the name of D. E. Shaw Research nor the names of its - contributors may be used to endorse or promote products derived - from this software without specific prior written permission. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - 14. Licensee's use of the lz4 third party component is - subject to the following terms and conditions: - - Copyright (C) 2011-2013, Yann Collet. - BSD 2-Clause License (http://www.opensource.org/licenses/bsd-license.php) - - Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions are - met: - - * Redistributions of source code must retain the above copyright - notice, this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following disclaimer - in the documentation and/or other materials provided with the - distribution. - - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS - "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT - LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR - A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT - OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT - LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, - DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY - THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT - (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE - OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - - 15. The NPP library uses code from the Boost Math Toolkit, - and is subject to the following license: - - Boost Software License - Version 1.0 - August 17th, 2003 - . . . . - - Permission is hereby granted, free of charge, to any person or - organization obtaining a copy of the software and accompanying - documentation covered by this license (the "Software") to use, - reproduce, display, distribute, execute, and transmit the Software, - and to prepare derivative works of the Software, and to permit - third-parties to whom the Software is furnished to do so, all - subject to the following: - - The copyright notices in the Software and this entire statement, - including the above license grant, this restriction and the following - disclaimer, must be included in all copies of the Software, in whole - or in part, and all derivative works of the Software, unless such - copies or derivative works are solely in the form of machine-executable - object code generated by a source language processor. - - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, - EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF - MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND - NON-INFRINGEMENT. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR - ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE FOR ANY DAMAGES OR - OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE, ARISING - FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR - OTHER DEALINGS IN THE SOFTWARE. - - -2. NVIDIA Corporation CUDA Samples End User License Agreement -------------------------------------------------------------- - -BY DOWNLOADING THE SOFTWARE AND OTHER AVAILABLE MATERIALS, YOU -("DEVELOPER" or "LICENSEE") AGREE TO BE BOUND BY THE FOLLOWING -TERMS AND CONDITIONS OF THIS AGREEMENT. IF DEVELOPER DOES NOT -AGREE TO THE TERMS AND CONDITIONS OF THIS AGREEMENT, THEN DO -NOT DOWNLOAD THE SOFTWARE AND MATERIALS. - -The materials available for download to Developers may include -software in both sample source ("Source Code") and object code -("Object Code") versions, documentation ("Documentation"), -certain art work ("Art Assets") and other materials -(collectively, these materials referred to herein as -"Materials"). Except as expressly indicated herein, all terms -and conditions of this Agreement apply to all of the -Materials. - -Except as expressly set forth herein, NVIDIA owns all of the -Materials and makes them available to Developer only under the -terms and conditions set forth in this Agreement. - - -2.1. License - -Subject to the terms of this Agreement, NVIDIA hereby grants -to Developer a royalty-free, non-exclusive license to possess -and to use the Materials. Developer may install and use -multiple copies of the Materials on a shared computer or -concurrently on different computers, and make multiple back-up -copies of the Materials, solely for Licensee's use within -Licensee's Enterprise. "Enterprise" shall mean individual use -by Licensee or any legal entity (such as a corporation or -university) and the subsidiaries it owns by more than 50 -percent. - -The following terms apply to the specified type of Material. - - -2.1.1. Source Code - -Developer shall have the right to modify and create derivative -works with the Source Code. Developer shall own any derivative -works ("Derivatives") it creates to the Source Code, provided -that Developer uses the Materials in accordance with the terms -and conditions of this Agreement. Developer may distribute the -Derivatives, provided that all NVIDIA copyright notices and -trademarks are propagated and used properly and the -Derivatives include the following statement: "This software -contains source code provided by NVIDIA Corporation." - - -2.1.2. Object Code - -Developer agrees not to disassemble, decompile or reverse -engineer the Object Code versions of any of the Materials. -Developer acknowledges that certain of the Materials provided -in Object Code version may contain third party components that -may be subject to restrictions, and expressly agrees not to -attempt to modify or distribute such Materials without first -receiving consent from NVIDIA. - - -2.1.3. Art Assets - -Developer shall have the right to modify and create -Derivatives of the Art Assets, but may not distribute any of -the Art Assets or Derivatives created therefrom without -NVIDIA's prior written consent. - - -2.1.4. Additional Licensing Obligations - -Licensee acknowledges and agrees that its use of certain third -party components included with the SOFTWARE may be subject to -additional licensing terms and conditions as set forth or -referenced in Attachment C of this Agreement. - - -2.1.5. No Other License - -No rights or licenses with respect to any proprietary -information or patent, copyright, trade secret or other -intellectual property right owned or controlled by NVIDIA are -granted by NVIDIA to Developer under this Agreement, expressly -or by implication, except as expressly provided in this -Agreement. Licensee represents and warrants that any and all -third party licensing and/or royalty payment obligations in -connection with Licensee's use of the H.264 video codecs are -solely the responsibility of Licensee. - - -2.1.6. Intellectual Property Ownership - -All rights, title, interest and copyrights in and to the -Materials (including but not limited to all images, -photographs, animations, video, audio, music, text, and other -information incorporated into the Materials), are owned by -NVIDIA, or its suppliers. The Materials are protected by -copyright laws and international treaty provisions. -Accordingly, Developer is required to treat the Materials like -any other copyrighted material, except as otherwise allowed -pursuant to this Agreement. - - -2.2. Term of Agreement - -This Agreement is effective until (i) automatically terminated -if Developer fails to comply with any of the terms and -conditions of this Agreement; or (ii) terminated by NVIDIA. -NVIDIA may terminate this Agreement (and with it, all of -Developer's right to the Materials) immediately upon written -notice (which may include email) to Developer, with or without -cause. For the sake of clarity, Licensee may continue to use -the Derivatives created pursuant to this Agreement, after the -termination or expiration of this Agreement. - - -2.3. Defensive Suspension - -If Developer commences or participates in any legal proceeding -against NVIDIA, then NVIDIA may, in its sole discretion, -suspend or terminate all license grants and any other rights -provided under this Agreement during the pendency of such -legal proceedings. - - -2.4. No Support - -NVIDIA has no obligation to support or to continue providing -or updating any of the Materials. - - -2.5. No Warranty - -THE SOFTWARE AND ANY OTHER MATERIALS PROVIDED BY NVIDIA TO -DEVELOPER HEREUNDER ARE PROVIDED "AS IS." NVIDIA DISCLAIMS ALL -WARRANTIES, EXPRESS, IMPLIED OR STATUTORY, INCLUDING, WITHOUT -LIMITATION, THE IMPLIED WARRANTIES OF TITLE, MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. - - -2.6. Limitation of Liability - -NVIDIA SHALL NOT BE LIABLE TO DEVELOPER, DEVELOPER'S -CUSTOMERS, OR ANY OTHER PERSON OR ENTITY CLAIMING THROUGH OR -UNDER DEVELOPER FOR ANY LOSS OF PROFITS, INCOME, SAVINGS, OR -ANY OTHER CONSEQUENTIAL, INCIDENTAL, SPECIAL, PUNITIVE, DIRECT -OR INDIRECT DAMAGES (WHETHER IN AN ACTION IN CONTRACT, TORT OR -BASED ON A WARRANTY), EVEN IF NVIDIA HAS BEEN ADVISED OF THE -POSSIBILITY OF SUCH DAMAGES. THESE LIMITATIONS SHALL APPLY -NOTWITHSTANDING ANY FAILURE OF THE ESSENTIAL PURPOSE OF ANY -LIMITED REMEDY. IN NO EVENT SHALL NVIDIA'S AGGREGATE LIABILITY -TO DEVELOPER OR ANY OTHER PERSON OR ENTITY CLAIMING THROUGH OR -UNDER DEVELOPER EXCEED THE AMOUNT OF MONEY ACTUALLY PAID BY -DEVELOPER TO NVIDIA FOR THE SOFTWARE OR ANY OTHER MATERIALS. - - -2.7. Applicable Law - -This Agreement shall be deemed to have been made in, and shall -be construed pursuant to, the laws of the State of Delaware. -The United Nations Convention on Contracts for the -International Sale of Goods is specifically disclaimed. - - -2.8. Feedback - -Notwithstanding any Non-Disclosure Agreement executed by and -between the parties, the parties agree that in the event -Licensee or NVIDIA provides Feedback (as defined below) to the -other party on how to design, implement, or improve the -SOFTWARE or Licensee's product(s) for use with the SOFTWARE, -the following terms and conditions apply the Feedback: - - -2.8.1. Exchange of Feedback - -Both parties agree that neither party has an obligation to -give the other party any suggestions, comments or other -feedback, whether verbally or in written or source code form, -relating to (i) the SOFTWARE; (ii) Licensee's products; (iii) -Licensee's use of the SOFTWARE; or (iv) -optimization/interoperability of Licensee's product with the -SOFTWARE (collectively defined as "Feedback"). In the event -either party provides Feedback to the other party, the party -receiving the Feedback may use any Feedback that the other -party voluntarily provides to improve the (i) SOFTWARE or -other related NVIDIA technologies, respectively for the -benefit of NVIDIA; or (ii) Licensee's product or other related -Licensee technologies, respectively for the benefit of -Licensee. Accordingly, if either party provides Feedback to -the other party, both parties agree that the other party and -its respective licensees may freely use, reproduce, license, -distribute, and otherwise commercialize the Feedback in the -(i) SOFTWARE or other related technologies; or (ii) Licensee's -products or other related technologies, respectively, without -the payment of any royalties or fees. - - -2.8.2. Residual Rights - -Licensee agrees that NVIDIA shall be free to use any general -knowledge, skills and experience, (including, but not limited -to, ideas, concepts, know-how, or techniques) ("Residuals"), -contained in the (i) Feedback provided by Licensee to NVIDIA; -(ii) Licensee's products shared or disclosed to NVIDIA in -connection with the Feedback; or (c) Licensee's confidential -information voluntarily provided to NVIDIA in connection with -the Feedback, which are retained in the memories of NVIDIA's -employees, agents, or contractors who have had access to such -Residuals. Subject to the terms and conditions of this -Agreement, NVIDIA's employees, agents, or contractors shall -not be prevented from using Residuals as part of such -employee's, agent's or contractor's general knowledge, skills, -experience, talent, and/or expertise. NVIDIA shall not have -any obligation to limit or restrict the assignment of such -employees, agents or contractors or to pay royalties for any -work resulting from the use of Residuals. - - -2.8.3. Disclaimer of Warranty - -FEEDBACK FROM EITHER PARTY IS PROVIDED FOR THE OTHER PARTY'S -USE "AS IS" AND BOTH PARTIES DISCLAIM ALL WARRANTIES, EXPRESS, -IMPLIED AND STATUTORY INCLUDING, WITHOUT LIMITATION, THE -IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A -PARTICULAR PURPOSE, OR NONINFRINGEMENT. BOTH PARTIES DO NOT -REPRESENT OR WARRANT THAT THE FEEDBACK WILL MEET THE OTHER -PARTY'S REQUIREMENTS OR THAT THE OPERATION OR IMPLEMENTATION -OF THE FEEDBACK WILL BE UNINTERRUPTED OR ERROR-FREE. - - -2.8.4. No Liability for Consequential Damages - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT -SHALL EITHER PARTY OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, -INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER -(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS -PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, -OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR -INABILITY TO USE THE FEEDBACK, EVEN IF THE OTHER PARTY HAS -BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. - - -2.9. Freedom of Action - -Developer agrees that this Agreement is nonexclusive and -NVIDIA may currently or in the future be developing software, -other technology or confidential information internally, or -receiving confidential information from other parties that -maybe similar to the Feedback and Developer's confidential -information (as provided in subsection 2 above), which may be -provided to NVIDIA in connection with Feedback by Developer. -Accordingly, Developer agrees that nothing in this Agreement -will be construed as a representation or inference that NVIDIA -will not develop, design, manufacture, acquire, market -products, or have products developed, designed, manufactured, -acquired, or marketed for NVIDIA, that compete with the -Developer's products or confidential information. - - -2.10. Restricted Rights Notice - -Materials have been developed entirely at private expense and -is commercial computer software provided with RESTRICTED -RIGHTS. Use, duplication or disclosure by the U.S. Government -or a U.S. Government subcontractor is subject to the -restrictions set forth in the license agreement under which -Materials was obtained pursuant to DFARS 227.7202-3(a) or as -set forth in subparagraphs (c)(1) and (2) of the Commercial -Computer Software - Restricted Rights clause at FAR 52.227-19, -as applicable. Contractor/manufacturer is NVIDIA, 2701 San -Tomas Expressway, Santa Clara, CA 95050. - - -2.11. Miscellaneous - -If any provision of this Agreement is inconsistent with, or -cannot be fully enforced under, the law, such provision will -be construed as limited to the extent necessary to be -consistent with and fully enforceable under the law. This -Agreement is the final, complete and exclusive agreement -between the parties relating to the subject matter hereof, and -supersedes all prior or contemporaneous understandings and -agreements relating to such subject matter, whether oral or -written. This Agreement may only be modified in writing signed -by an authorized officer of NVIDIA. Developer agrees that it -will not ship, transfer or export the Materials into any -country, or use the Materials in any manner, prohibited by the -United States Bureau of Industry and Security or any export -laws, restrictions or regulations. - - -2.12. Attachment C - - -Additional Licensing Obligations - -Licensee's use of the "libfreeimage" third party component is -subject to the following terms and conditions: - -The contents of this file are subject to the FreeImage Public -License Version 1.0 (the "License"); you may not use this file -except in compliance with the License. You may obtain a copy -of the License at http://home.wxs.nl/~flvdberg/freeimage- -license.txt. - -Software distributed under the License is distributed on an -"AS IS" basis, WITHOUT WARRANTY OF ANY KIND, either express or -implied. See the License for the specific language governing -rights and limitations under the License. - - -3. NVIDIA Driver License for Customer Use of NVIDIA Software -on Windows ------------------------------------------------------------- - - -IMPORTANT NOTICE -- READ CAREFULLY: ------------------------------------ - -This License For Customer Use of NVIDIA Software ("LICENSE") -is the agreement which governs use of the software of NVIDIA -Corporation and its subsidiaries ("NVIDIA") downloadable -herefrom, including GeForce Experience, computer software -(including drivers downloaded in connection with GeForce -Experience) and associated printed materials ("SOFTWARE"). By -downloading, installing, copying, or otherwise using the -SOFTWARE, you agree to be bound by the terms of this LICENSE. -If you do not agree to the terms of this LICENSE, do not -download the SOFTWARE. - - -RECITALS: ---------- - -Use of NVIDIA's products requires three elements: the -SOFTWARE, the hardware on a graphics controller board, and a -personal computer (collectively, such hardware and personal -computer is defined herein as "CUSTOMER SYSTEM"). The SOFTWARE -is protected by copyright laws and international copyright -treaties, as well as other intellectual property laws and -treaties. The SOFTWARE is not sold, and instead is only -licensed for use, strictly in accordance with this document. -The hardware is protected by various patents, and is sold, but -this LICENSE does not cover that sale, since it may not -necessarily be sold as a package with the SOFTWARE. This -LICENSE sets forth the terms and conditions of the SOFTWARE -LICENSE only. - - -3.1. Definitions - - -3.1.1. Customer - -Customer means the entity or individual that downloads and/or -installs the SOFTWARE. - - -3.2. Grant of License - - -3.2.1. Rights and Limitations of Grant - -Provided Customer complies with the terms in this LICENSE, -NVIDIA hereby grants Customer the following non-exclusive, -non-transferable right to use the SOFTWARE in the manner and -for the purposes described in the associated printed -materials, with the following limitations: - - -3.2.1.1. Rights - -Customer may install and use multiple copies of the SOFTWARE -on a shared computer or concurrently on different computers, -and make multiple back-up copies of the SOFTWARE, solely for -Customer's use within Customer's Enterprise. "Enterprise" -shall mean individual use by Customer or any legal entity -(such as a corporation or university) and the subsidiaries it -owns by more than fifty percent (50%). - - -3.2.1.2. Limitations - -No Reverse Engineering - -Customer may not reverse engineer, decompile, or disassemble -the SOFTWARE, nor attempt in any other manner to obtain the -source code. You may not remove any copyright notices from the -SOFTWARE. The SOFTWARE is licensed as a single product. Its -component parts may not be separated for use on more than one -computer, nor otherwise used separately from the other parts. - -No Rental - -Customer may not rent or lease the SOFTWARE to someone else. - - -3.2.2. Additional Information - -7-Zip. The SOFTWARE includes the 7-Zip software program -("7-Zip"). Use of the source code for 7-Zip is subject to the -terms and conditions at www.7-zip.org. - - -3.3. Consent to Collection and Use of Information - -Customer hereby acknowledges that the SOFTWARE accesses and -collects non-personally identifiable information about -Customer and CUSTOMER SYSTEM as well as configures CUSTOMER -SYSTEM in order to (a) properly optimize such system for use -with the SOFTWARE, (b) deliver content through the SOFTWARE, -and (c) improve NVIDIA products and services. Information -collected by the SOFTWARE includes, but is not limited to, -CUSTOMER SYSTEM'S (a) hardware configuration and ID, (b) -operating system and driver configuration, (c) installed games -and applications, (d) games and applications settings, -performance, and usage data, and (e) usage metrics of the -SOFTWARE. To the extent that Customer uses the SOFTWARE, -Customer hereby consents to all of the foregoing, and -represents and warrants that Customer has the right to grant -such consent. In addition, Customer agrees that Customer is -solely responsible for maintaining appropriate data backups -and system restore points for CUSTOMER SYSTEM, and that NVIDIA -will have no responsibility for any damage or loss to CUSTOMER -SYSTEM (including loss of data or access) arising from or -relating to (a) any changes to the configuration, application -settings, environment variables, registry, drivers, BIOS, or -other attributes of CUSTOMER SYSTEM (or any part of CUSTOMER -SYSTEM) initiated through the SOFTWARE; or (b) installation of -any SOFTWARE or third party software patches initiated through -the SOFTWARE. The SOFTWARE may contain links to websites and -services. We encourage you to review the privacy statements on -those sites and services that you choose to visit so that you -can understand how they may collect, use and share your -personal information. NVIDIA is not responsible for the -privacy statements or practices of sites and services -controlled by other companies or organizations. - -Customer and CUSTOMER SYSTEM information collection rules can -be configured on the "Preferences" tab of GeForce Experience. -For more information on NVIDIA's collection and use of -information policies for this SOFTWARE, visit -http://www.geforce.com/drivers/geforce-experience/faq. - -Customer represents and warrants that the non-personally -identifiable information that Customer has furnished in -connection with its registration for the SOFTWARE is complete -and accurate. Customer also acknowledges that from time to -time, NVIDIA may collect, use, and disclose such information -about Customer and/or Customer's system in connection with the -SOFTWARE in accordance with NVIDIA's privacy policy, available -at URL http://www.nvidia.com/object/privacy_policy.html. - - -3.4. Termination - -This LICENSE will automatically terminate if Customer fails to -comply with any of the terms and conditions hereof. In such -event, Customer must destroy all copies of the SOFTWARE and -all of its component parts. - -Defensive Suspension. If Customer commences or participates in -any legal proceeding against NVIDIA, then NVIDIA may, in its -sole discretion, suspend or terminate all license grants and -any other rights provided under this LICENSE during the -pendency of such legal proceedings. - - -3.5. Copyright - -All title and copyrights in and to the SOFTWARE (including but -not limited to all images, photographs, animations, video, -audio, music, text, and other information incorporated into -the SOFTWARE), the accompanying printed materials, and any -copies of the SOFTWARE, are owned by NVIDIA, or its licensors -or suppliers. The SOFTWARE is protected by copyright laws and -international treaty provisions. Accordingly, Customer is -required to treat the SOFTWARE like any other copyrighted -material, except as otherwise allowed pursuant to this LICENSE -and that it may make one copy of the SOFTWARE solely for -backup or archive purposes. The algorithms, structure, -organization and source code of the Software are the valuable -trade secrets and confidential information of NVIDIA. Except -as otherwise expressly provided herein, neither this LICENSE -nor NVIDIA grants Customer any express or implied right under -any NVIDIA patents, copyrights, trademarks, or other -intellectual property rights in the SOFTWARE, and all rights, -title and interest in and to the SOFTWARE not expressly -granted are reserved by NVIDIA or its licensors or suppliers. - - -3.6. Applicable Law - -This LICENSE shall be deemed to have been made in, and shall -be construed pursuant to, the laws of the State of Delaware. -The United Nations Convention on Contracts for the -International Sale of Goods is specifically disclaimed. The -state and/or federal courts residing in Santa Clara County, -California shall have exclusive jurisdiction over any dispute -or claim arising out of this Agreement. Customer may not -export the SOFTWARE in violation of applicable export laws and -regulations. - - -3.7. Disclaimer of Warranties and Limitations on Liability - - -3.7.1. No Warranties - -THE SOFTWARE IS PROVIDED "AS IS" AND TO THE MAXIMUM EXTENT -PERMITTED BY APPLICABLE LAW, NVIDIA AND ITS SUPPLIERS DISCLAIM -ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT -LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY, -NONINFRINGEMENT, TITLE AND FITNESS FOR A PARTICULAR PURPOSE. -Without limiting the foregoing, you are solely responsible for -determining and verifying that the SOFTWARE that you obtain -and install is the appropriate version for your model of -graphics controller board, operating system, and computer -hardware. - - -3.7.2. No Liability for Consequential Damages - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT -SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY DIRECT, -SPECIAL, INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES -WHATSOEVER (INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF -BUSINESS PROFITS, LOSS OF DATA, BUSINESS INTERRUPTION, LOSS OF -BUSINESS INFORMATION, OR ANY OTHER PECUNIARY LOSS) ARISING OUT -OF THE USE OF OR INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA -HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. SOME -JURISDICTIONS PROHIBIT EXCLUSION OR LIMITATION OF LIABILITY -FOR IMPLIED WARRANTIES OR CONSEQUENTIAL OR INCIDENTAL DAMAGES, -SO THE ABOVE LIMITATION MAY NOT APPLY TO YOU. YOU MAY ALSO -HAVE OTHER LEGAL RIGHTS THAT VARY FROM JURISDICTION TO -JURISDICTION. NOTWITHSTANDING THE FOREGOING, NVIDIA'S -AGGREGATE LIABILITY ARISING OUT OF THIS LICENSE AGREEMENT -SHALL NOT EXCEED ONE THOUSAND UNITED STATES DOLLARS -(USD$1000). - - -3.8. Miscellaneous - -If any provision of this LICENSE is inconsistent with, or -cannot be fully enforced under, the law, such provision will -be construed as limited to the extent necessary to be -consistent with and fully enforceable under the law. This -LICENSE is the final, complete and exclusive agreement between -the parties relating to the subject matter hereof, and -supersedes all prior or contemporaneous understandings and -agreements relating to such subject matter, whether oral or -written. This LICENSE may only be modified in writing signed -by an authorized officer of NVIDIA. Customer agrees that it -will not ship, transfer or export the SOFTWARE into any -country, or use the SOFTWARE in any manner, prohibited by the -United States Bureau of Industry and Security or any export -laws, restrictions or regulations. - - -4. NVIDIA Driver License for Customer Use of NVIDIA Software -on Linux and Mac OSX ------------------------------------------------------------- - - -IMPORTANT NOTICE -- READ CAREFULLY: ------------------------------------ - -This License For Customer Use of NVIDIA Software ("LICENSE") -is the agreement which governs use of the software of NVIDIA -Corporation and its subsidiaries ("NVIDIA") downloadable -herefrom, including computer software and associated printed -materials ("SOFTWARE"). By downloading, installing, copying, -or otherwise using the SOFTWARE, you agree to be bound by the -terms of this LICENSE. If you do not agree to the terms of -this LICENSE, do not download the SOFTWARE. - - -RECITALS: ---------- - -Use of NVIDIA's products requires three elements: the -SOFTWARE, the hardware on a graphics controller board, and a -personal computer. The SOFTWARE is protected by copyright laws -and international copyright treaties, as well as other -intellectual property laws and treaties. The SOFTWARE is not -sold, and instead is only licensed for use, strictly in -accordance with this document. The hardware is protected by -various patents, and is sold, but this agreement does not -cover that sale, since it may not necessarily be sold as a -package with the SOFTWARE. This agreement sets forth the terms -and conditions of the SOFTWARE LICENSE only. - - -4.1. DEFINITIONS - - -4.1.1. Customer - -Customer means the entity or individual that downloads the -SOFTWARE. - - -4.2. GRANT OF LICENSE - - -4.2.1. Rights and Limitations of Grant - -NVIDIA hereby grants Customer the following non-exclusive, -non-transferable right to use the SOFTWARE, with the following -limitations: - - -4.2.1.1. Rights - -Customer may install and use multiple copies of the SOFTWARE -on a shared computer or concurrently on different computers, -and make multiple back-up copies of the SOFTWARE, solely for -Customer's use within Customer's Enterprise. "Enterprise" -shall mean individual use by Customer or any legal entity -(such as a corporation or university) and the subsidiaries it -owns by more than fifty percent (50%). - - -4.2.1.2. Linux/FreeBSD Exception - -Notwithstanding the foregoing terms of Section 4.2.1.1, -SOFTWARE designed exclusively for use on the Linux or FreeBSD -operating systems, or other operating systems derived from the -source code to these operating systems, may be copied and -redistributed, provided that the binary files thereof are not -modified in any way (except for unzipping of compressed -files). - - -4.2.1.3. Limitations - -No Reverse Engineering - -Customer may not reverse engineer, decompile, or disassemble -the SOFTWARE, nor attempt in any other manner to obtain the -source code. - -No Separation of Components - -The SOFTWARE is licensed as a single product. Its component -parts may not be separated for use on more than one computer, -nor otherwise used separately from the other parts. - -No Rental - -Customer may not rent or lease the SOFTWARE to someone else. - - -4.3. TERMINATION - -This LICENSE will automatically terminate if Customer fails to -comply with any of the terms and conditions hereof. In such -event, Customer must destroy all copies of the SOFTWARE and -all of its component parts. - -Defensive Suspension. If Customer commences or participates in -any legal proceeding against NVIDIA, then NVIDIA may, in its -sole discretion, suspend or terminate all license grants and -any other rights provided under this LICENSE during the -pendency of such legal proceedings. - - -4.4. COPYRIGHT - -All title and copyrights in and to the SOFTWARE (including but -not limited to all images, photographs, animations, video, -audio, music, text, and other information incorporated into -the SOFTWARE), the accompanying printed materials, and any -copies of the SOFTWARE, are owned by NVIDIA, or its suppliers. -The SOFTWARE is protected by copyright laws and international -treaty provisions. Accordingly, Customer is required to treat -the SOFTWARE like any other copyrighted material, except as -otherwise allowed pursuant to this LICENSE and that it may -make one copy of the SOFTWARE solely for backup or archive -purposes. - - -4.5. APPLICABLE LAW - -This agreement shall be deemed to have been made in, and shall -be construed pursuant to, the laws of the State of California. - - -4.6. DISCLAIMER OF WARRANTIES AND LIMITATION ON LIABILITY - - -4.6.1. No Warranties - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, THE -SOFTWARE IS PROVIDED "AS IS" AND NVIDIA AND ITS SUPPLIERS -DISCLAIM ALL WARRANTIES, EITHER EXPRESS OR IMPLIED, INCLUDING, -BUT NOT LIMITED TO, IMPLIED WARRANTIES OF MERCHANTABILITY AND -FITNESS FOR A PARTICULAR PURPOSE. - - -4.6.2. No Liability for Consequential Damages - -TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT -SHALL NVIDIA OR ITS SUPPLIERS BE LIABLE FOR ANY SPECIAL, -INCIDENTAL, INDIRECT, OR CONSEQUENTIAL DAMAGES WHATSOEVER -(INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF BUSINESS -PROFITS, BUSINESS INTERRUPTION, LOSS OF BUSINESS INFORMATION, -OR ANY OTHER PECUNIARY LOSS) ARISING OUT OF THE USE OF OR -INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED -OF THE POSSIBILITY OF SUCH DAMAGES. - - -4.7. MISCELLANEOUS - -The United Nations Convention on Contracts for the -International Sale of Goods is specifically disclaimed. If any -provision of this LICENSE is inconsistent with, or cannot be -fully enforced under, the law, such provision will be -construed as limited to the extent necessary to be consistent -with and fully enforceable under the law. This agreement is -the final, complete and exclusive agreement between the -parties relating to the subject matter hereof, and supersedes -all prior or contemporaneous understandings and agreements -relating to such subject matter, whether oral or written. -Customer agrees that it will not ship, transfer or export the -SOFTWARE into any country, or use the SOFTWARE in any manner, -prohibited by the United States Bureau of Export -Administration or any export laws, restrictions or -regulations. This LICENSE may only be modified in writing -signed by an authorized officer of NVIDIA. - - -5. NVIDIA Nsight Development Platform, Visual Studio Edition -Software License Agreement (Windows only) ------------------------------------------------------------- - - -IMPORTANT - READ BEFORE COPYING, INSTALLING OR USING ----------------------------------------------------- - -Do not use or load this software and any associated materials -provided by NVIDIA on its extranet (collectively the -"Software") until You have carefully read the following terms -and conditions. By loading or using the Software, You agree to -fully comply with the terms and conditions of this Software -License Agreement ("Agreement") by and between NVIDIA -Corporation, a Delaware corporation with its principal place -of business at 2701 San Tomas Expressway, Santa Clara, -California 95050 U.S.A. ("NVIDIA"), and You. If You do not -wish to so agree, do not install or use the Software. - -For the purposes of this Agreement: - -"Licensee," "You" and/or "Your" shall mean, collectively and -individually, Original Equipment Manufacturers, Independent -Hardware Vendors, Independent Software Vendors, and End-Users -of the Software pursuant to the terms and conditions of this -Agreement. - -"Intellectual Property Rights" shall mean all proprietary -rights, including all patents, trademarks, copyrights, -know-how, trade secrets, mask works, including all -applications and registrations thereto, and any other similar -protected rights in any country. - - -5.1. Grant of License - -NVIDIA agrees to provide the Software and any associated -materials pursuant to this Agreement. Subject to the terms of -this Agreement, NVIDIA grants to You a nonexclusive, -transferable, worldwide, revocable, limited, royalty-free, -fully paid-up license under NVIDIA's copyrights to install, -deploy, use, have used execute, reproduce, display, perform, -run, the object code of the Software, to create Your products -to interoperate with NVIDIA hardware and software. - -Unless otherwise authorized in the Agreement, You shall not -otherwise assign, sublicense, lease, or in any other way -transfer or disclose Software to any third party. Unless -otherwise authorized in the Agreement, You shall not reverse- -compile, disassemble, reverse-engineer, or in any manner -attempt to derive the source code of the Software from the -object code portions of the Software. - -Except as expressly stated in this Agreement, no license or -right is granted to You directly or by implication, -inducement, estoppels or otherwise. NVIDIA shall have the -right to inspect or have an independent auditor inspect Your -relevant records to verify Your compliance with the terms and -conditions of this Agreement. - - -5.2. Confidentiality - -If applicable, any exchange of Confidential Information (as -defined in the NDA) shall be made pursuant to the terms and -conditions of a separately signed Non-Disclosure Agreement -("NDA") by and between NVIDIA and You. For the sake of -clarity, You agree that (a) the Software; and (b) Your use of -the Software/participation in the Software's pre-production -release is considered Confidential Information of NVIDIA. - -If You wish to have a third party consultant or subcontractor -("Contractor") perform work on Your behalf which involves -access to or use of Software, You shall obtain a written -confidentiality agreement from the Contractor which contains -terms and obligations with respect to access to or use of -Software no less restrictive than those set forth in this -Agreement and excluding any distribution or sublicense rights, -and use for any other purpose than permitted in this -Agreement. Otherwise, You shall not disclose the terms or -existence of this Agreement or use NVIDIA's name in any -publications, advertisements, or other announcements without -NVIDIA's prior written consent. Unless otherwise provided in -this Agreement, You do not have any rights to use any NVIDIA -trademarks or logos. - - -5.3. Ownership of Software and Intellectual Property Rights - -All rights, title and interest to all copies of the Software -remain with NVIDIA, subsidiaries, licensors, or its suppliers. -The Software is copyrighted and protected by the laws of the -United States and other countries, and international treaty -provisions. You may not remove any copyright notices from the -Software. NVIDIA may make changes to the Software, or to items -referenced therein, at any time and without notice, but is not -obligated to support or update the Software. Except as -otherwise expressly provided, NVIDIA grants no express or -implied right under any NVIDIA patents, copyrights, -trademarks, or other intellectual property rights. - -You have no obligation to give NVIDIA any suggestions, -comments or other feedback ("Feedback") relating to the -Software. However, NVIDIA may use and include any Feedback -that You voluntarily provide to improve the Software or other -related NVIDIA technologies. Accordingly, if You provide -Feedback, You agree NVIDIA and its licensees may freely use, -reproduce, license, distribute, and otherwise commercialize -the Feedback in the Software or other related technologies -without the payment of any royalties or fees. You also agree -that the Software may collect application specific session -data and target device information that shall be sent to -NVIDIA, solely for use by NVIDIA in improving the Software. - - -5.4. No Warranties - -THE SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY EXPRESS OR -IMPLIED WARRANTY OF ANY KIND, INCLUDING WARRANTIES OF -MERCHANTABILITY, NONINFRINGEMENT, OR FITNESS FOR A PARTICULAR -PURPOSE. NVIDIA does not warrant or assume responsibility for -the accuracy or completeness of any information, text, -graphics, links or other items contained within the Software. -NVIDIA does not represent that errors or other defects will be -identified or corrected. - - -5.5. Limitation of Liability - -EXCEPT WITH RESPECT TO THE MISUSE OF THE OTHER PARTY'S -INTELLECTUAL PROPERTY OR DISCLOSURE OF THE OTHER PARTY'S -CONFIDENTIAL INFORMATION IN BREACH OF THIS AGREEMENT, IN NO -EVENT SHALL NVIDIA, SUBSIDIARIES, LICENSORS, OR ITS SUPPLIERS -BE LIABLE FOR ANY DAMAGES WHATSOEVER (INCLUDING, WITHOUT -LIMITATION, INDIRECT, LOST PROFITS, CONSEQUENTIAL, BUSINESS -INTERRUPTION OR LOST INFORMATION) ARISING OUT OF THE USE OF OR -INABILITY TO USE THE SOFTWARE, EVEN IF NVIDIA HAS BEEN ADVISED -OF THE POSSIBILITY OF SUCH DAMAGES. SOME JURISDICTIONS -PROHIBIT EXCLUSION OR LIMITATION OF LIABILITY FOR IMPLIED -WARRANTIES OR CONSEQUENTIAL OR INCIDENTAL DAMAGES, SO THE -ABOVE LIMITATION MAY NOT APPLY TO YOU. YOU MAY ALSO HAVE OTHER -LEGAL RIGHTS THAT VARY FROM JURISDICTION TO JURISDICTION. -NOTWITHSTANDING THE FOREGOING, NVIDIA'S AGGREGATE LIABILITY -ARISING OUT OF THIS AGREEMENT SHALL NOT EXCEED ONE HUNDRED -UNITED STATES DOLLARS (USD$100). - - -5.6. Term - -This Agreement and the licenses granted hereunder shall be -effective as of the date You install/download the Software -("Effective Date") and continue perpetually, unless terminated -earlier in accordance with the "Termination" provision of this -Agreement. - - -5.7. Termination - -NVIDIA may terminate this Agreement at any time if You violate -its terms. Upon termination, You will immediately destroy the -Software or return all copies of the Software to NVIDIA, and -certify to NVIDIA in writing that such actions have been -completed. - - -5.8. Miscellaneous - - -5.8.1. Survival - -Those provisions in this Agreement, which by their nature need -to survive the termination or expiration of this Agreement, -shall survive termination or expiration of the Agreement, -including but not limited to Section 5.2, Section 5.3, -Section 5.4, Section 5.5, Section 5.7, and Section 5.8. - - -5.8.2. Applicable Laws - -Claims arising under this Agreement shall be governed by the -laws of Delaware, excluding its principles of conflict of laws -and the United Nations Convention on Contracts for the Sale of -Goods. The state and/or federal courts residing in Santa Clara -County, California shall have exclusive jurisdiction over any -dispute or claim arising out of this Agreement. You may not -export the Software in violation of applicable export laws and -regulations. - - -5.8.3. Amendment - -The Agreement shall not be modified except by a written -agreement that names this Agreement and any provision to be -modified, is dated subsequent to the Effective Date, and is -signed by duly authorized representatives of both parties. - - -5.8.4. No Waiver - -No failure or delay on the part of either party in the -exercise of any right, power or remedy under this Agreement or -under law, or to insist upon or enforce performance by the -other party of any of the provisions of this Agreement or -under law, shall operate as a waiver thereof, nor shall any -single or partial exercise of any right, power or remedy -preclude other or further exercise thereof, or the exercise of -any other right, power or remedy; rather the provision, right, -or remedy shall be and remain in full force and effect. - - -5.8.5. No Assignment - -This Agreement and Licensee's rights and obligations herein, -may not be assigned, subcontracted, delegated, or otherwise -transferred by Licensee without NVIDIA's prior written -consent, and any attempted assignment, subcontract, -delegation, or transfer in violation of the foregoing will be -null and void. The terms of this Agreement shall be binding -upon Licensee's assignees. - - -5.8.6. Government Restricted Rights - -The parties acknowledge that the Software is subject to U.S. -export control laws and regulations. The parties agree to -comply with all applicable international and national laws -that apply to the Software, including the U.S. Export -Administration Regulations, as well as end-user, end-use and -destination restrictions issued by U.S. and other governments. - -The Software has been developed entirely at private expense -and is commercial computer software provided with RESTRICTED -RIGHTS. Use, duplication or disclosure of the Software by the -U.S. Government or a U.S. Government subcontractor is subject -to the restrictions set forth in the Agreement under which the -Software was obtained pursuant to DFARS 227.7202-3(a) or as -set forth in subparagraphs (c)(1) and (2) of the Commercial -Computer Software - Restricted Rights clause at FAR 52.227-19, -as applicable. Contractor/manufacturer is NVIDIA, 2701 San -Tomas Expressway, Santa Clara, CA 95050. Use of the Software -by the Government constitutes acknowledgment of NVIDIA's -proprietary rights therein. - - -5.8.7. Independent Contractors - -Licensee's relationship to NVIDIA is that of an independent -contractor, and neither party is an agent or partner of the -other. Licensee will not have, and will not represent to any -third party that it has, any authority to act on behalf of -NVIDIA. - - -5.8.8. Severability - -If for any reason a court of competent jurisdiction finds any -provision of this Agreement, or portion thereof, to be -unenforceable, that provision of the Agreement will be -enforced to the maximum extent permissible so as to affect the -intent of the parties, and the remainder of this Agreement -will continue in full force and effect. This Agreement has -been negotiated by the parties and their respective counsel -and will be interpreted fairly in accordance with its terms -and without any strict construction in favor of or against -either party. - - -5.8.9. Entire Agreement - -This Agreement and NDA constitute the entire agreement between -the parties with respect to the subject matter contemplated -herein, and merges all prior and contemporaneous -communications. - -MICROSOFT SOFTWARE LICENSE TERMS -MICROSOFT DIRECTX END USER RUNTIME - -These license terms are an agreement between Microsoft Corporation (or based on -where you live, one of its affiliates) and you. Please read them. They apply -to the software named above, which includes the media on which you received it, -if any. The terms also apply to any Microsoft - -* updates, -* supplements, -* Internet-based services, and -* support services - -for this software, unless other terms accompany those items. If so, those -terms apply. - -BY USING THE SOFTWARE, YOU ACCEPT THESE TERMS. IF YOU DO NOT ACCEPT THEM, DO -NOT USE THE SOFTWARE. - -If you comply with these license terms, you have the rights below. - -1. INSTALLATION AND USE RIGHTS. You may install and use any number of copies -of the software on your devices. - -2. SCOPE OF LICENSE. The software is licensed, not sold. This agreement only -gives you some rights to use the software. Microsoft reserves all other -rights. Unless applicable law gives you more rights despite this limitation, -you may use the software only as expressly permitted in this agreement. In -doing so, you must comply with any technical limitations in the software that -only allow you to use it in certain ways. You may not - -* work around any technical limitations in the software; -* reverse engineer, decompile or disassemble the software, except and only to - the extent that applicable law expressly permits, despite this limitation; -* make more copies of the software than specified in this agreement or allowed - by applicable law, despite this limitation; -* publish the software for others to copy; -* rent, lease or lend the software; -* transfer the software or this agreement to any third party; or -* use the software for commercial software hosting services. - -3. BACKUP COPY. You may make one backup copy of the software. You may use it -only to reinstall the software. - -4. DOCUMENTATION. Any person that has valid access to your computer or -internal network may copy and use the documentation for your internal, -reference purposes. - -5. EXPORT RESTRICTIONS. The software is subject to United States export laws -and regulations. You must comply with all domestic and international export -laws and regulations that apply to the software. These laws include -restrictions on destinations, end users and end use. For additional -information, see www.microsoft.com/exporting. - -6. SUPPORT SERVICES. Because this software is "as is," we may not provide -support services for it. - -7. ENTIRE AGREEMENT. This agreement, and the terms for supplements, updates, -Internet-based services and support services that you use, are the entire -agreement for the software and support services. - -8. APPLICABLE LAW. - -a. United States. If you acquired the software in the United States, -Washington state law governs the interpretation of this agreement and applies -to claims for breach of it, regardless of conflict of laws principles. The -laws of the state where you live govern all other claims, including claims -under state consumer protection laws, unfair competition laws, and in tort. - -b. Outside the United States. If you acquired the software in any other -country, the laws of that country apply. - -9. LEGAL EFFECT. This agreement describes certain legal rights. You may have -other rights under the laws of your country. You may also have rights with -respect to the party from whom you acquired the software. This agreement does -not change your rights under the laws of your country if the laws of your -country do not permit it to do so. - -10. DISCLAIMER OF WARRANTY. THE SOFTWARE IS LICENSED "AS-IS." YOU BEAR THE -RISK OF USING IT. MICROSOFT GIVES NO EXPRESS WARRANTIES, GUARANTEES OR -CONDITIONS. YOU MAY HAVE ADDITIONAL CONSUMER RIGHTS UNDER YOUR LOCAL LAWS -WHICH THIS AGREEMENT CANNOT CHANGE. TO THE EXTENT PERMITTED UNDER YOUR LOCAL -LAWS, MICROSOFT EXCLUDES THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR -A PARTICULAR PURPOSE AND NON-INFRINGEMENT. - -11. LIMITATION ON AND EXCLUSION OF REMEDIES AND DAMAGES. YOU CAN RECOVER FROM -MICROSOFT AND ITS SUPPLIERS ONLY DIRECT DAMAGES UP TO U.S. $5.00. YOU CANNOT -RECOVER ANY OTHER DAMAGES, INCLUDING CONSEQUENTIAL, LOST PROFITS, SPECIAL, -INDIRECT OR INCIDENTAL DAMAGES. - -This limitation applies to - -* anything related to the software, services, content (including code) on third - party Internet sites, or third party programs; and -* claims for breach of contract, breach of warranty, guarantee or condition, - strict liability, negligence, or other tort to the extent permitted by - applicable law. - -It also applies even if Microsoft knew or should have known about the -possibility of the damages. The above limitation or exclusion may not apply to -you because your country may not allow the exclusion or limitation of -incidental, consequential or other damages. - -The Software contains components, as listed below that are -licensed to Licensee pursuant to the terms and conditions of -their respective End User License Agreements: - - * NVIDIA CUDA Samples - - * NVIDIA CUDA Toolkit - - * NVIDIA DirectX SDK - -More information, including licensing information, about the -NVIDIA CUDA Toolkit and the NVIDIA CUDA Samples can be found -at: http://www.nvidia.com/getcuda - -More information, including licensing information, about the -NVIDIA DirectX SDK can be found at: -http://developer.nvidia.com/object/sdk_home.html - - -6. NVIDIA CUDA General Terms ----------------------------- - -The Software, on the Windows platform, may collect -non-personally identifiable information for the purposes of -customizing information delivered to you and improving future -versions of the Software. Such information, including IP -address and system configuration, will only be collected on an -anonymous basis and cannot be linked to any personally -identifiable information. Personally identifiable information -such as your username or hostname is not collected. - -------------------------------------------------------------- diff --git a/licenses/UPennState b/licenses/UPennState new file mode 100644 index 000000000..8d2c6b44f --- /dev/null +++ b/licenses/UPennState @@ -0,0 +1,7 @@ +Copyright (c) 2012 University of Pennsylvania + +Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/licenses/hoomd-blue b/licenses/hoomd-blue new file mode 100644 index 000000000..4e38f05d2 --- /dev/null +++ b/licenses/hoomd-blue @@ -0,0 +1,46 @@ +Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition +(HOOMD-blue) Open Source Software License Copyright 2009-2014 The Regents of +the University of Michigan All rights reserved. + +HOOMD-blue may contain modifications ("Contributions") provided, and to which +copyright is held, by various Contributors who have granted The Regents of the +University of Michigan the right to modify and/or distribute such Contributions. + +You may redistribute, use, and create derivate works of HOOMD-blue, in source +and binary forms, provided you abide by the following conditions: + +* Redistributions of source code must retain the above copyright notice, this +list of conditions, and the following disclaimer both in the code and +prominently in any materials provided with the distribution. + +* Redistributions in binary form must reproduce the above copyright notice, this +list of conditions, and the following disclaimer in the documentation and/or +other materials provided with the distribution. + +* All publications and presentations based on HOOMD-blue, including any reports +or published results obtained, in whole or in part, with HOOMD-blue, will +acknowledge its use according to the terms posted at the time of submission on: +http://codeblue.umich.edu/hoomd-blue/citations.html + +* Any electronic documents citing HOOMD-Blue will link to the HOOMD-Blue website: +http://codeblue.umich.edu/hoomd-blue/ + +* Apart from the above required attributions, neither the name of the copyright +holder nor the names of HOOMD-blue's contributors may be used to endorse or +promote products derived from this software without specific prior written +permission. + +Disclaimer + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER AND CONTRIBUTORS ``AS IS'' AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND/OR ANY +WARRANTIES THAT THIS SOFTWARE IS FREE OF INFRINGEMENT ARE DISCLAIMED. + +IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, +INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, +BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF +LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE +OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/licenses/newmat b/licenses/newmat new file mode 100644 index 000000000..e31b4f4c0 --- /dev/null +++ b/licenses/newmat @@ -0,0 +1,30 @@ +Copyright: + + Copyright (C) 1990-2006 Robert Davies + +Licence: + + I place no restrictions on the use of newmat except that I take + no liability for any problems that may arise from its use, + distribution or other dealings with it. + + You can use it in your commercial projects. + + You can make and distribute modified or merged versions. You can + include parts of it in your own software. + + If you distribute modified or merged versions, please make it + clear which parts are mine and which parts are modified. + + For a substantially modified version, simply note that it is, + in part, derived from my software. A comment in the code will + be sufficient. + + The software is provided "as is", without warranty of any kind. + + Please understand that there may still be bugs and errors. + + Use at your own risk. I (Robert Davies) take no responsibility + for any errors or omissions in this package or for any misfortune + that may befall you or others as a result of your use, + distribution or other dealings with it. diff --git a/licenses/polyphen b/licenses/polyphen new file mode 100644 index 000000000..250b86ed7 --- /dev/null +++ b/licenses/polyphen @@ -0,0 +1,7 @@ +The software provided herein is free for academic instruction and research +use only. Commercial licenses are available to legal entities, including +companies and organizations (both for-profit and non-profit), requiring the +software for general commercial use. To obtain a commercial license please, +contact us via e-mail. + +e-mail: iadzhubey@rics.bwh.harvard.edu
\ No newline at end of file diff --git a/media-gfx/brlcad/ChangeLog b/media-gfx/brlcad/ChangeLog index d513a937c..584b0bb1a 100644 --- a/media-gfx/brlcad/ChangeLog +++ b/media-gfx/brlcad/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/media-gfx/brlcad/ChangeLog,v 1.3 2011/04/18 22:47:37 dilfridge Exp $ + 21 May 2015; Dongxu Li <dongxuli2011@gmail.com> + brlcad-7.24.2.ebuild, brlcad-9999.ebuild: + Fixed deps tcl/tk slots + + 28 April 2015; Dongxu Li <dongxuli2011@gmail.com> + brlcad-7.24.2.ebuild, brlcad-9999.ebuild: + Fixed a deps issue + 4 July 2013; Dongxu Li <dongxuli2011@gmail.com> +brlcad-7.24.0.ebuild: Version bumped to 7.24.0 diff --git a/media-gfx/brlcad/Manifest b/media-gfx/brlcad/Manifest index cd637e6b3..d07c8bf1e 100644 --- a/media-gfx/brlcad/Manifest +++ b/media-gfx/brlcad/Manifest @@ -1,2 +1,3 @@ -DIST brlcad-7.20.4.tar.gz 70674938 SHA256 ee6210890f9f2115613b40dc25af95091dc700b5cc1ae390758a62b64854b65e SHA512 ac75675af04bfad444f66c0597aae6738883f49a92b775e1324d981968671adb8ac2a9aec921135498be84d4f6724741a2eeab7c3b3da64add2b20681f87dfdd WHIRLPOOL 8ba8093428c8aeb281538dd0a17c871dd8500affc118e524b0b12356d5dec082db3b136af7f80b524ad25fab6e49b3590dd9ef1f8e1310936ef106d53ee33a29 DIST brlcad-7.22.0.tar.gz 80633583 SHA256 4cc10161efbf9713c9b5810d259a039431096a37c95eb87b52f4ac669e16bcb1 SHA512 515df65cf0e6a7a2109309c05a31abfad80889a40236f79bf09fe92528cd35742be76a3074d3aa12320c8e85a32d35661af8c7e2acef0b2a2a588de885a0e30d WHIRLPOOL bb5f30edbaf9455330df69406b07ab955b0dfc5d1dffd44c9a94ab0cb0438c5d938d67caeeb2be75e38c88761f1036425881eb3a8cb872b514b1eb480c371bf7 +DIST brlcad-7.24.0.tar.gz 80060095 SHA256 31ddffd14674a9c570dc17af2dbce2b75542f2a9f5b2007efc01855bfaaf1240 SHA512 53c549173b95640125fa22ee7eec8a891c327bb1a8d3d046cc23a53a8e34d4a1b03c1729be30ad69aa9e28f05ec2880786d0a972707fa974e50ff227677b3b51 WHIRLPOOL e5777e5fca958ec02ed29630a7cbd1fd26aab210a5f4d99640d3c7496ee59ded4dd0c21940ce324bfb49c5b16b92436fb849384dca3c8cdb584105964d70167b +DIST brlcad-7.24.2.tar.gz 81355643 SHA256 6fe54268230a08aee29e1448802706ae00a3c3d1d8a9601954f28f560da3de26 SHA512 c0280bd55ad07c267fc77c643f8d687f91c7b193dc40d23fb6757d43378891121be762e07fdefeb621d72bcde0be42fb6a7ad67088446cf97df3ec299c86db88 WHIRLPOOL 80c1f7910ad126eb63def685adf12eddb7601ea7f3cef890ba75c4d4562e12c2ee9b38c28c9a470fdb65b881b8f3354af68c40a63da07bbc9356cd79a7499dec diff --git a/media-gfx/brlcad/brlcad-7.22.0.ebuild b/media-gfx/brlcad/brlcad-7.22.0.ebuild index 7eae12be3..b089f9d86 100644 --- a/media-gfx/brlcad/brlcad-7.22.0.ebuild +++ b/media-gfx/brlcad/brlcad-7.22.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit cmake-utils eutils java-pkg-2 flag-o-matic DESCRIPTION="Constructive solid geometry modeling system" @@ -14,12 +14,12 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="benchmarks debug doc examples java opengl smp" -RDEPEND="media-libs/libpng +RDEPEND="media-libs/libpng:0 sys-libs/zlib >=sci-libs/tnt-3 sci-libs/jama - <dev-lang/tcl-8.6 - <dev-lang/tk-8.6 + <dev-lang/tcl-8.6:0 + <dev-lang/tk-8.6:0 <dev-tcltk/itcl-4.0 <dev-tcltk/itk-4.0 dev-tcltk/iwidgets @@ -29,14 +29,14 @@ RDEPEND="media-libs/libpng media-libs/urt x11-libs/libXt x11-libs/libXi - java? ( >=virtual/jre-1.5 ) + java? ( >=virtual/jre-1.5:* ) " DEPEND="${RDEPEND} sys-devel/bison sys-devel/flex dev-tcltk/tktable - >=virtual/jre-1.5 + >=virtual/jre-1.5:* doc? ( dev-libs/libxslt app-doc/doxygen @@ -50,7 +50,6 @@ BRLCAD_DIR="${EPREFIX}/usr/${PN}" src_configure() { filter-flags -std=c++0x -append-ldflags $(no-as-needed) if use Debug; then CMAKE_BUILD_TYPE=Debug else diff --git a/media-gfx/brlcad/brlcad-7.20.4.ebuild b/media-gfx/brlcad/brlcad-7.24.0.ebuild index 39a6f491a..7f3a4393b 100644 --- a/media-gfx/brlcad/brlcad-7.20.4.ebuild +++ b/media-gfx/brlcad/brlcad-7.24.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit cmake-utils eutils java-pkg-2 flag-o-matic DESCRIPTION="Constructive solid geometry modeling system" @@ -14,14 +14,14 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="benchmarks debug doc examples java opengl smp" -RDEPEND="media-libs/libpng +RDEPEND="media-libs/libpng:0 sys-libs/zlib >=sci-libs/tnt-3 sci-libs/jama - >=dev-lang/tcl-8.5 - >=dev-lang/tk-8.5 - =dev-tcltk/itcl-3.4* - =dev-tcltk/itk-3.4* + <dev-lang/tcl-8.6:0 + <dev-lang/tk-8.6:0 + <dev-tcltk/itcl-4.0 + <dev-tcltk/itk-4.0 dev-tcltk/iwidgets dev-tcltk/tkimg dev-tcltk/tkpng @@ -29,14 +29,14 @@ RDEPEND="media-libs/libpng media-libs/urt x11-libs/libXt x11-libs/libXi - java? ( >=virtual/jre-1.5 ) + java? ( >=virtual/jre-1.5:* ) " DEPEND="${RDEPEND} sys-devel/bison sys-devel/flex dev-tcltk/tktable - >=virtual/jre-1.5 + >=virtual/jre-1.5:* doc? ( dev-libs/libxslt app-doc/doxygen @@ -44,13 +44,12 @@ DEPEND="${RDEPEND} BRLCAD_DIR="${EPREFIX}/usr/${PN}" -src_prepare() { - epatch "${FILESDIR}/${P}-cmake.patch" -} +#src_prepare() { +# epatch "${FILESDIR}/${P}-cmake.patch" +#} src_configure() { filter-flags -std=c++0x -append-ldflags $(no-as-needed) if use Debug; then CMAKE_BUILD_TYPE=Debug else @@ -58,12 +57,12 @@ append-ldflags $(no-as-needed) fi local mycmakeargs=( -DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}" - -DBRLCAD_ENABLE_STRICT=OFF - -DBRLCAD-ENABLE_STRICT=OFF - -DBRLCAD-ENABLE_COMPILER_WARNINGS=OFF + -DBRLCAD_ENABLE_STRICT=NO + -DBRLCAD-ENABLE_COMPILER_WARNINGS=NO + -DBRLCAD_BUNDLED_LIBS=ON -DBRLCAD_FLAGS_OPTIMIZATION=ON -DBRLCAD_ENABLE_X11=ON - -DBRLCAD_BUNDLED_LIBS=AUTO + -DCMAKE_BUILD_TYPE=Release ) # use flag triggered options diff --git a/media-gfx/brlcad/brlcad-7.24.2.ebuild b/media-gfx/brlcad/brlcad-7.24.2.ebuild new file mode 100644 index 000000000..86477a34c --- /dev/null +++ b/media-gfx/brlcad/brlcad-7.24.2.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 +inherit cmake-utils eutils java-pkg-2 flag-o-matic + +DESCRIPTION="Constructive solid geometry modeling system" +HOMEPAGE="http://brlcad.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2 BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="benchmarks debug doc examples java opengl smp" + +RDEPEND=" + java? ( + >=virtual/jre-1.5:* + ) + " + +DEPEND="${RDEPEND} + >=sci-libs/tnt-3 + sys-devel/bison + sys-devel/flex + media-libs/libpng:0 + <dev-lang/tcl-8.6:0/8.5 + <dev-lang/tk-8.6:0/8.5 + dev-tcltk/tktable + sys-libs/zlib + sys-libs/libtermcap-compat + media-libs/urt + x11-libs/libXt + x11-libs/libXi + java? ( + sci-libs/jama + >=virtual/jre-1.5:* + ) + doc? ( + dev-libs/libxslt + app-doc/doxygen + )" + +BRLCAD_DIR="${EPREFIX}/usr/${PN}" + +src_prepare() { + epatch "${FILESDIR}/${P}-cmake.patch" +} + +src_configure() { + append-cflags "-w" + if use debug; then + CMAKE_BUILD_TYPE=Debug + else + CMAKE_BUILD_TYPE=Release + fi + local mycmakeargs=( + -DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}" + -DBRLCAD_ENABLE_STRICT=NO + -DBRLCAD-ENABLE_COMPILER_WARNINGS=NO + -DBRLCAD_BUNDLED_LIBS=AUTO + -DBRLCAD_FLAGS_OPTIMIZATION=ON + -DBRLCAD_ENABLE_X11=ON + -DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON + ) + + # use flag triggered options + if use debug; then + mycmakeargs += "-DCMAKE_BUILD_TYPE=Debug" + else + mycmakeargs += "-DCMAKE_BUILD_TYPE=Release" + fi + mycmakeargs+=( + $(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL) +#experimental RTGL support +# $(cmake-utils_use opengl BRLCAD_ENABLE_RTGL) + $(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT) + $(cmake-utils_use smp BRLCAD_ENABLE_SMP) + $(cmake-utils_use java BRLCAD_ENABLE_RTSERVER) + $(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY) + $(cmake-utils_use doc BRLCAD_EXTRADOCS) + $(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF) + $(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN) + ) + cmake-utils_src_configure +} + +src_compile() { + cmake-utils_src_compile +} + +src_test() { + cmake-utils_src_test + emake check || die "emake check failed" + if use benchmarks; then + emake benchmark || die "emake benchmark failed" + fi +} + +src_install() { + cmake-utils_src_install + rm -f "${D}"usr/share/brlcad/{README,NEWS,AUTHORS,HACKING,INSTALL,COPYING} + dodoc AUTHORS NEWS README HACKING TODO BUGS ChangeLog + echo "PATH=\"${BRLCAD_DIR}/bin\"" > 99brlcad + echo "MANPATH=\"${BRLCAD_DIR}/man\"" >> 99brlcad + doenvd 99brlcad || die + newicon misc/macosx/Resources/ReadMe.rtfd/brlcad_logo_tiny.png brlcad.png + make_desktop_entry mged "BRL-CAD" brlcad "Graphics;Engineering" +} diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild index c829549d7..fb891d8f2 100644 --- a/media-gfx/brlcad/brlcad-9999.ebuild +++ b/media-gfx/brlcad/brlcad-9999.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit cmake-utils eutils subversion java-pkg-2 flag-o-matic DESCRIPTION="Constructive solid geometry modeling system" @@ -14,25 +14,29 @@ SLOT="0" KEYWORDS="" IUSE="benchmarks debug doc examples java opengl smp" -RDEPEND="media-libs/libpng - sys-libs/zlib - >=sci-libs/tnt-3 - sci-libs/jama - dev-tcltk/iwidgets - dev-tcltk/tkimg - dev-tcltk/tkpng - sys-libs/libtermcap-compat - media-libs/urt - x11-libs/libXt - x11-libs/libXi - java? ( >=virtual/jre-1.5 ) +RDEPEND=" + java? ( + >=virtual/jre-1.5:* + ) " DEPEND="${RDEPEND} + >=sci-libs/tnt-3 sys-devel/bison sys-devel/flex + media-libs/libpng:0 + <dev-lang/tcl-8.6:0/8.5 + <dev-lang/tk-8.6:0/8.5 dev-tcltk/tktable - >=virtual/jre-1.5 + sys-libs/zlib + sys-libs/libtermcap-compat + media-libs/urt + x11-libs/libXt + x11-libs/libXi + java? ( + sci-libs/jama + >=virtual/jre-1.5:* + ) doc? ( dev-libs/libxslt app-doc/doxygen @@ -41,20 +45,20 @@ DEPEND="${RDEPEND} BRLCAD_DIR="${EPREFIX}/usr/${PN}" src_configure() { -filter-flags -std=c++0x - append-ldflags $(no-as-needed) - if use Debug; then + append-cflags "-w" + if use debug; then CMAKE_BUILD_TYPE=Debug else CMAKE_BUILD_TYPE=Release fi local mycmakeargs=( -DCMAKE_INSTALL_PREFIX="${BRLCAD_DIR}" - -DBRLCAD_ENABLE_STRICT=OFF - -DBRLCAD_ENABLE_COMPILER_WARNINGS=OFF + -DBRLCAD_ENABLE_STRICT=NO + -DBRLCAD-ENABLE_COMPILER_WARNINGS=NO + -DBRLCAD_BUNDLED_LIBS=AUTO -DBRLCAD_FLAGS_OPTIMIZATION=ON -DBRLCAD_ENABLE_X11=ON - -DBRLCAD_BUNDLED_LIBS=ON + -DBRLCAD_ENABLE_VERBOSE_PROGRESS=ON ) # use flag triggered options @@ -66,16 +70,15 @@ filter-flags -std=c++0x mycmakeargs+=( $(cmake-utils_use opengl BRLCAD_ENABLE_OPENGL) #experimental RTGL support - # $(cmake-utils_use opengl BRLCAD_ENABLE_RTGL) +# $(cmake-utils_use opengl BRLCAD_ENABLE_RTGL) $(cmake-utils_use amd64 BRLCAD_ENABLE_64BIT) $(cmake-utils_use smp BRLCAD_ENABLE_SMP) - # $(cmake-utils_use java BRLCAD_ENABLE_RTSERVER) + $(cmake-utils_use java BRLCAD_ENABLE_RTSERVER) $(cmake-utils_use examples BRLCAD_INSTALL_EXAMPLE_GEOMETRY) $(cmake-utils_use doc BRLCAD_EXTRADOCS) $(cmake-utils_use doc BRLCAD_EXTRADOCS_PDF) $(cmake-utils_use doc BRLCAD_EXTRADOCS_MAN) - $(cmake-utils_use debug BRLCAD_ENABLE_VERBOSE_PROGRESS) - ) + ) cmake-utils_src_configure } diff --git a/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch b/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch new file mode 100644 index 000000000..52d423d75 --- /dev/null +++ b/media-gfx/brlcad/files/brlcad-7.24.2-cmake.patch @@ -0,0 +1,13 @@ +--- a/misc/CMake/BRLCAD_CMakeFiles.cmake 2015-04-27 12:18:13.159285916 -0400 ++++ b/misc/CMake/BRLCAD_CMakeFiles.cmake 2015-04-27 12:19:40.722856052 -0400 +@@ -82,6 +82,10 @@ + endif("${ITEM}" MATCHES "${TARGET_FLAG}") + endforeach(TARGET_FLAG ${FUZZY_TARGET_FLAGS}) + ++ if("${ITEM}" MATCHES "MODULE") ++ set(CMAKEFILES_DO_TEST 0) ++ endif("") ++ + # Handled target flags, proceeding with tests. + if(CMAKEFILES_DO_TEST) + get_filename_component(ITEM_PATH "${ITEM}" PATH) diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog index ed65ea18c..f1965b136 100644 --- a/media-gfx/librecad/ChangeLog +++ b/media-gfx/librecad/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header$ + 05 Apr 2015; Dongxu Li <dongxuli2011@gmail.com> + librecad-2.0.7.ebuild librecad-9999.ebuild: + fixed doc and appdata installation + 15 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> librecad-2.0.7.ebuild: Cleanup diff --git a/media-gfx/librecad/librecad-2.0.7.ebuild b/media-gfx/librecad/librecad-2.0.7.ebuild index 7c3dd80de..61c4be023 100644 --- a/media-gfx/librecad/librecad-2.0.7.ebuild +++ b/media-gfx/librecad/librecad-2.0.7.ebuild @@ -36,7 +36,9 @@ src_install() { use tools && dobin unix/ttf2lff insinto /usr/share/${PN} doins -r unix/resources/* - use doc && dohtml -r support/doc/* + use doc && dohtml -r librecad/support/doc/* + insinto /usr/share/appdata + doins unix/appdata/librecad.appdata.xml doicon librecad/res/main/"${PN}".png make_desktop_entry ${PN} LibreCAD ${PN} Graphics } diff --git a/media-gfx/librecad/librecad-9999.ebuild b/media-gfx/librecad/librecad-9999.ebuild index d226025f6..f2f67d376 100644 --- a/media-gfx/librecad/librecad-9999.ebuild +++ b/media-gfx/librecad/librecad-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -37,6 +37,8 @@ src_install() { insinto /usr/share/${PN} doins -r unix/resources/* use doc && dohtml -r librecad/support/doc/* + insinto /usr/share/appdata + doins unix/appdata/librecad.appdata.xml doicon librecad/res/main/${PN}.png make_desktop_entry ${PN} LibreCAD ${PN} Graphics } diff --git a/media-libs/OpenMOIV/ChangeLog b/media-libs/OpenMOIV/ChangeLog new file mode 100644 index 000000000..678a9616f --- /dev/null +++ b/media-libs/OpenMOIV/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for media-libs/OpenMOIV +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> OpenMOIV-1.0.3a.ebuild: + Bump to EAPI=5 diff --git a/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild index 8ef1a1c35..c54aa76a0 100644 --- a/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild +++ b/media-libs/OpenMOIV/OpenMOIV-1.0.3a.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=5 inherit cmake-utils @@ -14,11 +14,7 @@ LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~x86 ~amd64" -IUSE="" - -RDEPEND=" - media-libs/coin - " +RDEPEND="media-libs/coin" DEPEND="${RDEPEND}" S="${WORKDIR}/${PN}.src.${PV/a//}" @@ -35,8 +31,8 @@ src_configure() { src_install() { insinto "/usr/$(get_libdir)" - doins "${CMAKE_BUILD_DIR}/libChemKit2.so" || die "doins for libChemKit2 failed" + doins "${CMAKE_BUILD_DIR}/libChemKit2.so" insinto "/usr/include" - doins -r "${S}/include/ChemKit2" || die "include install failed" + doins -r "${S}/include/ChemKit2" } diff --git a/media-libs/libgfx/ChangeLog b/media-libs/libgfx/ChangeLog index ff0ba09c8..ba7f04767 100644 --- a/media-libs/libgfx/ChangeLog +++ b/media-libs/libgfx/ChangeLog @@ -1,10 +1,12 @@ -# ChangeLog for media-gfx/libgfx -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# ChangeLog for media-libs/libgfx +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> libgfx-1.1.0.ebuild: + Bump to EAPI=5; Cleanup + *libgfx-1.1.0 (17 May 2009) 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +files/1.1.0-gcc4.3.patch, +libgfx-1.1.0.ebuild, +metadata.xml: Initial setup - diff --git a/media-libs/libgfx/libgfx-1.1.0.ebuild b/media-libs/libgfx/libgfx-1.1.0.ebuild index 88260e60f..f4df99e08 100644 --- a/media-libs/libgfx/libgfx-1.1.0.ebuild +++ b/media-libs/libgfx/libgfx-1.1.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 inherit eutils @@ -13,24 +13,20 @@ SRC_URI="http://mgarland.org/dist/${P}.tar.gz" LICENSE="LGPL-2.1" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND}" src_prepare() { epatch "${FILESDIR}"/${PV}-gcc4.3.patch } src_compile() { - cd src - emake || die + cd src || die + emake } src_install() { - dolib.a src/*.a ||die + dolib.a src/*.a insinto /usr/include/ - doins include/gfx/gfx.h || die + doins include/gfx/gfx.h - dohtml doc/* || die + dohtml doc/* } diff --git a/net-libs/xrootd/ChangeLog b/net-libs/xrootd/ChangeLog deleted file mode 100644 index e2b9ca42e..000000000 --- a/net-libs/xrootd/ChangeLog +++ /dev/null @@ -1,122 +0,0 @@ -# ChangeLog for net-libs/xrootd -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/ChangeLog,v 1.19 2014/06/19 18:13:17 bicatali Exp $ - - 01 Dec 2014; Justin Lecher <jlec@gentoo.org> xrootd-4.0.4.ebuild, - metadata.xml: - Use PATCHES - -*xrootd-4.0.0 (19 Jun 2014) - - 19 Jun 2014; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-4.0.0.ebuild: - Version bump - - 11 Mar 2014; Patrick Lauer <patrick@gentoo.org> xrootd-3.3.6.ebuild: - Whitespace - -*xrootd-3.3.6 (10 Mar 2014) - - 10 Mar 2014; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.6.ebuild: - Version bump - - 20 Nov 2013; Patrick Lauer <patrick@gentoo.org> xrootd-3.3.4.ebuild: - Whitespace - -*xrootd-3.3.4 (19 Nov 2013) - - 19 Nov 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.4.ebuild, - -xrootd-3.3.1.ebuild, metadata.xml: - Version bump - -*xrootd-3.3.2 (04 Jun 2013) - - 04 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.2.ebuild, - -xrootd-3.2.7.ebuild, files/cmsd.initd, files/frm_purged.initd, - files/frm_xfrd.initd: - Version bump. Keyword amd64-linux and x86-linux. Fixed non-bashism in init - scripts - -*xrootd-3.3.1 (23 Mar 2013) - - 23 Mar 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.3.1.ebuild, - -xrootd-3.2.6.ebuild: - Version bump - -*xrootd-3.2.7 (24 Jan 2013) - - 24 Jan 2013; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.7.ebuild: - Version bump - - 05 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> xrootd-3.2.6.ebuild: - add user eclass - -*xrootd-3.2.6 (05 Dec 2012) - - 05 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.6.ebuild, - -xrootd-3.2.2.ebuild, -xrootd-3.2.4.ebuild, files/cmsd.initd, - files/frm_purged.initd, files/frm_xfrd.initd, files/xrootd.initd, - metadata.xml, xrootd-3.2.1.ebuild: - Version bump. Transfering checks on /var/run and /var/spool at install time to - run-time (bug #445882) - -*xrootd-3.2.4 (29 Sep 2012) - - 29 Sep 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.4.ebuild: - Version bump - - 24 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> - +files/xrootd-3.2.2-glibc216.patch, xrootd-3.2.2.ebuild: - fixed for glibc-2.16, bug #426300 - -*xrootd-3.2.2 (09 Jul 2012) - - 09 Jul 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.2.ebuild: - Version bump - - 09 Jul 2012; Justin Lecher <jlec@gentoo.org> -xrootd-3.1.0.ebuild, - -xrootd-3.1.1.ebuild, xrootd-3.2.1.ebuild, metadata.xml: - Cleaned old, add missing eclass - - 08 Jul 2012; Jeff Horelick <jdhore@gentoo.org> xrootd-3.2.1.ebuild: - marked x86 per bug 425054 - - 06 Jul 2012; Agostino Sarubbo <ago@gentoo.org> xrootd-3.2.1.ebuild: - Stable for amd64, wrt bug #425054 - -*xrootd-3.2.1 (22 May 2012) - - 22 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.2.1.ebuild: - Version bump - -*xrootd-3.1.1 (06 Mar 2012) - - 06 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.1.1.ebuild: - Version bump - - 19 Dec 2011; Sébastien Fabbro <bicatali@gentoo.org> +xrootd-3.1.0.ebuild, - +files/cmsd.confd, +files/cmsd.initd, +files/frm_purged.initd, - +files/frm_xfrd.initd, +files/xrootd.confd, +files/xrootd.initd, - +metadata.xml: - Initial import to the main tree - -*xrootd-3.1.0 (03 Dec 2011) - - 03 Dec 2011; Andrew Savchenko <bircoph@gmail.com> +xrootd-3.1.0.ebuild, - +files/cmsd.initd, +files/frm_purged.initd, +files/frm_xfrd.initd, - +files/xrootd.confd, +files/xrootd.initd, +metadata.xml: - XRootD isn't really a new program in this overlay. It was - previously bundled within sci-physics/root, but now it is unbundled - upstream and needs to be installed as a separate package in order - to be used from ROOT. - - Aside from standard xrootd distribution, this ebuild may install - useful pdf documentation from the official web site. - - Program was tested on ~x86 and ~amd64 with some basic setup, though - no real production tests were done. Please note, that xrootd and - accompany daemons do not work with root privileges any longer, so - special xrootd user was used. - - Another note: all daemons MUST use the same config (-c - /etc/xrootd/your._config), that's why there is only one conf.d file - for all four daemons. diff --git a/net-libs/xrootd/Manifest b/net-libs/xrootd/Manifest deleted file mode 100644 index 70f4531c3..000000000 --- a/net-libs/xrootd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xrootd-4.0.4.tar.gz 1920380 SHA256 17091c1de35b06fccc0acbf2f2084d697e3cebea09dc4056338da5e11458b5f7 SHA512 6419c6d70d2e481963b74a9f23808ca889530079dc6e8bc6aa47ff888b6cc5613a1c6702dd3fb86f6e416255206f9db14f9d775896feae6ba70907c666615a79 WHIRLPOOL 0f3422ebf254750d2ca9e122b0eb4f00bd802d378f3d520006b3772cd511ec385a79dced9e111b46ce4296a1ca339fc71425b0a5877385084f0870707b45664b diff --git a/net-libs/xrootd/files/cmsd.confd b/net-libs/xrootd/files/cmsd.confd deleted file mode 100644 index ab5aa8c61..000000000 --- a/net-libs/xrootd/files/cmsd.confd +++ /dev/null @@ -1,9 +0,0 @@ -# conf.d file for cmsd daemon - -# User to run as (default is root) -CMSD_USER="root" - -# -# Please refer to the cmsd(1) man(1) page for more -# information on command line parameters. -CMSD_OPTS="" diff --git a/net-libs/xrootd/files/cmsd.initd b/net-libs/xrootd/files/cmsd.initd deleted file mode 100644 index b04ca579c..000000000 --- a/net-libs/xrootd/files/cmsd.initd +++ /dev/null @@ -1,35 +0,0 @@ -#!/sbin/runscript -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/cmsd.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $ - -. /etc/conf.d/xrootd - -depend() { - need net - use logger dns - provide root-file-server -} - -start_pre() { - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd -} - -start() { - ebegin "Starting Cluster Management Service daemon" - start-stop-daemon --start --quiet --user ${XROOTD_USER} \ - --make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} --background -- \ - -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \ - ${CMSD_OPTS} - eend $? -} - -stop() { - ebegin "Stopping Cluster Management Service daemon" - start-stop-daemon --stop --quiet \ - --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} - eend $? -} diff --git a/net-libs/xrootd/files/frm_purged.initd b/net-libs/xrootd/files/frm_purged.initd deleted file mode 100644 index 1e95d5c8c..000000000 --- a/net-libs/xrootd/files/frm_purged.initd +++ /dev/null @@ -1,35 +0,0 @@ -#!/sbin/runscript -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/frm_purged.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $ - -. /etc/conf.d/xrootd - -depend() { - need net - use logger dns - provide root-file-server -} - -start_pre() { - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd -} - -start() { - ebegin "Starting File Residency Manager purge daemon" - start-stop-daemon --start --quiet --user ${XROOTD_USER} \ - --make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} --background -- \ - -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \ - ${FRM_PURGED_OPTS} - eend $? -} - -stop() { - ebegin "Stopping File Residency Manager purge daemon" - start-stop-daemon --stop --quiet \ - --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} - eend $? -} diff --git a/net-libs/xrootd/files/frm_xfrd.initd b/net-libs/xrootd/files/frm_xfrd.initd deleted file mode 100644 index 0b28f873a..000000000 --- a/net-libs/xrootd/files/frm_xfrd.initd +++ /dev/null @@ -1,35 +0,0 @@ -#!/sbin/runscript -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/frm_xfrd.initd,v 1.3 2013/06/04 15:51:34 bicatali Exp $ - -. /etc/conf.d/xrootd - -depend() { - need net - use logger dns - provide root-file-server -} - -start_pre() { - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd -} - -start() { - ebegin "Starting File Residency Manager transfer daemon" - start-stop-daemon --start --quiet --user ${XROOTD_USER} \ - --make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} --background -- \ - -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \ - ${FRM_XFRD_OPTS} - eend $? -} - -stop() { - ebegin "Stopping File Residency Manager transfer daemon" - start-stop-daemon --stop --quiet \ - --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} - eend $? -} diff --git a/net-libs/xrootd/files/xrootd-no-werror.patch b/net-libs/xrootd/files/xrootd-no-werror.patch deleted file mode 100644 index d9f3b1c52..000000000 --- a/net-libs/xrootd/files/xrootd-no-werror.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- cmake/XRootDOSDefs.cmake.orig 2014-06-04 20:31:15.000000000 +0400 -+++ cmake/XRootDOSDefs.cmake 2014-08-21 12:12:55.397368485 +0400 -@@ -15,7 +15,7 @@ - # GCC - #------------------------------------------------------------------------------- - if( CMAKE_COMPILER_IS_GNUCXX ) -- set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -Werror" ) -+ set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra" ) - set( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-parameter" ) - # gcc 4.1 is retarded - execute_process( COMMAND ${CMAKE_C_COMPILER} -dumpversion diff --git a/net-libs/xrootd/files/xrootd.confd b/net-libs/xrootd/files/xrootd.confd deleted file mode 100644 index 0e847e53e..000000000 --- a/net-libs/xrootd/files/xrootd.confd +++ /dev/null @@ -1,21 +0,0 @@ -# conf.d file for xroot, cmsd, frm_purged, frm_xfrd daemons - -# User to run as, please note that: -# 1) daemons will refuse to run as root; -# 2) several dirs must be created with an appropriate permissions -# and ownership, so be careful when changing default 'xrootd' user. -XROOTD_USER="xrootd" - -# Configuration file MUST be the same for all four daemons. -# See /etc/xrootd for available simple defaults. -XROOTD_CONF="/etc/xrootd/xrootd-clustered.cfg" - -# Logdir for all daemons -XROOTD_LOGDIR="/var/log/xrootd" - -# Additional options for each daemon, please refer to their -# documentation for details -XROOTD_OPTS="" -CMSD_OPTS="" -FRM_PURGED="" -FRM_XFRD="" diff --git a/net-libs/xrootd/files/xrootd.initd b/net-libs/xrootd/files/xrootd.initd deleted file mode 100644 index 1685ccc5c..000000000 --- a/net-libs/xrootd/files/xrootd.initd +++ /dev/null @@ -1,33 +0,0 @@ -#!/sbin/runscript -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/files/xrootd.initd,v 1.2 2012/12/05 18:19:15 bicatali Exp $ - -depend() { - need net - use logger dns - provide root-file-server -} - -start_pre() { - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/spool - checkpath -q -d -m 0755 -o xrootd:xrootd /var/run/xrootd -} - -start() { - ebegin "Starting extended ROOTD file server" - start-stop-daemon --start --quiet --user ${XROOTD_USER} \ - --make-pidfile --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} --background -- \ - -c ${XROOTD_CONF} -l ${XROOTD_LOGDIR}/${RC_SVCNAME}.log \ - ${XROOTD_OPTS} - eend $? -} - -stop() { - ebegin "Stopping extended ROOTD file server" - start-stop-daemon --stop --quiet \ - --pidfile /var/run/${RC_SVCNAME}.pid \ - --exec /usr/bin/${RC_SVCNAME} - eend $? -} diff --git a/net-libs/xrootd/metadata.xml b/net-libs/xrootd/metadata.xml deleted file mode 100644 index 46f42a0f9..000000000 --- a/net-libs/xrootd/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-physics</herd> - <longdescription lang="en"> - XROOTD software framework is a fully generic suite for fast, low latency - and scalable data access, which can serve natively any kind of data, - organized as a hierarchical filesystem-like namespace, based on the - concept of directory. - It is usually used with <pkg>sci-physics/root</pkg> and its PROOF - facilities for cluster computing in high energy physics. -</longdescription> - <use> - <flag name="fuse">Enable the <pkg>sys-fs/fuse</pkg> filesystem driver</flag> - </use> -</pkgmetadata> diff --git a/net-libs/xrootd/xrootd-4.0.4.ebuild b/net-libs/xrootd/xrootd-4.0.4.ebuild deleted file mode 100644 index ff9f9b11a..000000000 --- a/net-libs/xrootd/xrootd-4.0.4.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/net-libs/xrootd/xrootd-4.0.0.ebuild,v 1.1 2014/06/19 18:13:17 bicatali Exp $ - -EAPI=5 - -inherit cmake-utils eutils user multilib - -DURI="http://xrootd.slac.stanford.edu/doc/prod" - -DESCRIPTION="Extended ROOT remote file server" -HOMEPAGE="http://xrootd.org/" -SRC_URI="${HOMEPAGE}/download/v${PV}/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc fuse kerberos perl readline ssl test" - -RDEPEND=" - !<sci-physics/root-5.32[xrootd] - sys-libs/zlib:0= - fuse? ( sys-fs/fuse:0= ) - kerberos? ( virtual/krb5 ) - perl? ( - dev-lang/perl - readline? ( dev-perl/Term-ReadLine-Perl ) - ) - readline? ( sys-libs/readline:0= ) - ssl? ( dev-libs/openssl:0= )" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen[dot] ) - perl? ( dev-lang/swig ) - test? ( dev-util/cppunit )" - -pkg_setup() { - enewgroup xrootd - enewuser xrootd -1 -1 "${EPREFIX}"/var/spool/xrootd xrootd -} - -PATCHES=( "${FILESDIR}"/${PN}-no-werror.patch ) - -src_configure() { - local mycmakeargs=( - $(cmake-utils_use_enable fuse) - $(cmake-utils_use_enable kerberos KRB5) - $(cmake-utils_use_enable perl) - $(cmake-utils_use_enable readline) - $(cmake-utils_use_enable ssl CRYPTO) - $(cmake-utils_use_enable test TESTS) - ) - cmake-utils_src_configure -} - -src_compile() { - cmake-utils_src_compile - use doc && doxygen Doxyfile -} - -src_install() { - cmake-utils_src_install - - # base configs - insinto /etc/xrootd - doins packaging/common/*.cfg - - fowners root:xrootd /etc/xrootd - keepdir /var/log/xrootd - fowners xrootd:xrootd /var/log/xrootd - - local i - for i in cmsd frm_purged frm_xfrd xrootd; do - newinitd "${FILESDIR}"/${i}.initd ${i} - done - # all daemons MUST use single master config file - newconfd "${FILESDIR}"/xrootd.confd xrootd - - dodoc docs/ReleaseNotes.txt - use doc && dohtml -r doxydoc/html/* -} diff --git a/profiles/categories b/profiles/categories index 609bef2c6..20ed0d65e 100644 --- a/profiles/categories +++ b/profiles/categories @@ -1,7 +1,6 @@ app-admin app-benchmarks app-doc -app-editors app-forensics app-portage app-text @@ -10,7 +9,6 @@ dev-cpp dev-java dev-lang dev-libs -dev-lua dev-ml dev-perl dev-python @@ -21,7 +19,6 @@ media-gfx media-libs net-firewall net-ftp -net-libs net-misc perl-core sci-astronomy @@ -34,11 +31,9 @@ sci-mathematics sci-misc sci-physics sci-visualization -sys-apps sys-cluster sys-devel sys-infiniband -sys-process virtual x11-libs x11-misc diff --git a/profiles/license_groups b/profiles/license_groups index a2ba71db5..86a807021 100644 --- a/profiles/license_groups +++ b/profiles/license_groups @@ -1 +1 @@ -EULA ACML-EULA NVIDIA-gdk +EULA ACML-EULA AMD-APPSDK NVIDIA-gdk diff --git a/sci-astronomy/bpz/bpz-1.99.3.ebuild b/sci-astronomy/bpz/bpz-1.99.3.ebuild index dffbf71c4..d857d3d78 100644 --- a/sci-astronomy/bpz/bpz-1.99.3.ebuild +++ b/sci-astronomy/bpz/bpz-1.99.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-single-r1 diff --git a/sci-astronomy/chealpix/ChangeLog b/sci-astronomy/chealpix/ChangeLog index 538bc3f08..5934ac20f 100644 --- a/sci-astronomy/chealpix/ChangeLog +++ b/sci-astronomy/chealpix/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/chealpix -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/chealpix: Updating remote-id in metadata.xml + *chealpix-3.11.2 (03 Feb 2014) 03 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> +chealpix-3.11.2.ebuild, diff --git a/sci-astronomy/chealpix/metadata.xml b/sci-astronomy/chealpix/metadata.xml index de81d6067..4a26a0dc1 100644 --- a/sci-astronomy/chealpix/metadata.xml +++ b/sci-astronomy/chealpix/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the C library. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/healpix_cxx/ChangeLog b/sci-astronomy/healpix_cxx/ChangeLog index 1e48b7415..72dc0ac7a 100644 --- a/sci-astronomy/healpix_cxx/ChangeLog +++ b/sci-astronomy/healpix_cxx/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/healpix_cxx -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/healpix_cxx: Updating remote-id in metadata.xml + *healpix_cxx-3.11.2 (03 Feb 2014) 03 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> diff --git a/sci-astronomy/healpix_cxx/metadata.xml b/sci-astronomy/healpix_cxx/metadata.xml index 391b83cad..fee3b68d3 100644 --- a/sci-astronomy/healpix_cxx/metadata.xml +++ b/sci-astronomy/healpix_cxx/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the C++ library and programs. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/healpix_idl/ChangeLog b/sci-astronomy/healpix_idl/ChangeLog index e12f4a5bc..969ed48d4 100644 --- a/sci-astronomy/healpix_idl/ChangeLog +++ b/sci-astronomy/healpix_idl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-astronomy/healpix_idl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/healpix_idl: Updating remote-id in metadata.xml + *healpix_idl-3.11 (16 Jun 2013) 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +healpix_idl-3.11.ebuild, diff --git a/sci-astronomy/healpix_idl/metadata.xml b/sci-astronomy/healpix_idl/metadata.xml index 020cd30c0..4f8d241a1 100644 --- a/sci-astronomy/healpix_idl/metadata.xml +++ b/sci-astronomy/healpix_idl/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-astronomy</herd> -<longdescription lang="en"> + <herd>sci-astronomy</herd> + <longdescription lang="en"> HEALPix is an acronym for Hierarchical Equal Area isoLatitude Pixelization of a sphere. As suggested in the name, this pixelization produces a subdivision of a spherical surface in which each pixel covers the same surface area as every other pixel. This package contains the IDL/GDL routines and plots. </longdescription> + <upstream> + <remote-id type="sourceforge">healpix_idl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-astronomy/libthesky/ChangeLog b/sci-astronomy/libthesky/ChangeLog new file mode 100644 index 000000000..a274b210d --- /dev/null +++ b/sci-astronomy/libthesky/ChangeLog @@ -0,0 +1,57 @@ +# ChangeLog for sci-astronomy/libthesky +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-astronomy/libthesky: Updating remote-id in metadata.xml + + 09 May 2015; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.3.2.ebuild, + +metadata.xml: + Moved ebuild to Science overlay + + 09 May 2015; AstroFloyd <AstroFloyd@gmail.com> libthesky-0.3.2.ebuild: + Cleaned up ebuild + +*libthesky-0.3.2 (26 Apr 2015) + + 26 Apr 2015; AstroFloyd <AstroFloyd@gmail.com> -libthesky-0.3.0.ebuild + +libthesky-0.3.2.ebuild: + Version bump + +*libthesky-0.3.1 (04 Apr 2015) +*libthesky-0.3.0 (04 Apr 2015) + + 04 Apr 2015; AstroFloyd <AstroFloyd@gmail.com> -libthesky-0.0.1.ebuild, + -libthesky-0.0.2.ebuild, -libthesky-0.0.2-r1.ebuild, -libthesky-0.0.3.ebuild, + -libthesky-0.1.0.ebuild, +libthesky-0.3.0.ebuild, +libthesky-0.3.1.ebuild: + Version bump + +*libthesky-0.2.0 (20 Oct 2013) + + 20 Oct 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.2.0.ebuild: + Version bump + +*libthesky-0.1.0 (31 Aug 2013) + + 31 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.1.0.ebuild: + Version bump + +*libthesky-0.0.3 (31 Aug 2013) + + 31 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.0.3.ebuild: + Version bump + +*libthesky-0.0.2-r1 (26 Aug 2013) + + 26 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.0.2-r1.ebuild: + Revision bump: adding asteroids.dat in separate download + +*libthesky-0.0.2 (26 Aug 2013) + + 26 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.0.2.ebuild: + Version bump + +*libthesky-0.0.1 (26 Aug 2013) + + 26 Aug 2013; AstroFloyd <AstroFloyd@gmail.com> +libthesky-0.0.1.ebuild, + +metadata.xml: diff --git a/sci-astronomy/libthesky/Manifest b/sci-astronomy/libthesky/Manifest new file mode 100644 index 000000000..53c596e00 --- /dev/null +++ b/sci-astronomy/libthesky/Manifest @@ -0,0 +1,2 @@ +DIST libthesky-0.3.2.tar.gz 124598 SHA256 38d05a11cc22991cc85438321d54b5e27b0bb5264822df991a53b751ee5a06ae SHA512 64fae18cf410c37d6bda5d65f8890a045734fa3bbaa23c76a8080ef06e15443af5159baf779b69594e24bb1fc8b0719ba03174764d46abed66f61750e8e9e68e WHIRLPOOL 3fee9a059a5122efb50b26cefdd15fa1ef6ac8b27df47e4a6d077d70dbf68db635e7bc975f9a256791e1ac622af75a44f9de30d152fae05f111c0d0d30110f7e +DIST libthesky-data-20131020.tar.bz2 3945800 SHA256 110fc72b68c44f6be5d71fa3076ff1b54ebec72079d854d52e60df4ac0c1e18b SHA512 2bbc2eaeb37a52f383625ecbb0c8d455741631b8cf212e5b8839a9d4276ca8bfc638087aca6d94a458e2889e8e0b9a37cd0392828fe24fb1f653d5956c27b27d WHIRLPOOL 5c2c540c718541f7b4f777d4432a17657c4262cd54e6fdc02b267e598122e558715a170f31285306180117056a037ba9facf296491ad20fd8cdf94c6f59cc627 diff --git a/sci-astronomy/libthesky/libthesky-0.3.2.ebuild b/sci-astronomy/libthesky/libthesky-0.3.2.ebuild new file mode 100644 index 000000000..3bf556b85 --- /dev/null +++ b/sci-astronomy/libthesky/libthesky-0.3.2.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils fortran-2 + +DESCRIPTION="Fortran library to compute positions of celestial bodies" +HOMEPAGE="http://libthesky.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz +mirror://sourceforge/${PN}/libthesky-data-20131020.tar.bz2" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=">=sci-libs/libsufr-0.5.4" +RDEPEND="${DEPEND}" + +src_configure() { + mycmakeargs=( + $(cmake-utils_use static-libs CREATE_STATICLIB) + ) + cmake-utils_src_configure +} + +# Install the data files as well as the libraries: +src_install() { + insinto /usr/share/libTheSky + doins "${WORKDIR}"/data/* + cmake-utils_src_install +} + +DOCS="CHANGELOG README VERSION" diff --git a/sci-astronomy/libthesky/metadata.xml b/sci-astronomy/libthesky/metadata.xml new file mode 100644 index 000000000..b27321594 --- /dev/null +++ b/sci-astronomy/libthesky/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-astronomy</herd> + <maintainer> + <email>AstroFloyd@gmail.com</email> + <name>AstroFloyd</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">libthesky</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild b/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild index 7650296f1..b2aa19227 100644 --- a/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild +++ b/sci-astronomy/mosstack/mosstack-0.6.1-r1.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{3_2,3_3} ) +PYTHON_COMPAT=( python3_3 ) inherit distutils-r1 diff --git a/sci-astronomy/mosstack/mosstack-0.6.1.ebuild b/sci-astronomy/mosstack/mosstack-0.6.1.ebuild index c589368b0..08ceeb874 100644 --- a/sci-astronomy/mosstack/mosstack-0.6.1.ebuild +++ b/sci-astronomy/mosstack/mosstack-0.6.1.ebuild @@ -3,7 +3,7 @@ # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{3_2,3_3} ) +PYTHON_COMPAT=( python3_3 ) inherit distutils-r1 diff --git a/sci-biology/AlignGraph/AlignGraph-9999.ebuild b/sci-biology/AlignGraph/AlignGraph-9999.ebuild new file mode 100644 index 000000000..b7e28666a --- /dev/null +++ b/sci-biology/AlignGraph/AlignGraph-9999.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +if [ "$PV" == "9999" ]; then + inherit git-r3 +fi + +DESCRIPTION="Asssemble contigs/scaffolds using related reference sequence" +HOMEPAGE="https://github.com/baoe/AlignGraph + http://bioinformatics.oxfordjournals.org/content/30/12/i319.long" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/baoe/AlignGraph.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="Artistic-2" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/blat + sci-biology/bowtie" + +# AlignGraph runs the alignment steps with BLAT and Bowtie2 automatically, but both +# need to be installed on the system. AlignGraph’s run time is currently 23–57 min +# per million aligned reads. In the performance tests of this study, the memory usage +# was 36–50 GB, and it stays <100 GB even for entire mammalian genomes. These requirements +# are more moderate than those of most de novo assemblers (Luo et al., 2012). + +# 8 threads are hardcoded. Currently users cannot make changes to this, since this is +# a moderate choice for either single CPU machines (overhead for parallelization would +# not be too large) or multiple CPU machines. Another reason is, the bottleneck for the +# runtime is usually from BLAT, no matter how many threads there are for Bowtie2. +src_compile(){ + cd AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o AlignGraph AlignGraph.cpp -lpthread + cd ../Eval-AlignGraph || die + $(tc-getCXX) ${CXXFLAGS} -o Eval-AlignGraph Eval-AlignGraph.cpp -lpthread +} + +src_install(){ + dobin AlignGraph/AlignGraph Eval-AlignGraph/Eval-AlignGraph + dodoc README.md +} diff --git a/sci-biology/AlignGraph/ChangeLog b/sci-biology/AlignGraph/ChangeLog new file mode 100644 index 000000000..d1a50d2ba --- /dev/null +++ b/sci-biology/AlignGraph/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/AlignGraph +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/AlignGraph: Add github to remote-id in metadata.xml + +*AlignGraph-9999 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +AlignGraph-9999.ebuild, +metadata.xml: + sci-biology/AlignGraph: new package diff --git a/sci-biology/AlignGraph/metadata.xml b/sci-biology/AlignGraph/metadata.xml new file mode 100644 index 000000000..91aa93dea --- /dev/null +++ b/sci-biology/AlignGraph/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">baoe/AlignGraph</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/BBmap/BBmap-31.40.ebuild b/sci-biology/BBmap/BBmap-31.40.ebuild deleted file mode 100644 index e28c005c8..000000000 --- a/sci-biology/BBmap/BBmap-31.40.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/FASTQ conversion" -HOMEPAGE="http://sourceforge.net/projects/bbmap/" -SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java7.tar.gz" -#SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_31.40_java6.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=" - >=virtual/jdk-1.7:* - dev-java/ant-core" -RDEPEND="${DEPEND} - >=virtual/jre-1.7:*" - -S="${WORKDIR}"/bbmap diff --git a/sci-biology/BBmap/BBmap-34.56.ebuild b/sci-biology/BBmap/BBmap-34.56.ebuild new file mode 100644 index 000000000..e41097f2b --- /dev/null +++ b/sci-biology/BBmap/BBmap-34.56.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Short read aligner, K-mer-based error-correction and normalization, FASTA/Q conversion" +HOMEPAGE="http://sourceforge.net/projects/bbmap/" +SRC_URI="http://sourceforge.net/projects/bbmap/files/BBMap_"${PV}".tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="" + +# needs USE=java, see bug #542700 +DEPEND=" + sys-cluster/openmpi[java] + >=virtual/jdk-1.7:* + dev-java/ant-core" +RDEPEND="${DEPEND} + >=virtual/jre-1.7:*" + +S="${WORKDIR}"/bbmap + +#src_prepare(){ +# # fix the line in build.xml to point to mpi.jar location +# # <property name="mpijar" location="/tmp/mpi.jar" ></property> +#} + +src_compile(){ + ant dist || die +} + +src_install(){ + dobin *.sh + dodoc docs/readme.txt + java-pkg_dojar dist/lib/BBTools.jar +} diff --git a/sci-biology/BBmap/ChangeLog b/sci-biology/BBmap/ChangeLog index 53acebd3d..8a5e70684 100644 --- a/sci-biology/BBmap/ChangeLog +++ b/sci-biology/BBmap/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> BBmap-34.56.ebuild: + new package, needs openmpi with java support to provide mpi.jar, see bug + #542700 + +*BBmap-34.56 (05 Mar 2015) + + 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BBmap-34.56.ebuild, + -BBmap-31.40.ebuild: + version bump + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> BBmap-31.40.ebuild: sci-biology/BBmap: fix SLOT operators diff --git a/sci-biology/BBmap/Manifest b/sci-biology/BBmap/Manifest index f1826f34f..e5a5ea55f 100644 --- a/sci-biology/BBmap/Manifest +++ b/sci-biology/BBmap/Manifest @@ -1 +1 @@ -DIST BBMap_31.40_java7.tar.gz 2971946 SHA256 f2ddbea680d9364b41245ff00f26c020ad7b7286080efcfab0e9f4bc187b64dc SHA512 609cc8600fbb4e6de82cd239dea66761daab0097fdb90ec6d04b11e49bc2eaa576c8102d140de7fb971aa1eb8629193cc44177802d71544bd1d3fc775bdfdb8e WHIRLPOOL 30beb865a98474bac7221b79109468738cc802df029dfffb4ccf04742dcf5770a3f1307792db5f3dea76c07940f540ec7331a28c9ef03031548d03e7d22c8187 +DIST BBMap_34.56.tar.gz 3764341 SHA256 fa0632489d20fbe7ee98e47230696715c311e68a1270f56f44a6da3ab8eb20e6 SHA512 2adb526c2e5abb7d6b3d1e2c3c0ee8390b3c439d028723f6c200fd43904ce6c02ce9104307b02ca2bcaae10d3d343cfef374b5292ff4221190a40e1e16a4b89c WHIRLPOOL 2e3c12f058fa6bed15fa43cd1c57c8cfc02ed5c89d8ce04051edbc70aa878bb06117228a6c5f1bbec226ac250cb4e66bb346ff8bb95e504a600f9c584b10269e diff --git a/sci-biology/BRAKER/BRAKER-20150330.ebuild b/sci-biology/BRAKER/BRAKER-20150330.ebuild new file mode 100644 index 000000000..63fe5f176 --- /dev/null +++ b/sci-biology/BRAKER/BRAKER-20150330.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module + +DESCRIPTION="Gene prediction based on RNA-Seq using GeneMark-ET and AUGUSTUS" +# http://bioinf.uni-greifswald.de/bioinf/publications/pag2015.pdf +HOMEPAGE="http://bioinf.uni-greifswald.de/augustus/downloads" +SRC_URI=" http://bioinf.uni-greifswald.de/augustus/binaries/BRAKER1.tar.gz -> ${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + virtual/perl-Scalar-List-Utils" +# +# BUG: +# this causes: +# [blocks B ] <perl-core/Scalar-List-Utils-1.380.0 ("<perl-core/Scalar-List-Utils-1.380.0" is blocking virtual/perl-Scalar-List-Utils-1.380.0) + +S="${WORKDIR}" + +src_install(){ + perl_set_version + dobin *.pl + insinto ${VENDOR_LIB}/${PN} + doins *.pm + dodoc README.braker +} diff --git a/sci-biology/BRAKER/ChangeLog b/sci-biology/BRAKER/ChangeLog new file mode 100644 index 000000000..0a1fbb2ce --- /dev/null +++ b/sci-biology/BRAKER/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/BRAKER +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*BRAKER-20150330 (27 Apr 2015) + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +BRAKER-20150330.ebuild, +metadata.xml: + sci-biology/BRAKER: new package; somehow RDEPENDs are installed wrongly: Can't + locate Scalar/Util/Numeric.pm in @INC (you may need to install the + Scalar::Util::Numeric module) diff --git a/sci-biology/BRAKER/Manifest b/sci-biology/BRAKER/Manifest new file mode 100644 index 000000000..d4e70141e --- /dev/null +++ b/sci-biology/BRAKER/Manifest @@ -0,0 +1 @@ +DIST BRAKER-20150330.tar.gz 29237 SHA256 9229862127c7b81e47c4947a7d9b34221c2eb0a41b523c20e7e948deb16e6b80 SHA512 bbb1a29827616d43acd4c19953ae719f0269974cd1ea11fa551c7f8664d6702ed8787f64d82f31fbd045c0ac8208278190587cf6447283dfc865ab4819ca424c WHIRLPOOL 2ffad5d89ca7cd04339bc1761774dfc50037f77fce066105b08122e5dc3a77a9267a7a6c29e47255f1820626aa294181c7ec00166f8f01ecab4ab9ef88722159 diff --git a/sci-biology/CAutils/metadata.xml b/sci-biology/BRAKER/metadata.xml index 2bc893037..2bc893037 100644 --- a/sci-biology/CAutils/metadata.xml +++ b/sci-biology/BRAKER/metadata.xml diff --git a/sci-biology/BRANCH/ChangeLog b/sci-biology/BRANCH/ChangeLog index 03ab1fc78..73a69afe4 100644 --- a/sci-biology/BRANCH/ChangeLog +++ b/sci-biology/BRANCH/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/BRANCH: Add github to remote-id in metadata.xml + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> BRANCH-9999.ebuild: Move from git-2 to git-r3 eclass; add HOMEPAGE; be verbose during compilation; install docs @@ -11,4 +14,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +BRANCH-9999.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/BRANCH/metadata.xml b/sci-biology/BRANCH/metadata.xml index 2bc893037..a41257bf2 100644 --- a/sci-biology/BRANCH/metadata.xml +++ b/sci-biology/BRANCH/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">baoe/BRANCH</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BlastToSam/BlastToSam-9999.ebuild b/sci-biology/BlastToSam/BlastToSam-9999.ebuild new file mode 100644 index 000000000..7b476cdaa --- /dev/null +++ b/sci-biology/BlastToSam/BlastToSam-9999.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 java-pkg-2 java-ant-2 + +DESCRIPTION="Convert NCBI BLAST output to SAM format" +HOMEPAGE="https://github.com/AstrorEnales/BlastToSam" +EGIT_REPO_URI="https://github.com/AstrorEnales/BlastToSam.git" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +RDEPEND=">=virtual/jre-1.5:*" +DEPEND="${RDEPEND} + >=virtual/jdk-1.5:* + dev-java/ant-core" + +src_compile() { + ant compile || die +} + +src_install() { + java-pkg_dojar build/jar/BlastToSam.jar + java-pkg_dolauncher + dodoc README.md +} diff --git a/sci-biology/BlastToSam/ChangeLog b/sci-biology/BlastToSam/ChangeLog new file mode 100644 index 000000000..c90d4ecd1 --- /dev/null +++ b/sci-biology/BlastToSam/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/BlastToSam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/BlastToSam: Add github to remote-id in metadata.xml + +*BlastToSam-9999 (29 Apr 2015) + + 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +BlastToSam-9999.ebuild, +metadata.xml: + sci-biology/BlastToSam: new package, works diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml new file mode 100644 index 000000000..5be99c3d3 --- /dev/null +++ b/sci-biology/BlastToSam/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">AstrorEnales/BlastToSam</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/CAutils/CAutils-20120126.ebuild b/sci-biology/CAutils/CAutils-20120126.ebuild deleted file mode 100644 index 24478ec81..000000000 --- a/sci-biology/CAutils/CAutils-20120126.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Additional utilities for Celera assembler (wgs-assembler) from UMD" -HOMEPAGE="http://www.cbcb.umd.edu/software/celera-assembler" -SRC_URI="ftp://ftp.cbcb.umd.edu/pub/software/CAutils.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND} - dev-lang/perl" - -# is partially included in amos-3.1.0 diff --git a/sci-biology/CAutils/ChangeLog b/sci-biology/CAutils/ChangeLog deleted file mode 100644 index 8e70c1a94..000000000 --- a/sci-biology/CAutils/ChangeLog +++ /dev/null @@ -1,7 +0,0 @@ -# ChangeLog for sci-biology/CAutils -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 10 Jan 2015; Justin Lecher <jlec@gentoo.org> CAutils-20120126.ebuild: - Fix license - diff --git a/sci-biology/CAutils/Manifest b/sci-biology/CAutils/Manifest deleted file mode 100644 index 5f12e80e2..000000000 --- a/sci-biology/CAutils/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST CAutils.tar.gz 16800 SHA256 d772b338ade65ac59c6190885219053fd8c613c1b53a024df7899ef187a929e6 SHA512 382578957510f8bab3688510a1ec37c864ff48de2e94cbbd532cbe4b318a3a286ce2a456704f48055e4d27aac972748a61944c061b22b35c76402f5d58f20a83 WHIRLPOOL 141e3b46d7373fed27239493adb124a913c1b2693923959b2a4d53543a637847b492a22b21bd719cbbf4a40de3c782956692114cd73f5743b6d62a00f0f5dc4e diff --git a/sci-biology/ESTate/ChangeLog b/sci-biology/ESTate/ChangeLog index 879e7b407..7d523e9be 100644 --- a/sci-biology/ESTate/ChangeLog +++ b/sci-biology/ESTate/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> ESTate-0.5.ebuild: + sci-biology/ESTate: track file collision + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> ESTate-0.5.ebuild: Soma QA and polishing diff --git a/sci-biology/ESTate/ESTate-0.5.ebuild b/sci-biology/ESTate/ESTate-0.5.ebuild index 1622516b0..63c896611 100644 --- a/sci-biology/ESTate/ESTate-0.5.ebuild +++ b/sci-biology/ESTate/ESTate-0.5.ebuild @@ -28,6 +28,11 @@ src_prepare(){ -i src/Makefile || die } +# Detected file collision(s) versus sci-biology/hmmer-2.3.2-r2: +# * sci-biology/ESTate-0.5:0::science +# * /usr/bin/revcomp +# * /usr/bin/translate + src_install(){ dobin bin/* doman doc/man/man1/*.1 doc/man/man7/*.7 diff --git a/sci-biology/Gambit/Manifest b/sci-biology/Gambit/Manifest index b53686f60..f22f3245b 100644 --- a/sci-biology/Gambit/Manifest +++ b/sci-biology/Gambit/Manifest @@ -1,2 +1,2 @@ -DIST GambitDocumentation_v0.4.145.pdf 1061985 SHA256 f0d28fedab07007244a2a6f6292b7c445843a336878583ae177c22528ede30c9 -DIST Gambit_v0.4.145_src.tar.gz 246624 SHA256 1c1ed7fdb3b9a5007f2daeef2b96033d7145a767dd526339dbb928dd27626268 +DIST GambitDocumentation_v0.4.145.pdf 1061985 SHA256 f0d28fedab07007244a2a6f6292b7c445843a336878583ae177c22528ede30c9 SHA512 c16c1928a9c4edb31204a43d206328a34090ca7b4d2cefb0999f93d6e559f84773b515ac2972350739f9f5f0d45e54b3b584c763f25de1b5464eca4a0ba03a57 WHIRLPOOL 8d78b5bd7bfe0a8ccb9b249bdf92d9bcc6bc2e350382c8c001753176d39f53b7e23322e3b897bec597631c35f9d969796277d494a90c876b11dfbe4fd71f9371 +DIST Gambit_v0.4.145_src.tar.gz 246624 SHA256 1c1ed7fdb3b9a5007f2daeef2b96033d7145a767dd526339dbb928dd27626268 SHA512 5fd650acc6acbfdf5dbb085b7a641883bf833aa0c7c156a7358675cc35f71f2dc1cc82c25b651df56a99f43015eda14574167252703c84a22f792e9df52ee501 WHIRLPOOL e7da4f63b0a6771d816f76fa0a6482c985c4b7015ca288106f04e4587cc50bba26719236d0e3d79c1b9085cfad4634c52eea359d880d7af2eac4bb98ded004e1 diff --git a/sci-biology/HTSeq/HTSeq-0.6.1.ebuild b/sci-biology/HTSeq/HTSeq-0.6.1.ebuild index 37af947ad..c15e14c89 100644 --- a/sci-biology/HTSeq/HTSeq-0.6.1.ebuild +++ b/sci-biology/HTSeq/HTSeq-0.6.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml index 2bc893037..d5d97aa75 100644 --- a/sci-biology/HTSeq/metadata.xml +++ b/sci-biology/HTSeq/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">HTSeq</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/InterMine/ChangeLog b/sci-biology/InterMine/ChangeLog index 48beb17c4..a78e71a5f 100644 --- a/sci-biology/InterMine/ChangeLog +++ b/sci-biology/InterMine/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/InterMine: Add github to remote-id in metadata.xml + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> InterMine-0.98.ebuild: Fix license, homepage and move from git-2 to git-r3 @@ -11,4 +14,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +InterMine-0.98.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/InterMine/metadata.xml b/sci-biology/InterMine/metadata.xml index 2bc893037..b370f551e 100644 --- a/sci-biology/InterMine/metadata.xml +++ b/sci-biology/InterMine/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">intermine/intermine</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Jannovar-bin/ChangeLog b/sci-biology/Jannovar-bin/ChangeLog new file mode 100644 index 000000000..5a6ec92c4 --- /dev/null +++ b/sci-biology/Jannovar-bin/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/Jannovar-bin +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*Jannovar-bin-20150503 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Jannovar-bin-20150503.ebuild, +metadata.xml: + sci-biology/Jannovar-bin: new package diff --git a/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild new file mode 100644 index 000000000..890494af2 --- /dev/null +++ b/sci-biology/Jannovar-bin/Jannovar-bin-20150503.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 + +DESCRIPTION="Exome annotation tool" +HOMEPAGE="http://compbio.charite.de/contao/index.php/jannovar.html" +SRC_URI="http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/Jannovar.jar -> Jannovar-bin-20150503.jar + http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/JannovarTutorial.pdf -> JannovarTutorial.pdf + http://compbio.charite.de/contao/index.php/jannovar.html?file=tl_files/Jannovar/tutorial.tgz -> Jannovar_tutorial.tgz" + +# https://github.com/charite/jannovar +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=">=virtual/jdk-1.7" +RDEPEND=">=virtual/jre-1.7" + +S="${WORKDIR}" + +src_install(){ + cp "${DISTDIR}"/Jannovar-bin-20150503.jar Jannovar-bin.jar + java-pkg_newjar Jannovar-bin.jar + java-pkg_dolauncher Jannovar-bin --jar Jannovar-bin.jar +} diff --git a/sci-biology/Jannovar-bin/Manifest b/sci-biology/Jannovar-bin/Manifest new file mode 100644 index 000000000..2bb4bf7dd --- /dev/null +++ b/sci-biology/Jannovar-bin/Manifest @@ -0,0 +1,3 @@ +DIST Jannovar-bin-20150503.jar 231228 SHA256 86fa6637bac2618781d3f437fe572e1a4d84e12edba2a33130f0e9152a7ac9d6 SHA512 4878efaa14679bc8a0e95aa0231a99953360725ba018cae4298063b3620cd8240ed52bc21514c85a6f185048b9801381421b9f33a79a32237089981c88b1e673 WHIRLPOOL 774fd24880d7a6dd44f5222c56ce7850d04d31f200377792602f7458ed121821abca9538ecb92daf88d363c07b0e54fbac17d7b40b047212c6b65122c935f599 +DIST JannovarTutorial.pdf 303393 SHA256 6fb580dd6e3724823da0a4818e6270bced355bcf9c8ca0935a06a65966b97803 SHA512 852535388cf64d09213e8c775394d1de0768efee184da2302f08f88126b334463f5889da5fcbb99898ea708c6be078066e89aed95b85de6b79f73eedc47c2083 WHIRLPOOL 957829100fe89cbef4049120a6fa28d43dfa0a2a84996728e921ec45d2c61fc2418a0a58c1162b15944661e2b5105109e2b0af0a3792c29f3ff0a2f1a813df99 +DIST Jannovar_tutorial.tgz 259723 SHA256 dab9726544fe921829712d71f7a7d8c2c6819b640d6aac97c73b661f40f2539f SHA512 6b0a044c63b709b1be7243ca9e55dc258da12a09f794087eb13489eea180460e110ecc24f77f97abd57d0ddae7fc1b2a679ffcf5df33b8fe3bc1675ad766ec25 WHIRLPOOL d33d343ccddbe1ac6114347ef1a87a41654fa134324aa8332f4c4bb282b54bb64d72d11207324a9abc56471988024589b645d32be02206879c2a80c005fe1b6a diff --git a/sci-biology/MAKER/metadata.xml b/sci-biology/Jannovar-bin/metadata.xml index 2bc893037..2bc893037 100644 --- a/sci-biology/MAKER/metadata.xml +++ b/sci-biology/Jannovar-bin/metadata.xml diff --git a/sci-biology/KaKs_Calculator/ChangeLog b/sci-biology/KaKs_Calculator/ChangeLog new file mode 100644 index 000000000..2a3e92fe4 --- /dev/null +++ b/sci-biology/KaKs_Calculator/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/KaKs_Calculator +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*KaKs_Calculator-1.2 (21 Mar 2015) + + 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +KaKs_Calculator-1.2.ebuild, +metadata.xml: + sci-biology/KaKs_Calculator: new package but code does not compile; awaiting + some answer from upstream http://cbb.big.ac.cn/Zhang_Zhang diff --git a/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild new file mode 100644 index 000000000..5d9bb674c --- /dev/null +++ b/sci-biology/KaKs_Calculator/KaKs_Calculator-1.2.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates" +HOMEPAGE="https://code.google.com/p/kaks-calculator" +SRC_URI="https://kaks-calculator.googlecode.com/files/KaKs_Calculator"${PV}".tar.gz + https://kaks-calculator.googlecode.com/files/parseFastaIntoAXT.pl" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/ParaAT" +RDEPEND=" + dev-lang/perl + ${DEPEND}" + +S="${WORKDIR}"/KaKs_Calculator"${PV}" + +src_prepare(){ + sed -e "s/^CC = g++/CC="$(tc-getCXX)"/; s/^CFLAGS/#CFLAGS/" -i src/makefile +} + +src_compile(){ + cd src || die + emake +} + +src_install(){ + dobin "${DISTDIR}"/parseFastaIntoAXT.pl + dobin src/{KaKs_Calculator,AXTConvertor,ConPairs} +} diff --git a/sci-biology/KaKs_Calculator/Manifest b/sci-biology/KaKs_Calculator/Manifest new file mode 100644 index 000000000..778eb13c0 --- /dev/null +++ b/sci-biology/KaKs_Calculator/Manifest @@ -0,0 +1,2 @@ +DIST KaKs_Calculator1.2.tar.gz 2301729 SHA256 92b7f7bdd1b090b5f16e83968263e1e58886cdb7fe832e2dfd0a636bdfd4840a SHA512 a1a18229d89262425f879695a1f44ebecbe473c32bcf7ee0d2a2d5d36d34a45b88f5fdcedbacdf0070eb5f0feedff9d74616849aff3cf44f210fdbc65ed56e2c WHIRLPOOL 54a36ba47473342953f5d80aae6e8b2abe5d8e296b381222a15bbb86815931a7a79c5bedf4d261a63ab9776da3b11545adfb2edba04fb61e6a4e0e06feb158e7 +DIST parseFastaIntoAXT.pl 1483 SHA256 4cd376404e93647343ba23d48496d2e275ae82bfbeff6ae6f224145e3d74e382 SHA512 38d39d0fe1f788cf45d742e9fd6b0918a78973faecdb10d98d39384670abdef7212dbd2cdea777f0d5fcbbf202f5331f9fe178ef0f48fafe9e0a31625ab532a1 WHIRLPOOL cdd50eb4a228f88886a5810a4274806cb8514b79d49e8ded63c3d602f3f95f383958730f897470461cd6db2b73b3db2535cbca8449089ea81c80df7224bf42e1 diff --git a/sci-biology/transdecoder/metadata.xml b/sci-biology/KaKs_Calculator/metadata.xml index 2bc893037..2bc893037 100644 --- a/sci-biology/transdecoder/metadata.xml +++ b/sci-biology/KaKs_Calculator/metadata.xml diff --git a/sci-biology/MAKER/MAKER-9999.ebuild b/sci-biology/MAKER/MAKER-9999.ebuild deleted file mode 100644 index fa4733e5a..000000000 --- a/sci-biology/MAKER/MAKER-9999.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" -HOMEPAGE="http://www.yandell-lab.org/software/maker.html" -SRC_URI="" - -RESTRICT="fetch" - -# for academia: GPL-v2 or Artistic-2 -# for commercial: ask -LICENSE="|| ( GPL-2 Artistic-2 )" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-biology/MaSuRCA/ChangeLog b/sci-biology/MaSuRCA/ChangeLog index e9d6a2cee..4014eea12 100644 --- a/sci-biology/MaSuRCA/ChangeLog +++ b/sci-biology/MaSuRCA/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/MaSuRCA -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*MaSuRCA-2.3.2b (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +MaSuRCA-2.3.2b.ebuild, -MaSuRCA-2.1.0.ebuild: + sci-biology/MaSuRCA: version bump + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> MaSuRCA-2.1.0.ebuild: added license diff --git a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild index 04e817245..01eeeeb46 100644 --- a/sci-biology/MaSuRCA/MaSuRCA-2.1.0.ebuild +++ b/sci-biology/MaSuRCA/MaSuRCA-2.3.2b.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -16,33 +16,27 @@ IUSE="" DEPEND="dev-lang/perl app-arch/bzip2" -RDEPEND="${DEPEND}" - #sci-biology/quorum" +RDEPEND="${DEPEND} + >=sci-biology/quorum-0.2.1 + >=sci-biology/jellyfish-1.1.11" # the ebuild mimics "${S}"/install.sh src_configure(){ - cd jellyfish-1.1.11 || die + cd jellyfish || die econf - cd ../jellyfish-2.0.0rc1 || die - econf --program-suffix=-2.0 - cd ../CA/kmer || die - sh ./configure.sh econf - cd ../../SuperReads-0.3.2 || die + cd ../../SuperReads || die econf - cd ../quorum-0.3.2 || die + cd ../quorum || die econf --enable-relative-paths --with-relative-jf-path } src_compile(){ - cd jellyfish-1.1.11 || die - emake - - cd ../jellyfish-2.0.0rc1 || die + cd jellyfish || die emake cd ../CA/kmer || die @@ -51,10 +45,10 @@ src_compile(){ cd ../../CA/src || die emake - cd ../SuperReads-0.3.2 || die + cd ../SuperReads || die emake - cd ../quorum-0.3.2 || die + cd ../quorum || die emake } diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest index 73d86433e..3366274b4 100644 --- a/sci-biology/MaSuRCA/Manifest +++ b/sci-biology/MaSuRCA/Manifest @@ -1,2 +1,2 @@ -DIST MaSuRCA-2.1.0.tar.gz 8333371 SHA256 c0e816cc461af55972b4fc55351ab5943026eb5e0553ddf3cc316b3c44ffd49c SHA512 1b095148b4083503953ba9c745ca587870b7f605f02b1d5c5c733753c1e3d0f630c9925cedb8b1b4318356bc42124a26191e14d0587613007ccdf00d65b58c07 WHIRLPOOL af72eebbf80b105f9524601bbddb66f4781a44b91d526871038fd6902999bbe5d39bed927a3b081c93dc7ea95a40b3918c510723cc03271c6ff1534a1b7142f8 +DIST MaSuRCA-2.3.2b.tar.gz 7506105 SHA256 837cb144d3dba206a778e88a06f2af67f2cc9ca4f5e6e97dd48ad4ac783aec70 SHA512 042040899a8fafe99145390701f2ced0d100cebf4abad4d5d02ccfe3cfe4406e0a887740752ae81a75fc055629c1580c3f99dff007e4330190c732164cad0f35 WHIRLPOOL ef123be71b4deaaec961451fdc6250162d222345ba1307c59dc8f4ba6deddc52f25ee269b9d5b5ce44bab1f2332018c10da0cc9386e1a49718338c88516507b4 DIST MaSuRCA_QuickStartGuide.pdf 152644 SHA256 3a1e9fa83608f6138355aa0e6c5b1db337e2fca67d0a7275c0b54e85780e421d SHA512 e911a7b092f68a1f60e45c996e25b53b65260fad9e465488d30a066b00db2cdef0e0bb422d9731d37cfa3958eac74943d54019ac9e538560b66da0a64d6ce800 WHIRLPOOL a7d1ef0798b0ee0810b0fe6ac6bda4e0b6f4655a7109d5dc5dfc797ed6669ad5353a2f3b988e9efe1dcde485dc69bdc2b1d3887ee2d026e99cf8a14fe4075a95 diff --git a/sci-biology/ONTO-PERL/ChangeLog b/sci-biology/ONTO-PERL/ChangeLog index 2d1f1e2c9..e88acf703 100644 --- a/sci-biology/ONTO-PERL/ChangeLog +++ b/sci-biology/ONTO-PERL/ChangeLog @@ -4,7 +4,7 @@ 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -ONTO-PERL-1.31.ebuild, +ONTO-PERL-1.41.ebuild, metadata.xml: - Version BUmp; Bump to EAPI=5 + Version Bump; Bump to EAPI=5 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ONTO-PERL-1.31.ebuild: Cleaned ebuild, 'http://search.cpan.org/CPAN' found in thirdpartymirrors diff --git a/sci-biology/ORFcor/ChangeLog b/sci-biology/ORFcor/ChangeLog new file mode 100644 index 000000000..86b3882de --- /dev/null +++ b/sci-biology/ORFcor/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/ORFcor +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ORFcor-20130507.ebuild: + sci-biology/ORFcor: more cleanup + +*ORFcor-20130507 (09 Mar 2015) + + 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +ORFcor-20130507.ebuild, +metadata.xml: + new package, working ebuild diff --git a/sci-biology/ORFcor/Manifest b/sci-biology/ORFcor/Manifest new file mode 100644 index 000000000..881c8d80d --- /dev/null +++ b/sci-biology/ORFcor/Manifest @@ -0,0 +1 @@ +DIST ORFcor.tar.gz 3499343 SHA256 32609f3a0ceebfc98eba4987b57ccabeb52fb8c4f7ec26bc2a9c4ba1839b09bc SHA512 2a0c57e94a71294f115c769aced754e8e3f6d0f8ad2b577add8f65f9f45fed2486946244ea99109dbac7dfcaf3bae1a14ebe4d6ffb194c285675e361ddd12141 WHIRLPOOL 94d48efc48b372733466f594ed7e9fb3ce4a531636f38e20cb7328c91c600ad70cd7e611fa1cd6514272273526a2c472b920b089b3380c5fb1eaa887dad2ec52 diff --git a/sci-biology/ORFcor/ORFcor-20130507.ebuild b/sci-biology/ORFcor/ORFcor-20130507.ebuild new file mode 100644 index 000000000..f338df021 --- /dev/null +++ b/sci-biology/ORFcor/ORFcor-20130507.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Automated editor of protein-coding sequences" +HOMEPAGE="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058387" +SRC_URI="http://www.currielab.wisc.edu/files/ORFcor.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-lang/perl + sci-biology/muscle + dev-perl/Parallel-ForkManager" + # >=sci-biology/hmmer-3.0 +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/ORFcor + +src_install(){ + dobin *.pl + dodoc README + insinto /usr/share/${PN} + doins 31_HMM* + insinto /usr/share/${PN}/test_data + doins test_data/* +} diff --git a/sci-biology/ORFcor/metadata.xml b/sci-biology/ORFcor/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/ORFcor/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/SEECER/ChangeLog b/sci-biology/SEECER/ChangeLog index 1ac7a3886..a57cf306e 100644 --- a/sci-biology/SEECER/ChangeLog +++ b/sci-biology/SEECER/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*SEECER-0.1.3-r1 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +SEECER-0.1.3-r1.ebuild, +files/replace_ids.cc, -SEECER-0.1.3.ebuild: + sci-biology/SEECER: added upstream 'patch'; do more proper install process + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> SEECER-0.1.3.ebuild: Fix license @@ -10,4 +16,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +SEECER-0.1.3.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/SEECER/Manifest b/sci-biology/SEECER/Manifest index 72d9cd2b8..8f7967346 100644 --- a/sci-biology/SEECER/Manifest +++ b/sci-biology/SEECER/Manifest @@ -1,2 +1,2 @@ DIST SEECER-0.1.3.tar.gz 9457477 SHA256 bfe7885170810e99d0b2459fa84b94f6695457c393f6153c8d74db15a688e2c2 SHA512 7e7c4a8525ffd9104402d7eb10f7fd99648214dfdc6dc2cd40ed22a641dbf80ddc2e5945cdc5d3a8776f781e069c5490825f3c132843d2ea6ce26440f84e07d3 WHIRLPOOL af60f230f014a7231b0a4b5ac41056f193dabdd8af57b4d142a2f0f005d6d613526c4b5220c790437382923b386481ac45ef2a243d8f7b44323be1fb87a3a723 -DIST manual.pdf 233688 SHA256 f8f1bbc6053158ed080545692dbd9db47a8429d0900d5df9109e6a9e55295ee6 SHA512 735132309c00ff5b46d9495e0b248727bb7fac98fff830ce0f9b9d6620e592c65b4850945157706fafcf81b396fc52071bd7671cb31ea20dfcb959b16b51cab6 WHIRLPOOL 38d8fe7d904c155728c12a26fee79b64ff9695be616babfc38f83c17c03a1d3c396834447bc97e8345e770984c138d09dc0bfc9d8eef1e5dc037170711d78811 +DIST SEECER-manual.pdf 233688 SHA256 f8f1bbc6053158ed080545692dbd9db47a8429d0900d5df9109e6a9e55295ee6 SHA512 735132309c00ff5b46d9495e0b248727bb7fac98fff830ce0f9b9d6620e592c65b4850945157706fafcf81b396fc52071bd7671cb31ea20dfcb959b16b51cab6 WHIRLPOOL 38d8fe7d904c155728c12a26fee79b64ff9695be616babfc38f83c17c03a1d3c396834447bc97e8345e770984c138d09dc0bfc9d8eef1e5dc037170711d78811 diff --git a/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild new file mode 100644 index 000000000..bfebed989 --- /dev/null +++ b/sci-biology/SEECER/SEECER-0.1.3-r1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="SEquencing Error Corrector for RNA-Seq reads" +HOMEPAGE="http://sb.cs.cmu.edu/seecer/" +SRC_URI=" + http://sb.cs.cmu.edu/seecer/downloads/"${P}".tar.gz + http://sb.cs.cmu.edu/seecer/downloads/manual.pdf -> "${PN}"-manual.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# although has bundled jellyfish-1.1.11 copy it just calls the executable during runtime +DEPEND=" + sci-libs/gsl + sci-biology/seqan" +RDEPEND="${DEPEND} + sci-biology/jellyfish" + +S="${S}"/SEECER + +src_prepare(){ + # http://seecer-rna-read-error-correction-mailing-list.21961.x6.nabble.com/Segmentation-fault-in-step-4-td41.html + cp -p "${FILESDIR}"/replace_ids.cc "${S}"/src/ || die +} + +src_install(){ + dobin bin/seecer bin/random_sub_N bin/replace_ids bin/run_jellyfish.sh + dodoc README "${DISTDIR}"/"${PN}"-manual.pdf +} diff --git a/sci-biology/SEECER/SEECER-0.1.3.ebuild b/sci-biology/SEECER/SEECER-0.1.3.ebuild deleted file mode 100644 index d415a0151..000000000 --- a/sci-biology/SEECER/SEECER-0.1.3.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Error corrector for RNA-Seq reads" -HOMEPAGE="http://sb.cs.cmu.edu/seecer/" -SRC_URI=" - http://sb.cs.cmu.edu/seecer/downloads/SEECER-0.1.3.tar.gz - http://sb.cs.cmu.edu/seecer/downloads/manual.pdf" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND=" - sci-libs/gsl - sci-biology/seqan - sci-biology/jellyfish" -RDEPEND="${DEPEND}" - -S="${S}"/SEECER - -# doh, it install /usr/bin/seecer (note the lowercase letters) - -# checking for x86_64-pc-linux-gnu-gcc option to support OpenMP... -fopenmp -# -# Uses: -# libgomp.so.1 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.8.3/libgomp.so.1 (0x00007f7853faf000) - -# dobin bin/run_seecer.sh -# dodoc "${DISTDIR}"/manual.pdf diff --git a/sci-biology/SEECER/files/replace_ids.cc b/sci-biology/SEECER/files/replace_ids.cc Binary files differnew file mode 100644 index 000000000..0a778197e --- /dev/null +++ b/sci-biology/SEECER/files/replace_ids.cc diff --git a/sci-biology/SSAKE/ChangeLog b/sci-biology/SSAKE/ChangeLog new file mode 100644 index 000000000..f11515c1a --- /dev/null +++ b/sci-biology/SSAKE/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/SSAKE +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*SSAKE-3.8.2 (17 Apr 2015) + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +SSAKE-3.8.2.ebuild, + +metadata.xml: + sci-biology/SSAKE: new package diff --git a/sci-biology/SSAKE/Manifest b/sci-biology/SSAKE/Manifest new file mode 100644 index 000000000..74b276a0c --- /dev/null +++ b/sci-biology/SSAKE/Manifest @@ -0,0 +1 @@ +DIST ssake_v3-8-2.tar.gz 2390868 SHA256 254740c04ce2dc3afd8a4c3615be56baebb8b98a5e22bad6c3dd166a4dfdcb10 SHA512 12d05a37847a4c10291e75ac60d48b8cedd4f5380c8ef5668204728858684ef1f0847e3a8d5e7c08f31edd37fdf7ac0b16bae64139fee34e47d8e4f8a777965a WHIRLPOOL 2b60b9bb46a9564a54e18dcc2bc4d7a5166d8444f0ff9429c7040f57cbf013f75515581af4d67a759dcf4841be3a4fb0c8ac8ec5f45fa0117cd243a1cadc6ef7 diff --git a/sci-biology/SSAKE/SSAKE-3.8.2.ebuild b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild new file mode 100644 index 000000000..4aba1f778 --- /dev/null +++ b/sci-biology/SSAKE/SSAKE-3.8.2.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Short-read trimmer, assembler, scaffolder in PERL using the 3'-most k-mers" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/ssake" +SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/ssake/releases/${PV}/ssake_v3-8-2.tar.gz" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# pure perl +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/ssake_v3-8-2 + +src_install(){ + dobin SSAKE + dodoc SSAKE.pdf SSAKE.readme + insinto /usr/share/${PN}/tools + doins tools/* + insinto /usr/share/${PN}/test + doins test/* +} diff --git a/sci-biology/SSAKE/metadata.xml b/sci-biology/SSAKE/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/SSAKE/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/STAR/ChangeLog b/sci-biology/STAR/ChangeLog new file mode 100644 index 000000000..b718477c8 --- /dev/null +++ b/sci-biology/STAR/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/STAR +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*STAR-2.4.1c (05 May 2015) +*STAR-9999 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +STAR-2.4.1c.ebuild, + +STAR-9999.ebuild, +metadata.xml: + sci-biology/STAR: new package diff --git a/sci-biology/STAR/Manifest b/sci-biology/STAR/Manifest new file mode 100644 index 000000000..037124090 --- /dev/null +++ b/sci-biology/STAR/Manifest @@ -0,0 +1 @@ +DIST STAR_2.4.1c.tar.gz 27129701 SHA256 7ac598be3f06ee7ce54d27624ea6ce40f0a44cc4144698460e7dc6a6542b9f2d SHA512 595e65634d976e31d75f397cfebf120730b302ce16a0ea6e4a59ecf8dced9f649f4b9a40a0ea2d9b9766acff96823769cf47c2fe1d6d268b569ffa669679fee0 WHIRLPOOL a28001153e8836f31c6cc4f527a19e1605ae1302c0f18453e936906d8a21ad166759c567f82356ff82eefa3ce0f7368a1f33f5d4ca8e412b84b9c199a37bf3ed diff --git a/sci-biology/STAR/STAR-2.4.1c.ebuild b/sci-biology/STAR/STAR-2.4.1c.ebuild new file mode 100644 index 000000000..bed7e73e1 --- /dev/null +++ b/sci-biology/STAR/STAR-2.4.1c.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" +HOMEPAGE="http://code.google.com/p/rna-star/" +SRC_URI="https://github.com/alexdobin/STAR/archive/STAR_"${PV}".tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# sci-biology/htslib +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/STAR-STAR_"${PV}" + +# contains bundled STAR-Fusion +src_prepare(){ + sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die + sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die +} + +src_compile(){ + cd source || die + emake STAR +} + +src_install(){ + dobin source/STAR + dodoc doc/STARmanual.pdf +} diff --git a/sci-biology/STAR/STAR-9999.ebuild b/sci-biology/STAR/STAR-9999.ebuild new file mode 100644 index 000000000..149226a98 --- /dev/null +++ b/sci-biology/STAR/STAR-9999.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 toolchain-funcs + +DESCRIPTION="STAR aligner: align RNA-seq reads to reference genome uncompressed suffix arrays" +HOMEPAGE="http://code.google.com/p/rna-star/" +EGIT_REPO_URI="https://github.com/alexdobin/STAR.git" +# http://rna-star.googlecode.com/files/STARmanual_2.3.0.1.pdf + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# contains bundled version sci-biology/htslib-0.0.1 +DEPEND="" +RDEPEND="${DEPEND}" + +# contains bundled STAR-Fusion +src_prepare(){ + sed -e "s/= gcc/= $(tc-getCC)/;s/-O2/${CFLAGS}/g" -i source/htslib/Makefile || die + sed -e "s/-O3/${CFLAGS}/g" -i source/Makefile || die +} + +src_compile(){ + cd source || die + emake STAR +} + +src_install(){ + dobin source/STAR + dodoc doc/STARmanual.pdf +} diff --git a/sci-biology/STAR/metadata.xml b/sci-biology/STAR/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/STAR/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/StarORF/ChangeLog b/sci-biology/StarORF/ChangeLog new file mode 100644 index 000000000..d1fbadfca --- /dev/null +++ b/sci-biology/StarORF/ChangeLog @@ -0,0 +1,11 @@ +# ChangeLog for sci-biology/StarORF +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*StarORF-9999 (06 May 2015) + + 06 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +StarORF-9999.ebuild, +metadata.xml: + sci-biology/StarORF: new package, somehow build.xml needs dev- + java/jreleaseinfo but it does not see it: 'build.xml:3: taskdef class + ch.oscg.jreleaseinfo.anttask.JReleaseInfoAntTask cannot be found' diff --git a/sci-biology/StarORF/StarORF-9999.ebuild b/sci-biology/StarORF/StarORF-9999.ebuild new file mode 100644 index 000000000..2affa2e33 --- /dev/null +++ b/sci-biology/StarORF/StarORF-9999.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="Java-based utility to show ORFs in a sequence" +HOMEPAGE="http://star.mit.edu/orf" +EGIT_REPO_URI="https://github.com/starteam/starorf_java.git" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=" + >=virtual/jdk-1.5:* + dev-java/jreleaseinfo" +RDEPEND="${DEPEND} + >=virtual/jre-1.5:*" + +#src_compile() { +# ant compile || die +#} + +src_install() { + java-pkg_dojar StarORF.jar +} diff --git a/sci-biology/StarORF/metadata.xml b/sci-biology/StarORF/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/StarORF/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/TransDecoder/ChangeLog b/sci-biology/TransDecoder/ChangeLog new file mode 100644 index 000000000..4e2164c0b --- /dev/null +++ b/sci-biology/TransDecoder/ChangeLog @@ -0,0 +1,57 @@ +# ChangeLog for sci-biology/TransDecoder +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/TransDecoder: Add github to remote-id in metadata.xml + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-2.0.1.ebuild: + sci-biology/transdecoder: more ebuild cleanup + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-2.0.1.ebuild: + sci-biology/transdecoder: ebuild cleanup + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + -transdecoder-20140704.ebuild, transdecoder-2.0.1.ebuild: + sci-biology/transdecoder: drop old + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: + sci-biology/transdecoder: fixed installation of perl-related files + + 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-2.0.1.ebuild: + dropped hmmer dependency altogether, added pkg_postinst() with + usage/dependency info + +*transdecoder-2.0.1 (19 Mar 2015) + + 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +transdecoder-2.0.1.ebuild, transdecoder-20140704.ebuild: + removing KEYWORDS until the perl files are installed to some other place. At + the moment I get: 'perl-module.eclass: Suspicious environment values found. + PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/TransDecoder"' + + 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-20140704.ebuild: + drop hmmer-3 dependency, it is an optional dependency only + + 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + transdecoder-20140704.ebuild: + install *.pm into PERL5LIB/TransDecoder and pass that via env.d + + 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/TransDecoder.patch, +files/pfam_runner.pl.patch, + transdecoder-20140704.ebuild: + sci-biology/transdecoder: added patches so that we use PATH to loclate + binaries and not in a local subdirectory named 'util', drop sys- + cluster/openmpi requirement, it does not link against it all all, this is a + bunch of perl and shell scripts + +*transdecoder-20140704 (08 Jan 2015) + + 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +transdecoder-20140704.ebuild: + sci-biology/transdecoder: new package diff --git a/sci-biology/TransDecoder/Manifest b/sci-biology/TransDecoder/Manifest new file mode 100644 index 000000000..83f501c15 --- /dev/null +++ b/sci-biology/TransDecoder/Manifest @@ -0,0 +1 @@ +DIST TransDecoder-2.0.1.tar.gz 9925281 SHA256 ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22 SHA512 fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de WHIRLPOOL 61c6b7fe5684becdb28a3bccb113fea07889a2c4e6627e92cd27c1a90ca53f5a88504e048363a1322f1108dd6ebd5549c52aee9d438fbcfb2023390c79c126ec diff --git a/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild new file mode 100644 index 000000000..e8f513431 --- /dev/null +++ b/sci-biology/TransDecoder/TransDecoder-2.0.1.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" +HOMEPAGE="http://sourceforge.net/projects/transdecoder/" +SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/"${PV}".tar.gz -> ${P}.tar.gz" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/cd-hit + sci-biology/hmmer + sci-biology/parafly + sci-biology/ffindex" +# cdhit-4.6.1 is a real dependency, at least hmmer is optional (also ncbi-tools++ is now used for ORF searches) + +S="${WORKDIR}"/TransDecoder-2.0.1 + +##src_prepare(){ +# #mv Makefile Makefile.old +# #epatch "${FILESDIR}"/TransDecoder.patch +# #epatch "${FILESDIR}"/pfam_runner.pl.patch +#} + +# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see +# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives +# +# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin + +src_install(){ + dobin TransDecoder.Predict TransDecoder.LongOrfs + insinto /usr/share/${PN}/util + dobin util/*.pl + # zap the bundled cdhit binaries copied from transdecoder_plugins/cdhit/ to util/bin + rm -rf util/bin + # + # * sci-biology/trinityrnaseq-20140413:0::science + # * /usr/bin/Fasta_reader.pm + # * /usr/bin/GFF3_utils.pm + # * /usr/bin/Gene_obj.pm + # * /usr/bin/Gene_obj_indexer.pm + # * /usr/bin/Longest_orf.pm + # * /usr/bin/Nuc_translator.pm + # * /usr/bin/TiedHash.pm + # + perl_set_version + insinto ${VENDOR_LIB}/${PN} + dobin PerlLib/*.pm # BUG: install into /usr/bin but wanted to have it readable and executable in ${VENDOR_LIB}/${PN} instead + einfo "Fetch on your own:" + einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin" + einfo "hmmpress Pfam-AB.hmm.bin" +} + +pkg_postinst(){ + einfo "It is recommended to use TransDecoder with hmmer-3 or at least NCBI blast" + einfo "from either sci-biology/ncbi-blast+ (released more often) or" + einfo "from sci-biology/ncbi-toolkit++ (huge bundle with releases and less frequent bugfixes)" + einfo "Author says the minimum requirement is sci-biology/cd-hit" +} diff --git a/sci-biology/transdecoder/files/TransDecoder.patch b/sci-biology/TransDecoder/files/TransDecoder.patch index c0cff94d4..c0cff94d4 100644 --- a/sci-biology/transdecoder/files/TransDecoder.patch +++ b/sci-biology/TransDecoder/files/TransDecoder.patch diff --git a/sci-biology/transdecoder/files/pfam_runner.pl.patch b/sci-biology/TransDecoder/files/pfam_runner.pl.patch index 7809b1aaa..7809b1aaa 100644 --- a/sci-biology/transdecoder/files/pfam_runner.pl.patch +++ b/sci-biology/TransDecoder/files/pfam_runner.pl.patch diff --git a/sci-biology/TransDecoder/metadata.xml b/sci-biology/TransDecoder/metadata.xml new file mode 100644 index 000000000..33de46b4c --- /dev/null +++ b/sci-biology/TransDecoder/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/Trinotate/ChangeLog b/sci-biology/Trinotate/ChangeLog new file mode 100644 index 000000000..86519b975 --- /dev/null +++ b/sci-biology/Trinotate/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/Trinotate +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> Trinotate-2.0.1.ebuild: + sci-biology/Trinotate: Fix whitespaces + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/Trinotate: Add github to remote-id in metadata.xml + +*Trinotate-2.0.1 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +Trinotate-2.0.1.ebuild, +metadata.xml: + sci-biology/Trinotate: new package diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest new file mode 100644 index 000000000..8e5dca6ff --- /dev/null +++ b/sci-biology/Trinotate/Manifest @@ -0,0 +1 @@ +DIST v2.0.1.tar.gz 29226683 SHA256 9411b51c5a40a4885a96fb7df2b8f398d176a7cc23b12d642ab85dcaf1b00a93 SHA512 389ae53c53910b26cc78578cd3803cf14925964e2209e1baabdce78f3a2a73d064f6484e0355cc9597f4cd13ec09ba93da97b19cdc5646fb9f8f4ab91fbc98db WHIRLPOOL eded82cee2f82baa50b21f8735a0fb3087bca6d0ea42b6dad098e5d2d64d42639f16189e1d12369b7317b6768542fcd536a875a1363dbc3f722608fa125491f3 diff --git a/sci-biology/Trinotate/Trinotate-2.0.1.ebuild b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild new file mode 100644 index 000000000..0cf111604 --- /dev/null +++ b/sci-biology/Trinotate/Trinotate-2.0.1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes" +HOMEPAGE="http://trinotate.github.io" +SRC_URI="https://github.com/Trinotate/Trinotate/archive/v${PV}.tar.gz" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/ncbi-tools++ + sci-biology/trinityrnaseq + sci-biology/TransDecoder" + +# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer +# >=sci-biology/rnammer-2.3.2 +# +# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp +# >=sci-biology/signalp-4 +# +# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm + +# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'. +# In the 'rnammer' software configuration, edit the rnammer script to point +# $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; + +src_install(){ + perl_set_version + dobin Trinotate + insinto /usr/share/"${PN}" + doins -r admin java sample_data util TrinotateWeb + insinto ${VENDOR_LIB}/${PN} + doins -r PerlLib/* + dodoc Release.Notes +} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml new file mode 100644 index 000000000..2fa34fe9c --- /dev/null +++ b/sci-biology/Trinotate/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">Trinotate/Trinotate</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/VarScan/ChangeLog b/sci-biology/VarScan/ChangeLog index bfcfc5c96..a7470a6cf 100644 --- a/sci-biology/VarScan/ChangeLog +++ b/sci-biology/VarScan/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*VarScan-2.3.7 (13 Mar 2015) + + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +VarScan-2.3.7.ebuild, -VarScan-2.3.6.ebuild: + fix SRC_URI to fetch real source code, ebuild improvements but not working + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> VarScan-2.3.6.ebuild, metadata.xml: sci-biology/VarScan: fix SLOT operators diff --git a/sci-biology/VarScan/Manifest b/sci-biology/VarScan/Manifest index 51896321c..060b85b5e 100644 --- a/sci-biology/VarScan/Manifest +++ b/sci-biology/VarScan/Manifest @@ -1 +1 @@ -DIST VarScan.v2.3.6.jar 102394 SHA256 13edaee278c8a5be2926e48c03ce2ed8916e4a10b9e8817beaee74c3dd00a4b8 SHA512 cfcbc13bdddf319e8d9dbc696ea0c20e1939305048fb8e07cf5db8f4d0ff692535c2a314bbf5825838f272348593e7f095f6d0a53314bb1116da94a9c1aeb68d WHIRLPOOL b6b7c557cdf3db3f34d7d587b521259275aedbb1bc7879aba0a895b411bfb57f478cdd15b88d360be955eea90d648aa439fc3b4bb1a8bb2bb40fe0ba3563605b +DIST VarScan.v2.3.7.source.jar 183371 SHA256 ea19129b2ebbee1840630bf98abbdf2318cc62c66767fae542963db8ed1967a1 SHA512 530aa2000fc8e3763205781c8d9b9de91b876f9c474dde7795387b47d02c965d4766fb8476608c518dcc53cb6704ac83f5187db384c77450581a975040730c50 WHIRLPOOL eae94c91e7e6622dbef259d156bee596346e3b9ea9e919c3a35a2ba5de5c8b7480b9872af999bf6b12b3d0d1ac374bd629c080375c9d9438e14a254b6eff305c diff --git a/sci-biology/VarScan/VarScan-2.3.6.ebuild b/sci-biology/VarScan/VarScan-2.3.7.ebuild index a9a9a07d6..ad7eaa80f 100644 --- a/sci-biology/VarScan/VarScan-2.3.6.ebuild +++ b/sci-biology/VarScan/VarScan-2.3.7.ebuild @@ -8,7 +8,11 @@ inherit java-pkg-2 DESCRIPTION="Variant detection (germline, multi-sample, somatic mut., som. cp nr alterations (CNA)), SNP calls" HOMEPAGE="http://varscan.sourceforge.net/" -SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar" + +# binary +#http://downloads.sourceforge.net/project/varscan/VarScan.v2.3.7.jar +#SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.jar" +SRC_URI="http://downloads.sourceforge.net/project/varscan/${PN}.v${PV}.source.jar" LICENSE="Non-profit-OSL-3.0" SLOT="0" @@ -16,6 +20,11 @@ KEYWORDS="" IUSE="" DEPEND=" - >=virtual/jdk-1.5:* - dev-java/ant-core" + >=virtual/jdk-1.5:*" RDEPEND=">=virtual/jre-1.5:*" + +S="${WORKDIR}"/net/sf/varscan + +src_compile(){ + javac *.java +} diff --git a/sci-biology/VelvetOptimiser/ChangeLog b/sci-biology/VelvetOptimiser/ChangeLog index 44fa73b05..6c91c0b3d 100644 --- a/sci-biology/VelvetOptimiser/ChangeLog +++ b/sci-biology/VelvetOptimiser/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/VelvetOptimiser -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + VelvetOptimiser-2.2.5.ebuild: + sci-biology/VelvetOptimiser: fixed installation of perl-related files + 15 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> VelvetOptimiser-2.2.5.ebuild: sci-biology/VelvetOptimiser: add requirement for threaded perl diff --git a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild index 55290bcef..69a7bd0cd 100644 --- a/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild +++ b/sci-biology/VelvetOptimiser/VelvetOptimiser-2.2.5.ebuild @@ -1,10 +1,11 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -inherit perl-module +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils DESCRIPTION="Optimise three primary parameter options (K, -exp_cov, -cov_cutoff) for Velvet sequence assembler." HOMEPAGE="http://www.vicbioinformatics.com/software.velvetoptimiser.shtml" @@ -23,7 +24,8 @@ RDEPEND="${DEPEND} src_install(){ dobin VelvetOptimiser.pl - insinto ${VENDOR_LIB}/${PN} + perl_set_version + insinto ${VENDOR_LIB}/VelvetOpt doins VelvetOpt/*.pm - dodoc README INSTALL CHANGELOG || die + dodoc README INSTALL CHANGELOG } diff --git a/sci-biology/abacas/ChangeLog b/sci-biology/abacas/ChangeLog new file mode 100644 index 000000000..9c7e05d33 --- /dev/null +++ b/sci-biology/abacas/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/abacas +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> abacas-1.3.1.ebuild: + sci-biology/abacas: clarify description + +*abacas-1.3.1 (31 Mar 2015) + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +abacas-1.3.1.ebuild, +metadata.xml: + sci-biology/abacas: new package diff --git a/sci-biology/abacas/Manifest b/sci-biology/abacas/Manifest new file mode 100644 index 000000000..f95aff4f7 --- /dev/null +++ b/sci-biology/abacas/Manifest @@ -0,0 +1 @@ +DIST abacas.1.3.1.pl 64936 SHA256 0afee209a4f879987b320e2f882bc0eab540a7a712a81a5f01b9795d2749310d SHA512 5b60f85439ab751e4b43eba827dc8b4a8ad7d3acbbdc1f13a0f83e227cf8eb4d94dd5a32c4e6e37aa4e263758973ada5ab8e476685c56b6856c06218b547f76f WHIRLPOOL 5b99ee3aab66f06ccd74f4393dff42f1525a8b2c2c7679dfde180bb2262dd4c9d2d3a45585ed39d10f38c6f53d3b3089be9c65ee1b22d90938fcc09c8da14500 diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild new file mode 100644 index 000000000..e0cdf72ab --- /dev/null +++ b/sci-biology/abacas/abacas-1.3.1.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments, design primers for gap closing" +HOMEPAGE="http://abacas.sourceforge.net" +SRC_URI="http://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + sci-biology/mummer" + +S="${WORKDIR}" + +src_prepare(){ + cp -p "${DISTDIR}"/abacas.1.3.1.pl abacas.pl || die + sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' -i abacas.pl || die +} +src_install(){ + dobin abacas.pl +} + +pkg_postinst(){ + einfo "To view the results use Artemis ACT (sci-biology/artemis)" +} diff --git a/sci-biology/abacas/metadata.xml b/sci-biology/abacas/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/abacas/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/abyss/ChangeLog b/sci-biology/abyss/ChangeLog new file mode 100644 index 000000000..c6809596c --- /dev/null +++ b/sci-biology/abyss/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for sci-biology/abyss +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*abyss-1.3.3-r1 (23 May 2015) +*abyss-1.3.4-r1 (23 May 2015) +*abyss-1.3.6-r1 (23 May 2015) + + 23 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +abyss-1.3.3-r1.ebuild, +abyss-1.3.4-r1.ebuild, +abyss-1.3.6-r1.ebuild, + +files/abyss-1.3.3-ac_prog_ar.patch, +files/abyss-1.3.3-gcc-4.7.patch, + +files/abyss-1.3.3-samtoafg.patch, +files/abyss-1.3.4-gcc-4.7.patch, + +files/abyss-1.3.4-samtoafg.patch, +files/abyss-1.3.6-ac_prog_ar.patch, + +files/abyss-1.3.6-gcc-4.7.patch, +files/abyss-1.3.6-samtoafg.patch, + +metadata.xml: + sci-biology/amos: bring in upstream patch to cope with secondary alignments + from 'bwa mem -M' diff --git a/sci-biology/abyss/Manifest b/sci-biology/abyss/Manifest new file mode 100644 index 000000000..77dfde1ec --- /dev/null +++ b/sci-biology/abyss/Manifest @@ -0,0 +1,3 @@ +DIST abyss-1.3.3.tar.gz 621480 SHA256 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 SHA512 4ec7fdd24bdb1e3d66e2bda50929122ff347107010701703e81ca1609fb1b4913c713991b3fe84a48ccfbc069e126f4f4120aafbab81e54e567a95a2f1099fb2 WHIRLPOOL 35f6fdfe60b70316e67bcbbb0a9c67e952302333e9ec71d893f2de7a94482dca1a604dc8cfef1ecee49e464244bb5df7469a8ad7bdc37bd54ff455b0f75b7914 +DIST abyss-1.3.4.tar.gz 640545 SHA256 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf SHA512 0fa4c14117699945e007412deaeeccca27124a210669accbc1444baf5a4de1a17e1f9b48e6ee43fefed63f0d56b933c847363e59a0fc2bad60ae6d603cd8c09e WHIRLPOOL 42b16f22bc47c8f29b07c256d504d6f58119c64fdcf0e198fd8b836ceb45139fd5cadc7feec72adf958800e55eb1065a449ce7dd288339887dcea4ab13623c01 +DIST abyss-1.3.6.tar.gz 678880 SHA256 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 SHA512 2c6d72e0227c4af2d5740a989168ad35a84b9236dc53b65a29a010c4e5f77e5c4bfaa38bfaa2f14fd530ae6df204294ff167bd40e79f61e8bad6a7489bf34ace WHIRLPOOL 0677b1fd4090ba155fb876c0047a1ccd2ec2e220950e1e9940e1f3df05ef0abd3ba2e3dbabd500d6fab39a8f7d94e02e0a07410934733682a70fa605d2a8bc07 diff --git a/sci-biology/abyss/abyss-1.3.3-r1.ebuild b/sci-biology/abyss/abyss-1.3.3-r1.ebuild new file mode 100644 index 000000000..b7278619c --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.3-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.3.ebuild,v 1.5 2013/08/11 14:55:22 jlec Exp $ + +EAPI="4" + +inherit autotools eutils toolchain-funcs + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +src_prepare() { + tc-export AR + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-ac_prog_ar.patch \ + "${FILESDIR}"/${P}-samtoafg.patch + + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + eautoreconf +} + +src_configure() { + econf \ + --docdir="${EPREFIX}/usr/share/doc/${PF}" \ + $(use_enable openmp) +} diff --git a/sci-biology/abyss/abyss-1.3.4-r1.ebuild b/sci-biology/abyss/abyss-1.3.4-r1.ebuild new file mode 100644 index 000000000..48d767122 --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.4-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.4.ebuild,v 1.3 2013/08/11 14:55:22 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${PN}-1.3.3-ac_prog_ar.patch + "${FILESDIR}"/${P}-samtoafg.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/abyss-1.3.6-r1.ebuild b/sci-biology/abyss/abyss-1.3.6-r1.ebuild new file mode 100644 index 000000000..d5d019eca --- /dev/null +++ b/sci-biology/abyss/abyss-1.3.6-r1.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/abyss/abyss-1.3.6.ebuild,v 1.2 2014/07/06 11:12:45 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/abyss/" +SRC_URI="http://www.bcgsc.ca/downloads/abyss/${P}.tar.gz" + +LICENSE="abyss" +SLOT="0" +IUSE="+mpi openmp" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + dev-cpp/sparsehash + dev-libs/boost + mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +# todo: --enable-maxk=N configure option +# todo: fix automagic mpi toggling + +PATCHES=( + "${FILESDIR}"/${P}-gcc-4.7.patch + "${FILESDIR}"/${P}-ac_prog_ar.patch + "${FILESDIR}"/${P}-samtoafg.patch + ) + +src_prepare() { + tc-export AR + sed -i -e "s/-Werror//" configure.ac || die #365195 + sed -i -e "/dist_pkgdoc_DATA/d" Makefile.am || die + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --docdir="${EPREFIX}/usr/share/doc/${PF}" + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch new file mode 100644 index 000000000..300868f52 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 5c6cb92..b99bedd 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + + # Checks for header files. + AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \ diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch new file mode 100644 index 000000000..42066f7f2 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 506ea0c..a0a403c 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -15,6 +15,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch new file mode 100644 index 000000000..cb7dfb08a --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch @@ -0,0 +1,40 @@ +Hello, + +I see Shaun Jackmans' (abyss-)sam2afg script is available within the +Amos source repository. I find this very useful for coercing output from +assemblers which which don't track read location into amos by remapping +reads against the assembly and converting to afg - not ideal but better +than nothing when you don't have the 'real' read locations to work with. + +This fails, however when reads are aligned with 'bwa mem', which can +output multi-part alignments. sam2afg checks for reuse of the same read +id (presumably to prevent the generation of non-unique eid values), +consequently encountering multiple alignments for a read causes it to die. + +The following one-line patch allows sam2afg to skip these secondary +alignments present in 'bwa mem' output, provided bwa mem has been run +with the '-M' argument which sets the SAM 'secondary alignment' flag on +the alignments in question. + +Hopefully this will also be of use to others... + +Best Regards, +James + +-- +Dr. James Abbott +Lead Bioinformatician +Bioinformatics Support Service +Imperial College, London + + +--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 ++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 +@@ -105,6 +105,7 @@ + die unless defined $qqual; + + $tstart--; # convert to zero-based coordinate ++ next if $flag & 0x100; # secondary alignment + $qid .= "/1" if $flag & 0x40; #FREAD1 + $qid .= "/2" if $flag & 0x80; #FREAD2 + diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch new file mode 100644 index 000000000..c2cc35c31 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch new file mode 100644 index 000000000..cb7dfb08a --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch @@ -0,0 +1,40 @@ +Hello, + +I see Shaun Jackmans' (abyss-)sam2afg script is available within the +Amos source repository. I find this very useful for coercing output from +assemblers which which don't track read location into amos by remapping +reads against the assembly and converting to afg - not ideal but better +than nothing when you don't have the 'real' read locations to work with. + +This fails, however when reads are aligned with 'bwa mem', which can +output multi-part alignments. sam2afg checks for reuse of the same read +id (presumably to prevent the generation of non-unique eid values), +consequently encountering multiple alignments for a read causes it to die. + +The following one-line patch allows sam2afg to skip these secondary +alignments present in 'bwa mem' output, provided bwa mem has been run +with the '-M' argument which sets the SAM 'secondary alignment' flag on +the alignments in question. + +Hopefully this will also be of use to others... + +Best Regards, +James + +-- +Dr. James Abbott +Lead Bioinformatician +Bioinformatics Support Service +Imperial College, London + + +--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 ++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 +@@ -105,6 +105,7 @@ + die unless defined $qqual; + + $tstart--; # convert to zero-based coordinate ++ next if $flag & 0x100; # secondary alignment + $qid .= "/1" if $flag & 0x40; #FREAD1 + $qid .= "/2" if $flag & 0x80; #FREAD2 + diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch new file mode 100644 index 000000000..158e9b126 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch @@ -0,0 +1,18 @@ + configure.ac | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/configure.ac b/configure.ac +index 9d4bb66..aa94364 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -12,6 +12,10 @@ AC_PROG_CPP + AC_PROG_CXX + AC_PROG_INSTALL + AC_PROG_RANLIB ++AN_MAKEVAR([AR], [AC_PROG_AR]) ++AN_PROGRAM([ar], [AC_PROG_AR]) ++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)]) ++AC_PROG_AR + AC_CHECK_TOOL(GHC, ghc) + AM_CONDITIONAL([HAVE_GHC], [test "$GHC"]) + diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch new file mode 100644 index 000000000..c2cc35c31 --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch @@ -0,0 +1,15 @@ + ParseAligns/abyss-fixmate.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc +index 1a169cf..36cc05b 100644 +--- a/ParseAligns/abyss-fixmate.cc ++++ b/ParseAligns/abyss-fixmate.cc +@@ -16,6 +16,7 @@ + #include <iterator> + #include <sstream> + #include <string> ++#include <unistd.h> + + using namespace std; + diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch new file mode 100644 index 000000000..cb7dfb08a --- /dev/null +++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch @@ -0,0 +1,40 @@ +Hello, + +I see Shaun Jackmans' (abyss-)sam2afg script is available within the +Amos source repository. I find this very useful for coercing output from +assemblers which which don't track read location into amos by remapping +reads against the assembly and converting to afg - not ideal but better +than nothing when you don't have the 'real' read locations to work with. + +This fails, however when reads are aligned with 'bwa mem', which can +output multi-part alignments. sam2afg checks for reuse of the same read +id (presumably to prevent the generation of non-unique eid values), +consequently encountering multiple alignments for a read causes it to die. + +The following one-line patch allows sam2afg to skip these secondary +alignments present in 'bwa mem' output, provided bwa mem has been run +with the '-M' argument which sets the SAM 'secondary alignment' flag on +the alignments in question. + +Hopefully this will also be of use to others... + +Best Regards, +James + +-- +Dr. James Abbott +Lead Bioinformatician +Bioinformatics Support Service +Imperial College, London + + +--- abyss-1.3.6/bin/abyss-samtoafg.ori 2015-05-23 23:43:46.797747928 +0200 ++++ abyss-1.3.6/bin/abyss-samtoafg 2015-05-23 23:44:09.227747743 +0200 +@@ -105,6 +105,7 @@ + die unless defined $qqual; + + $tstart--; # convert to zero-based coordinate ++ next if $flag & 0x100; # secondary alignment + $qid .= "/1" if $flag & 0x40; #FREAD1 + $qid .= "/2" if $flag & 0x80; #FREAD2 + diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/abyss/metadata.xml index f17a827e3..f17a827e3 100644 --- a/sci-biology/bwa/metadata.xml +++ b/sci-biology/abyss/metadata.xml diff --git a/sci-biology/amos-short/ChangeLog b/sci-biology/amos-short/ChangeLog new file mode 100644 index 000000000..5a2a78fed --- /dev/null +++ b/sci-biology/amos-short/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/amos-short +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + amos-short-0.9.3.ebuild: + Bump to EAPI=5, but drop KEYWORDS as SRC is + unavailable diff --git a/sci-biology/amos-short/amos-short-0.9.3.ebuild b/sci-biology/amos-short/amos-short-0.9.3.ebuild index 3dcfac928..ad261eb4f 100644 --- a/sci-biology/amos-short/amos-short-0.9.3.ebuild +++ b/sci-biology/amos-short/amos-short-0.9.3.ebuild @@ -1,20 +1,18 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 inherit eutils DESCRIPTION="A Modular, Open-Source whole genome assembler with defaults for short reads" HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="http://sourceforge.net/projects/amos/files/short_read_assembly/0.9.3/AMOS-short.tgz" -#SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" +SRC_URI="http://sourceforge.net/projects/amos/files/short_read_assembly/${PV}/AMOS-short.tgz" LICENSE="GPL-2" SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" DEPEND="" RDEPEND="${DEPEND}" @@ -26,9 +24,9 @@ src_prepare() { } src_compile() { - emake -j1 || die "emake failed" + emake -j1 } src_install() { - emake DESTDIR="${D}" install || die "emake install failed" + emake DESTDIR="${D}" install } diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog index 7d1df6d02..74d1a5dbf 100644 --- a/sci-biology/amos/ChangeLog +++ b/sci-biology/amos/ChangeLog @@ -1,7 +1,31 @@ # ChangeLog for sci-biology/amos -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + amos-3.1.0-r2.ebuild, amos-9999.ebuild: + added dev-qt/qt3support:4 to DEPEND because 'scanelf -qn /usr/bin/hawkeye' + confirms libQt3Support.so is used (thanks to Davide Pesavento pesa@g.o) + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + amos-3.1.0-r2.ebuild, amos-9999.ebuild: + sci-biology/amos: fixed installation of perl-related files + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + amos-3.1.0-r2.ebuild, amos-9999.ebuild: + sci-biology/amos: use doins instead of dobin + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + amos-3.1.0-r2.ebuild, amos-9999.ebuild: + sci-biology/amos: fixed installation of perl-related files + +*amos-3.1.0-r2 (31 Mar 2015) + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +amos-3.1.0-r2.ebuild, +files/amos-3.1.0-gcc-4.7.patch, + +files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, amos-9999.ebuild: + sci-biology/amos: fix installation process and dependencies + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> -amos-3.1.0-r1.ebuild, amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch, -files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest new file mode 100644 index 000000000..27ad50ff2 --- /dev/null +++ b/sci-biology/amos/Manifest @@ -0,0 +1 @@ +DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild new file mode 100644 index 000000000..0b777e2a2 --- /dev/null +++ b/sci-biology/amos/amos-3.1.0-r2.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) +inherit eutils python-r1 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="A Modular, Open-Source whole genome assembler" +HOMEPAGE="http://amos.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="mpi qt4" + +DEPEND=" + mpi? ( virtual/mpi ) + dev-libs/boost + qt4? ( dev-qt/qtcore:4[qt3support] + dev-qt/qt3support:4 ) + sci-biology/blat + sci-biology/jellyfish" +RDEPEND="${DEPEND} + dev-lang/perl + dev-perl/DBI + dev-perl/Statistics-Descriptive + sci-biology/mummer" + +MAKEOPTS+=" -j1" + +src_prepare() { + epatch \ + "${FILESDIR}"/${P}-gcc-4.7.patch \ + "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch +} + +# --with-jellyfish location of Jellyfish headers + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 + # bambus needs TIGR::FASTAreader.pm and others + # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it + perl_set_version + insinto ${VENDOR_LIB}/AMOS + doins "${D}"/usr/lib64/AMOS/*.pm + insinto ${VENDOR_LIB}/TIGR + doins "${D}"/usr/lib64/TIGR/*.pm + # move also /usr/lib64/AMOS/AMOS.py to /usr/bin + mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die + # zap the mis-placed files ('make install' is at fault) + rm -f "${D}"/usr/lib64/AMOS/*.pm + rm -rf "${D}"/usr/lib64/TIGR +} diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild index baecc2f9e..9ac9c4c2d 100644 --- a/sci-biology/amos/amos-9999.ebuild +++ b/sci-biology/amos/amos-9999.ebuild @@ -1,11 +1,13 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -AUTOTOOLS_AUTORECONF=true +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs +AUTOTOOLS_AUTORECONF=true inherit autotools-utils git-r3 DESCRIPTION="Genome assembly package live cvs sources" @@ -16,11 +18,35 @@ EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos" LICENSE="Artistic" SLOT="0" KEYWORDS="" -IUSE="" +IUSE="mpi qt4" DEPEND=" + mpi? ( virtual/mpi ) dev-libs/boost - dev-qt/qtcore:4" + qt4? ( dev-qt/qtcore:4[qt3support] + dev-qt/qt3support:4 ) + sci-biology/blat + sci-biology/jellyfish" RDEPEND="${DEPEND} dev-perl/DBI + dev-perl/Statistics-Descriptive sci-biology/mummer" + +# --with-jellyfish location of Jellyfish headers + +src_install() { + default + python_replicate_script "${ED}"/usr/bin/goBambus2 + # bambus needs TIGR::FASTAreader.pm and others + # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it + perl_set_version + insinto ${VENDOR_LIB}/AMOS + doins "${D}"/usr/lib64/AMOS/*.pm + insinto ${VENDOR_LIB}/TIGR + doins "${D}"/usr/lib64/TIGR/*.pm + # move also /usr/lib64/AMOS/AMOS.py to /usr/bin + mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die + # zap the mis-placed files ('make install' is at fault) + rm -f "${D}"/usr/lib64/AMOS/*.pm + rm -rf "${D}"/usr/lib64/TIGR +} diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch new file mode 100644 index 000000000..de2a41184 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch @@ -0,0 +1,15 @@ + src/Align/find-tandem.cc | 1 + + 1 files changed, 1 insertions(+), 0 deletions(-) + +diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc +index ddf1cab..a29e21e 100644 +--- a/src/Align/find-tandem.cc ++++ b/src/Align/find-tandem.cc +@@ -7,6 +7,7 @@ + #include <vector> + #include <ctime> + #include <sys/time.h> ++#include <unistd.h> + using namespace std; + + const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch new file mode 100644 index 000000000..97a8f59d0 --- /dev/null +++ b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch @@ -0,0 +1,25 @@ +--- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 ++++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 +@@ -1,7 +1,7 @@ + #pipeline script for assembly + Bambus 2 + #contributed by Todd J Treangen + +-import string, sys, os, subprocess#, spincursor ++import sys, os, subprocess#, spincursor + + RED = "\033[0;31m" + GREEN = "\033[0;32m" +@@ -360,7 +360,7 @@ + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) + +- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) ++ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) + + if xopt_dict["verbose"] == 1: + print "10) running OutputResults" +@@ -388,4 +388,3 @@ + else: + print "\t\t%s...failed%s"%(RED,NONE) + sys.exit(1) +-) diff --git a/sci-biology/angsd/ChangeLog b/sci-biology/angsd/ChangeLog new file mode 100644 index 000000000..a0ed7633e --- /dev/null +++ b/sci-biology/angsd/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/angsd +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*angsd-9999 (20 Mar 2015) + + 20 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +angsd-9999.ebuild, + +metadata.xml: + sci-biology/angsd: new package, -9999 compiles fine, need a snapshot for 0.700 + version or whichever diff --git a/sci-biology/angsd/angsd-9999.ebuild b/sci-biology/angsd/angsd-9999.ebuild new file mode 100644 index 000000000..2850ddc45 --- /dev/null +++ b/sci-biology/angsd/angsd-9999.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-2 + +[ "$PV" == "9999" ] && inherit git-2 + +DESCRIPTION="Population genetics analysis package" +HOMEPAGE="http://www.popgen.dk/angsd" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/ANGSD/angsd.git" + KEYWORDS="" +else + EGIT_REPO_URI="https://github.com/ANGSD/angsd.git" + EGIT_BRANCH="0.700" + KEYWORDS="" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="" + +DEPEND="dev-lang/R + sci-libs/htslib" +RDEPEND="${DEPEND}" + +# https://github.com/ANGSD/angsd/issues/9 +src_prepare(){ + sed -e 's@FLAGS=-O3@FLAGS=@' \ + -e 's@HTSLIB = .*@HTSLIB = -lhts@' \ + -e 's@all: htshook angsd misc@all: angsd misc@' -i Makefile || die + sed -e 's@HTSLIB = .*@HTSLIB = -lhts@' \ + -e 's@HTSDIR = .*@HTSDIR = /usr/include@' -i misc/Makefile || die + sed -e 's@include "../htslib/bgzf.h@include "bgzf.h@' -i misc/thetaStat.cpp || die +} + +src_compile(){ + emake HTS=/usr/include +} + +src_install(){ + dobin angsd + dodoc README.md + cd misc || die + dobin supersim thetaStat realSFS emOptim2 msToGlf smartCount printIcounts splitgl contamination NGSadmix +} diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/angsd/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/argo-bin/ChangeLog b/sci-biology/argo-bin/ChangeLog index 7f9152a7a..1bf8c1aa9 100644 --- a/sci-biology/argo-bin/ChangeLog +++ b/sci-biology/argo-bin/ChangeLog @@ -1,7 +1,21 @@ # ChangeLog for sci-biology/argo-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + argo-bin-1.0.31.ebuild, argo-bin-2.0.3.ebuild: + sci-biology/argo-bin: remove IUSE + +*argo-bin-2.0.3 (26 May 2015) + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +argo-bin-2.0.3.ebuild, argo-bin-1.0.31.ebuild: + sci-biology/argo-bin: ebuild cleanup; version bump + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + argo-bin-1.0.31.ebuild: + sci-biology/argo-bin: redefine S variable so we can chdir to a WORKDIR (not + sure why the jar archive must be unpacked there at all ...) + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> argo-bin-1.0.31.ebuild: Cleaned ebuild - diff --git a/sci-biology/argo-bin/Manifest b/sci-biology/argo-bin/Manifest index 7cda4c55d..73550affb 100644 --- a/sci-biology/argo-bin/Manifest +++ b/sci-biology/argo-bin/Manifest @@ -1 +1,2 @@ -DIST argo.jar 26624770 SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf +DIST argo.jar 26624770 SHA256 33ece2dba7ee5cc36f5aab99b3e7df2d641b261d86aacac00745e9d4a2e914cf SHA512 fc1aaa39453502054d402386d3551014d71a81a73593420fe5073a462b3f605e00e8b32e21e54a4f669a3f09a25e8946db17928c65c17beea26ec4316e91458d WHIRLPOOL a1a83d721f4273cee97ac04e9935c5254adf84f9187c5a7330339f71cad826cab3eb375105ba454835d5803de5d476615b6c497fb47af37536a1211d48a6b09e +DIST argo2.jar 27685069 SHA256 7ebcb16d7dcf85d1a7c8ef427f78a4cb6a48b9ff2a1814b6d4931cf4f9218002 SHA512 8a03cfe6016ffa2d661dbf04ce9fde6e5474fcf111336399c934c481a4c71758b3007a20f3af931725c9e2f5f2bf3bc0c1d131cdda6e57992c10a6c0854207a8 WHIRLPOOL c89249b732c6450eb69170f0d00950a854a613eba10aee53290f1bf50ac1888bcbd7a2902788e824125702e2002e80015d0b21fcbd89bd0593688c4878d981e4 diff --git a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild index 6a708d5c3..a59ae7a06 100644 --- a/sci-biology/argo-bin/argo-bin-1.0.31.ebuild +++ b/sci-biology/argo-bin/argo-bin-1.0.31.ebuild @@ -1,24 +1,28 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit java-utils-2 toolchain-funcs DESCRIPTION="Visualization and manually annotating whole genomes" -HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" SRC_URI="http://www.broadinstitute.org/annotation/argo/argo.jar" -#SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" +# +# Release Number: 1.0.31 +# Release Date: 2010-02-05 LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="java" +IUSE="" -DEPEND="" +DEPEND="!sci-biology/argo" RDEPEND="${DEPEND} - java? ( >=virtual/jre-1.4 )" + >=virtual/jre-1.5:*" +S="${WORKDIR}" src_install() { java-pkg_newjar "${DISTDIR}"/argo.jar argo.jar diff --git a/sci-biology/argo-bin/argo-bin-2.0.3.ebuild b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild new file mode 100644 index 000000000..8e475e6c3 --- /dev/null +++ b/sci-biology/argo-bin/argo-bin-2.0.3.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-utils-2 toolchain-funcs + +DESCRIPTION="Visualization and manually annotating whole genomes" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" +SRC_URI="http://www.broadinstitute.org/annotation/argo2/releases/argo2.jar" +# +# Release Number: 3 +# Release Date: 2010-06-23 + +LICENSE="LGPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="!sci-biology/argo" +RDEPEND="${DEPEND} + >=virtual/jre-1.5:*" +S="${WORKDIR}" + +src_install() { + java-pkg_newjar "${DISTDIR}"/argo2.jar argo2.jar + java-pkg_dolauncher +} diff --git a/sci-biology/argo/ChangeLog b/sci-biology/argo/ChangeLog new file mode 100644 index 000000000..72a3d3cb9 --- /dev/null +++ b/sci-biology/argo/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/argo +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: + sci-biology/argo: ebuild cleanup + + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> argo-1.0.24.ebuild: + fix java depencies syntax diff --git a/sci-biology/argo/Manifest b/sci-biology/argo/Manifest index b3a1cb088..6a14974aa 100644 --- a/sci-biology/argo/Manifest +++ b/sci-biology/argo/Manifest @@ -1 +1 @@ -DIST workspace-2008-03-11.tgz 109194467 SHA256 0ee6acb0ebdc17cfbedfedb8559ba950ddd4c5c4ef5f7875fa93f3fad885b99e +DIST workspace-2008-03-11.tgz 109194467 SHA256 0ee6acb0ebdc17cfbedfedb8559ba950ddd4c5c4ef5f7875fa93f3fad885b99e SHA512 42696ac2a4dc0167d9fb84d8420254e4ba9256447ef320c1ca3906aac48944635397098962ee5a207b39afacc0faa2dc584e96c29ab1dead9892d6ff85228820 WHIRLPOOL d6ce9bad3039fb77eb9b0ebc00b0b6e966fa26436ed90e8942f0489cf024602b3cad817e0696e6c8770d68c497715a1841222cf68839be44efff921210a496af diff --git a/sci-biology/argo/argo-1.0.24.ebuild b/sci-biology/argo/argo-1.0.24.ebuild index c58dfe443..6e522b616 100644 --- a/sci-biology/argo/argo-1.0.24.ebuild +++ b/sci-biology/argo/argo-1.0.24.ebuild @@ -1,24 +1,29 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit java-pkg-2 java-ant-2 java-utils-2 toolchain-funcs DESCRIPTION="Production tool for visualizing and manually annotating whole genomes" -HOMEPAGE="http://www.broadinstitute.org/annotation/argo/" +HOMEPAGE="http://www.broadinstitute.org/annotation/argo2 + http://www.broadinstitute.org/annotation/argo" SRC_URI="http://www.broadinstitute.org/annotation/argo/src/workspace-2008-03-11.tgz" +# +# cat workspace-2008-03-11/annotation/argo/version.txt +# Gebo-1.0.17-build-1313 LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND=">=virtual/jre-1.5" DEPEND=" - >=virtual/jdk-1.5 + !sci-biology/argo-bin + >=virtual/jdk-1.5:* dev-java/ant-core" +RDEPEND=">=virtual/jre-1.5:*" S="${WORKDIR}"/workspace-2008-03-11 @@ -29,5 +34,7 @@ src_compile(){ src_install() { java-pkg_dojar annotation/dist/argo/argo.jar + #java-pkg_dolauncher --jar argo.jar java-pkg_dojar annotation/dist/argo/argo-applet-unproguarded.jar + #java-pkg_dolauncher --jar argo-applet-unproguarded.jar } diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog index d1286af50..4320cdcff 100644 --- a/sci-biology/artemis-bin/ChangeLog +++ b/sci-biology/artemis-bin/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + artemis-bin-16.0.11.ebuild: + sci-biology/artemis-bin: EAPI bump + *artemis-bin-16.0.11 (08 Jan 2015) 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/artemis-bin/Manifest b/sci-biology/artemis-bin/Manifest index d9651ab45..3bd261d96 100644 --- a/sci-biology/artemis-bin/Manifest +++ b/sci-biology/artemis-bin/Manifest @@ -1,2 +1,4 @@ DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f DIST artemis_compiled_v16.0.11.tar.gz 10722613 SHA256 0413c3f0deab4d813bc4f3af7aef8cca09ad2111b3497a0696c18a31857ffd4b SHA512 a0fb9f64b0fb869bde9fe2d1788ed938a16ea0bd75315abd93e65af89772fe9d4589b7e7813286c9b1d90f1f3133c16d9bc35ce78d1740c5631ca0e32633e421 WHIRLPOOL 0682bdfead9f95a17180816ed445226c128a804f8db3549c78627b510330694b60fd7ab0e419766bf08295f3a266eefd0dfd85c0d1244c80009b5aba0c29052a +DIST artemis_v16.0.11.jar 11292419 SHA256 f368714105646cfc31460cfcfb72b8b33490c7684ee5323d7dd181060039c80f SHA512 2fbd7c5ab12c2ca710906324eb5ee861d4821eaf923f630a800ce2b2de4e43c3971cf6c470140aa2654741ab79440a2039e8b9a17502ca955432d9ef311e9f84 WHIRLPOOL fc605625b536853ee7657b09bca93f04b9f1da67a093875bcfac0d4948f7daf020c26f0624b551aba36f21e87a7ee8b933e0e26c45a715ea2fe6cb9211d0f78f +DIST sartemis_v16.0.11.jar 11832144 SHA256 834ad0464405843904b173f38220f47867ec8eb779cb2c37d6de7ba585ef133c SHA512 6fd63ac81eed727816fe633cde3e9fab9eaf71a61c74aef4f82c8c4dc24efe93ce86494ebdf3fcb3d82e50aed5c277f383f67c1b7b68ae81cf872f2982bc1850 WHIRLPOOL 874ab57f11b011a222efd4b91278614941b096756faf0259b844453dfb082d99bae503faa2ffaeb6c4d56b4317b3bcc00a49f8b5b16d6c7cc02968b4911c503a diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild index 69b26ca35..3c0415906 100644 --- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild +++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit java-pkg-2 @@ -10,22 +10,35 @@ MY_V="16" DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz + ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar + ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf" - LICENSE="GPL-2" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="" -DEPEND="sci-biology/samtools - sci-biology/BamView" +S="${WORKDIR}"/artemis + +DEPEND=" + !sci-biology/artemis + sci-biology/samtools" RDEPEND="${DEPEND} >=virtual/jre-1.6" src_install(){ - dodoc artemis.pdf + cp -p "${DISTDIR}"/artemis_v"${PV}".jar artemis.jar || die + java-pkg_dojar artemis.jar + cp -p "${DISTDIR}"/sartemis_v"${PV}".jar sartemis.jar || die + java-pkg_dojar sartemis.jar + dodoc "${DISTDIR}"/artemis.pdf README } -# do not know what is the diffeerence between artemis_compiled_v16.0.6.tar.gz, artemis_v16.0.6.jar and sartemis_v16.0.6.jar -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.6/ +# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files +# artemis_v16.0.11.jar and sartemis_v16.0.11.jar +# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/ + +pkg_postinst(){ + einfo "For BAM file support please install sci-biology/BamView" +} diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog index 4bebaffc8..818f34c42 100644 --- a/sci-biology/artemis/ChangeLog +++ b/sci-biology/artemis/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 09 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild: + sci-biology/artemis: ebuild cleanup; officially there is not install and one + needs to keep the structure of the source tree and execute directly from + there; therefore the ebuild does not work yet + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild: sci-biology/artemis: fix SLOT operators diff --git a/sci-biology/artemis/Manifest b/sci-biology/artemis/Manifest new file mode 100644 index 000000000..1c027d782 --- /dev/null +++ b/sci-biology/artemis/Manifest @@ -0,0 +1 @@ +DIST artemis.pdf 1149449 SHA256 ab573b4ea7b895cb7d2a97e4d42a71938f1feda44e2da22fe5b079583ad87ba6 SHA512 1c3056dab7239c3a68b2e76491d77612f22ac8f83eaf32e0ab0a3901e03d3c65d5ac02f5758d2d7728d94dd44c29517a498fa94a947d5d319ded43ddec4ba5fb WHIRLPOOL a75266ae72075ea7547560a9046c1e0f813956b94a5c3d9af3cd08a579ed60af842c6ece94e6b1dfa5db1820094069edb7d88b4ee6256410ebced4310739d79f diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild index 630e392f3..8db550951 100644 --- a/sci-biology/artemis/artemis-9999.ebuild +++ b/sci-biology/artemis/artemis-9999.ebuild @@ -6,9 +6,9 @@ EAPI=5 inherit java-pkg-2 java-ant-2 git-r3 -DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool" +DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool" HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis" -SRC_URI="" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf" EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis" LICENSE="GPL-2" @@ -21,13 +21,41 @@ RDEPEND=" sci-biology/samtools >=virtual/jre-1.6:*" DEPEND="${RDEPEND} + !sci-biology/artemis-bin dev-java/ant-core - >=virtual/jdk-1.6:*" + >=virtual/jdk-1.6:* + dev-java/log4j + dev-java/jdbc-postgresql + dev-java/jakarta-regexp + dev-java/batik + dev-java/j2ssh + sci-biology/picard + dev-java/biojava" +# some more dependencies extracted from /usr/bin/act +# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar, +# # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html # http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html # http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial -# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf - # BamView is at http://bamview.sourceforge.net/ + +src_compile(){ + ant || die +} + +src_install(){ + dobin act act.command art dnaplotter gff2embl + java-pkg_dojar ant-build/artemis.jar + dodoc "${DISTDIR}"/artemis.pdf README +} + +# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files +# artemis_v16.0.11.jar and sartemis_v16.0.11.jar +# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/ + +pkg_postinst(){ + einfo "For BAM file support please install sci-biology/BamView" + einfo " from http://bamview.sourceforge.net" +} diff --git a/sci-biology/augustus/ChangeLog b/sci-biology/augustus/ChangeLog new file mode 100644 index 000000000..d24d31d94 --- /dev/null +++ b/sci-biology/augustus/ChangeLog @@ -0,0 +1,90 @@ +# ChangeLog for sci-biology/augustus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/augustus/ChangeLog,v 1.19 2013/03/11 14:37:00 jlec Exp $ + +*augustus-3.1 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +augustus-3.1.ebuild, -augustus-3.0.3.ebuild: + sci-biology/augustus: version bump + + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild: + sci-biology/augustus: Switch RDEPEND - DEPEND + + 08 Apr 2015; Justin Lecher <jlec@gentoo.org> augustus-3.0.3.ebuild: + sci-biology/augustus: Drop suspect DEPEND + + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + + 31 Jan 2013; Justin Lecher <jlec@gentoo.org> -augustus-2.3.1.ebuild, + -augustus-2.4.ebuild, -augustus-2.5.ebuild, metadata.xml: + Drop old, fixes multiple QA issues, #454822 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for x86, wrt bug #454842 + + 31 Jan 2013; Agostino Sarubbo <ago@gentoo.org> augustus-2.5.5.ebuild: + Stable for amd64, wrt bug #454842 + +*augustus-2.5.5 (23 Jun 2011) + + 23 Jun 2011; Justin Lecher <jlec@gentoo.org> augustus-2.3.1.ebuild, + augustus-2.4.ebuild, augustus-2.5.ebuild, +augustus-2.5.5.ebuild, + +files/augustus-2.5.5-sane-build.patch: + Version Bump, respect LDFLAGS, #337655 + + 09 Mar 2011; Markos Chandras <hwoarang@gentoo.org> augustus-2.4.ebuild: + Stable on amd64 wrt bug #353573 + + 09 Mar 2011; Thomas Kahle <tomka@gentoo.org> augustus-2.4.ebuild: + x86 stable per bug 353573 + + 04 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + augustus-2.5.ebuild: + Respect LDFLAGS + +*augustus-2.5 (03 Feb 2011) + + 03 Feb 2011; Andrey Kislyuk <weaver@gentoo.org> augustus-2.4.ebuild, + +augustus-2.5.ebuild: + Version bump, update SRC_URI + +*augustus-2.4 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -augustus-2.1.ebuild, + -files/augustus-2.1-glibc-2.10.patch, +augustus-2.4.ebuild: + Version bump, drop old + + 09 Feb 2010; Pacho Ramos <pacho@gentoo.org> augustus-2.3.1.ebuild: + amd64 stable, bug 298767 + + 29 Dec 2009; Christian Faulhammer <fauli@gentoo.org> + augustus-2.3.1.ebuild: + stable x86, bug 298767 + +*augustus-2.3.1 (16 Nov 2009) + + 16 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> +augustus-2.3.1.ebuild: + Version bump + + 31 Oct 2009; Markus Meier <maekke@gentoo.org> augustus-2.1.ebuild: + amd64/x86 stable, bug #290924 + + 09 Aug 2009; Samuli Suominen <ssuominen@gentoo.org> augustus-2.1.ebuild, + +files/augustus-2.1-glibc-2.10.patch: + Fix building with GLIBC 2.10+ wrt #276719. + +*augustus-2.1 (19 Mar 2009) + + 19 Mar 2009; Andrey Kislyuk <weaver@gentoo.org> + -files/augustus-2.0.3-cflags.patch, -files/augustus-2.0.3-gcc4.3.patch, + -augustus-2.0.3.ebuild, +augustus-2.1.ebuild: + Version bump + +*augustus-2.0.3 (04 Jan 2009) + + 04 Jan 2009; weaver <weaver@gentoo.org> + +files/augustus-2.0.3-cflags.patch, +files/augustus-2.0.3-gcc4.3.patch, + +metadata.xml, +augustus-2.0.3.ebuild: + Initial commit, ebuild written by me diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest new file mode 100644 index 000000000..2de508495 --- /dev/null +++ b/sci-biology/augustus/Manifest @@ -0,0 +1 @@ +DIST augustus-3.1.tar.gz 75867488 SHA256 6db15a859537ccab8739e09c9c28f59c31dd9781e19d91f0d4489f60c7c15486 SHA512 7662b9610d8c1fa7311e3c94b698f0051d4ec885645f5def8df0a9c65a42bd11d2e538c640170716b5f6a4064ad52549be80be977724cd2d52d9623fcd85e061 WHIRLPOOL 9409cd8c6272a39b52c8338d7a59099c86ba4b106ab6227927ea8e0afc3016db3914cacacf8873d259483d73d10d143b3123780fe39591e5b54b91ccba161288 diff --git a/sci-biology/augustus/augustus-3.1.ebuild b/sci-biology/augustus/augustus-3.1.ebuild new file mode 100644 index 000000000..d0fe711cf --- /dev/null +++ b/sci-biology/augustus/augustus-3.1.ebuild @@ -0,0 +1,59 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Eukaryotic gene predictor" +HOMEPAGE="http://augustus.gobics.de/" +SRC_URI="http://bioinf.uni-greifswald.de/augustus/binaries/${P}.tar.gz" + +LICENSE="GPL-3" +# temporary drop in licensing scheme, see http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/HISTORY.TXT +# http://stubber.math-inf.uni-greifswald.de/bioinf/augustus/binaries/LICENCE.TXT +# LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="examples" + +RDEPEND=" + sci-libs/gsl + dev-libs/boost + sys-libs/zlib" +DEPEND="${RDEPEND} + sys-devel/flex" + +src_prepare() { + # TODO: do we need anything from the 2.5.5 patch? + # epatch "${FILESDIR}"/${P}-sane-build.patch + tc-export CC CXX +} + +src_compile() { + emake clean && emake +} + +src_install() { + dobin bin/* +# dobin src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign} + + exeinto /usr/libexec/${PN} + doexe scripts/*.p* + insinto /usr/libexec/${PN} + doins scripts/*.conf + + insinto /usr/share/${PN} + doins -r config + + echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + + dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt} + + if use examples; then + insinto /usr/share/${PN}/ + doins -r docs/tutorial examples + fi +} diff --git a/sci-biology/embassy-cbstools/metadata.xml b/sci-biology/augustus/metadata.xml index f17a827e3..f17a827e3 100644 --- a/sci-biology/embassy-cbstools/metadata.xml +++ b/sci-biology/augustus/metadata.xml diff --git a/sci-biology/bambino/ChangeLog b/sci-biology/bambino/ChangeLog index ddfd6bee9..0078ba794 100644 --- a/sci-biology/bambino/ChangeLog +++ b/sci-biology/bambino/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/bambino -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambino-1.02.ebuild, + bambino-1.06.ebuild: + fix java dependencies syntax + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> bambino-1.02.ebuild, bambino-1.06.ebuild: fixed DESCRIPTION diff --git a/sci-biology/bambino/bambino-1.02.ebuild b/sci-biology/bambino/bambino-1.02.ebuild index 2a6d7f5d4..1fd268d70 100644 --- a/sci-biology/bambino/bambino-1.02.ebuild +++ b/sci-biology/bambino/bambino-1.02.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -19,9 +19,9 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" +DEPEND=">=virtual/jdk-1.6:*" RDEPEND="${DEPEND} - >=virtual/jdk-1.6 + >=virtual/jre-1.6:* sci-biology/picard dev-java/jdbc-mysql" diff --git a/sci-biology/bambino/bambino-1.06.ebuild b/sci-biology/bambino/bambino-1.06.ebuild index c717ffed3..b13b855bc 100644 --- a/sci-biology/bambino/bambino-1.06.ebuild +++ b/sci-biology/bambino/bambino-1.06.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -19,9 +19,9 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" +DEPEND=">=virtual/jdk-1.6:*" RDEPEND="${DEPEND} - >=virtual/jdk-1.6 + >=virtual/jre-1.6:* sci-biology/picard dev-java/jdbc-mysql" diff --git a/sci-biology/bambus/ChangeLog b/sci-biology/bambus/ChangeLog new file mode 100644 index 000000000..a1f191be9 --- /dev/null +++ b/sci-biology/bambus/ChangeLog @@ -0,0 +1,14 @@ +# ChangeLog for sci-biology/bambus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: + sci-biology/bambus: actually do not install the outdated *.pm files but rely + on them from sci-biology/amos + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: + sci-biology/bambus: fixed installation of perl-related files + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bambus-2.33.ebuild: + sci-biology/bambus: fix installation process and use current perl-module files + from amos package instead diff --git a/sci-biology/bambus/Manifest b/sci-biology/bambus/Manifest index 1625f9a2b..117e5e97f 100644 --- a/sci-biology/bambus/Manifest +++ b/sci-biology/bambus/Manifest @@ -1 +1,2 @@ -DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc +DIST bambus-2.33.tar.gz 504535 SHA256 bc8e3c712719bccb00357001713e56f58aac57ae452fd73148eeccff291eefdc SHA512 b31360439938bd88a19694af0addceafa658e144c2d6dcc156f7b5a3a2df0e806d55f4e4e7cd31dbbdd9464201506da61b3d0b288ba34138770d3023ab40795a WHIRLPOOL de070bc2b8972b2563446dc2f2b130310110926dc8e7e8f08477992b7f43aa5636a65ce66f21781fdb3a0751e49f5072f0080204b07d7ea866631c81b2902d62 +DIST scaffolding_MIRA_BAMBUS.pdf 181237 SHA256 1a86233ab1cfaef6b23a09267129fd3eeec0a81a4d90995d69c3c72da5cca68c SHA512 fcdf458917b09613dea2769921dee625528b08fbb92c5bc0d8b32bb0f29f6b8d163e4b0a2fdf6c338ba4a872cd29cffd7d0a7aeb8beb6c9afc76d0cc812bbc29 WHIRLPOOL 780bf5d38357377477becae03feee14c8f2603cd337716c12b9011785897830edf48a35423003b57e0bc1dc550a9921800d0ff64c49f44ca01c928bf3df36bbf diff --git a/sci-biology/bambus/bambus-2.33.ebuild b/sci-biology/bambus/bambus-2.33.ebuild index 2c05ad171..7ac757aee 100644 --- a/sci-biology/bambus/bambus-2.33.ebuild +++ b/sci-biology/bambus/bambus-2.33.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 -inherit eutils +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs DESCRIPTION="Scaffolding Polymorphic Genomes and Metagenomes, a part of AMOS bundle" HOMEPAGE="http://sourceforge.net/apps/mediawiki/amos/index.php?title=AMOS + http://sourceforge.net/projects/amos/files/bambus http://www.tigr.org/software/bambus" -SRC_URI="http://sourceforge.net/projects/amos/files/bambus/2.33/bambus-2.33.tar.gz" +SRC_URI="http://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz + http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" LICENSE="Artistic" SLOT="0" @@ -26,28 +29,32 @@ RDEPEND="${DEPEND} src_prepare() { # epatch "${FILESDIR}"/amos-2.0.8-gcc44.patch - sed -i 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' Makefile || die - sed -i 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' doc/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/IO/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/DotLib/Makefile || die - sed -i 's:INSTDIR:DESTDIR:g' src/grommit/Makefile || die - sed -i 's:^CC:#CC:' Makefile || die - sed -i 's:^CXX:#CXX:' Makefile || die - sed -i 's:^LD:#LD:' Makefile || die - sed -i 's:^AR:#AR:' Makefile || die - sed -i 's:^export:#export:' Makefile || die - sed -i 's:-Wl::' src/grommit/Makefile || die - sed -i 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/ -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:make all:make all DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:make install:make install DESTDIR=$(DESTDIR):' Makefile || die - sed -i 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)) -shared -fPIC:' src/grommit/Makefile || die - sed -i 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS):' src/grommit/Makefile || die - sed -i 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' src/goBambus.pl || die + sed -e 's:BASEDIR = /usr/local/packages/bambus:BASEDIR = /usr:' -i Makefile || die + sed -e 's:PERL = /usr/local/bin/perl:PERL = /usr/bin/perl:' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i doc/Makefile || die + sed -e 's:make all;:make all || exit 255;:' -i src/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/IO/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/DotLib/Makefile || die + sed -e 's:INSTDIR:DESTDIR:g' -i src/grommit/Makefile || die + sed -e "s:^CC\t=:CC=$(tc-getCXX):" -i Makefile || die + sed -e "s:^CXX\t=:CXX=$(tc-getCXX):" -i Makefile || die + sed -e "s:^LD\t:LD=$(tc-getCXX):" -i Makefile || die + sed -e 's:^AR\t=:#AR=:' -i Makefile || die + sed -e 's:^export:#export:' -i Makefile || die + sed -e 's:-Wl::' -i src/grommit/Makefile || die + # sed -e 's:-L../TIGR_Foundation_CC/:-L../TIGR_Foundation_CC/:' -i src/grommit/Makefile || die + sed -e 's:make all:make all DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e 's:make install:make install DESTDIR=$(DESTDIR):' -i Makefile || die + sed -e "s:# Main targets:LD=$(tc-getCXX):" -i src/grommit/Makefile || die + sed -e 's:^LDFLAGS =$(STATIC_$(OSTYPE)):LDFLAGS += $(STATIC_$(OSTYPE)):' -i src/grommit/Makefile || die + sed -e 's:CFLAGS = $(HEADERS) -g:CFLAGS += $(HEADERS) -fPIC:' -i src/grommit/Makefile || die + sed -e 's:^$ENV{PERLLIB}:$ENV{PERL5LIB}:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/goBambus.pl || die + sed -e 's:^#!.*:#!/usr/bin/perl:' -i src/IO/*.pl || die einfo "Argh, cannot delete src/TIGR_Foundation_CC/ because it has some extra files getopt.* not present" - einfo "in sci-biology/tigr-foundation-libs. It sees bambus-2.33/src/TIGR_Foundation_CC/ contains" + einfo "in sci-biology/tigr-foundation-libs. It seems bambus-2.33/src/TIGR_Foundation_CC/ contains" einfo "the following 3 files getopt.cc getopt.hh getopt1.cc which were possibly copied" einfo "over from some old GNU libc and maybe could be completely dropped?" einfo "Affected would be:" @@ -59,7 +66,7 @@ src_prepare() { #sed -i 's:TIGR_Foundation_CC::' src/Makefile || die "Failed to zap last pointer to local copy of tigr-foundation-libs" cd src/TIGR_Foundation_CC || die "Failed to cd src/TIGR_Foundation_CC/" epatch "${FILESDIR}"/TigrFoundation-all-patches.patch || die - sed -i "s:/export/usr/local:${D}/usr:g" Makefile || die + sed -e "s:/export/usr/local:${D}/usr:g" -i Makefile || die } src_compile() { @@ -99,6 +106,8 @@ src_install() { rmdir "${D}"/usr/doc || die dobin "${FILESDIR}"/goBambus.pl || die "Failed to install the alternative of goBambus.py written in perl" + dodoc "${DISTDIR}"/scaffolding_MIRA_BAMBUS.pdf + rm -rf "${D}"/usr/lib } pkg_postinst(){ diff --git a/sci-biology/bamtools/ChangeLog b/sci-biology/bamtools/ChangeLog index 8afcd01cf..54378eb20 100644 --- a/sci-biology/bamtools/ChangeLog +++ b/sci-biology/bamtools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/bamtools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bamtools: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 @@ -25,4 +28,3 @@ 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bamtools-9999.ebuild: Moved from 'git' to 'git-2' - diff --git a/sci-biology/bamtools/metadata.xml b/sci-biology/bamtools/metadata.xml index e304b1287..1bb8db887 100644 --- a/sci-biology/bamtools/metadata.xml +++ b/sci-biology/bamtools/metadata.xml @@ -7,4 +7,7 @@ <name>Martin Mokrejs</name> </maintainer> <longdescription>BAM (Binary Alignment/Map) format is useful for storing large DNA sequence alignments. It is closely related to the text-based SAM format, but optimized for random-access. BamTools provides a fast, flexible C++ API for reading and writing BAM files.</longdescription> + <upstream> + <remote-id type="github">pezmaster31/bamtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/barnacle/ChangeLog b/sci-biology/barnacle/ChangeLog new file mode 100644 index 000000000..7d5b98162 --- /dev/null +++ b/sci-biology/barnacle/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/barnacle +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*barnacle-1.0.3 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +barnacle-1.0.3.ebuild, +metadata.xml: + sci-biology/barnacle: a skeleton of a messy package diff --git a/sci-biology/barnacle/Manifest b/sci-biology/barnacle/Manifest new file mode 100644 index 000000000..a45d8326b --- /dev/null +++ b/sci-biology/barnacle/Manifest @@ -0,0 +1 @@ +DIST barnacle-1.0.3.tar.gz 472057 SHA256 f97ea85d3f70e52da56c47dec391ff693255d225b66fa2016f079ab223bc2a52 SHA512 6ae6c85c52ed5ac093f2f5bd179fc3347dcef44237af717f58dee6bd59f84e4952241c7f4b0456cd575c0bdbfdd4019386bdcd6a03cad9f5f5ca6d224814c180 WHIRLPOOL e85e4d36fae226d840219c0c4b66101832d267e4b01fd2a2f717bfa730f05bb1954fd8c30ccfcd4df94586d32b51fbfac720c6072684170d7b87b19dda28f4c8 diff --git a/sci-biology/barnacle/barnacle-1.0.3.ebuild b/sci-biology/barnacle/barnacle-1.0.3.ebuild new file mode 100644 index 000000000..de565f329 --- /dev/null +++ b/sci-biology/barnacle/barnacle-1.0.3.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Check de novo assembly for chimeric contigs/transcripts" +HOMEPAGE="http://www.bcgsc.ca/platform/bioinfo/software/barnacle" +#SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.0/"${P}".tar.gz" +SRC_URI="http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/${PV}/${P}.tar.gz" +# ftp://ftp.bcgsc.ca/supplementary/Barnacle_BMC_Genomics/aml_data.tar.gz +# http://www.bcgsc.ca/platform/bioinfo/software/barnacle/releases/1.0.3 + +LICENSE="bcca_2010" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${S}" + +# follow README.txt +src_compile(){ + cd src || die + # Run setup.py to compile the portions of Barnacle that require compilation, and download and setup the default annotations + ./setup.py || die +} + +src_install(){ + dodoc README.txt + cd src || die + # do something +} diff --git a/sci-biology/barnacle/metadata.xml b/sci-biology/barnacle/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/barnacle/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/barrnap/ChangeLog b/sci-biology/barrnap/ChangeLog index 50bd6cd18..05d6b32c1 100644 --- a/sci-biology/barrnap/ChangeLog +++ b/sci-biology/barrnap/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*barrnap-0.4 (27 Apr 2015) + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +barrnap-0.4.ebuild, + barrnap-0.3.ebuild: + sci-biology/barrnap: version bump; adjust the ebuild to new install layout + 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> barrnap-0.3.ebuild: generalized dependency on perl diff --git a/sci-biology/barrnap/Manifest b/sci-biology/barrnap/Manifest index 25eaaab3d..11284c5d9 100644 --- a/sci-biology/barrnap/Manifest +++ b/sci-biology/barrnap/Manifest @@ -1 +1,2 @@ DIST barrnap-0.3.tar.gz 4102752 SHA256 f99a808a3b304748fff0394e4e048a8efb0a52ee309b6a4f7296e3e2cf05ce69 SHA512 4b67e995b335e9e8397481c60058bf3a21044e1829781f277027ce2b3e4836c17c30dc2453c6d7d3c00ef8c07394fc5cb46719bfd397e66db7d4ba3c5bfdd514 WHIRLPOOL 7c43f9eec8aa644de7b1f53d626b13fb1b838bef81680a7e96063f79e80ce2d23a101d1fef8cd7ad87165e24555f2bd866c02ff36d45bd5068c56f37c7a27542 +DIST barrnap-0.4.tar.gz 8053614 SHA256 9e31936283f1fbb4822afdfb589f82cc736d8a9c3e70bd8c46928b4cc8110f04 SHA512 77490398978df73cd2c5529403674cdb2142fa57506a997a95bd4c90a897756554a2d10598e28bac396b8b611b8c9b1c6eaf3bfb4e0d22724c4175d18c2e16ea WHIRLPOOL e721bc9859c633339ad6012373b116e730c5c3e68a810a75105a70e46cbba1c6609d128289feab5c6b192594c393c02c42a6e4b412cc35ed377beba926fb4bef diff --git a/sci-biology/barrnap/barrnap-0.3.ebuild b/sci-biology/barrnap/barrnap-0.3.ebuild index 43d1a135c..06d01c30f 100644 --- a/sci-biology/barrnap/barrnap-0.3.ebuild +++ b/sci-biology/barrnap/barrnap-0.3.ebuild @@ -12,7 +12,7 @@ SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz" LICENSE="GPL-3" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="" # contains bundled binaries of hmmer-3.1 (dev version) diff --git a/sci-biology/barrnap/barrnap-0.4.ebuild b/sci-biology/barrnap/barrnap-0.4.ebuild new file mode 100644 index 000000000..8855b27cc --- /dev/null +++ b/sci-biology/barrnap/barrnap-0.4.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit perl-module + +DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format" +HOMEPAGE="http://www.vicbioinformatics.com/software.barrnap.shtml" +SRC_URI="http://www.vicbioinformatics.com/"${P}".tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# contains bundled binaries of hmmer-3.1 (dev version) +# needs >=perl-5.6 + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl + sci-biology/nesoni" + +src_install(){ + # the below recreates the whole layout + insinto /usr/share/"${PN}"/bin + doins bin/barrnap + chmod a+rx "${D}"/usr/share/"${PN}"/bin/barrnap || die + insinto /usr/share/"${PN}"/binaries/linux + doins binaries/linux/nhmmer + chmod a+rx "${D}"/usr/share/"${PN}"/binaries/linux/nhmmer || die + insinto /usr/share/"${PN}"/db + doins db/* + insinto /usr/share/"${PN}"/examples + doins examples/* + + echo PATH=/usr/share/"${PN}"/bin:$PATH > "${S}"/99barrnap + doenvd "${S}"/99barrnap + + dodoc README.md +} diff --git a/sci-biology/bcftools/ChangeLog b/sci-biology/bcftools/ChangeLog index fc2086f24..a53d27c16 100644 --- a/sci-biology/bcftools/ChangeLog +++ b/sci-biology/bcftools/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bcftools: Add github to remote-id in metadata.xml + +*bcftools-1.2 (02 Mar 2015) + + 02 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +bcftools-1.2.ebuild, -bcftools-1.1.ebuild: + version bump, respect CC and CFLAGS + 15 Jan 2015; Christoph Junghans <ottxor@gentoo.org> bcftools-1.1.ebuild: fixed license diff --git a/sci-biology/bcftools/Manifest b/sci-biology/bcftools/Manifest index d9fae6d7b..1099bffd2 100644 --- a/sci-biology/bcftools/Manifest +++ b/sci-biology/bcftools/Manifest @@ -1 +1 @@ -DIST bcftools-1.1.tar.bz2 1197465 SHA256 6d0d1610e942a1c0388f9ae8402e1508eb6451c58929ac5200c89ed572fdd65e SHA512 15892de6fd417da8efd8fc9ab20578113d3b764738bcbefc88ac309dd953e39b844d4d93fce6f19b4e63f3a8b28d2d2574041b414e71ae16842224593032f522 WHIRLPOOL 7714856354c7544eba305e01005b6a75673c6786c78d360d6ee4c279cdad3c22bdef95eb6f5f558b30e65ded8f41d79ceccf1bf2c5ae6c49c8eb146f2332c613 +DIST bcftools-1.2.tar.bz2 1302282 SHA256 53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6 SHA512 893f03c0fec344113440ffee4503f88643defb17e68be845aecf0beafc71edb44ce45fc3e5e9e4901bb31ad976e55d1ad64952890266d98101cb68e310edb2e5 WHIRLPOOL 57557748bee07e51bb62786f763a3dfd9f7798fd1c96fff1853dbdbd50be1964b9a03a4a744c4cd5a18b1beec57215350680f1ccf1c1128436e71901b8c0c0be diff --git a/sci-biology/bcftools/bcftools-1.1.ebuild b/sci-biology/bcftools/bcftools-1.1.ebuild deleted file mode 100644 index 73032781c..000000000 --- a/sci-biology/bcftools/bcftools-1.1.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" -HOMEPAGE="http://www.htslib.org/bcftools_release_notes" -SRC_URI="http://sourceforge.net/projects/samtools/files/samtools/1.1/bcftools-1.1.tar.bz2" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND="sci-libs/htslib - dev-lang/perl" -RDEPEND="${DEPEND}" - -src_prepare(){ - sed -e 's#prefix = /usr/local#prefix = /usr#' \ - -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall -Wc++-compat -O2@' -i Makefile - - sed -e 's#prefix = /usr/local#prefix = /usr#' \ - -e 's@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = -g -Wall -Wc++-compat -O2@' -i htslib-1.1/Makefile -} diff --git a/sci-biology/bcftools/bcftools-1.2.ebuild b/sci-biology/bcftools/bcftools-1.2.ebuild new file mode 100644 index 000000000..3207a0177 --- /dev/null +++ b/sci-biology/bcftools/bcftools-1.2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files" +HOMEPAGE="http://www.htslib.org" +SRC_URI="https://github.com/samtools/bcftools/releases/download/"${PV}"/"${P}".tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sci-libs/htslib + dev-lang/perl" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e "s@gcc@$(tc-getCC)@" \ + -e 's#prefix = /usr/local#prefix = /usr#' \ + -e "s@CFLAGS = -g -Wall -Wc++-compat -O2@#CFLAGS = ${CFLAGS}@" -i Makefile || die + + sed -e "s@gcc@$(tc-getCC)@" \ + -e 's#prefix = /usr/local#prefix = /usr#' \ + -e "s@CFLAGS = -g -Wall -O2@#CFLAGS = ${CFLAGS}@" -i htslib-*/Makefile || die +} diff --git a/sci-biology/bcftools/metadata.xml b/sci-biology/bcftools/metadata.xml index 2bc893037..39c1d32fa 100644 --- a/sci-biology/bcftools/metadata.xml +++ b/sci-biology/bcftools/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">samtools/bcftools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/beagle/ChangeLog b/sci-biology/beagle/ChangeLog new file mode 100644 index 000000000..99f4578b2 --- /dev/null +++ b/sci-biology/beagle/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/beagle +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*beagle-4.0 (10 May 2015) + + 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +beagle-4.0.ebuild, + +metadata.xml: + sci-biology/beagle: a skeleton for a new java package with just *.java files + provided diff --git a/sci-biology/beagle/Manifest b/sci-biology/beagle/Manifest new file mode 100644 index 000000000..9834eb02d --- /dev/null +++ b/sci-biology/beagle/Manifest @@ -0,0 +1,4 @@ +DIST beagle-example.sh 976 SHA256 d2748d065fc6669264a88b9aeafbb6a7d45609fc646fedd7773f1cc414a5ca6e SHA512 db07b8e7753b1fa7b314301227fd4da3f80e2f5ea47357cb7f17d1ab1ad11b498ff763d82dc034a3cdc914071285e8186dcc85d0e829b537a9407ce11a6e4e80 WHIRLPOOL d9ab743a2b18376d78672c5206d7c8afc51cc2ffde3314e494e5287dd169a48c57c0113290f9928c539316354c39d30984171b48e1463c0fe45f87af3ee2b379 +DIST beagle-release_notes.txt 1208 SHA256 f632bbf3d9531ef449ccb1ae14e5ec0ddd19fe41be83d8b973cda4f3379099c3 SHA512 fa347608eb76bea7ba65d8aa109a578ba43900e29b6854160b58acb2c78a19999542901e5f9ebe703d2feb5e46b60e318c23d78a5eb63ad6e7df1d9850902067 WHIRLPOOL 2366a37f477b6e78b9ea8b34a38e54db0e3fc0a67396d3374d6528d5a9c98cf8f44a3a9d4912ce227b13760fdc398b64ae3423c09f093887e0487394baf66330 +DIST beagle.03Mar15.pdf 655574 SHA256 e630b38f3c4eee884798e344a328fa6938453ff7595803de5647ac326711ee5c SHA512 78dfcffae1bdb29b7a9741d9a3610905222030d91ab74b7be09f46c9fc3742333f1f26d330c9fe532d9127771de2c36ffda229d8603b082478b5b90528c7a649 WHIRLPOOL 66977729d5233bf0935c0907fa005f90e2e70a05ada3f910aa45baa9f4541d3ba9fb47bbb839d13ed32e969eb8da77ca263acd26a72d75ee45faa2f28256f2df +DIST beagle.r1399.src.zip 307214 SHA256 6e19b7b8e37a7c0d3e270a0f92425d1adc410920135630ac8fde719c0e4a9292 SHA512 b22b6ba3c67e01cf3e7c332723af781d32c3b2b9dad15b2eb1e1f47a216ff89911f89617eb95214723554059314dc312271a5320677937df48c7c4f3bb889253 WHIRLPOOL 805641ce255b5f3c8ae1d40f286e9442f80ee2cd78353e66ca5cf2b20de9441f8a9cbe05888ffc9d77cd8fc78d8eb2f36463d9a43cd3baa690463816090329d1 diff --git a/sci-biology/beagle/beagle-4.0.ebuild b/sci-biology/beagle/beagle-4.0.ebuild new file mode 100644 index 000000000..9652198bd --- /dev/null +++ b/sci-biology/beagle/beagle-4.0.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Genotype calling, genotype phasing, imputation of ungenotyped markers, identity-by-descent segment detection" +HOMEPAGE="http://faculty.washington.edu/browning/beagle/beagle.html" +SRC_URI="http://faculty.washington.edu/browning/beagle/beagle.r1399.src.zip + http://faculty.washington.edu/browning/beagle/beagle.03Mar15.pdf + http://faculty.washington.edu/browning/beagle/run.beagle.r1399.example -> ${PN}-example.sh + http://faculty.washington.edu/browning/beagle/release_notes -> ${PN}-release_notes.txt" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=virtual/jdk-1.7" +RDEPEND="${DEPEND} + >=virtual/jdk-1.7 + sci-biology/conform-gt" diff --git a/sci-biology/beagle/metadata.xml b/sci-biology/beagle/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/beagle/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/beaglecall/ChangeLog b/sci-biology/beaglecall/ChangeLog new file mode 100644 index 000000000..385fc8642 --- /dev/null +++ b/sci-biology/beaglecall/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/beaglecall +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*beaglecall-20101115 (10 May 2015) + + 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +beaglecall-20101115.ebuild, +metadata.xml: + sci-biology/beaglecall: a skeleton for a new java package with just *.java + files provided diff --git a/sci-biology/beaglecall/Manifest b/sci-biology/beaglecall/Manifest new file mode 100644 index 000000000..c7ee33d22 --- /dev/null +++ b/sci-biology/beaglecall/Manifest @@ -0,0 +1,3 @@ +DIST beaglecall_1.0.1_15Nov10.src.zip 109726 SHA256 c00125754dac6db36ffd982fd78140ceafaa3abf28b8e0f8e78fcae0f3e45985 SHA512 7a4485ea74f4ca5f00f952aa469d3f551d80a05bb4b0c41d3a9ffa680fac94a9d415595a6a46bc3048372af7de99aa14bc2c85f20d6a470ef2110e3c97d98236 WHIRLPOOL 0f0662ce403a00d9dff9928dab9910dc8ba355e76bf6332d43a40b12271069038acf7e0c477471c5c86b902872ff2e92a67a3fea55a504e034a7a28dbf7c69de +DIST beaglecall_1.0_15Nov10.pdf 1134881 SHA256 82b491f72eacd8c6fa6b83900c42f94de06b9aafda55f94f3fa872e0de9f7a5f SHA512 70bc1c9a05bc28941ee0be428929cbf07e602fda0f3afabca383ad5df5461269e4415c3da25a57a6b5072647112464516cc052ef3fa2be3a642b765ba518deac WHIRLPOOL 119331ae25ae95de495fbdc4c22a6a345712e739ed495a3aa2f02102b5705ca1889460e01bfae1de0cc01361993a27fc9dc589be40aa9407d10e3399bde99f01 +DIST beaglecall_example.zip 1556387 SHA256 c125a36b3b08f9f68f44fbe26872276fee4ccb4db586569e6403555ec2ffbe10 SHA512 35e66ddfa67b13e0f076994773d99de7c0daacf0308204729cb6fefae011e50d3fc65b42205d00f9b82c83be8323b1def8cd3e9ba63b1bee87369f140b717b63 WHIRLPOOL f8cd72d928eda88a9d2ba0e15c825876704d5e59bec1e2bd3c924b7b67d9819f3a60a4ca2fd90e41b85deb3f171a66f375e1b445bc29409a75076e2473dca998 diff --git a/sci-biology/beaglecall/beaglecall-20101115.ebuild b/sci-biology/beaglecall/beaglecall-20101115.ebuild new file mode 100644 index 000000000..c13e09780 --- /dev/null +++ b/sci-biology/beaglecall/beaglecall-20101115.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Simultaneous genotype calling and haplotype phasing for unrelated individuals" +HOMEPAGE="http://faculty.washington.edu/browning/beaglecall/beaglecall.html" +SRC_URI="http://faculty.washington.edu/browning/beaglecall/beaglecall_1.0.1_15Nov10.src.zip + http://faculty.washington.edu/browning/beaglecall/beaglecall_1.0_15Nov10.pdf + http://faculty.washington.edu/browning/beaglecall/beaglecall_example.zip" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=virtual/jdk-1.5:*" +RDEPEND="${DEPEND} + >=virtual/jre-1.5:*" + +# src/ contains *.java files only +# example/ diff --git a/sci-biology/beaglecall/metadata.xml b/sci-biology/beaglecall/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/beaglecall/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/bedtools/ChangeLog b/sci-biology/bedtools/ChangeLog index a36ef570b..e72833e57 100644 --- a/sci-biology/bedtools/ChangeLog +++ b/sci-biology/bedtools/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> bedtools-2.22.1.ebuild: + sci-biology/bedtools: Bump to EAPI=5 + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bedtools: Add github to remote-id in metadata.xml + *bedtools-2.22.1 (14 Jan 2015) 14 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/bedtools/bedtools-2.22.1.ebuild b/sci-biology/bedtools/bedtools-2.22.1.ebuild index 877dcadc0..97a20b3f7 100644 --- a/sci-biology/bedtools/bedtools-2.22.1.ebuild +++ b/sci-biology/bedtools/bedtools-2.22.1.ebuild @@ -1,8 +1,8 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/bedtools/bedtools-2.16.2.ebuild,v 1.1 2012/05/29 02:54:40 weaver Exp $ +# $Header: $ -EAPI=4 +EAPI=5 inherit flag-o-matic diff --git a/sci-biology/bedtools/metadata.xml b/sci-biology/bedtools/metadata.xml index d841c4bcb..6edffa4a6 100644 --- a/sci-biology/bedtools/metadata.xml +++ b/sci-biology/bedtools/metadata.xml @@ -12,5 +12,6 @@ </longdescription> <upstream> <remote-id type="google-code">bedtools</remote-id> + <remote-id type="github">arq5x/bedtools2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/biobambam/ChangeLog b/sci-biology/biobambam/ChangeLog new file mode 100644 index 000000000..79127ede4 --- /dev/null +++ b/sci-biology/biobambam/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-biology/biobambam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/biobambam: Add github to remote-id in metadata.xml diff --git a/sci-biology/biobambam/metadata.xml b/sci-biology/biobambam/metadata.xml index 9dab65018..7f3371953 100644 --- a/sci-biology/biobambam/metadata.xml +++ b/sci-biology/biobambam/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription lang="en"> + <herd>sci-biology</herd> + <longdescription lang="en"> This package contains some tools for processing BAM files including bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name @@ -12,4 +12,7 @@ bamrecompress: reads BAM and writes BAM with a defined compression setting. This bamsort: reads BAM and writes BAM resorted by coordinates or query name bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name </longdescription> + <upstream> + <remote-id type="github">gt1/biobambam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/biopieces/ChangeLog b/sci-biology/biopieces/ChangeLog index db06e7663..615109a06 100644 --- a/sci-biology/biopieces/ChangeLog +++ b/sci-biology/biopieces/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Mar 2015; Justin Lecher <jlec@gentoo.org> biopieces-9999.ebuild: + Fix missing test in IUSE and missing dep in python + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -Manifest, biopieces-9999.ebuild: sci-biology/biopieces: fix SLOT operators; correct ruby and python deps diff --git a/sci-biology/biopieces/biopieces-9999.ebuild b/sci-biology/biopieces/biopieces-9999.ebuild index d33a63fc5..0e3731d66 100644 --- a/sci-biology/biopieces/biopieces-9999.ebuild +++ b/sci-biology/biopieces/biopieces-9999.ebuild @@ -25,13 +25,13 @@ SRC_URI="" LICENSE="GPL-2" SLOT="0" -IUSE="" +IUSE="test" REQUIRED_USE="${PYTHON_REQUIRED_USE}" # Ruby terminal-table ? -DEPEND=" +CDEPEND="${PYTHON_DEPS} >=dev-lang/perl-5.8 dev-perl/libwww-perl dev-perl/Bit-Vector @@ -51,13 +51,15 @@ DEPEND=" virtual/perl-DB_File virtual/perl-Time-HiRes" +DEPEND="${CDEPEND}" + ruby_add_bdepend "dev-ruby/RubyInline" ruby_add_rdepend "dev-ruby/gnuplot dev-ruby/narray" # sci-biology/vmatch # http://www.vmatch.de/ # fecth restrict # sci-biology/usearch-bin # http://www.drive5.com/usearch/ # fecth restrict -RDEPEND="${DEPEND} +RDEPEND="${CDEPEND} sci-biology/ncbi-tools sci-biology/muscle sci-biology/mummer diff --git a/sci-biology/blue/ChangeLog b/sci-biology/blue/ChangeLog index 9dcc13400..97f68443b 100644 --- a/sci-biology/blue/ChangeLog +++ b/sci-biology/blue/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*blue-1.1.3 (26 May 2015) + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.3.ebuild, + blue-1.1.2.ebuild: + sci-biology/blue: version bump, updated HOMEPAGE and SRC_URI + + 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> blue-1.1.2.ebuild: + improved comments based on email from upstream + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> blue-1.1.2.ebuild: Fix license @@ -10,4 +19,3 @@ 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +blue-1.1.2.ebuild, +metadata.xml: Initial ebuild, does not install the *.exe.so files. Do we need them? - diff --git a/sci-biology/blue/Manifest b/sci-biology/blue/Manifest index eaacef198..91292c1f6 100644 --- a/sci-biology/blue/Manifest +++ b/sci-biology/blue/Manifest @@ -1,2 +1,6 @@ -DIST Correcting_reads_with_Blue.pdf 821286 SHA256 b20cf2524740a2fbacee6bf0dbb652c06a00a3a1b112d448114cebe900bc970d SHA512 73906f2844d89dbf7dcf6a163d8763b8995669871082abf362c4cc4fa8b21fa180cad0c4f024ea4d82a32a0fcda8d4e85a563d58cc7fd2b49dc63c09c88ef714 WHIRLPOOL 754b77f034f1df878f8b942f6985212a3da0f57576a6a5bbd06564591ac41c40396c147a91a2792ab226a7c30a23179e3118724f72ee289bd2133b61c14a2ec1 +DIST blue-1.1.2-Changes_for_Blue_1.1.2.pdf 310372 SHA256 c40a06a780223642152d30cf12c11b35af80c5778e2b584c490ded7acb962e36 SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73 WHIRLPOOL 7ead99964d95a3a6c77acde87c9b90e4d031838eb60e000f20c7e96f85e854b8118b57a0a69d4d927ece7e58fccfa322ce0b4eb9d7420f0bfb58f71b06ae7296 +DIST blue-1.1.2-Correcting_reads_with_Blue.pdf 560129 SHA256 4938a9e98851a8c13d96fd0ce3be15f97c00cb008751594884fa2f13bac9c561 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585 WHIRLPOOL e6089c2e895d7c693c2f2dd30ffe7c3911d9cc67f971e9da8551333f75b99a35927927a3cea728438de4310acc9da4ad99e51ec75ac49acd306a60b53b395f9d DIST blue-1.1.2.tar.gz 658544 SHA256 c038fa9fd76330cb70059cd47979327708368e2d6b6d7edae00825ba39dc23bd SHA512 933b2a8bb1e1f3fed241cff2eac9566d49d77c3f97b2f22f4a8194f3cdf25c09ae474b4d681ff65914d695598579fded6433f6a47ad06b78879c36d58402ea4b WHIRLPOOL 32c89ae39cfadab9beae038afd530cf85d8c8775a84bd5e2c29a2e67246d9b09d5c872492c1836dfab6fe20e9f59a1b0aaddc5dc051393030ccff39bb08fec8e +DIST blue-1.1.3-Changes_for_Blue_1.1.3.pdf 310372 SHA256 c40a06a780223642152d30cf12c11b35af80c5778e2b584c490ded7acb962e36 SHA512 1f6d595018e880a9d10197816881fa88bbc1da9613fb83d0c3b77fe3ea22e614a9fc9783abfa7f649c242a4966a6929c53fcd1b845f98280d50c491b4cff8f73 WHIRLPOOL 7ead99964d95a3a6c77acde87c9b90e4d031838eb60e000f20c7e96f85e854b8118b57a0a69d4d927ece7e58fccfa322ce0b4eb9d7420f0bfb58f71b06ae7296 +DIST blue-1.1.3-Correcting_reads_with_Blue.pdf 560129 SHA256 4938a9e98851a8c13d96fd0ce3be15f97c00cb008751594884fa2f13bac9c561 SHA512 1341a7f3d4c77b3a3f8d66f57b4cc976930bf7d28219d77a3a91efde0bc76f08bf0159c98df3227a2484dc0fe7d40904dbbde74dc03b6c110649285314a07585 WHIRLPOOL e6089c2e895d7c693c2f2dd30ffe7c3911d9cc67f971e9da8551333f75b99a35927927a3cea728438de4310acc9da4ad99e51ec75ac49acd306a60b53b395f9d +DIST blue-1.1.3.tar.gz 717341 SHA256 42c5b3a2156712e34d0537bcdc97aedf72ea0ab363527f1448e20969ebc4b355 SHA512 fc51965a063ced80304b3e59eb538742f6f4a2970d02cecc346aa8b15e961a242b6ce6cc3a847c8e4f478bee997ed5794f304d201554398130c1a16bceb84c30 WHIRLPOOL 087552bfd7f9e9b9be578519cdb31802cec82b140da80bdd30f9b0fe14cdaeea58b0277e33c6c3603201e293d463ec03631fa1395334e8f38f812ed97b6f04af diff --git a/sci-biology/blue/blue-1.1.2.ebuild b/sci-biology/blue/blue-1.1.2.ebuild index 834db7cad..945a35d12 100644 --- a/sci-biology/blue/blue-1.1.2.ebuild +++ b/sci-biology/blue/blue-1.1.2.ebuild @@ -5,11 +5,11 @@ EAPI=5 DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions" -HOMEPAGE="http://www.csiro.au/Outcomes/ICT-and-Services/Software/Blue.aspx" +HOMEPAGE="http://www.bioinformatics.csiro.au/blue" SRC_URI=" - http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Linux112.ashx -> ${P}.tar.gz - http://www.csiro.au/~/media/CSIROau/Images/Bioinformatics/Blue_software/Version_1-1-2/Correcting_reads_with_Blue.ashx -> Correcting_reads_with_Blue.pdf" - + http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz + http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf + http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf" LICENSE="GPL-2+" SLOT="0" KEYWORDS="" @@ -28,5 +28,11 @@ src_compile(){ src_install(){ dobin Tessel.exe GenerateMerPairs.exe Blue.exe - # BUG: probably have to install also the *.exe.so files + # one could install also the *.exe.so files for speedup into /usr/bin/ + + # The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. + + # In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently? } + +# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector diff --git a/sci-biology/blue/blue-1.1.3.ebuild b/sci-biology/blue/blue-1.1.3.ebuild new file mode 100644 index 000000000..945a35d12 --- /dev/null +++ b/sci-biology/blue/blue-1.1.3.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Error corrector for Illummina and Roche/454 able to also fix insertions and deletions" +HOMEPAGE="http://www.bioinformatics.csiro.au/blue" +SRC_URI=" + http://www.bioinformatics.csiro.au/public/files/Linux-${PV}.tar.gz -> ${P}.tar.gz + http://www.bioinformatics.csiro.au/public/files/Correcting_reads_with_Blue.pdf -> ${P}-Correcting_reads_with_Blue.pdf + http://www.bioinformatics.csiro.au/public/files/Changes_for_Blue_1.1.3.pdf -> ${P}-Changes_for_Blue_${PV}.pdf" +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-lang/mono" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/Linux + +src_compile(){ + Blue/compile.sh || die + Tessel/compile.sh || die + GenerateMerPairs/compile.sh || die +} + +src_install(){ + dobin Tessel.exe GenerateMerPairs.exe Blue.exe + # one could install also the *.exe.so files for speedup into /usr/bin/ + + # The -hp option sets a flag that is checked when Blue is scanning along a read trying to find errors that could be corrected. There are a number of tests done at every base position, all based on depth of coverage. These tests will pick up random indel errors, but indels are so common at the end of homopolymer runs in 454 and IonTorrent data that multiple hp run lengths all look to be OK. For example, if our genome had AAAAAA then with Illumina data this is what we'd see almost all the time, with very rare indels at the end of the hp run resulting in runs of 5 or 7 As. With 454-like data, we'd probably get 5 As as frequently as 6 As so depth of coverage would say that neither of them are errors. The -hp flag looks out for the end of hp runs and forces an attempt at correction at that point. If the read wasn't in error, then no correction will be made. + + # In general Blue will correct Ns - if a correct replacement can be found. The only time it doesn't do this is if there are too many consecutive Ns - as the process of finding likely replacements is combinatoric and the cost goes up exponentially with the number of consecutive Ns. In these cases, the read is abandoned and passed through uncorrected. Can you give an example of a read that you would like to see corrected differently? +} + +# it's author uses 'mono-sgen /usr/bin/Blue.exe' to use the alternative garbage collector diff --git a/sci-biology/bowtie/ChangeLog b/sci-biology/bowtie/ChangeLog index f3d98e2c4..d2248db7b 100644 --- a/sci-biology/bowtie/ChangeLog +++ b/sci-biology/bowtie/ChangeLog @@ -2,10 +2,23 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bowtie: Updating remote-id in metadata.xml + + 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> bowtie-1.1.1.ebuild, + bowtie-2.2.3.ebuild, bowtie-2.2.5.ebuild: + sci-biology/bowtie: clarified package descriptions (bowtie1 vs. bowtie2) + +*bowtie-2.2.3 (27 Apr 2015) +*bowtie-2.2.5 (27 Apr 2015) + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +bowtie-2.2.3.ebuild, +bowtie-2.2.5.ebuild, -bowtie-2.2.4.ebuild: + sci-biology/bowtie: version bump + 06 Feb 2015; Ted Tanberry <ted.tanberry@gmail.com> bowtie-1.1.1.ebuild, bowtie-2.2.4.ebuild: Version bump, updated ebuild, fixed small build system bugs 28 Sep 2013; Justin Lecher <jlec@gentoo.org> bowtie-2.1.0.ebuild: Exchange common variables, fix SRC_URI - diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest index b9cb1c316..df99ece11 100644 --- a/sci-biology/bowtie/Manifest +++ b/sci-biology/bowtie/Manifest @@ -1,2 +1,3 @@ DIST bowtie-1.1.1-src.zip 7711451 SHA256 92aacb2d32065ebee433ce76eff673c24ed12591eb6c20e22ad7e4a790c48f72 SHA512 b7e2604902d846e5e1ce79ae79eceed5401070e7db76f6875d1617e277f8244a32930b334b20869c712bab58d7d88ae26f2569350c8324df4dddae0400c013f9 WHIRLPOOL 65d1248280b32ca1f6cf7c270895abdfbec27f32128915b13a01e43a7697a743f1872440f528b29413140c260e9b7f61b6a4d435f3f83be486972b6b1533d6a5 -DIST bowtie2-2.2.4-source.zip 5725498 SHA256 1f3482bf31111dbfb8b547f984c4755296316f6c48c33c7d3cf19c814785d0aa SHA512 f4d40cb9d6d8f6b956d9ac6e109dba15d2e3815bb7e6498465e7ee81b59b725ae118fd6ec385482605b0218e99ee13350127926df3efe6e6ab0da7ff816b654f WHIRLPOOL 561b67d206a5e5791d3034c28700e371bca18005ff13ae895a816d95e92f606c1f5f1ffdd41e581ce052417ebb386b8ca36f1dc9dc3ed30fb4b5b8607164befd +DIST bowtie2-2.2.3-source.zip 5724584 SHA256 c4f5ce9f0f53a6b8c7f573a26e96f6909f25bd4e0e8bd77191eaa10671baf0bf SHA512 3baf0e764a79e34b6767a62d52777fc528a82481f417ea5f1b24f38e01fac68c2870daff3060c8da11681d3270e15a10ede034356522336a94f0936d70874684 WHIRLPOOL e19ea1cee85c5ccbc198a981587e8832ebfb4bd9a02332d8171d218e89e6c84df5760db6cd1f8195b712097c6ff3ae7790415d1e63afd2632979392709de26ab +DIST bowtie2-2.2.5-source.zip 5725798 SHA256 e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 SHA512 8b97860fea73ef36a60dee3dbccdfc956ac7f619ec47a7b820d1df09cff8f77362ddc8071b59ea8021444bda59757d68bdf486fb453d5c4e4b896198bc465d60 WHIRLPOOL 7a8eb7e6d723ccb807a1db3b724326764f8f339017c0b4eb6b234e034458e736ba521106bcc8347c3c428008d8f138f463f3c3e6033b781e1c41898735c2a878 diff --git a/sci-biology/bowtie/bowtie-1.1.1.ebuild b/sci-biology/bowtie/bowtie-1.1.1.ebuild index 536e9d8c4..e6e5c3a9b 100644 --- a/sci-biology/bowtie/bowtie-1.1.1.ebuild +++ b/sci-biology/bowtie/bowtie-1.1.1.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="An ultrafast memory-efficient short read aligner" +DESCRIPTION="Short read (below 50nt) aligner requiring end-to-end match, no gaps" HOMEPAGE="http://bowtie-bio.sourceforge.net/" SRC_URI="mirror://sourceforge/bowtie-bio/${P}-src.zip" diff --git a/sci-biology/bowtie/bowtie-2.2.4.ebuild b/sci-biology/bowtie/bowtie-2.2.3.ebuild index d8059fc9d..e987cdb85 100644 --- a/sci-biology/bowtie/bowtie-2.2.4.ebuild +++ b/sci-biology/bowtie/bowtie-2.2.3.ebuild @@ -6,7 +6,7 @@ EAPI=5 inherit eutils toolchain-funcs -DESCRIPTION="An ultrafast memory-efficient short read aligner" +DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" diff --git a/sci-biology/bowtie/bowtie-2.2.5.ebuild b/sci-biology/bowtie/bowtie-2.2.5.ebuild new file mode 100644 index 000000000..e987cdb85 --- /dev/null +++ b/sci-biology/bowtie/bowtie-2.2.5.ebuild @@ -0,0 +1,52 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="Short read aligner supporting gaps, matches to N nucleotides, no end-to-end requirement" +HOMEPAGE="http://bowtie-bio.sourceforge.net/bowtie2/" +SRC_URI="mirror://sourceforge/project/${PN}-bio/${PN}2/${PV}/${PN}2-${PV}-source.zip" + +LICENSE="GPL-3" +SLOT="2" +KEYWORDS="~amd64 ~x86" + +IUSE="examples cpu_flags_x86_sse2" +REQUIRED_USE="cpu_flags_x86_sse2" + +RDEPEND="dev-lang/perl" +DEPEND="${RDEPEND} + app-arch/unzip" + +S="${WORKDIR}/${PN}2-${PV}" + +DOCS=( AUTHORS NEWS TUTORIAL ) +HTML_DOCS=( doc/{manual.html,style.css} ) + +src_compile() { + emake \ + CC="$(tc-getCC)" \ + CPP="$(tc-getCXX)" \ + CFLAGS="" \ + CXXFLAGS="" \ + EXTRA_FLAGS="${LDFLAGS}" \ + RELEASE_FLAGS="${CXXFLAGS} -msse2" +} + +src_install() { + dobin ${PN}2 ${PN}2-* + + exeinto /usr/libexec/${PN}2 + doexe scripts/* + + newman MANUAL ${PN}2.1 + einstalldocs + + if use examples; then + insinto /usr/share/${PN}2 + doins -r example + fi +} diff --git a/sci-biology/bowtie/metadata.xml b/sci-biology/bowtie/metadata.xml index f17a827e3..e49341707 100644 --- a/sci-biology/bowtie/metadata.xml +++ b/sci-biology/bowtie/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">bowtie-bio</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/breakdancer/ChangeLog b/sci-biology/breakdancer/ChangeLog index 2dfc56969..d577653b8 100644 --- a/sci-biology/breakdancer/ChangeLog +++ b/sci-biology/breakdancer/ChangeLog @@ -1,7 +1,21 @@ # ChangeLog for sci-biology/breakdancer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + breakdancer-9999.ebuild: + sci-biology/breakdancer: added inherit cmake + + 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + breakdancer-9999.ebuild: + sci-biology/breakdancer: update homepage + +*breakdancer-9999 (18 May 2015) + + 18 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +breakdancer-9999.ebuild, -Manifest, -breakdancer-1.1.2.ebuild: + sci-biology/breakdancer: upstream moved to github + *breakdancer-1.1.2 (23 Mar 2014) 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/breakdancer/Manifest b/sci-biology/breakdancer/Manifest deleted file mode 100644 index 980727e37..000000000 --- a/sci-biology/breakdancer/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST breakdancer-1.1.2_2013_03_08.zip 43732 SHA256 09c66c4d64735e89d893581a10804c66ac43f7bd7b07253bbd10efbe42db9cf2 SHA512 5f5e8ae097217f33a72a8977c5abb1e392800311623e25f126d5d96423f76d03a3fc8afe78b5f13560d125fe4bec7999e81da4b2a1cef5db218b7e40385b1e65 WHIRLPOOL 6b25ea4c63fdcd73707e410ca041731e6caa08fce39115306bc3107d4329e80353d9d5795b47575cd10f11747965193486f54348dc7eea4df7f1393010c4369b diff --git a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild b/sci-biology/breakdancer/breakdancer-1.1.2.ebuild deleted file mode 100644 index 6aff8687d..000000000 --- a/sci-biology/breakdancer/breakdancer-1.1.2.ebuild +++ /dev/null @@ -1,20 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads" -HOMEPAGE="http://breakdancer.sourceforge.net" -SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="dev-lang/perl - dev-perl/Statistics-Descriptive - dev-perl/Math-CDF - sci-biology/samtools" -RDEPEND="${DEPEND}" diff --git a/sci-biology/breakdancer/breakdancer-9999.ebuild b/sci-biology/breakdancer/breakdancer-9999.ebuild new file mode 100644 index 000000000..c0599b3bb --- /dev/null +++ b/sci-biology/breakdancer/breakdancer-9999.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +[ "$PV" == "9999" ] && inherit git-r3 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Genome-wide detection of structural variants from next generation paired-end sequencing reads" +HOMEPAGE="http://gmt.genome.wustl.edu/packages/breakdancer" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/genome/breakdancer.git" + KEYWORDS="" +else + # TODO: fish out 1.3.6 version from github + SRC_URI="http://sourceforge.net/projects/breakdancer/files/breakdancer-1.1.2_2013_03_08.zip" + KEYWORDS="" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="" + +# http://search.cpan.org/~callahan/Math-CDF-0.1/CDF.pm +DEPEND="dev-lang/perl + dev-perl/Statistics-Descriptive + sci-biology/samtools" +RDEPEND="${DEPEND}" diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest deleted file mode 100644 index 9c0d995bf..000000000 --- a/sci-biology/bwa/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bwa-0.7.12.tar.bz2 184599 SHA256 701dcad147ae470d741717a72c369b338df7f80bff4bb8eee8176c66f16d608c SHA512 3ea093b861c1596d20b1ee0336468b66e52bc9f26e3d0bcbba0ddccc7fe9b1af2c7e1ed2a4e1366fe93fec348152becc126d5f4685dae54f05e6c582488b3abd WHIRLPOOL 4b8651dedf2e09980850e7212fc2a77dc86b06f708af2077cff28cc843858b15825a203e3e02e7728418e9eb539004404f7c4b234c1f65de6a7b7dfe4dcfd1d0 diff --git a/sci-biology/bwa/bwa-0.7.12.ebuild b/sci-biology/bwa/bwa-0.7.12.ebuild deleted file mode 100644 index 62488f328..000000000 --- a/sci-biology/bwa/bwa-0.7.12.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils toolchain-funcs - -DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" -HOMEPAGE="http://bio-bwa.sourceforge.net/" -SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -PATCHES=( "${FILESDIR}"/${PN}_Makefile.patch ) - -src_prepare() { - epatch ${PATCHES[@]} - tc-export CC AR -} - -src_install() { - dobin bwa - - doman bwa.1 - - exeinto /usr/libexec/${PN} - doexe qualfa2fq.pl xa2multi.pl - - dodoc NEWS.md README-alt.md README.md -} diff --git a/sci-biology/bwa/files/bwa_Makefile.patch b/sci-biology/bwa/files/bwa_Makefile.patch deleted file mode 100644 index 406e9b052..000000000 --- a/sci-biology/bwa/files/bwa_Makefile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- Makefile -+++ Makefile -@@ -1,8 +1,8 @@ --CC= gcc -+CC?= gcc - #CC= clang --analyze --CFLAGS= -g -Wall -Wno-unused-function -O2 -+CFLAGS?= -g -Wall -Wno-unused-function -O2 - WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS --AR= ar -+AR?= ar - DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) - LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o - AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ -@@ -26,10 +26,10 @@ - all:$(PROG) - - bwa:libbwa.a $(AOBJS) main.o -- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) - - bwamem-lite:libbwa.a example.o -- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) - - libbwa.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog new file mode 100644 index 000000000..6c3346626 --- /dev/null +++ b/sci-biology/bx-python/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for sci-biology/bx-python +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/bx-python: Add bitbucket to remote-id in metadata.xml + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> bx-python-0.7.2.ebuild, + bx-python-9999.ebuild: + sci-biology/bx-python: Streamline ebuild + +*bx-python-0.7.2 (12 Apr 2015) +*bx-python-9999 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +bx-python-0.7.2.ebuild, + +bx-python-9999.ebuild, +metadata.xml: + sci-biology/bx-python: add bx-python diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest new file mode 100644 index 000000000..604cca2f5 --- /dev/null +++ b/sci-biology/bx-python/Manifest @@ -0,0 +1 @@ +DIST bx-python-0.7.2.tar.gz 939454 SHA256 b083b2c87807bbfa5b11196754768147ca5bb15001cb0dd76ef217065b4ca451 SHA512 6757250909be72daf61daef865b4c5ee29a823ca7444a70b17dd25db8cec22e39dd0b93186634a9ed9ac036fdb7054e225270141c9ffd63a231d82f0eee8c8cd WHIRLPOOL 3f795403c82b4bcbf45e32fa0e56869fac0069be99919586655dd5c5b9f72d295826ef0dc64127127d665c7d4280a8c7ddebe8b8a70bb8ef03da8d4e768e2bd3 diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.7.2.ebuild new file mode 100644 index 000000000..4167df923 --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.7.2.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild new file mode 100644 index 000000000..3cb8abe22 --- /dev/null +++ b/sci-biology/bx-python/bx-python-9999.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 mercurial + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home" +SRC_URI="" +EHG_REPO_URI="https://bitbucket.org/james_taylor/bx-python" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml new file mode 100644 index 000000000..1e685c91f --- /dev/null +++ b/sci-biology/bx-python/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="pypi">bx-python</remote-id> + <remote-id type="bitbucket">james_taylor/bx-python</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog index 12f9e49f7..682f31ee5 100644 --- a/sci-biology/caftools/ChangeLog +++ b/sci-biology/caftools/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-biology/caftools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + caftools-2.0.2.ebuild: + sci-biology/caftools: added a link to the original publication; Simon Dear + <sd@sanger.ac.uk>: host extmail.sanger.ac.uk[193.62.203.50] said: 550 unknown + 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> caftools-2.0.2.ebuild: sci-biology/caftools: clarified package description diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild index 07c11852a..56d61dde9 100644 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ b/sci-biology/caftools/caftools-2.0.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -7,7 +7,8 @@ EAPI=5 inherit eutils DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf + http://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697" SRC_URI=" ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz" diff --git a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild index e220e16a8..95a3e07d9 100644 --- a/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild +++ b/sci-biology/cd-hit-auxtools/cd-hit-auxtools-0.5.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $ +# $Header: $ EAPI=4 diff --git a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild index d7c573fa0..2850f79c6 100644 --- a/sci-biology/cd-hit/cd-hit-4.6.1.ebuild +++ b/sci-biology/cd-hit/cd-hit-4.6.1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/cd-hit/cd-hit-4.6.ebuild,v 1.1 2012/06/20 18:39:24 jlec Exp $ +# $Header: $ EAPI=4 diff --git a/sci-biology/cegma/ChangeLog b/sci-biology/cegma/ChangeLog index aae608683..760074c38 100644 --- a/sci-biology/cegma/ChangeLog +++ b/sci-biology/cegma/ChangeLog @@ -2,10 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> cegma-2.5.ebuild: + sci-biology/cegma: re-added KEYWORDS because sci-biology/ncbi-tools++ is now + available; fixed installation of perl-related files; dropped hmmer from DEPEND + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> cegma-2.5.ebuild: Fix license;drop keywords due to missing keyowrds of deps 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +cegma-2.5.ebuild, +metadata.xml: new package; install *.pm into PERL5LIB/cegma and pass that via env.d - diff --git a/sci-biology/cegma/cegma-2.5.ebuild b/sci-biology/cegma/cegma-2.5.ebuild index bbc11996f..ba9f79961 100644 --- a/sci-biology/cegma/cegma-2.5.ebuild +++ b/sci-biology/cegma/cegma-2.5.ebuild @@ -4,34 +4,36 @@ EAPI=5 +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + DESCRIPTION="Predict genes in a genome and use them for training to find all genes" HOMEPAGE="http://korflab.ucdavis.edu/datasets/cegma" SRC_URI="http://korflab.ucdavis.edu/datasets/cegma/CEGMA_v${PV}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64" IUSE="" DEPEND=" - dev-lang/perl sci-biology/wise - >=sci-biology/hmmer-3.0 sci-biology/geneid sci-biology/ncbi-tools++" + # >=sci-biology/hmmer-3.0 RDEPEND="${DEPEND}" S="${WORKDIR}"/CEGMA_v${PV} src_install(){ dobin bin/* - eval `perl '-V:installvendorlib'` - vendor_lib_install_dir="${installvendorlib}" - dodir ${vendor_lib_install_dir}/cegma - insinto ${vendor_lib_install_dir}/cegma + perl_set_version + insinto ${VENDOR_LIB} doins lib/*.pm +} - echo "PERL5LIB="${vendor_lib_install_dir}"/cegma" > ${S}"/99cegma" - # echo "CEGMATMP=/var/tmp" >> ${S}"/99cegma" - doenvd ${S}"/99cegma" || die +pkg_postinst(){ + ewarn "cegma needs >=sci-biology/hmmer-3.0 but sci-biology/wise uses sci-biology/hmmer-2.3" + ewarn "hmmer-3 is not backwards compatible and does not even have all its previous features" + ewarn "Therefore, we do not list hmmer in the list of DEPENDENCIES." } diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog index e3de2154b..3ab418154 100644 --- a/sci-biology/cgview-bin/ChangeLog +++ b/sci-biology/cgview-bin/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + cgview-bin-20131130.ebuild: + sci-biology/cgview-bin: fixed installation of perl-related files + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> cgview-bin-20131130.ebuild: sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild index 61141e3d2..74a954086 100644 --- a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild +++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild @@ -6,6 +6,9 @@ EAPI=5 inherit java-pkg-2 +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)" HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT" SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip" @@ -34,11 +37,16 @@ src_test(){ } src_install() { - echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview" + insinto /usr/share/${PN}/scripts + chmod a+x scripts/* # BUG: this does not work + doins scripts/* + echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview" echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview" doenvd "${S}/99cgview" - #export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin - #export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB" - - dobin bin/cgview.jar + perl_set_version + insinto ${VENDOR_LIB}/cgview + doins lib/perl_modules/Util/*.pm + # + # Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException + java-pkg_dojar bin/cgview.jar } diff --git a/sci-biology/codonw/ChangeLog b/sci-biology/codonw/ChangeLog index 00b6629e0..4226f0e7e 100644 --- a/sci-biology/codonw/ChangeLog +++ b/sci-biology/codonw/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/codonw: Updating remote-id in metadata.xml + +*codonw-1.4.4-r2 (30 May 2015) + + 30 May 2015; Justin Lecher <jlec@gentoo.org> +codonw-1.4.4-r2.ebuild, + -codonw-1.4.4-r1.ebuild, metadata.xml: + sci-biology/codonw: Workaround file collision by appending PN to every + command, bug #344713, bug #550388 + 10 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> condow-1.4.4-r1.ebuild: Move to EAPI=5. @@ -14,4 +24,3 @@ 28 Feb 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package sci-biology/codonw, ebuild written by me - diff --git a/sci-biology/codonw/codonw-1.4.4-r1.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 85c0c5e9e..99c6994a7 100644 --- a/sci-biology/codonw/codonw-1.4.4-r1.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -20,7 +20,8 @@ KEYWORDS="~amd64 ~x86" S=${WORKDIR}/codonW src_prepare() { - sed -e 's/$(CC) -c/& -DBSD/' \ + sed \ + -e 's/$(CC) -c/& -DBSD/' \ -e 's/$(CFLAGS) $(objects)/$(CFLAGS) $(LDFLAGS) $(objects)/' \ -i Makefile || die } @@ -30,10 +31,11 @@ src_compile() { } src_install() { - dobin codonw + local i + dobin ${PN} # woohoo watch out for collisions for i in rscu cu aau raau tidy reader cutab cutot transl bases base3s dinuc cai fop gc3s gc cbi enc; do - dosym codonw /usr/bin/${i} + dosym codonw /usr/bin/${i}-${PN} done dodoc *.txt } diff --git a/sci-biology/codonw/metadata.xml b/sci-biology/codonw/metadata.xml index 3302123e5..1930fee10 100644 --- a/sci-biology/codonw/metadata.xml +++ b/sci-biology/codonw/metadata.xml @@ -1,9 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">codonw</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/conform-gt/ChangeLog b/sci-biology/conform-gt/ChangeLog new file mode 100644 index 000000000..dcc6850f8 --- /dev/null +++ b/sci-biology/conform-gt/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/conform-gt +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*conform-gt-1174 (10 May 2015) + + 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +conform-gt-1174.ebuild, +metadata.xml: + sci-biology/conform-gt: a skeleton for a new java package with just *.java + files provided diff --git a/sci-biology/conform-gt/Manifest b/sci-biology/conform-gt/Manifest new file mode 100644 index 000000000..28c2db2ae --- /dev/null +++ b/sci-biology/conform-gt/Manifest @@ -0,0 +1 @@ +DIST conform-gt.r1174.zip 128608 SHA256 d9f9447514c0825bf156581e38db81325b898145a6f74c34a8af411389571f78 SHA512 8547f122c4298e19d5284969ca7410d7a1581028e8155b554acedff16fed5d07ddb4f6f8e986279b8fec5012d7d95d278abd9af4049fa9d0ea08e5dfc775fffc WHIRLPOOL b5101faedebf87cfa4483a202442768e95c7d0607d26766d8b492da8b3a908e2aae48394bb913e6144abf513537bba4b11adf2ba458e8c4aa1eee68f16944ee5 diff --git a/sci-biology/conform-gt/conform-gt-1174.ebuild b/sci-biology/conform-gt/conform-gt-1174.ebuild new file mode 100644 index 000000000..3429a259c --- /dev/null +++ b/sci-biology/conform-gt/conform-gt-1174.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Modify your Variant Call Format file to be consistent with reference VCF" +HOMEPAGE="http://faculty.washington.edu/browning/conform-gt.html" +SRC_URI="http://faculty.washington.edu/browning/conform-gt/conform-gt.r1174.zip" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" +# Some source files in the net.sf.samtools package are licensed under the MIT License. + +# http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase1_vcf/ + +S="${WORKDIR}"/src diff --git a/sci-biology/conform-gt/metadata.xml b/sci-biology/conform-gt/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/conform-gt/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/coral/ChangeLog b/sci-biology/coral/ChangeLog new file mode 100644 index 000000000..06fd2f3b5 --- /dev/null +++ b/sci-biology/coral/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/coral +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*coral-1.4 (17 Mar 2015) + + 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +coral-1.4.ebuild, + +metadata.xml: + new package diff --git a/sci-biology/coral/Manifest b/sci-biology/coral/Manifest new file mode 100644 index 000000000..afe45a7cb --- /dev/null +++ b/sci-biology/coral/Manifest @@ -0,0 +1 @@ +DIST coral-1.4.tar.gz 34953 SHA256 a74be95ebe726117d5128ee1b4dc1a9e49af8a21958d4efc4b94b6f14cfe30ad SHA512 eefc34a233b73a9eb1bfc0ba3836c7e736787c9774ca9716c3230379d31d37f3e2b3a0dcbc9bf396583461519d45e4bf0ac12db6d386b22b8d1f365e84305a0d WHIRLPOOL b93c9e915297e25e4dfd35c8b8c93bb62a174c950ba83f6d84465ea734037de4eee25f7d8086d9e88273ffb9394d2ae5b2289b837c96546bcca4ffb6a60cfa48 diff --git a/sci-biology/coral/coral-1.4.ebuild b/sci-biology/coral/coral-1.4.ebuild new file mode 100644 index 000000000..f7161469a --- /dev/null +++ b/sci-biology/coral/coral-1.4.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Error corrector for Illumina and Roche/454 reads using multiple alignment info" +HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/coral" +SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/coral/coral-1.4.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e "s#-O3 -Wall -g#${CXXFLAGS}#; s#g++#$(tc-getCXX)#" -i Makefile || die +} + +src_install(){ + dobin coral + dodoc README +} diff --git a/sci-biology/coral/metadata.xml b/sci-biology/coral/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/coral/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/cortex_var/ChangeLog b/sci-biology/cortex_var/ChangeLog new file mode 100644 index 000000000..645e30645 --- /dev/null +++ b/sci-biology/cortex_var/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/cortex_var +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + cortex_var-1.0.5.21.ebuild: + sci-biology/cortex_var: cleanup ebuild syntax + +*cortex_var-1.0.5.21 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +cortex_var-1.0.5.21.ebuild, +metadata.xml: + sci-biology/cortex_var: new package with bundled htslib and gsl libraries diff --git a/sci-biology/cortex_var/Manifest b/sci-biology/cortex_var/Manifest new file mode 100644 index 000000000..af8ef8f9d --- /dev/null +++ b/sci-biology/cortex_var/Manifest @@ -0,0 +1,2 @@ +DIST CORTEX_release_v1.0.5.21.tgz 26902149 SHA256 cac63d5458890f85628542c1e19fe9a3c60066ba836855a13cafa15e394e14fa SHA512 92200cc1e886e519a8e54c9054a2901a03001091654a0534c7a92a5fa7a0ac43aba782b59731d588525902adf749cabca64cdb9cdb25c215be9afb01690215e3 WHIRLPOOL 2cdff42afa80c2a06cf3234ea046b9fb14f00f42707db0f300cece93e9b5e437b1ef8467511e342359cca7fd563260412b012f5fc5bc0f15ae1e5685eb0bb731 +DIST cortex_var_user_manual.pdf 265899 SHA256 b3cb4aa90efd0a817c9246ad9aaf7f7d1a17a900f593bf472dca26c5a8ce4801 SHA512 e4ff442f9280e9eee384c2b82c75493bdb90589b354333fc8b2bee8cf9c9baa432ec09dce5325b2e12c1e1930971616065713858565d56f9a361c573ac0c4f65 WHIRLPOOL 5353cf0f100a33c693904b97ae3381046a92522a7824c70bc2acfb5d24dbb51506b4ef8974fd38649fc1f45837f32f40108a596fb5bd832d609d7bed5c2160bc diff --git a/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild new file mode 100644 index 000000000..70118b8dc --- /dev/null +++ b/sci-biology/cortex_var/cortex_var-1.0.5.21.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Assemble and compare genotype variants (variant discovery without reference sequence)" +HOMEPAGE="http://cortexassembler.sourceforge.net/index_cortex_var.html" +SRC_URI="http://sourceforge.net/projects/cortexassembler/files/cortex_var/latest/CORTEX_release_v1.0.5.21.tgz + http://cortexassembler.sourceforge.net/cortex_var_user_manual.pdf" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://www.well.ox.ac.uk/project-stampy + +DEPEND="sci-biology/vcftools + sci-libs/gsl + sci-libs/htslib + dev-lang/perl" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/CORTEX_release_v1.0.5.21 + +src_prepare(){ + sed -e "s/ -O3 / ${CFLAGS} /" Makefile || die +} + +src_compile(){ + rm -rf libs/htslib libs/gsl-1.15 + make NUM_COLS=1 MAXK=31 cortex_var || die +} + +src_install(){ + bash install.sh || die + perl_set_version + insinto ${VENDOR_LIB} + doins scripts/analyse_variants/bioinf-perl/lib/* scripts/calling/* + echo "PATH=/usr/share/${PN}/scripts/analyse_variants/needleman_wunsch" > "${S}/99${PN}" + doenvd "${S}/99${PN}" + dodoc "${DISTDIR}"/cortex_var_user_manual.pdf +} diff --git a/sci-biology/cortex_var/metadata.xml b/sci-biology/cortex_var/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/cortex_var/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild index 49d7ae6de..6debbc14c 100644 --- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild +++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild index 49d7ae6de..6debbc14c 100644 --- a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild +++ b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-biology/cutadapt/cutadapt-1.5.ebuild b/sci-biology/cutadapt/cutadapt-1.5.ebuild index 49d7ae6de..6debbc14c 100644 --- a/sci-biology/cutadapt/cutadapt-1.5.ebuild +++ b/sci-biology/cutadapt/cutadapt-1.5.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-biology/cutadapt/cutadapt-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild index 985fa125a..ac45c8673 100644 --- a/sci-biology/cutadapt/cutadapt-9999.ebuild +++ b/sci-biology/cutadapt/cutadapt-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index 2bc893037..21184a5d6 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">cutadapt</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dcmstack/ChangeLog b/sci-biology/dcmstack/ChangeLog new file mode 100644 index 000000000..6b8c0b1b5 --- /dev/null +++ b/sci-biology/dcmstack/ChangeLog @@ -0,0 +1,24 @@ +# ChangeLog for sci-biology/dcmstack +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: + gentoo does not support python 2_6 + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: + corrected python compatibilities + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: + added python 3.3 compatibility + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: + removed unneeded bits, sorted eclasses + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> dcmstack-9999.ebuild: + updated deps + +*dcmstack-9999 (31 Mar 2015) + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> +dcmstack-9999.ebuild, + +metadata.xml: + new package, initial draft diff --git a/sci-biology/dcmstack/dcmstack-9999.ebuild b/sci-biology/dcmstack/dcmstack-9999.ebuild new file mode 100644 index 000000000..c165551a5 --- /dev/null +++ b/sci-biology/dcmstack/dcmstack-9999.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 git-r3 multilib + +DESCRIPTION="DICOM to Nifti coversion" +HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/moloney/dcmstack" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="" + +DEPEND=" + dev-python/setuptools[${PYTHON_USEDEP}]" +RDEPEND="sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/pydicom-0.9.7[${PYTHON_USEDEP}]" diff --git a/app-editors/neovim/metadata.xml b/sci-biology/dcmstack/metadata.xml index 897aa2e6b..897aa2e6b 100644 --- a/app-editors/neovim/metadata.xml +++ b/sci-biology/dcmstack/metadata.xml diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog index aba75b4ed..b3b197f41 100644 --- a/sci-biology/discrover/ChangeLog +++ b/sci-biology/discrover/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/discrover: Add github to remote-id in metadata.xml + +*discrover-1.6.0 (18 Mar 2015) + + 18 Mar 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.6.0.ebuild, + -discrover-1.5.2.ebuild, discrover-9999.ebuild, metadata.xml: + sci-biology/discrover: version bump; drop USE flag + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> discrover-1.5.2.ebuild, discrover-9999.ebuild, metadata.xml: sci-biology/discrover: fix SLOT operators; correct ruby deps diff --git a/sci-biology/discrover/Manifest b/sci-biology/discrover/Manifest index 761387b9b..a8c14d997 100644 --- a/sci-biology/discrover/Manifest +++ b/sci-biology/discrover/Manifest @@ -1 +1 @@ -DIST discrover-1.5.2.tar.gz 257926 SHA256 047222c605b8e49096bb6d003a3aa1bea10fb489f990441c6d02804acd957d8b SHA512 31e8414f625dd3cfc2564145ffebdc0f69dad9cbe1c70034b874be04922b3867694ea5a525b8bff9823135527b7eed84ed3592a53705ba8f113d54f08c9f9438 WHIRLPOOL 76365fa0db51fe94186b8524e17a3a15c820dfe982af71c6ac02c649fc030b8d92b895ed600444235ba23887b422a9683e1ebeffddfb7c21fe9c471e958ded45 +DIST discrover-1.6.0.tar.gz 251285 SHA256 1399eb8249a712d331c24eeb8ef30f7cc7cc737a6a9bd6682d34834a944c5065 SHA512 78215b8c05da214928934b63f78753d707fbbe5de8cf7dbd03ddededfaf8cedf232b6769755718748735ff504e129ce02bdef3b29d0ece2b57e3745ab2e1669b WHIRLPOOL f2716730dd9310194170f78177d73ab2c856769cf04c54fa1493515c26454a1af5df2f15fa246aeeeaf7fc7b966da6d6f30a8f4ca7beeaa2e1e9b44aca73d2ea diff --git a/sci-biology/discrover/discrover-1.5.2.ebuild b/sci-biology/discrover/discrover-1.6.0.ebuild index f0992e2f5..5f1281c4a 100644 --- a/sci-biology/discrover/discrover-1.5.2.ebuild +++ b/sci-biology/discrover/discrover-1.6.0.ebuild @@ -3,11 +3,7 @@ # $Header: $ EAPI=5 - -USE_RUBY="ruby19" -RUBY_OPTIONAL=yes - -inherit cmake-utils ruby-fakegem +inherit cmake-utils DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" HOMEPAGE="https://github.com/maaskola/discrover" @@ -16,21 +12,12 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar. LICENSE="GPL-3+" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc" +IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc" RDEPEND=" dev-libs/boost cairo? ( x11-libs/cairo ) dreme? ( sci-biology/meme ) - tikzlogo? ( - $(ruby_implementations_depend) - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - dev-tex/pgf - dev-tex/xcolor - media-gfx/imagemagick - ) - misc_scripts? ( $(ruby_implementations_depend) ) rmathlib? ( dev-lang/R ) tcmalloc? ( dev-util/google-perftools ) " @@ -58,7 +45,6 @@ src_configure() { $(cmake-utils_use_with dreme DREME) $(cmake-utils_use_with doc DOC) $(cmake-utils_use_with lto LTO) - $(cmake-utils_use_with tikzlogo TIKZLOGO) $(cmake-utils_use_with misc_scripts MISC_SCRIPTS) $(cmake-utils_use_with rmathlib RMATHLIB) $(cmake-utils_use_with tcmalloc TCMALLOC) diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild index 8131e9bf4..69588034c 100644 --- a/sci-biology/discrover/discrover-9999.ebuild +++ b/sci-biology/discrover/discrover-9999.ebuild @@ -3,11 +3,7 @@ # $Header: $ EAPI=5 - -USE_RUBY="ruby19" -RUBY_OPTIONAL=yes - -inherit cmake-utils git-r3 ruby-fakegem +inherit cmake-utils git-r3 DESCRIPTION="A sequence motif discovery tool that uses discriminative learning" HOMEPAGE="https://github.com/maaskola/discrover" @@ -17,21 +13,12 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}" LICENSE="GPL-3+" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="+cairo dreme doc +lto tikzlogo misc_scripts +rmathlib tcmalloc" +IUSE="+cairo dreme doc +lto misc_scripts +rmathlib tcmalloc" RDEPEND=" dev-libs/boost cairo? ( x11-libs/cairo ) dreme? ( sci-biology/meme ) - tikzlogo? ( - $(ruby_implementations_depend) - dev-texlive/texlive-latex - dev-texlive/texlive-latexextra - dev-tex/pgf - dev-tex/xcolor - media-gfx/imagemagick - ) - misc_scripts? ( $(ruby_implementations_depend) ) rmathlib? ( dev-lang/R ) tcmalloc? ( dev-util/google-perftools ) " @@ -59,7 +46,6 @@ src_configure() { $(cmake-utils_use_with dreme DREME) $(cmake-utils_use_with doc DOC) $(cmake-utils_use_with lto LTO) - $(cmake-utils_use_with tikzlogo TIKZLOGO) $(cmake-utils_use_with misc_scripts MISC_SCRIPTS) $(cmake-utils_use_with rmathlib RMATHLIB) $(cmake-utils_use_with tcmalloc TCMALLOC) diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml index 6bfaf6cfe..85d16cfe7 100644 --- a/sci-biology/discrover/metadata.xml +++ b/sci-biology/discrover/metadata.xml @@ -7,22 +7,22 @@ </maintainer> <use> <flag name="cairo"> - Use Cairo for sequence logo plotting capabilities - </flag> + Use Cairo for sequence logo plotting capabilities + </flag> <flag name="dreme"> - Enable usage of DREME from the MEME package for seeding - </flag> + Enable usage of DREME from the MEME package for seeding + </flag> <flag name="lto"> - Compile with link-time optimization (LTO) - </flag> - <flag name="tikzlogo"> - Enable LaTeX/TikZ based ruby script for sequence logo drawing - </flag> + Compile with link-time optimization (LTO) + </flag> <flag name="misc_scripts"> - Install miscellaneous scripts, e.g. for sequence length statistics - </flag> + Install miscellaneous scripts + </flag> <flag name="rmathlib"> - Link to the standalone Rmathlib for statistical routines - </flag> + Link to the standalone Rmathlib for statistical routines + </flag> </use> + <upstream> + <remote-id type="github">maaskola/discrover</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/embassy-cbstools/ChangeLog b/sci-biology/embassy-cbstools/ChangeLog deleted file mode 100644 index d7fb20f44..000000000 --- a/sci-biology/embassy-cbstools/ChangeLog +++ /dev/null @@ -1,61 +0,0 @@ -# ChangeLog for sci-biology/embassy-cbstools -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-cbstools/ChangeLog,v 1.5 2010/01/15 22:44:35 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-cbstools-1.0.0-r3.ebuild, embassy-cbstools-1.0.0.650.ebuild, - -files/embassy-cbstools-1.0.0-r2.patch, metadata.xml: - Bump eclass, Drop old - -*embassy-cbstools-1.0.0-r3 (19 Sep 2011) - - 19 Sep 2011; Justin Lecher <jlec@gentoo.org> - -embassy-cbstools-1.0.0-r2.ebuild, +embassy-cbstools-1.0.0-r3.ebuild: - Silent upstream bump - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-cbstools-1.0.0-r2.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 19 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-cbstools-1.0.0-r2.ebuild, files/embassy-cbstools-1.0.0-r2.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-cbstools-1.0.0-r2.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-cbstools-1.0.0-r2.ebuild: - EOV not needed to be set anymore - -*embassy-cbstools-1.0.0-r2 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-cbstools-1.0.0-r2.ebuild, +files/embassy-cbstools-1.0.0-r2.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-cbstools-1.0.0-r1.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-cbstools-1.0.0-r1 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-cbstools-1.0.0-r1.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-cbstools-1.0.0.ebuild: - Stabilised on amd64 and x86. - -*embassy-cbstools-1.0.0 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-cbstools-1.0.0.ebuild: - Initial import for EMBASSY 6.0.1. - diff --git a/sci-biology/embassy-cbstools/Manifest b/sci-biology/embassy-cbstools/Manifest deleted file mode 100644 index 6d7c74656..000000000 --- a/sci-biology/embassy-cbstools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-cbstools-1.0.0.650.tar.gz 452594 SHA256 adb97baa5c7c44c1451537c8cb608024322435d5a4a2693a063a501e42f7127c SHA512 8f16f726220a36f998d8a0f1d8aec9ec6b2db8160b15bed7bafc5a65d57a937bd91ee831ecabe2e9aaa8cecaa18d050f16439a276a882730fde3fa4937bec384 WHIRLPOOL 82813e295f5576d30d474eb9294c2c2c75c577abb59f57baae35cc8cceaccd5a9216f50be43d61523feea80ad6212c955a084bcd9f84da9b5802d050cdc4092a diff --git a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild b/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild deleted file mode 100644 index dd78911a8..000000000 --- a/sci-biology/embassy-cbstools/embassy-cbstools-1.0.0.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="applications from the CBS group" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch deleted file mode 100644 index 63c67a160..000000000 --- a/sci-biology/embassy-cbstools/files/embassy-cbstools-1.0.0.650_fix-build-system.patch +++ /dev/null @@ -1,97 +0,0 @@ ---- CBSTOOLS-1.0.0.650/configure.ac -+++ CBSTOOLS-1.0.0.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- CBSTOOLS-1.0.0.650/src/Makefile.am -+++ CBSTOOLS-1.0.0.650/src/Makefile.am -@@ -19,9 +19,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -65,5 +63,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif ---- CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am -+++ CBSTOOLS-1.0.0.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-clustalomega/ChangeLog b/sci-biology/embassy-clustalomega/ChangeLog deleted file mode 100644 index 8d022543c..000000000 --- a/sci-biology/embassy-clustalomega/ChangeLog +++ /dev/null @@ -1,117 +0,0 @@ -# ChangeLog for sci-biology/embassy-clustalomega -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - embassy-clustalomega-1.1.0.ebuild, metadata.xml: - Bump eclass - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 19 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-domalign-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-domalign-0.1.0-r5.ebuild, +files/embassy-domalign-0.1.0-r5.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-domalign-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-domalign-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-domalign-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-domalign-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-domalign-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-domalign-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-domalign-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domalign-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Removed hidden file .#embassy-domalign-0.1.0-r1.ebuild.1.2 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-domalign-0.1.0.ebuild, embassy-domalign-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0-r1.ebuild: - Added to x86. - -*embassy-domalign-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Added to x86. - -*embassy-domalign-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-domalign-0.1.0.ebuild: - Initial import. Part of EMBASSY 3.0.0. - diff --git a/sci-biology/embassy-clustalomega/Manifest b/sci-biology/embassy-clustalomega/Manifest deleted file mode 100644 index 43c85d868..000000000 --- a/sci-biology/embassy-clustalomega/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-clustalomega-1.1.0.tar.gz 618177 SHA256 98bcb7e561a6f0373ddf96c5d98c0f043da1cddb75dc94a1dca439c54b5a27b5 SHA512 fc16f9505e0300ae184e292fb1d96ce6b90eaf80298f847769466a84726d10ea58e3f4c14ed21a9e2c36d7fa533c7ad248b4995bf41c8abbd0fed1faf1fd4801 WHIRLPOOL f06e66144845b85cdc253571f126bdc9074d3efaad45c92c83bfc8abfc8a0a70b75435e2917f76519a53e94f8649805e99c88137bd04e59cc5c15dc6dabc6b54 diff --git a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild b/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild deleted file mode 100644 index e6636aced..000000000 --- a/sci-biology/embassy-clustalomega/embassy-clustalomega-1.1.0.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Clustal Omega - Scalable multiple protein sequences alignment" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" - -RDEPEND+=" sci-biology/clustal-omega" diff --git a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch b/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch deleted file mode 100644 index 7847da78a..000000000 --- a/sci-biology/embassy-clustalomega/files/embassy-clustalomega-1.1.0_fix-build-system.patch +++ /dev/null @@ -1,90 +0,0 @@ ---- CLUSTALOMEGA-1.1.0/configure.ac -+++ CLUSTALOMEGA-1.1.0/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- CLUSTALOMEGA-1.1.0/src/Makefile.am -+++ CLUSTALOMEGA-1.1.0/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -62,5 +60,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-domainatrix/ChangeLog b/sci-biology/embassy-domainatrix/ChangeLog deleted file mode 100644 index e55b3b7d3..000000000 --- a/sci-biology/embassy-domainatrix/ChangeLog +++ /dev/null @@ -1,174 +0,0 @@ -# ChangeLog for sci-biology/embassy-domainatrix -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domainatrix/ChangeLog,v 1.29 2010/01/01 21:48:13 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-domainatrix-0.1.0-r6.ebuild, embassy-domainatrix-0.1.650.ebuild, - -files/embassy-domainatrix-0.1.0-r5.patch, metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-domainatrix-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 19 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domainatrix-0.1.0-r5.ebuild, - files/embassy-domainatrix-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domainatrix-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domainatrix-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-domainatrix-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-domainatrix-0.1.0-r5.ebuild, - +files/embassy-domainatrix-0.1.0-r5.patch, +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-domainatrix-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-domainatrix-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-domainatrix-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-domainatrix-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-domainatrix-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-domainatrix-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-domainatrix-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-domainatrix-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-domainatrix-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-domainatrix-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> - embassy-domainatrix-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-domainatrix-0.1.0-r1.ebuild: - Added ~sparc - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-0.1.0-r1.ebuild: - Added to x86. - -*embassy-domainatrix-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-domainatrix-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -files/embassy-domainatrix-1.0.0-r1.patch, - -embassy-domainatrix-1.0.0-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-domainatrix-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-0.1.0.ebuild: - Added to x86. - -*embassy-domainatrix-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - +embassy-domainatrix-0.1.0.ebuild, embassy-domainatrix-1.0.0-r1.ebuild: - Ported version 1.0.0-r1 to the improved embassy.eclass. Version 0.1.0 is - really an upgrade; it is normal to be required to downgrade from 1.0.0 to - 0.1.0 to upgrade to EMBASSY 3.0.0. This is an issue with upstream's - versionning scheme. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-domainatrix-1.0.0.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-domainatrix-1.0.0-r1.ebuild: - Stable ppc-macos - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> - embassy-domainatrix-1.0.0-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-1.0.0-r1.ebuild: - Added to x86. - -*embassy-domainatrix-1.0.0-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +files/embassy-domainatrix-1.0.0-r1.patch, - +embassy-domainatrix-1.0.0-r1.ebuild: - Patched version for EMBOSS-2.10. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-domainatrix-1.0.0.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-domainatrix-1.0.0.ebuild: - Unstable ppc-macos. - -*embassy-domainatrix-1.0.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-domainatrix-1.0.0.ebuild: - Moved from app-sci/embassy-domainatrix to sci-biology/embassy-domainatrix. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-1.0.0.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-domainatrix-1.0.0.ebuild: - Added to ~ppc. - -* domainatrix-1.0.0 (19 Jul 2004) - - 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-domainatrix-1.0.0.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-domainatrix/Manifest b/sci-biology/embassy-domainatrix/Manifest deleted file mode 100644 index 3170b29e2..000000000 --- a/sci-biology/embassy-domainatrix/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-domainatrix-0.1.650.tar.gz 474066 SHA256 122cae02e529385eb98d51caa3a21b613545b5dbc763e17524afeab1f7d1cb18 SHA512 151e026445abb171a9141ae5576442307121646c66dc811320a6f73be1103203bf04d37b813e5c95ef0873be261cd474835f4dffd042f33f99d7dd4fda19be7b WHIRLPOOL 82689cbedec77da2c7eb62a78e4407e2153d9dc6e4c51608705bc4bfed3556516ca61619982a3fcb02cdf8e37eee68f87aeba9fec23d054b660dad15d81553c0 diff --git a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild b/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild deleted file mode 100644 index 238053286..000000000 --- a/sci-biology/embassy-domainatrix/embassy-domainatrix-0.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Protein domain analysis add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch b/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch deleted file mode 100644 index f76b0237c..000000000 --- a/sci-biology/embassy-domainatrix/files/embassy-domainatrix-0.1.650_fix-build-system.patch +++ /dev/null @@ -1,91 +0,0 @@ ---- DOMAINATRIX-0.1.650/configure.ac -+++ DOMAINATRIX-0.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- DOMAINATRIX-0.1.650/src/Makefile.am -+++ DOMAINATRIX-0.1.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -64,5 +62,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif - diff --git a/sci-biology/embassy-domalign/ChangeLog b/sci-biology/embassy-domalign/ChangeLog deleted file mode 100644 index 35ad6db18..000000000 --- a/sci-biology/embassy-domalign/ChangeLog +++ /dev/null @@ -1,118 +0,0 @@ -# ChangeLog for sci-biology/embassy-domalign -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domalign/ChangeLog,v 1.20 2010/01/01 21:51:36 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-domalign-0.1.0-r5.ebuild, embassy-domalign-0.1.650.ebuild, - -files/embassy-domalign-0.1.0-r5.patch, metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 19 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild, files/embassy-domalign-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domalign-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-domalign-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-domalign-0.1.0-r5.ebuild, +files/embassy-domalign-0.1.0-r5.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-domalign-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-domalign-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-domalign-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-domalign-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-domalign-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-domalign-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-domalign-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domalign-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Removed hidden file .#embassy-domalign-0.1.0-r1.ebuild.1.2 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-domalign-0.1.0.ebuild, embassy-domalign-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0-r1.ebuild: - Added to x86. - -*embassy-domalign-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-domalign-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domalign-0.1.0.ebuild: - Added to x86. - -*embassy-domalign-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-domalign-0.1.0.ebuild: - Initial import. Part of EMBASSY 3.0.0. - diff --git a/sci-biology/embassy-domalign/Manifest b/sci-biology/embassy-domalign/Manifest deleted file mode 100644 index 9a48247a7..000000000 --- a/sci-biology/embassy-domalign/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-domalign-0.1.650.tar.gz 498669 SHA256 df64428f965f3bf7636b649d60fbfc68450b6ff6981d1b971840b55ac7996509 SHA512 14e86664e9038acc60fbec92fa218e218921fb1e51cc2e482fb1760ccd9ea16041dc8a2a9f5f320fca3340b7efdc48ea9d753b048a43966fc3431acdaddc7846 WHIRLPOOL c7de34abbfaf407e3c4d5dc3582ad9a45adc4c7c91a7376e5cedaaa620711ffb315d647fbd813315d93edbbfed38b130ace7a5b3d016f638af64d02432c6db37 diff --git a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild b/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild deleted file mode 100644 index 157e1af36..000000000 --- a/sci-biology/embassy-domalign/embassy-domalign-0.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Protein domain alignment add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch b/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch deleted file mode 100644 index d87bae393..000000000 --- a/sci-biology/embassy-domalign/files/embassy-domalign-0.1.650_fix-build-system.patch +++ /dev/null @@ -1,92 +0,0 @@ ---- DOMALIGN-0.1.650/configure.ac -+++ DOMALIGN-0.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- DOMALIGN-0.1.650/src/Makefile.am -+++ DOMALIGN-0.1.650/src/Makefile.am -@@ -17,10 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I../include -I${embprefix}/include \ -- -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -63,5 +60,5 @@ - ../../../plplot/libeplplot.la $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif - diff --git a/sci-biology/embassy-domsearch/ChangeLog b/sci-biology/embassy-domsearch/ChangeLog deleted file mode 100644 index db2a175d0..000000000 --- a/sci-biology/embassy-domsearch/ChangeLog +++ /dev/null @@ -1,116 +0,0 @@ -# ChangeLog for sci-biology/embassy-domsearch -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-domsearch/ChangeLog,v 1.19 2010/01/01 21:53:24 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-domsearch-0.1.0-r5.ebuild, embassy-domsearch-0.1.650.ebuild, - -files/embassy-domsearch-0.1.0-r5.patch, metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-domsearch-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 19 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domsearch-0.1.0-r5.ebuild, files/embassy-domsearch-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domsearch-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-domsearch-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-domsearch-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-domsearch-0.1.0-r5.ebuild, +files/embassy-domsearch-0.1.0-r5.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-domsearch-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-domsearch-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-domsearch-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-domsearch-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-domsearch-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-domsearch-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-domsearch-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-domsearch-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-domsearch-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-domsearch-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-domsearch-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-domsearch-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-domsearch-0.1.0.ebuild, embassy-domsearch-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-domsearch-0.1.0-r1.ebuild: - Added ~sparc - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domsearch-0.1.0-r1.ebuild: - Added to x86. - -*embassy-domsearch-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-domsearch-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-domsearch-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domsearch-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-domsearch-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-domsearch-0.1.0.ebuild: - Added to x86. - -*embassy-domsearch-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-domsearch-0.1.0.ebuild: - Initial import. Part of EMBASSY 3.0.0. - diff --git a/sci-biology/embassy-domsearch/Manifest b/sci-biology/embassy-domsearch/Manifest deleted file mode 100644 index 89f5e90a6..000000000 --- a/sci-biology/embassy-domsearch/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-domsearch-0.1.650.tar.gz 504183 SHA256 43c1d99723f42d0f79c4e9d11abaff084bed8262ec958f237a51465cd7afa168 SHA512 a242100dc7b4b1f4a838dbf65dffb0475b6b890c7d68efae6a74beb3d4784d031f92365a50a41c0d7ea7d1b4be5e65a298626a798970c74df0d5f85427a51589 WHIRLPOOL 02afa5cdf4d82b127317537c088b91592f6c4624769b7b13f030fd59590b533fb8ec62189b165bbf885d967069883f5e08f562e7187294468700ce9571a47111 diff --git a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild b/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild deleted file mode 100644 index f0d1265c5..000000000 --- a/sci-biology/embassy-domsearch/embassy-domsearch-0.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Protein domain search add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch b/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch deleted file mode 100644 index f3f4b3950..000000000 --- a/sci-biology/embassy-domsearch/files/embassy-domsearch-0.1.650_fix-build-system.patch +++ /dev/null @@ -1,91 +0,0 @@ ---- DOMSEARCH-0.1.650/configure.ac -+++ DOMSEARCH-0.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- DOMSEARCH-0.1.650/src/Makefile.am -+++ DOMSEARCH-0.1.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -62,5 +60,5 @@ - ../../../plplot/libeplplot.la $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif - diff --git a/sci-biology/embassy-emnu/ChangeLog b/sci-biology/embassy-emnu/ChangeLog deleted file mode 100644 index a497db7a4..000000000 --- a/sci-biology/embassy-emnu/ChangeLog +++ /dev/null @@ -1,157 +0,0 @@ -# ChangeLog for sci-biology/embassy-emnu -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-emnu/ChangeLog,v 1.29 2010/01/01 21:55:20 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-emnu-1.05-r7.ebuild, - embassy-emnu-1.05.650.ebuild, -files/embassy-emnu-1.05-r7.patch, - metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild, - files/embassy-emnu-1.05-r7.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-emnu-1.05-r7.ebuild: - EOV not needed to be set anymore - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - -files/embassy-emnu-1.05-r6.patch, +files/embassy-emnu-1.05-r7.patch: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-emnu-1.05-r6.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-emnu-1.05-r6 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-emnu-1.05-r6.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r5.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-emnu-1.05-r4.ebuild: - Pruning version that will never be stabilised. - -*embassy-emnu-1.05-r5 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-emnu-1.05-r5.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-emnu-1.05-r4 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-emnu-1.05-r4.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> embassy-emnu-1.05-r3.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-emnu-1.05-r2.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-emnu-1.05-r3.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-emnu-1.05-r2.ebuild, embassy-emnu-1.05-r3.ebuild: - Dropped ppc-macos, see you in prefix. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-emnu-1.05-r3.ebuild: - Added ~sparc - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r3.ebuild: - Added to x86. - -*embassy-emnu-1.05-r3 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-emnu-1.05-r3.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r2.ebuild: - Fixed digest mismatch due to silent upstream repackaging. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -files/embassy-emnu-1.05-r1.patch, -embassy-emnu-1.05-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r2.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-emnu-1.05-r2.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r2.ebuild: - Added to x86. - -*embassy-emnu-1.05-r2 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r1.ebuild, +embassy-emnu-1.05-r2.ebuild: - Ported 1.05-r1 to the improved embassy.eclass. The new version is part of - EMBASSY 3.0.0. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-emnu-1.05.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-emnu-1.05-r1.ebuild: - Stable ppc-macos - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-emnu-1.05-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05-r1.ebuild: - Added to x86. - -*embassy-emnu-1.05-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +files/embassy-emnu-1.05-r1.patch, +embassy-emnu-1.05-r1.ebuild: - Patched version for EMBOSS 2.10. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-emnu-1.05.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-emnu-1.05.ebuild: - Unstable ppc-macos. - -*embassy-emnu-1.05 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-emnu-1.05.ebuild: - Moved from app-sci/embassy-emnu to sci-biology/embassy-emnu. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-emnu-1.05.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-emnu-1.05.ebuild: - Added to ~ppc. - -* embassy-emnu-1.05 (19 Jul 2004) - - 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-emnu-1.05.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-emnu/Manifest b/sci-biology/embassy-emnu/Manifest deleted file mode 100644 index 1813061e4..000000000 --- a/sci-biology/embassy-emnu/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-emnu-1.05.650.tar.gz 425595 SHA256 0a5ae3a1fbaf7952ba5e28cf89bf9cbf521cea9fe4703170b532c50542c8ea0e SHA512 0cb0dafd53c4fd410409430dc12353989d2c226191acace26e81b457602b6b6c60f8eb1d0d9b36ea90b2420010c1a3e887a2458e8487008a36775961e378d0dd WHIRLPOOL ab62608ab9a1f433a0781c672c80daf6447f81e98159adc506e4a6fd22c7c6376fd6b5ae14f91aba5bdad76f66c3e0a9a89638cf2288f90aa70c36402c41cc6a diff --git a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild b/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild deleted file mode 100644 index fe88b98a7..000000000 --- a/sci-biology/embassy-emnu/embassy-emnu-1.05.650.ebuild +++ /dev/null @@ -1,15 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Simple menu of EMBOSS applications" -EBO_EXTRA_ECONF="$(use_enable ncurses curses)" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" -IUSE+=" ncurses" - -RDEPEND+=" ncurses? ( sys-libs/ncurses )" diff --git a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch b/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch deleted file mode 100644 index e73eb7b17..000000000 --- a/sci-biology/embassy-emnu/files/embassy-emnu-1.05.650_fix-build-system.patch +++ /dev/null @@ -1,127 +0,0 @@ ---- EMNU-1.05.650/configure.ac -+++ EMNU-1.05.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -899,20 +862,16 @@ - - - dnl emnu and mse only: uses curses --dnl Test if --with-curses is given --AC_ARG_WITH([curses], --[AS_HELP_STRING([--with-curses], [curses (or ncurses)])]) -- --AC_MSG_CHECKING([for curses]) -- --AS_IF([test "${with_curses}"], --[ -- CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" -- LDFLAGS="$LDFLAGS -L${with_curses}/lib" -+dnl Test if --enable-curses is given -+AC_ARG_ENABLE([curses], -+[AS_HELP_STRING([--enable-curses], [curses])]) -+ -+AS_IF([test "x$enable_curses" = "xyes"], [ -+ PKG_CHECK_MODULES([NCURSES], [ncurses]) -+ PKG_CHECK_MODULES([FORM], [form]) -+ PKG_CHECK_MODULES([MENU], [menu]) - ]) - --AC_CHECK_LIB([ncurses], [main], [LIBS="$LIBS -lncurses"], [LIBS="$LIBS -lcurses"]) -- - - - ---- EMNU-1.05.650/src/Makefile.am -+++ EMNU-1.05.650/src/Makefile.am -@@ -17,9 +17,8 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) \ -+ $(NCURSES_CFLAGS) $(FORM_CFLAGS) $(MENU_CFLAGS) - endif - - if ISSHARED -@@ -57,5 +56,5 @@ - ../../../plplot/libeplplot.la -lmenu -lform $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot -lmenu -lform $(XLIB) -+ -lajax $(NLADD) $(NCURSES_LIBS) $(FORM_LIBS) $(MENU_LIBS) $(XLIB) - endif ---- EMNU-1.05.650/emboss_acd/Makefile.am -+++ EMNU-1.05.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-esim4/ChangeLog b/sci-biology/embassy-esim4/ChangeLog deleted file mode 100644 index 9c25b667a..000000000 --- a/sci-biology/embassy-esim4/ChangeLog +++ /dev/null @@ -1,160 +0,0 @@ -# ChangeLog for sci-biology/embassy-esim4 -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-esim4/ChangeLog,v 1.28 2010/01/01 21:58:14 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-esim4-1.0.0-r7.ebuild, - embassy-esim4-1.0.0.650.ebuild, -files/embassy-esim4-1.0.0-r7.patch, - metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild, - files/embassy-esim4-1.0.0-r7.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-esim4-1.0.0-r7.ebuild: - EOV not needed to be set anymore - -*embassy-esim4-1.0.0-r7 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-esim4-1.0.0-r7.ebuild, - +files/embassy-esim4-1.0.0-r7.patch, +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-esim4-1.0.0-r6.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-esim4-1.0.0-r6 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-esim4-1.0.0-r6.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r5.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-esim4-1.0.0-r4.ebuild: - Pruning version that will never be stabilised. - -*embassy-esim4-1.0.0-r5 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-esim4-1.0.0-r5.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-esim4-1.0.0-r4 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-esim4-1.0.0-r4.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-esim4-1.0.0-r3.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-esim4-1.0.0-r2.ebuild: - Pruning old version. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-esim4-1.0.0-r3.ebuild: - Marked ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-esim4-1.0.0-r2.ebuild, embassy-esim4-1.0.0-r3.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r3.ebuild: - Added to x86. - -*embassy-esim4-1.0.0-r3 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-esim4-1.0.0-r3.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r2.ebuild: - Fixed digest mismatch due to silent upstream repackaging. - - 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-esim4-1.0.0-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r2.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-esim4-1.0.0-r2.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r2.ebuild: - Added to x86. - -*embassy-esim4-1.0.0-r2 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r1.ebuild, +embassy-esim4-1.0.0-r2.ebuild: - Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of - EMBASSY 3.0.0. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-esim4-1.0.0.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-esim4-1.0.0-r1.ebuild: - Stable ppc-macos - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> - embassy-esim4-1.0.0-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0-r1.ebuild: - Added to x86. - -*embassy-esim4-1.0.0-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +embassy-esim4-1.0.0-r1.ebuild: - Build against the EMBOSS 2.10 source tree. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-esim4-1.0.0.ebuild: - Unstable ppc-macos. - -*embassy-esim4-1.0.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-esim4-1.0.0.ebuild: - Moved from app-sci/embassy-esim4 to sci-biology/embassy-esim4. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-esim4-1.0.0.ebuild: - Added to ~ppc. - -* embassy-esim4-1.0.0 (19 Jul 2004) - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-esim4-1.0.0.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-esim4/Manifest b/sci-biology/embassy-esim4/Manifest deleted file mode 100644 index d6b2e7d7e..000000000 --- a/sci-biology/embassy-esim4/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-esim4-1.0.0.650.tar.gz 473261 SHA256 ce2f8a4e802da7e11ac3cbaf24406d9b33d4aa488f1c68bbbc8e969ec7e0b671 SHA512 623b241915217ffb314e3fc4ca6aed5e1683b78b6c76f899b67c4e5d48ce83c9920d79b1c5a1508d61856c332e614020d0804b7252c535d9622f9623f29cd152 WHIRLPOOL ea34bd05cc41f8e1e4af8eebfca9f1c0888c96f0dbb11df79c2cd8966b27d72f019c8ec3043ca7c9e276e015232476165a77336590ace448766a45163f654d62 diff --git a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild b/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild deleted file mode 100644 index 308596049..000000000 --- a/sci-biology/embassy-esim4/embassy-esim4-1.0.0.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="sim4 - Alignment of cDNA and genomic DNA" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch b/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch deleted file mode 100644 index 827907180..000000000 --- a/sci-biology/embassy-esim4/files/embassy-esim4-1.0.0.650_fix-build-system.patch +++ /dev/null @@ -1,97 +0,0 @@ ---- ESIM4-1.0.0.650/configure.ac -+++ ESIM4-1.0.0.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- ESIM4-1.0.0.650/src/Makefile.am -+++ ESIM4-1.0.0.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -63,5 +61,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif ---- ESIM4-1.0.0.650/emboss_acd/Makefile.am -+++ ESIM4-1.0.0.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-hmmer/ChangeLog b/sci-biology/embassy-hmmer/ChangeLog deleted file mode 100644 index fa2844cae..000000000 --- a/sci-biology/embassy-hmmer/ChangeLog +++ /dev/null @@ -1,166 +0,0 @@ -# ChangeLog for sci-biology/embassy-hmmer -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-hmmer/ChangeLog,v 1.30 2010/01/01 22:00:05 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-hmmer-2.3.2-r4.ebuild, - embassy-hmmer-2.3.2.650.ebuild, -files/embassy-hmmer-2.3.2-r4.patch, - metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild, - files/embassy-hmmer-2.3.2-r4.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-hmmer-2.3.2-r4.ebuild: - EOV not needed to be set anymore - -*embassy-hmmer-2.3.2-r4 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-hmmer-2.3.2-r4.ebuild, - +files/embassy-hmmer-2.3.2-r4.patch, +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-hmmer-2.3.2-r3.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-hmmer-2.3.2-r3 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-hmmer-2.3.2-r3.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.3.2-r2.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-hmmer-2.3.2-r1.ebuild: - Pruning version that will never be stabilised. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.3.2-r1.ebuild, embassy-hmmer-2.3.2-r2.ebuild: - Fixed description. Added dependency on HMMER. - -*embassy-hmmer-2.3.2-r2 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-hmmer-2.3.2-r2.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-hmmer-2.3.2-r1 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-hmmer-2.3.2-r1.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> embassy-hmmer-2.3.2.ebuild: - Added ~amd64 - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-hmmer-2.1.1-r2.ebuild: - Pruning old version. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-hmmer-2.3.2.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild, embassy-hmmer-2.3.2.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.3.2.ebuild: - Added to x86. - -*embassy-hmmer-2.3.2 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild, +embassy-hmmer-2.3.2.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 20 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild: - Fixed download URL (silent upstream repackaging). - - 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-hmmer-2.1.1-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r2.ebuild: - Added to x86. - -*embassy-hmmer-2.1.1-r2 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r1.ebuild, +embassy-hmmer-2.1.1-r2.ebuild: - Ported 2.1.1-r1 to the improved embassy.eclass. The new version is part of - EMBASSY 3.0.0. - - 30 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r1.ebuild: - Fixed bug #100672. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-hmmer-2.1.1.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-hmmer-2.1.1-r1.ebuild: - Stable ppc-macos Bug 96819 - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> - embassy-hmmer-2.1.1-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1-r1.ebuild: - Added to x86. - -*embassy-hmmer-2.1.1-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +embassy-hmmer-2.1.1-r1.ebuild: - Build against the EMBOSS 2.10 source tree. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-hmmer-2.1.1.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-hmmer-2.1.1.ebuild: - Unstable ppc-macos - -*embassy-hmmer-2.1.1 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-hmmer-2.1.1.ebuild: - Moved from app-sci/embassy-hmmer to sci-biology/embassy-hmmer. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-hmmer-2.1.1.ebuild: - Added to ~ppc. - -* embassy-hmmer-2.1.1 (19 Jul 2004) - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-hmmer-2.1.1.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-hmmer/Manifest b/sci-biology/embassy-hmmer/Manifest deleted file mode 100644 index cfef1c3b4..000000000 --- a/sci-biology/embassy-hmmer/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-hmmer-2.3.2.650.tar.gz 587775 SHA256 1464ff5e87c7c429f2fc78ac3554f8bd32cdaf49b8bed095fce6268b9afd4f6a SHA512 eb2c037fec70f4113b9ab59cc4eca9a608e8d0971a7bcc4612d60b1e28556444dd3ecdea4ff7b8f8b34711ad9f655334857e7510e89060459c81994a3abcc02a WHIRLPOOL 59027e96d3e629eb771fa966be95cd30138d6b97223056c95c1cc19d21ec0ffe555ff12f2cadc372ea303a0e06a9c1e673c4e32b2a50d8fd2ab2071d2c04cb83 diff --git a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild b/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild deleted file mode 100644 index 8f2a68a80..000000000 --- a/sci-biology/embassy-hmmer/embassy-hmmer-2.3.2.650.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="wrappers for HMMER - Biological sequence analysis with profile HMMs" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" - -RDEPEND+="sci-biology/hmmer" diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch deleted file mode 100644 index 78d0c254f..000000000 --- a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.650_fix-build-system.patch +++ /dev/null @@ -1,90 +0,0 @@ ---- HMMER-2.3.2.650/configure.ac -+++ HMMER-2.3.2.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- HMMER-2.3.2.650/src/Makefile.am -+++ HMMER-2.3.2.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -67,5 +65,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-hmmer/metadata.xml b/sci-biology/embassy-hmmer/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-hmmer/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-iprscan/ChangeLog b/sci-biology/embassy-iprscan/ChangeLog deleted file mode 100644 index 497766bba..000000000 --- a/sci-biology/embassy-iprscan/ChangeLog +++ /dev/null @@ -1,45 +0,0 @@ -# ChangeLog for sci-biology/embassy-iprscan -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-iprscan/ChangeLog,v 1.5 2010/01/15 22:45:28 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-iprscan-4.3.1-r2.ebuild, embassy-iprscan-4.3.1.650.ebuild, - -files/embassy-iprscan-4.3.1-r2.patch, metadata.xml: - Bump eclass, Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild, - files/embassy-iprscan-4.3.1-r2.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-iprscan-4.3.1-r2.ebuild: - EOV not needed to be set anymore - - 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-iprscan-4.3.1-r1.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-iprscan-4.3.1-r1 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-iprscan-4.3.1-r1.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-iprscan-4.3.1.ebuild: - Stabilised on amd64 and x86. - -*embassy-iprscan-4.3.1 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-iprscan-4.3.1.ebuild: - Initial import for EMBASSY 6.0.1. - diff --git a/sci-biology/embassy-iprscan/Manifest b/sci-biology/embassy-iprscan/Manifest deleted file mode 100644 index 5b8f21827..000000000 --- a/sci-biology/embassy-iprscan/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-iprscan-4.3.1.650.tar.gz 406720 SHA256 9534de155a4efd765a588f567b9b502052360719278e492b1c0dd9e50aa78013 SHA512 eed75693557f141331dfb6bec6961a8f6eab93780cad3b629d547b8635be2df6ec85e5ae0e9646d174a562a0f6d31c3c487a4dacac9efdd393a7144cd5716878 WHIRLPOOL 25b3ac80d0f5e7bb3e4ffe21fcd2657894f23ca4f7e182d527d97b5b869e11206e2ab4f265fca027e419ef7fdd2752b3d11c8ef9518edb72b93dddff4d7dcfc8 diff --git a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild b/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild deleted file mode 100644 index 11c44d8dd..000000000 --- a/sci-biology/embassy-iprscan/embassy-iprscan-4.3.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="InterProScan motif detection add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch b/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch deleted file mode 100644 index 955005d51..000000000 --- a/sci-biology/embassy-iprscan/files/embassy-iprscan-4.3.1.650_fix-build-system.patch +++ /dev/null @@ -1,97 +0,0 @@ ---- IPRSCAN-4.3.1.650/configure.ac -+++ IPRSCAN-4.3.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- IPRSCAN-4.3.1.650/src/Makefile.am -+++ IPRSCAN-4.3.1.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -58,5 +56,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif ---- IPRSCAN-4.3.1.650/emboss_acd/Makefile.am -+++ IPRSCAN-4.3.1.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-iprscan/metadata.xml b/sci-biology/embassy-iprscan/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-iprscan/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-meme/ChangeLog b/sci-biology/embassy-meme/ChangeLog deleted file mode 100644 index 746ddda9b..000000000 --- a/sci-biology/embassy-meme/ChangeLog +++ /dev/null @@ -1,75 +0,0 @@ -# ChangeLog for sci-biology/embassy-meme -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-memenew/ChangeLog,v 1.11 2010/01/01 22:03:00 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> embassy-meme-4.7.650.ebuild, - metadata.xml: - Bump eclass, Drop old - - 14 Jan 2012; Andreas K. Huettel <dilfridge@gentoo.org> - -embassy-memenew-4.0.0-r1.ebuild: - Removed because the file is non-fetchable - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild, - files/embassy-memenew-4.0.0-r1.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-memenew-4.0.0-r1.ebuild: - EOV not needed to be set anymore - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-memenew-4.0.0.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-memenew-4.0.0 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-memenew-4.0.0.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-memenew-0.1.0-r1.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - embassy-memenew-0.1.0.ebuild, embassy-memenew-0.1.0-r1.ebuild: - Fixed description. - -*embassy-memenew-0.1.0-r1 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-memenew-0.1.0-r1.ebuild: - New upstream version/package for EMBASSY 6.0.1. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-memenew-0.1.0.ebuild: - Added ~amd64. - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-memenew-0.1.0.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-memenew-0.1.0.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-memenew-0.1.0.ebuild: - Added to x86. - -*embassy-memenew-0.1.0 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-memenew-0.1.0.ebuild: - Initial import. This package will probably replace EMBASSY-MEME in new - EMBASSY releases. - diff --git a/sci-biology/embassy-meme/Manifest b/sci-biology/embassy-meme/Manifest deleted file mode 100644 index 13e38d3a7..000000000 --- a/sci-biology/embassy-meme/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-meme-4.7.650.tar.gz 622448 SHA256 a9ce0af5f8e05d82cf7678c9781041520bb9889a5706e38480940003ef2a9e8f SHA512 0536531b198aac09a9fe6c17cf1c60c766789c94a7f83f743a90aaa65061c95534bf398c53611a34549b7ec1a4928fdc45fe0d2553f25f85eeda41f90c2e8c6f WHIRLPOOL 041fec3789c86375edb64b34a0190484cda6a59aab564c5deee19930a8cec0455ed9689d726cb647cca30e7c3c59f728aff5546ab8ad491aed4f331e76497b51 diff --git a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild b/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild deleted file mode 100644 index ffc88d1df..000000000 --- a/sci-biology/embassy-meme/embassy-meme-4.7.650.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="wrappers for MEME - Multiple Em for Motif Elicitation" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" - -RDEPEND+=" sci-biology/meme" diff --git a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch b/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch deleted file mode 100644 index 03c424604..000000000 --- a/sci-biology/embassy-meme/files/embassy-meme-4.7.650_fix-build-system.patch +++ /dev/null @@ -1,90 +0,0 @@ ---- MEME-4.7.650/configure.ac -+++ MEME-4.7.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- MEME-4.7.650/src/Makefile.am -+++ MEME-4.7.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -60,5 +58,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-meme/metadata.xml b/sci-biology/embassy-meme/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-meme/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-mse/ChangeLog b/sci-biology/embassy-mse/ChangeLog deleted file mode 100644 index 13160995e..000000000 --- a/sci-biology/embassy-mse/ChangeLog +++ /dev/null @@ -1,185 +0,0 @@ -# ChangeLog for sci-biology/embassy-mse -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-mse/ChangeLog,v 1.35 2010/01/01 22:05:28 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-mse-3.0.0.ebuild, - embassy-mse-3.0.0.650.ebuild, -files/embassy-mse-3.0.0.patch, metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild, - files/embassy-mse-3.0.0.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-mse-3.0.0.ebuild: - EOV not needed to be set anymore - -*embassy-mse-3.0.0 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-mse-3.0.0.ebuild, - +files/embassy-mse-3.0.0.patch, +metadata.xml: - Version Bump, Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-mse-1.0.0-r7.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-mse-1.0.0-r7 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r7.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r6.ebuild: - Stabilised on amd64 and x86. - - 28 Aug 2008; Olivier Fisette <ribosome@gentoo.org> ChangeLog: - Fixing broken Manifest. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-mse-1.0.0-r5.ebuild: - Pruning version that will never be stabilised. - -*embassy-mse-1.0.0-r6 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r6.ebuild: - New upstream version/package for EMBASSY 6.0.1. - - 07 Aug 2007; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r5.ebuild: - Removed multilib-strict fix, as it was moved to the embassy eclass. - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r4.ebuild: - We still need an AMD64 ebuild for EMBOSS 4.0.0 (my mistake). - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - -embassy-mse-1.0.0-r4.ebuild: - Pruned old version that will never be stabilised. - -*embassy-mse-1.0.0-r5 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r5.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r4.ebuild: - Added to ~amd64. - -*embassy-mse-1.0.0-r4 (17 Feb 2007) - - 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r4.ebuild: - Added a fix for multilib-strict on AMD64 suggested by Jeff Gardner - <je_fro@gentoo.org>. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-mse-1.0.0-r2.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-mse-1.0.0-r3.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-mse-1.0.0-r3.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-mse-1.0.0-r2.ebuild, embassy-mse-1.0.0-r3.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r3.ebuild: - Added to x86. - -*embassy-mse-1.0.0-r3 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r3.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r2.ebuild: - Fixed download URL (silent upstream repackaging). - - 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-mse-1.0.0-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r2.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-mse-1.0.0-r2.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r2.ebuild: - Added to x86. - -*embassy-mse-1.0.0-r2 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r1.ebuild, +embassy-mse-1.0.0-r2.ebuild: - Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of - EMBASSY 3.0.0. - - 30 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r1.ebuild: - Fixed bug #100672. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-mse-1.0.0.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-mse-1.0.0-r1.ebuild: - Stable ppc-macos Bug 96819 - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-mse-1.0.0-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0-r1.ebuild: - Added to x86. - -*embassy-mse-1.0.0-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +embassy-mse-1.0.0-r1.ebuild: - Build against the EMBOSS 2.10 source tree. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-mse-1.0.0.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-mse-1.0.0.ebuild: - Unstable ppc-macos - -*embassy-mse-1.0.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-mse-1.0.0.ebuild: - Moved from app-sci/embassy-mse to sci-biology/embassy-mse. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-mse-1.0.0.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-mse-1.0.0.ebuild: - Added to ~ppc. - -* embassy-mse-1.0.0 (19 Jul 2004) - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-mse-1.0.0.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-mse/Manifest b/sci-biology/embassy-mse/Manifest deleted file mode 100644 index c69712e0a..000000000 --- a/sci-biology/embassy-mse/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-mse-3.0.0.650.tar.gz 491747 SHA256 2744c2a447cc16d7ad4d9049c61793fc2803659b83b0666b3ca9c30648dac88c SHA512 4ae34de71566464e4352ff7b3bbd19b8bf0571013f34253495cf5cc57240bac9c75192c302eb0231763db1745a7e3e79ebcdcb006e36ea4621a886b213eb96d3 WHIRLPOOL 8d257e79161d5989ac2fe3fe5e55e073402b57795121693fd43ac0d2d348032abb7927d4e40faf2b4db182145f9bcdcc7ba5d7b0534df10dd844c256b8dacb9b diff --git a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild b/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild deleted file mode 100644 index f692c9191..000000000 --- a/sci-biology/embassy-mse/embassy-mse-3.0.0.650.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="MSE - Multiple Sequence Screen Editor" -EBO_EXTRA_ECONF="$(use_enable ncurses curses)" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" -IUSE+=" ncurses" - -RDEPEND+=" ncurses? ( sys-libs/ncurses )" - -src_install() { - emboss-r1_src_install - insinto /usr/include/emboss/mse - doins h/*.h -} diff --git a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch b/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch deleted file mode 100644 index 8b2f0574e..000000000 --- a/sci-biology/embassy-mse/files/embassy-mse-3.0.0.650_fix-build-system.patch +++ /dev/null @@ -1,133 +0,0 @@ ---- MSE-3.0.0.650/configure.ac -+++ MSE-3.0.0.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL -@@ -1000,17 +963,13 @@ - - - --dnl emnu and mse only: uses curses --dnl Test if --with-curses is given --AC_ARG_WITH([curses], -- [AS_HELP_STRING([--with-curses], -- [curses (or ncurses)])]) --if test "${with_curses}" ; then --AC_MSG_CHECKING([for curses]) --CPPFLAGS="$CPPFLAGS -I${with_curses}/include -I${with_curses}/include/ncurses" --LDFLAGS="$LDFLAGS -L${with_curses}/lib" --fi --AC_CHECK_LIB(ncurses, main, LIBS="$LIBS -lncurses", LIBS="$LIBS -lcurses") -+dnl Test if --enable-curses is given -+AC_ARG_ENABLE([curses], -+[AS_HELP_STRING([--enable-curses], [curses])]) -+ -+AS_IF([test "x$enable_curses" = "xyes"], [ -+ PKG_CHECK_MODULES([NCURSES], [ncurses]) -+]) - - - ---- MSE-3.0.0.650/src/Makefile.am -+++ MSE-3.0.0.650/src/Makefile.am -@@ -18,9 +18,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I../h -I${embprefix}/include \ -- -I${embprefix}/include/eplplot -I${embprefix}/include/epcre \ -- $(NLINCLUDES) -+AM_CPPFLAGS = -I$(top_srcdir)/h -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) $(NCURSES_CFLAGS) - endif - - if ISSHARED -@@ -60,5 +58,5 @@ - $(XLIB) - else - LDADD = ../ckit/libckit.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ -- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lensembl -lajaxg -lajax $(NLADD) $(NCURSES_LIBS) $(XLIB) - endif ---- MSE-3.0.0.650/ckit/Makefile.am -+++ MSE-3.0.0.650/ckit/Makefile.am -@@ -2,7 +2,7 @@ - - lib_LTLIBRARIES = libckit.la - --AM_CPPFLAGS = -I../h -+AM_CPPFLAGS = -I$(top_srcdir)/h - - CKITSRC = datafiles.c next.c seqentry.c strings.c gcg.c pir.c \ - seqspec.c ttyinterface.c nextseqentry.c \ ---- MSE-3.0.0.650/emboss_acd/Makefile.am -+++ MSE-3.0.0.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-mse/metadata.xml b/sci-biology/embassy-mse/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-mse/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-phylipnew/ChangeLog b/sci-biology/embassy-phylipnew/ChangeLog deleted file mode 100644 index 7c9443a80..000000000 --- a/sci-biology/embassy-phylipnew/ChangeLog +++ /dev/null @@ -1,81 +0,0 @@ -# ChangeLog for sci-biology/embassy-phylipnew -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-phylipnew/ChangeLog,v 1.12 2010/01/01 22:02:06 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-phylipnew-3.69.ebuild, - embassy-phylipnew-3.69.650.ebuild, -files/embassy-phylipnew-3.69.patch, - metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild, - files/embassy-phylipnew-3.69.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-phylipnew-3.69.ebuild: - EOV not needed to be set anymore - -*embassy-phylipnew-3.69 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-phylipnew-3.69.ebuild, - +files/embassy-phylipnew-3.69.patch, +metadata.xml: - Version Bump, Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-phylipnew-3.68.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-phylipnew-3.68 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-phylipnew-3.68.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-phylipnew-3.67.ebuild: - Stabilised on amd64 and x86. - -*embassy-phylipnew-3.67 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-phylipnew-3.67.ebuild: - New upstream version/package for EMBASSY 6.0.1. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - embassy-phylipnew-3.6b.ebuild: - Fixed description. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-phylipnew-3.6b.ebuild: - Adding ~amd64. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-phylipnew-3.6b.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-phylipnew-3.6b.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-phylipnew-3.6b.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-phylipnew-3.6b.ebuild: - Added to x86. - -*embassy-phylipnew-3.6b (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-phylipnew-3.6b.ebuild: - Initial import. This package will probably replace EMBASSY-PHYLIP in new - EMBASSY releases. - diff --git a/sci-biology/embassy-phylipnew/Manifest b/sci-biology/embassy-phylipnew/Manifest deleted file mode 100644 index 6b25968a7..000000000 --- a/sci-biology/embassy-phylipnew/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-phylipnew-3.69.650.tar.gz 1741298 SHA256 af385d01826e67e05295955f05721728abbd4feb9e11a944189414da6590bfeb SHA512 b41a31285e05a418e4fbfae7241c3658fe458e3d5d84bff472d98b7c145340a55bee1d744b5c056d0e88407074947b5f37b2182c9cb800c8a8d43dfa76d026d5 WHIRLPOOL 94cbe384a1575c322c7e3cdba7ccdb79e3e24cec7bd24776872f3e7d425d85c64fdcdc1cae6c079b40ca943b84a039ba2c7c5c059c40ceaf95c5c2e11e4a3e58 diff --git a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild b/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild deleted file mode 100644 index 602bec9ac..000000000 --- a/sci-biology/embassy-phylipnew/embassy-phylipnew-3.69.650.ebuild +++ /dev/null @@ -1,13 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="the Phylogeny Inference Package" - -inherit emboss-r1 - -LICENSE+=" freedist" - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch b/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch deleted file mode 100644 index e0efb74bd..000000000 --- a/sci-biology/embassy-phylipnew/files/embassy-phylipnew-3.69.650_fix-build-system.patch +++ /dev/null @@ -1,98 +0,0 @@ ---- PHYLIPNEW-3.69.650/configure.ac -+++ PHYLIPNEW-3.69.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -781,21 +754,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -918,6 +876,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- PHYLIPNEW-3.69.650/src/Makefile.am -+++ PHYLIPNEW-3.69.650/src/Makefile.am -@@ -16,10 +16,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I../include -I${embprefix}/include \ -- -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I$(top_srcdir)/include -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -120,5 +117,5 @@ - ../../../plplot/libeplplot.la $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif ---- PHYLIPNEW-3.69.650/emboss_acd/Makefile.am -+++ PHYLIPNEW-3.69.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-phylipnew/metadata.xml b/sci-biology/embassy-phylipnew/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-phylipnew/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-signature/ChangeLog b/sci-biology/embassy-signature/ChangeLog deleted file mode 100644 index 2d3399062..000000000 --- a/sci-biology/embassy-signature/ChangeLog +++ /dev/null @@ -1,116 +0,0 @@ -# ChangeLog for sci-biology/embassy-signature -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-signature/ChangeLog,v 1.19 2010/01/01 21:59:44 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-signature-0.1.0-r5.ebuild, embassy-signature-0.1.650.ebuild, - -files/embassy-signature-0.1.0-r5.patch, metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-signature-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-signature-0.1.0-r5.ebuild, files/embassy-signature-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-signature-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-signature-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-signature-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-signature-0.1.0-r5.ebuild, +files/embassy-signature-0.1.0-r5.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-signature-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-signature-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-signature-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-signature-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-signature-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-signature-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-signature-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-signature-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-signature-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 16 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-signature-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-signature-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-signature-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-signature-0.1.0-r1.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-signature-0.1.0.ebuild, embassy-signature-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-signature-0.1.0-r1.ebuild: - Added to x86. - -*embassy-signature-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-signature-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-signature-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-signature-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-signature-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-signature-0.1.0.ebuild: - Added to x86. - -*embassy-signature-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-signature-0.1.0.ebuild: - New import. This package is part of the EMBASSY 3.0.0 distribution. - diff --git a/sci-biology/embassy-signature/Manifest b/sci-biology/embassy-signature/Manifest deleted file mode 100644 index 0e33ccc50..000000000 --- a/sci-biology/embassy-signature/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-signature-0.1.650.tar.gz 622294 SHA256 2ab34cc76caaaefe7914e9b00dd12ee81a32d7a7ccca20ba901d67f1e2c2f27e SHA512 4989693b17c29ece16f94934e1b2f5e62f31c345bc8cbac938450db0d8f5d56ae37be6090c46e96725e63621c5951f8a65461cd36d4aafb1b509f3f554b4e952 WHIRLPOOL 1a943266ee9092f13fb3ad0779cdfe70e3cb5c1ed7d31164a93da90aaea2df95150970e0ef22df89c3cc97dfe7564092f2cab8aad7fb720e2f456cb363666de3 diff --git a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild b/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild deleted file mode 100644 index 693de26df..000000000 --- a/sci-biology/embassy-signature/embassy-signature-0.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Protein signature add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch b/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch deleted file mode 100644 index 5197c6422..000000000 --- a/sci-biology/embassy-signature/files/embassy-signature-0.1.650_fix-build-system.patch +++ /dev/null @@ -1,90 +0,0 @@ ---- SIGNATURE-0.1.650/configure.ac -+++ SIGNATURE-0.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- SIGNATURE-0.1.650/src/Makefile.am -+++ SIGNATURE-0.1.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -68,5 +66,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-signature/metadata.xml b/sci-biology/embassy-signature/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-signature/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-structure/ChangeLog b/sci-biology/embassy-structure/ChangeLog deleted file mode 100644 index 06ab2b204..000000000 --- a/sci-biology/embassy-structure/ChangeLog +++ /dev/null @@ -1,116 +0,0 @@ -# ChangeLog for sci-biology/embassy-structure -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-structure/ChangeLog,v 1.19 2010/01/01 21:57:51 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> - -embassy-structure-0.1.0-r5.ebuild, embassy-structure-0.1.650.ebuild, - -files/embassy-structure-0.1.0-r5.patch, metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> - embassy-structure-0.1.0-r5.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-structure-0.1.0-r5.ebuild, files/embassy-structure-0.1.0-r5.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-structure-0.1.0-r5.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> - embassy-structure-0.1.0-r5.ebuild: - EOV not needed to be set anymore - -*embassy-structure-0.1.0-r5 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> - +embassy-structure-0.1.0-r5.ebuild, +files/embassy-structure-0.1.0-r5.patch, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-structure-0.1.0-r4.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-structure-0.1.0-r4 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-structure-0.1.0-r4.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-structure-0.1.0-r3.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-structure-0.1.0-r2.ebuild: - Pruning version that will never be stabilised. - -*embassy-structure-0.1.0-r3 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-structure-0.1.0-r3.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-structure-0.1.0-r2 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-structure-0.1.0-r2.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-structure-0.1.0-r1.ebuild: - Added ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-structure-0.1.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-structure-0.1.0-r1.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-structure-0.1.0-r1.ebuild: - Added ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-structure-0.1.0.ebuild, embassy-structure-0.1.0-r1.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-structure-0.1.0-r1.ebuild: - Added to x86. - -*embassy-structure-0.1.0-r1 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-structure-0.1.0-r1.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-structure-0.1.0.ebuild: - Fixed download URL (silent upstream repackaging). - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-structure-0.1.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-structure-0.1.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-structure-0.1.0.ebuild: - Added to x86. - -*embassy-structure-0.1.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-structure-0.1.0.ebuild: - New import. This package is part of the EMBASSY 3.0.0 distribution. - diff --git a/sci-biology/embassy-structure/Manifest b/sci-biology/embassy-structure/Manifest deleted file mode 100644 index 0d6171d95..000000000 --- a/sci-biology/embassy-structure/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-structure-0.1.650.tar.gz 588118 SHA256 06c3d07f495247d1427e91887fa00df053486e2b59f0ec722735bb0b957502f1 SHA512 56fb0ed975bfd95b1fbbccaf694e0617ec23971d53bdc230eeb6ca177907e784805697193e7630e4a513f1b4ee7a1a7974136520963557c452185be4ed22b641 WHIRLPOOL db988aab3f6d2165f44039385fd0a7ab2d6a7dce12906714d5932b411e3dfeac7e06a219af048ef120ea22acab3c1e958fefe68e6e1f19eec56de82c5c1b8c03 diff --git a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild b/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild deleted file mode 100644 index 896612d10..000000000 --- a/sci-biology/embassy-structure/embassy-structure-0.1.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Protein structure add-on package" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch b/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch deleted file mode 100644 index c87eefde1..000000000 --- a/sci-biology/embassy-structure/files/embassy-structure-0.1.650_fix-build-system.patch +++ /dev/null @@ -1,90 +0,0 @@ ---- STRUCTURE-0.1.650/configure.ac -+++ STRUCTURE-0.1.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- STRUCTURE-0.1.650/src/Makefile.am -+++ STRUCTURE-0.1.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -66,5 +64,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-structure/metadata.xml b/sci-biology/embassy-structure/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-structure/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-topo/ChangeLog b/sci-biology/embassy-topo/ChangeLog deleted file mode 100644 index 0bc873963..000000000 --- a/sci-biology/embassy-topo/ChangeLog +++ /dev/null @@ -1,161 +0,0 @@ -# ChangeLog for sci-biology/embassy-topo -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-topo/ChangeLog,v 1.29 2010/01/01 21:54:52 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-topo-2.0.0.ebuild, - embassy-topo-2.0.650.ebuild, -files/embassy-topo-2.0.0.patch, metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild, - files/embassy-topo-2.0.0.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-topo-2.0.0.ebuild: - EOV not needed to be set anymore - -*embassy-topo-2.0.0 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-topo-2.0.0.ebuild, - +files/embassy-topo-2.0.0.patch, +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-topo-1.0.0-r6.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-topo-1.0.0-r6 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-topo-1.0.0-r6.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r5.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-topo-1.0.0-r4.ebuild: - Pruning version that will never be stabilised. - -*embassy-topo-1.0.0-r5 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-topo-1.0.0-r5.ebuild: - New upstream version/package for EMBASSY 6.0.1. - -*embassy-topo-1.0.0-r4 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-topo-1.0.0-r4.ebuild: - New upstream packaging for EMBOSS 5.0.0. - - 15 Feb 2007; Jeff Gardner <je_fro@gentoo.org> - embassy-topo-1.0.0-r3.ebuild: - Adding ~amd64 - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -embassy-topo-1.0.0-r2.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-topo-1.0.0-r3.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> - embassy-topo-1.0.0-r3.ebuild: - Marked ~sparc - - 02 Nov 2006; Fabian Groffen <grobian@gentoo.org> - embassy-topo-1.0.0-r2.ebuild, embassy-topo-1.0.0-r3.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r3.ebuild: - Added to x86. - -*embassy-topo-1.0.0-r3 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - +embassy-topo-1.0.0-r3.ebuild: - New upstream version building against EMBOSS 4.0.0. - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r2.ebuild: - Fixed download URL (silent upstream repackaging). - - 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-topo-1.0.0-r1.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r2.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> - embassy-topo-1.0.0-r2.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r2.ebuild: - Added to x86. - -*embassy-topo-1.0.0-r2 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r1.ebuild, +embassy-topo-1.0.0-r2.ebuild: - Ported 1.0.0-r1 to the improved embassy.eclass. The new version is part of - EMBASSY 3.0.0. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> - -embassy-topo-1.0.0.ebuild: - Removed old version. - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> - embassy-topo-1.0.0-r1.ebuild: - Stable ppc-macos Bug 96819 - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> - embassy-topo-1.0.0-r1.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0-r1.ebuild: - Added to x86. - -*embassy-topo-1.0.0-r1 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> - +embassy-topo-1.0.0-r1.ebuild: - Build against the EMBOSS 2.10 source tree. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-topo-1.0.0.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-topo-1.0.0.ebuild: - Unstable ppc-macos - -*embassy-topo-1.0.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-topo-1.0.0.ebuild: - Moved from app-sci/embassy-topo to sci-biology/embassy-topo. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-topo-1.0.0.ebuild: - Added to x86. - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-topo-1.0.0.ebuild: - Added to ~ppc. - -* embassy-topo-1.0.0 (19 Jul 2004) - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-topo-1.0.0.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy-topo/Manifest b/sci-biology/embassy-topo/Manifest deleted file mode 100644 index 79de5917d..000000000 --- a/sci-biology/embassy-topo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-topo-2.0.650.tar.gz 443510 SHA256 a8b8b7c1e04be44b5d6982614a9af44b84d0282bb917ed29e23a0a710241ad6f SHA512 8ef157a61ac47680734bed3d07cfe2bcd86730998453daa704b74aad667944ad6b0cc6f7fce36be4566cb19a626f1648d5f6793ce227cf57939fcfd0d10690a8 WHIRLPOOL fbe0edadeafe14b4b24be6fd65ed51dc9572f89e12e6f038017e9dd208a867138219350ccde6ca3eeab94ccedf34e5ec672a65cbf30c3819387407e778caeb55 diff --git a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild b/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild deleted file mode 100644 index 0a77dfbd5..000000000 --- a/sci-biology/embassy-topo/embassy-topo-2.0.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Transmembrane protein display" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch b/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch deleted file mode 100644 index 7ddda05cb..000000000 --- a/sci-biology/embassy-topo/files/embassy-topo-2.0.650_fix-build-system.patch +++ /dev/null @@ -1,97 +0,0 @@ ---- TOPO-2.0.650/configure.ac -+++ TOPO-2.0.650/configure.ac -@@ -635,33 +635,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -737,21 +710,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -874,6 +832,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- TOPO-2.0.650/src/Makefile.am -+++ TOPO-2.0.650/src/Makefile.am -@@ -17,9 +17,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -60,5 +58,5 @@ - $(XLIB) - else - LDADD = -L${embprefix}/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg \ -- -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lajax $(NLADD) $(XLIB) - endif ---- TOPO-2.0.650/emboss_acd/Makefile.am -+++ TOPO-2.0.650/emboss_acd/Makefile.am -@@ -1,3 +1,3 @@ - --pkgdata_DATA = *.acd -+pkgdata_DATA = $(srcdir)/*.acd - pkgdatadir=$(prefix)/share/EMBOSS/acd diff --git a/sci-biology/embassy-topo/metadata.xml b/sci-biology/embassy-topo/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-topo/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy-vienna/ChangeLog b/sci-biology/embassy-vienna/ChangeLog deleted file mode 100644 index 1000b17f9..000000000 --- a/sci-biology/embassy-vienna/ChangeLog +++ /dev/null @@ -1,65 +0,0 @@ -# ChangeLog for sci-biology/embassy-vienna -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy-vienna/ChangeLog,v 1.8 2010/01/15 22:47:16 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-vienna-1.7.2-r2.ebuild, - embassy-vienna-1.7.2.650.ebuild, -files/embassy-vienna-1.7.2-r2.patch, - metadata.xml: - Bump eclass, drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild, - files/embassy-vienna-1.7.2-r2.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-vienna-1.7.2-r2.ebuild: - EOV not needed to be set anymore - -*embassy-vienna-1.7.2-r2 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-vienna-1.7.2-r2.ebuild, - +files/embassy-vienna-1.7.2-r2.patch, +metadata.xml: - Version Bump, Move to new embassy-ng.eclass - - 15 Jan 2010; Christian Faulhammer <fauli@gentoo.org> - embassy-vienna-1.7.2-r1.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-vienna-1.7.2-r1 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - +embassy-vienna-1.7.2-r1.ebuild: - Updated version for EMBASSY 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> - embassy-vienna-1.7.2.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - -embassy-vienna-1.6.ebuild: - Pruning version that will never be stabilised. - -*embassy-vienna-1.7.2 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - +embassy-vienna-1.7.2.ebuild: - New upstream version/package for EMBASSY 6.0.1. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> - embassy-vienna-1.6.ebuild: - Fixed description. - -*embassy-vienna-1.6 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +embassy-vienna-1.6.ebuild: - Initial import. - diff --git a/sci-biology/embassy-vienna/Manifest b/sci-biology/embassy-vienna/Manifest deleted file mode 100644 index f0c2dcc5f..000000000 --- a/sci-biology/embassy-vienna/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST embassy-vienna-1.7.2.650.tar.gz 873165 SHA256 d3c9f64394a5c59151a345c3a2d8e2b3fcab3b59918584776316c204f0bb6c6d SHA512 1484ca419ebcb7776d8f92dd633d4fda1a752a73ccb5189b58f7417a5611e015e9b42cbb37b51f4d5c7a27df0d5cab2cdf1e95ebd70a8359ffc8fa1633d28103 WHIRLPOOL 78679a7aca7db9b67774c9a07e11ecb081b0297c3e9c23e0f98d08ee96f62bef7b861ae223f2962ff79f67b0d9582168e21d869ae0ef6c9c23beb53102a351d2 diff --git a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild b/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild deleted file mode 100644 index e6af9a500..000000000 --- a/sci-biology/embassy-vienna/embassy-vienna-1.7.2.650.ebuild +++ /dev/null @@ -1,11 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -EBO_DESCRIPTION="Vienna RNA package - RNA folding" - -inherit emboss-r1 - -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos" diff --git a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch b/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch deleted file mode 100644 index c9ece6912..000000000 --- a/sci-biology/embassy-vienna/files/embassy-vienna-1.7.2.650_fix-build-system.patch +++ /dev/null @@ -1,98 +0,0 @@ ---- VIENNA-1.7.2.650/configure.ac -+++ VIENNA-1.7.2.650/configure.ac -@@ -649,33 +649,6 @@ - - - --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- -- -- - dnl FIXME: This does no longer seem required with Autoconf 2.67? - dnl Intel MacOSX 10.6 puts X11 in a non-standard place - dnl AS_IF([test "x${with_x}" != "xno"], -@@ -751,21 +724,6 @@ - - - --dnl "Export" these variables for PCRE -- --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) -- -- -- -- - dnl Test if --enable-localforce given - locallink="no" - embprefix="/usr/local" -@@ -888,6 +846,11 @@ - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - - -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- VIENNA-1.7.2.650/src/Makefile.am -+++ VIENNA-1.7.2.650/src/Makefile.am -@@ -32,9 +32,7 @@ - -I../../../ajax/ensembl -I../../../ajax/ajaxdb \ - -I../../../ajax/acd -I../../../plplot - else --AM_CPPFLAGS = -I../H -I${embprefix}/include -I${embprefix}/include/eplplot \ -- $(NLINCLUDES) \ -- -I${embprefix}/include/epcre -+AM_CPPFLAGS = -I$(top_srcdir)/H -I${embprefix}/include $(NLINCLUDES) $(PLPLOT_CFLAGS) - endif - - if ISSHARED -@@ -87,6 +85,7 @@ - endif - - liboviennarna_la_LDFLAGS = $(LINKFLAGS) -+liboviennarna_la_LIBADD = -lajax - - ovrnaalifold_SOURCES = vrnaalifold.c - ovrnaalifoldpf_SOURCES = vrnaalifoldpf.c -@@ -119,5 +118,5 @@ - $(XLIB) - else - LDADD = liboviennarna.la -L${embprefix}/lib -lnucleus -lacd -lajaxdb \ -- -lensembl -lajaxg -lajax -lepcre $(NLADD) -leplplot $(XLIB) -+ -lensembl -lajaxg -lajax $(NLADD) $(XLIB) - endif diff --git a/sci-biology/embassy-vienna/metadata.xml b/sci-biology/embassy-vienna/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy-vienna/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/embassy/ChangeLog b/sci-biology/embassy/ChangeLog deleted file mode 100644 index 8f07f9fce..000000000 --- a/sci-biology/embassy/ChangeLog +++ /dev/null @@ -1,160 +0,0 @@ -# ChangeLog for sci-biology/embassy -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/embassy/ChangeLog,v 1.33 2010/01/01 21:35:29 fauli Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -embassy-6.3.1.ebuild, - metadata.xml: - Drop old - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Dropped ~ppc due to missing keywording of sci-libs/plplot, #358035 - - 21 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Fixed for reviewed eclass - - 21 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Fixed for reviewed eclass - - 20 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Naming of eclass changed - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Unset DOCS as we do not have any - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> embassy-6.3.1.ebuild: - Unset DOCS as we do not have any - -*embassy-6.3.1 (10 Mar 2011) - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> +embassy-6.3.1.ebuild, - +metadata.xml: - Move to new embassy-ng.eclass - - 01 Jan 2010; Christian Faulhammer <fauli@gentoo.org> embassy-6.1.0.ebuild: - Transfer Prefix keywords - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*embassy-6.1.0 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +embassy-6.1.0.ebuild: - New meta-package for EMBASSY packages building against EMBOSS 6.1.0. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> embassy-6.0.1.ebuild: - Stabilised on amd64 and x86. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -embassy-5.0.0.ebuild: - Pruning version that will never be stabilised. - -*embassy-6.0.1 (27 Aug 2008) - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +embassy-6.0.1.ebuild: - New meta-package for EMBASSY packages building against EMBOSS 6.0.1. - -*embassy-5.0.0 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +embassy-5.0.0.ebuild: - New meta-package for EMBASSY packages building against EMBOSS 5.0.0. - - 17 Feb 2007; Olivier Fisette <ribosome@gentoo.org> embassy-4.0.0.ebuild: - Added to ~amd64. - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> -embassy-3.0.0.ebuild: - Pruning old version. - - 03 Nov 2006; nixnut <nixnut@gentoo.org> embassy-4.0.0.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> embassy-4.0.0.ebuild: - Added ~sparc - - 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> embassy-3.0.0.ebuild, - embassy-4.0.0.ebuild: - Dropped ppc-macos, see you in prefix. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> embassy-4.0.0.ebuild: - Added to x86. - -*embassy-4.0.0 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +embassy-4.0.0.ebuild: - New meta-package for EMBASSY packages building against EMBOSS 4.0.0. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -embassy-2.10.0.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> embassy-3.0.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> embassy-3.0.0.ebuild: - Stable on ppc. - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> embassy-3.0.0.ebuild: - Added to x86. - -*embassy-3.0.0 (07 Aug 2005) - - 07 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +embassy-3.0.0.ebuild: - New version. This meta-package is for EMBASSY software distributed with - EMBOSS 3.0.0. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -embassy-2.9.0.ebuild: - Removed old version. - - 27 Jul 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.10.0.ebuild: - Stable ppc-macos - - 26 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.10.0.ebuild: - Testing ppc-macos due to embassy-construct being testing. - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> embassy-2.10.0.ebuild: - Marked ppc stable. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.10.0.ebuild: - Added to x86. - - 06 May 2005; David Holm <dholm@gentoo.org> embassy-2.10.0.ebuild: - Added to ~ppc. - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.10.0.ebuild: - Added patched versions of DOMAINATRIX and EMNU that work with EMBOSS 2.10. - -*embassy-2.10.0 (25 Mar 2005) - - 25 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild, - +embassy-2.10.0.ebuild: - Ebuilds for the 2.9 and 2.10 branches of EMBOSS. - - 23 Mar 2005; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild: - EMBOSS 2.10 is incompatible with EMBASSY 2.9 packages. - - 02 Mar 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.9.0.ebuild: - Stable ppc-macos - - 25 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> embassy-2.9.0.ebuild: - Unstable ppc-macos - -*embassy-2.9.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +embassy-2.9.0.ebuild: - Moved from app-sci/embassy to sci-biology/embassy. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> embassy-2.9.0.ebuild: - Added to x86. - - 04 Sep 2004; Thomas Matthijs <axxo@gentoo.org> embassy-2.9.0.ebuild: - fix depend syntax 58347 - - 21 Jul 2004; David Holm <dholm@gentoo.org> embassy-2.9.0.ebuild: - Added to ~ppc. - -* embassy-2.9.0 (19 Jul 2004) - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - embassy-2.9.0.ebuild, metadata.xml, ChangeLog - Initial import. diff --git a/sci-biology/embassy/embassy-6.6.0.ebuild b/sci-biology/embassy/embassy-6.6.0.ebuild deleted file mode 100644 index 2d1d95922..000000000 --- a/sci-biology/embassy/embassy-6.6.0.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="A meta-package for installing all EMBASSY packages (EMBOSS add-ons)" -HOMEPAGE="http://emboss.sourceforge.net/embassy/" - -LICENSE+=" freedist" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~x86-linux ~ppc-macos" - -RDEPEND+=" - >=sci-biology/embassy-cbstools-1.0.0.650 - >=sci-biology/embassy-clustalomega-1.1.0 - >=sci-biology/embassy-domainatrix-0.1.650 - >=sci-biology/embassy-domalign-0.1.650 - >=sci-biology/embassy-domsearch-0.1.650 - >=sci-biology/embassy-emnu-1.05.650 - >=sci-biology/embassy-esim4-1.0.0.650 - >=sci-biology/embassy-hmmer-2.3.2.650 - >=sci-biology/embassy-iprscan-4.3.1.650 - >=sci-biology/embassy-meme-4.7.650 - >=sci-biology/embassy-mse-3.0.0.650 - >=sci-biology/embassy-phylipnew-3.69.650 - >=sci-biology/embassy-signature-0.1.650 - >=sci-biology/embassy-structure-0.1.650 - >=sci-biology/embassy-topo-2.0.650 - >=sci-biology/embassy-vienna-1.7.2.650" diff --git a/sci-biology/embassy/metadata.xml b/sci-biology/embassy/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/embassy/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-biology/emboss/ChangeLog b/sci-biology/emboss/ChangeLog deleted file mode 100644 index a6558c1a6..000000000 --- a/sci-biology/emboss/ChangeLog +++ /dev/null @@ -1,407 +0,0 @@ -# ChangeLog for sci-biology/emboss -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/emboss/ChangeLog,v 1.61 2011/03/09 16:29:05 jlec Exp $ - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4-r2.ebuild: - Drop old - - 04 Feb 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: - Clean a bit, user readme.gentoo.eclass - - 04 Jul 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/emboss-6.3.1_p4-r2_rename_plwid_to_plwidth.patch, - emboss-6.3.1_p4-r2.ebuild: - sci-biology/emboss-6.3.1_p4-r2: added a patch for 'undefined reference to - c_plwid' bug #493724 - - 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - emboss-6.3.1_p4-r2.ebuild: - sci-biology/emboss-6.3.1_p4-r2: add plplot dependency, trying to get rid of a - Makefile.patch using sed hackery - - 16 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - emboss-6.6.0.ebuild, +files/emboss-6.6.0_plcol.patch: - emboss-6.6.0.ebuild files/emboss-6.6.0_plcol.patch - Added the misisng patch, disabled searches for Gentoo-patches, - fixed patch-related variable values in the 6.6.0 ebuild, BUT - 1) the ebuild does not work, configure exits after looking for - -lhpdf or later -lpng (that can be obeyed by omitting --with-hpdf - --with-pngdriver) - 2) if one relies on whatever configure detects compilation aborts - while compiling embossversion.c or because -lexpat is not in LIBS. - Well, expat is not in configure flags at all. - - Maybe something is caused by the --enable-systemlibs configure switch, - I think it actually enables inclusion of these from their bundled - copies in the EMBOSS tarball (and not use of the system-wide headers - and libs). - -*emboss-6.3.1_p4-r2 (11 Sep 2013) -*emboss-6.5.7 (11 Sep 2013) -*emboss-6.6.0 (11 Sep 2013) - - 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +emboss-6.3.1_p4-r2.ebuild, +emboss-6.5.7.ebuild, +emboss-6.6.0.ebuild, - +files/ax_lib_mysql.m4, +files/emboss-6.3.1_p4-r2_Makefile.patch, - +files/emboss-6.3.1_p4-r2_compilations-paths.patch, - +files/emboss-6.3.1_p4-r2_libtool.patch, - +files/emboss-6.3.1_p4-r2_plcol.patch, -emboss-6.3.1_p4-r1.ebuild, - -files/emboss-6.3.1_p4-r1_plcol.patch: - Partial success on removal of all crazy libraries and includes from CFLAGS and - LDFLAGS used throught EMBOSS sources. While compile commandline are now clean - still libtool is passed with LDFLAGS carrying over the many X11 and graphics - libraries. Seems the source is ltmain.sh which uses on the linker lines but - editing m4/libtool.m4 is not the right way to do it. Same applies to ltmain.sh - in top-level directory. Any volunteers? Bug #394425 - - 19 Jul 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/emboss-6.3.1_p4-r1_plcol.patch, emboss-6.3.1_p4-r1.ebuild: - added plcol patch with increased diff line count, bug #391669; same patch - needs to go into offical emboss-6.3.1_p4 - - 22 May 2012; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - Add missing eutils.eclass - - 24 Sep 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - Use Fedora hosting because unpstream removed the patches - - 27 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild, - -files/emboss-6.3.1_p4-r1.patch: - Last fix for 64bitness - - 22 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch: - Fix compile correctly against postgresql, #359959 - - 21 Mar 2011; Justin Lecher <jlec@gentoo.org> files/emboss-6.3.1_p4-r1.patch: - Implicit decs fix, thanks bicatali for help - - 21 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild, - files/emboss-6.3.1_p4-r1.patch: - Fixed for reviewed eclass - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - Straighten ENV - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - New emboss_src_install used - - 15 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - Naming of eclass changed - - 14 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4-r1.ebuild: - Ebov not needed to be set anymore - -*emboss-6.3.1_p4-r1 (11 Mar 2011) - - 11 Mar 2011; Justin Lecher <jlec@gentoo.org> -emboss-6.3.1_p4.ebuild, - +emboss-6.3.1_p4-r1.ebuild, +files/emboss-6.3.1_p4-r1.patch, - -files/emboss-6.3.1_p4.patch: - Rev bump, to ahead of the tree ebuild - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> -files/6.3.1_p4.patch, - emboss-6.3.1_p4.ebuild, +files/emboss-6.3.1_p4.patch: - Correct naming of patch - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: - Removed largefile from local USE description - - 10 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild: - Move to new embassy-ng.eclass - - 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild: - Move to new embassy-ng.eclass - - 09 Mar 2011; Justin Lecher <jlec@gentoo.org> emboss-6.3.1_p4.ebuild: - EAPI=4 takes three arguments on use_with - -*emboss-6.3.1_p4 (09 Mar 2011) - - 09 Mar 2011; Justin Lecher <jlec@gentoo.org> - +files/6.3.1_p4-unbundle-libs.patch, -files/6.3.1-unbundle-libs.patch, - -emboss-6.3.1.ebuild, +emboss-6.3.1_p4.ebuild: - Bump to latest upstream patches - -*emboss-6.3.1 (09 Mar 2011) - - 09 Mar 2011; Justin Lecher <jlec@gentoo.org> - +files/6.3.1-unbundle-libs.patch, +files/emboss-README.Gentoo-2, - emboss-4.0.0.ebuild, emboss-6.0.1.ebuild, emboss-6.1.0-r1.ebuild, - +emboss-6.3.1.ebuild, metadata.xml: - Version Bump #335603, Unbundled libs, removed old, fix clash with - /usr/bin/digest, #330507 - - 18 Jul 2010; <nixnut@gentoo.org> emboss-6.0.1.ebuild: - ppc stable #325457 - - 09 Jul 2010; Samuli Suominen <ssuominen@gentoo.org> emboss-6.0.1.ebuild: - ppc64 stable wrt #325457 - - 23 Jun 2010; Justin Lecher <jlec@gentoo.org> emboss-4.0.0.ebuild, - emboss-6.0.1.ebuild, emboss-6.1.0.ebuild, emboss-6.1.0-r1.ebuild: - Blocking sys-devel/cons, bug 248792 - -*emboss-6.1.0-r1 (07 Mar 2010) - - 07 Mar 2010; Justin Lecher (jlec) <jlec@gentoo.org> - +emboss-6.1.0-r1.ebuild: - Moved to EAPI=3 for PREFIX support, imported prefix patches from overlay, - keyworded as in overlay - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.1.0.ebuild: - Remove documentation that conflicts with EMBASSY phylipnew. - -*emboss-6.1.0 (01 Sep 2009) - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> +emboss-6.1.0.ebuild: - New upstream version. - - 01 Sep 2009; Olivier Fisette <ribosome@gentoo.org> emboss-6.0.1.ebuild: - Stabilised on x86 and amd64. - - 31 Aug 2009; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild, - emboss-6.0.1.ebuild: - Q.A. fixes, including better dependency on ClustalW. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> -emboss-5.0.0.ebuild: - Pruning version that will never be stabilised. - - 27 Aug 2008; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild: - Depend on ClustalW 1.83 since version 2.x will soon be added to Portage - and is incompatible with EMBOSS wrapper programs. - -*emboss-6.0.1 (26 Aug 2008) - - 26 Aug 2008; Olivier Fisette <ribosome@gentoo.org> +emboss-6.0.1.ebuild: - New upstream version. - - 25 Jan 2008; Markus Dittrich <markusle@gentoo.org> - +files/emboss-5.0.0-as-needed.patch, emboss-4.0.0.ebuild, - emboss-5.0.0.ebuild: - Fixed unresolved symbols with as-needed (see bug #207304). - - 22 Jul 2007; Donnie Berkholz <dberkholz@gentoo.org>; emboss-4.0.0.ebuild: - Drop virtual/x11 references. - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> - +files/emboss-README.Gentoo-1: - Added updated Gentoo README file in reStructuredText format. - -*emboss-5.0.0 (18 Jul 2007) - - 18 Jul 2007; Olivier Fisette <ribosome@gentoo.org> +emboss-5.0.0.ebuild: - New upstream version. - - 09 Apr 2007; Jeff Gardner <je_fro@gentoo.org> +files/22emboss, - -files/22emboss-r1, emboss-4.0.0.ebuild: - Fixed to use doenvd wrt bug #173884 - - 10 Dec 2006; Olivier Fisette <ribosome@gentoo.org> - -emboss-3.0.0-r1.ebuild, emboss-4.0.0.ebuild: - Pruned old version. Removed ppc-macos keyword, as grobian said the - package and its dependencies were fully moved into "prefix". - - 20 Nov 2006; <blubb@gentoo.org> emboss-4.0.0.ebuild: - stable on amd64 - - 15 Nov 2006; Markus Rothe <corsair@gentoo.org> emboss-4.0.0.ebuild: - Stable on ppc64; bug #153766 - - 03 Nov 2006; nixnut <nixnut@gentoo.org> emboss-4.0.0.ebuild: - Stable on ppc wrt bug 153766 - - 03 Nov 2006; Jeff Gardner <je_fro@gentoo.org> emboss-3.0.0-r1.ebuild: - Added ~sparc to emboss-3 for embassy-phylip-3.6b. - - 02 Nov 2006; Olivier Fisette <ribosome@gentoo.org> emboss-4.0.0.ebuild: - Added to x86. - - 18 Aug 2006; Jason Wever <weeve@gentoo.org> emboss-4.0.0.ebuild: - Added ~sparc keyword wrt bug #144241. - -*emboss-4.0.0 (21 Jul 2006) - - 21 Jul 2006; Olivier Fisette <ribosome@gentoo.org> +emboss-4.0.0.ebuild: - New upstream version. See change log: - "http://emboss.sourceforge.net/developers/changelog.html". - - 20 Apr 2006; Olivier Fisette <ribosome@gentoo.org> -emboss-3.0.0.ebuild: - Removed old revision. - - 08 Apr 2006; Simon Stelling <blubb@gentoo.org> emboss-3.0.0-r1.ebuild: - stable on amd64 - - 22 Feb 2006; Fabian Groffen <grobian@gentoo.org> ChangeLog: - Marked ppc-macos stable (bug #123332) - - 22 Feb 2006; <nixnut@gentoo.org> emboss-3.0.0-r1.ebuild: - Stable on ppc. bug 123332 - - 21 Feb 2006; Markus Rothe <corsair@gentoo.org> emboss-3.0.0-r1.ebuild: - Stable on ppc64; bug #123332 - - 20 Feb 2006; Joshua Jackson <tsunam@gentoo.org> emboss-3.0.0-r1.ebuild: - Stable on x86; bug #123332 - - 19 Feb 2006; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0-r1.ebuild: - Block old versions of pscan to avoid file collisions (see bug #116236). - - 23 Jan 2006; Olivier Fisette <ribosome@gentoo.org> +files/README.Gentoo: - Added missing README file (fixes bug #120071). - -*emboss-3.0.0-r1 (21 Jan 2006) - - 21 Jan 2006; Olivier Fisette <ribosome@gentoo.org> - +emboss-3.0.0-r1.ebuild: - Install codons and restriction enzyme equivalence files in alternative - directories. This avoids file collisions on case insensitive filesystems - (see bug #115446), allows the installation of an updated enzyme prototypes - file that will give more consistent results (see bug #118832). - - 14 Dec 2005; Donnie Berkholz <spyderous@gentoo.org>; emboss-3.0.0.ebuild: - Add modular X dependencies. - - 19 Nov 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild: - stable on amd64 - - 04 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.10.0.ebuild: - Removed obsolete version. - - 03 Oct 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild: - Stable on ppc-macos (with j4rg0n's permission, bug #102420). - - 02 Oct 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-3.0.0.ebuild: - Stable on ppc. - - 24 Sep 2005; Markus Rothe <corsair@gentoo.org> emboss-3.0.0.ebuild: - Stable on ppc64 - - 21 Sep 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild: - Added to x86. - - 04 Sep 2005; Simon Stelling <blubb@gentoo.org> emboss-3.0.0.ebuild: - added ~amd64 keyword - - 13 Aug 2005; Olivier Fisette <ribosome@gentoo.org> emboss-3.0.0.ebuild, - emboss-2.10.0.ebuild: - Fixed Prosite dependency. - -*emboss-3.0.0 (06 Aug 2005) - - 06 Aug 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-3.0.0.ebuild: - New version. - - 28 Jul 2005; Olivier Fisette <ribosome@gentoo.org> -emboss-2.9.0.ebuild: - Removed old version. - - 25 Jun 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.10.0.ebuild: - Stable ppc-macos - - 24 Jun 2005; Joseph Jezak <josejx@gentoo.org> emboss-2.10.0.ebuild: - Marked ppc stable for bug #96819. - - 19 Jun 2005; Markus Rothe <corsair@gentoo.org> emboss-2.10.0.ebuild: - Stable on ppc64 - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.10.0.ebuild: - Added to x86. - - 02 May 2005; Omkhar Arasaratnam <omkhar@gentoo.org> emboss-2.10.0.ebuild: - Added ~ppc64 - - 02 May 2005; Michael Hanselmann <hansmi@gentoo.org> emboss-2.9.0.ebuild: - Stable on ppc. - -*emboss-2.10.0 (22 Mar 2005) - - 22 Mar 2005; Olivier Fisette <ribosome@gentoo.org> +emboss-2.10.0.ebuild: - New version. - - 22 Feb 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: - Added support for minimal build. - - 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild: - Stable ppc-macos - - 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: - Ebuild cleanup. - - 01 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> emboss-2.9.0.ebuild: - Unstable ppc-macos. - -*emboss-2.9.0 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +files/22emboss-r1, +emboss-2.9.0.ebuild: - Moved from app-sci/emboss to sci-biology/emboss. - - 31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild, - -emboss-2.8.0-r3.ebuild: - Removed old version. Added 2.9.0 to x86. - - 10 Aug 2004; Olivier Fisette <ribosome@gentoo.org> - emboss-2.8.0-r3.ebuild: - Added to x86. - emboss-2.8.0-r2.ebuild: - Removed obsolete ebuild. - - 21 Jul 2004; David Holm <dholm@gentoo.org> emboss-2.9.0.ebuild: - Added to ~ppc. - - 20 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - emboss-2.8.0-r3.ebuild, emboss-2.9.0.ebuild: - Removed icc support since no patching is needed. - - 19 Jul 2004; Olivier Fisette <ribosome@gentoo.org> emboss-2.9.0.ebuild: - Version bump. Changed the configuration and install steps a bit to - reflect the fact that header files are now installed automatically. - - 14 Jul 2004; Olivier Fisette <ribosome@gentoo.org> - emboss-2.8.0-r3.ebuild: Modified configuration step to make the X and png - USE flags independent; Added support for icc; Added primer3 and clustalw - to the dependencies since some EMBOSS programs won't work without them; - Added support for the biological databases aaindex, cutg, prints, prosite, - rebase and transfac, which are needed for many EMBOSS programs (the databases - are PDEPENDencies since they all must be indexed with an EMBOSS program before - use) (this database support is optional); Added header files installation for - EMBOSS development. - emboss-2.8.0-r2.ebuild: Added to x86. - emboss-2.8.0-r1.ebuild, emboss-2.8.0.ebuild, emboss-2.7.1.ebuild: Removed files. - metadata.xml: Added long description; Set myself as maintainer. - - 02 Jun 2004; Aron Griffis <agriffis@gentoo.org> emboss-2.8.0-r1.ebuild, - emboss-2.8.0-r2.ebuild: - Fix use invocation - - 12 May 2004; David Holm <dholm@gentoo.org> emboss-2.8.0-r2.ebuild: - Added to ~ppc. - -*emboss-2.8.0-r2 (11 May 2004) - - 11 May 2004; Patrick Kursawe <phosphan@gentoo.org> emboss-2.8.0-r2.ebuild, - files/22emboss-r1: - Adjusted value of PLPLOT_LIB, see bug #50176 - -*emboss-2.8.0-r1 (30 Jan 2004) - - 30 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0-r1.ebuild: - Modified to use X and png properly for servers - - 28 Jan 2004; Stephen Diener <sediener@gentoo.org> emboss-2.8.0.ebuild: - Modified 2.8.0 ebuild to require X not just USE it. - -*emboss-2.8.0 (13 Dec 2003) - - 13 Dec 2003; Stephen Diener <sediener@gentoo.org> emboss-2.7.1.ebuild, - emboss-2.8.0.ebuild: - Version bump... - - 20 Oct 2003; George Shapovalov <george@gentoo.org> metdata.xml : - added metadata.xml, marked ebuild stable - -*emboss-2.7.1 (03 Sep 2003) - - 03 Sep 2003; <sediener@gentoo.org> emboss-2.7.1.ebuild: - Initial ebuild diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest deleted file mode 100644 index 42ec06043..000000000 --- a/sci-biology/emboss/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe diff --git a/sci-biology/emboss/emboss-6.6.0.ebuild b/sci-biology/emboss/emboss-6.6.0.ebuild deleted file mode 100644 index 59285d753..000000000 --- a/sci-biology/emboss/emboss-6.6.0.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools-utils emboss-r1 eutils readme.gentoo - -DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package" -SRC_URI="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${PV}.tar.gz" - -KEYWORDS="~amd64 ~x86" -IUSE+=" minimal" - -RDEPEND+=" !sys-devel/cons" -PDEPEND+=" - !minimal? ( - sci-biology/aaindex - sci-biology/cutg - sci-biology/prints - sci-biology/prosite - sci-biology/rebase - )" - -S="${WORKDIR}"/EMBOSS-${PV} - -DOCS=( ChangeLog AUTHORS NEWS THANKS FAQ ) - -PATCHES=( - "${FILESDIR}"/${P}_FORTIFY_SOURCE-fix.patch - "${FILESDIR}"/${P}_plplot-declarations.patch - "${FILESDIR}"/${P}_qa-implicit-declarations.patch -) - -src_install() { - # Use autotools-utils_* to remove useless *.la files - autotools-utils_src_install - - readme.gentoo_create_doc - - # Install env file for setting libplplot and acd files path. - cat > 22emboss <<- EOF - # ACD files location - EMBOSS_ACDROOT="${EPREFIX}/usr/share/EMBOSS/acd" - EMBOSS_DATA="${EPREFIX}/usr/share/EMBOSS/data" - EOF - doenvd 22emboss - - # Remove useless dummy files - find "${ED}"/usr/share/EMBOSS -name dummyfile -delete || die "Failed to remove dummy files." - - # Move the provided codon files to a different directory. This will avoid - # user confusion and file collisions on case-insensitive file systems (see - # bug #115446). This change is documented in "README.gentoo". - mv "${ED}"/usr/share/EMBOSS/data/CODONS{,.orig} || \ - die "Failed to move CODON directory." -} diff --git a/sci-biology/emboss/files/README.gentoo b/sci-biology/emboss/files/README.gentoo deleted file mode 100644 index d1879bd08..000000000 --- a/sci-biology/emboss/files/README.gentoo +++ /dev/null @@ -1,34 +0,0 @@ -Administrating EMBOSS on Gentoo systems -======================================= - - -Codon data files location -------------------------- - -The codon data files that are distributed with EMBOSS are installed in the -``EPREFIX/usr/share/EMBOSS/data/CODONS.orig`` directory instead of the usual -``EPREFIX/usr/share/EMBOSS/data/CODONS``. This is done to avoid confusion between -these codon files and those installed with the CUTG database. The names of -these files sometimes vary only by their case. Having both sets of files in -the same directory is also impossible on systems such as MacOSX, where the -root filesystem is case insensitive. If you do not have the CUTG database -installed and want to use the codon files distributed with EMBOSS, you can -symlink the ``CODONS.orig`` directory to ``CODONS``:: - - # cd ${EPREFIX}/usr/share/EMBOSS/data - # ln -s CODONS.orig CODONS - - -Restriction enzymes equivalence file location ---------------------------------------------- - -The restriction enzymes equivalence file distributed with EMBOSS is installed -as ``EPREFIX/usr/share/EMBOSS/data/embossre.equ.orig`` rather than the usual -``EPREFIX/usr/share/EMBOSS/data/embossre.equ``. This is done to avoid a file -collision with the equivalence file provided by the Rebase database. If you do -not have the Rebase database installed and want to use the equivalence file -distributed with EMBOSS, you can symlink the ``embossre.equ.orig`` file to -``embossre.equ``:: - - # cd ${EPREFIX}/usr/share/EMBOSS/data - # ln -s embossre.equ.orig embossre.equ diff --git a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch b/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch deleted file mode 100644 index 7704873e9..000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_FORTIFY_SOURCE-fix.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- EMBOSS-6.6.0/emboss/embossversion.c -+++ EMBOSS-6.6.0/emboss/embossversion.c -@@ -415,7 +415,7 @@ - ajFmtPrintF(outfile, "X_DISPLAY_MISSING %d\n", X_DISPLAY_MISSING); - #endif - #ifdef _FORTIFY_SOURCE -- ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", _FORTIFY_SOURCE); -+ ajFmtPrintF(outfile, "_FORTIFY_SOURCE %d\n", __USE_FORTIFY_LEVEL); - #endif - ajFmtPrintF(outfile, "\n"); - ajFmtPrintF(outfile, "Sizes (bytes):\n"); diff --git a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch b/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch deleted file mode 100644 index c831c3ba7..000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_fix-build-system.patch +++ /dev/null @@ -1,368 +0,0 @@ ---- EMBOSS-6.6.0/ajax/acd/Makefile.am -+++ EMBOSS-6.6.0/ajax/acd/Makefile.am -@@ -3,16 +3,20 @@ - lib_LTLIBRARIES = libacd.la - - libacd_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libacd_la_LIBADD = ../core/libajax.la ../graphics/libajaxg.la - - libacd_la_CPPFLAGS = -I$(top_srcdir)/ajax/ajaxdb -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics --libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - if !ESYSTEMLIBS -+libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libacd_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libacd_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libacd_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libacd_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libacd_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am -+++ EMBOSS-6.6.0/ajax/ajaxdb/Makefile.am -@@ -3,14 +3,16 @@ - lib_LTLIBRARIES = libajaxdb.la - - libajaxdb_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxdb_la_LIBADD = ../core/libajax.la ../ensembl/libensembl.la - - libajaxdb_la_CPPFLAGS = -I$(top_srcdir)/ajax/ensembl --libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajaxdb_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajaxdb_la_CPPFLAGS += $(AXIS2C_CPPFLAGS) - libajaxdb_la_CPPFLAGS += $(JAVA_CPPFLAGS) - ---- EMBOSS-6.6.0/ajax/core/ajreg.h -+++ EMBOSS-6.6.0/ajax/core/ajreg.h -@@ -39,9 +39,8 @@ - #include "ajdefine.h" - #include "ajstr.h" - --#include "pcre_config.h" --#include "pcre_internal.h" --#include "pcreposix.h" -+#include <pcre.h> -+#include <pcreposix.h> - - AJ_BEGIN_DECLS - -@@ -84,7 +83,7 @@ - - typedef struct AjSRegexp - { -- real_pcre *pcre; -+ struct real_pcre *pcre; - pcre_extra *extra; - int *ovector; - const char* orig; ---- EMBOSS-6.6.0/ajax/core/Makefile.am -+++ EMBOSS-6.6.0/ajax/core/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libajax.la - - libajax_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajax_la_LIBADD = $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) - --libajax_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajax_la_CPPFLAGS = - if !ESYSTEMLIBS -+libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libajax_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libajax_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libajax_la_CPPFLAGS += $(JAVA_CPPFLAGS) - libajax_la_CPPFLAGS += $(MYSQL_CPPFLAGS) - libajax_la_CPPFLAGS += $(POSTGRESQL_CPPFLAGS) ---- EMBOSS-6.6.0/ajax/ensembl/Makefile.am -+++ EMBOSS-6.6.0/ajax/ensembl/Makefile.am -@@ -3,13 +3,15 @@ - lib_LTLIBRARIES = libensembl.la - - libensembl_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libensembl_la_LIBADD = ../core/libajax.la - --libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libensembl_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libensembl_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib --endif - libensembl_la_CPPFLAGS += -I$(top_srcdir)/plplot -+endif - libensembl_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libensembl_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/graphics/Makefile.am -+++ EMBOSS-6.6.0/ajax/graphics/Makefile.am -@@ -3,12 +3,16 @@ - lib_LTLIBRARIES = libajaxg.la - - libajaxg_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libajaxg_la_LIBADD = ../core/libajax.la $(PLPLOT_LIBS) - --libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/pcre -+libajaxg_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat --endif - libajaxg_la_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+libajaxg_la_CFLAGS += $(PLPLOT_CFLAGS) -+endif - libajaxg_la_CPPFLAGS += $(JAVA_CPPFLAGS) - - libajaxg_la_LDFLAGS = -version-info 6:5:0 ---- EMBOSS-6.6.0/ajax/Makefile.am -+++ EMBOSS-6.6.0/ajax/Makefile.am -@@ -1,7 +1,7 @@ - ## Process this file with automake to produce Makefile.in - --SUBDIRS = pcre -+SUBDIRS = - if !ESYSTEMLIBS --SUBDIRS += expat zlib -+SUBDIRS += pcre expat zlib - endif - SUBDIRS += core graphics ensembl ajaxdb acd ---- EMBOSS-6.6.0/configure.ac -+++ EMBOSS-6.6.0/configure.ac -@@ -629,32 +629,6 @@ - - - -- --dnl PCRE library definitions - see the MAJOR and MINOR values --dnl to see which version's configure.in these lines come from -- --dnl Provide the current PCRE version information. Do not use numbers --dnl with leading zeros for the minor version, as they end up in a C --dnl macro, and may be treated as octal constants. Stick to single --dnl digits for minor numbers less than 10. There are unlikely to be --dnl that many releases anyway. -- --PCRE_MAJOR="7" --PCRE_MINOR="9" --PCRE_DATE="11-Apr-2009" --PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -- --dnl Default values for miscellaneous macros -- --POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -- --dnl Provide versioning information for libtool shared libraries that --dnl are built by default on Unix systems. -- --PCRE_LIB_VERSION="0:1:0" --PCRE_POSIXLIB_VERSION="0:0:0" -- -- - dnl Define where the EMBOSS package is located - AC_SUBST([AJAX_FIXED_ROOT]) - AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\"" -@@ -743,17 +717,7 @@ - - - --dnl "Export" these variables for PCRE - --AC_SUBST([HAVE_MEMMOVE]) --AC_SUBST([HAVE_STRERROR]) --AC_SUBST([PCRE_MAJOR]) --AC_SUBST([PCRE_MINOR]) --AC_SUBST([PCRE_DATE]) --AC_SUBST([PCRE_VERSION]) --AC_SUBST([PCRE_LIB_VERSION]) --AC_SUBST([PCRE_POSIXLIB_VERSION]) --AC_SUBST([POSIX_MALLOC_THRESHOLD]) - - - -@@ -849,7 +813,51 @@ - - AM_CONDITIONAL([ESYSTEMLIBS], [test "x${enable_systemlibs}" = "xyes"]) - -- -+AS_IF([test "x${enable_systemlibs}" = "xyes"], -+[ -+dnl using system libraries -+ PKG_CHECK_MODULES([PCRE], [libpcre]) -+ PKG_CHECK_MODULES([EXPAT], [expat]) -+ PKG_CHECK_MODULES([ZLIB], [zlib]) -+ PKG_CHECK_MODULES([PLPLOT], [plplotd]) -+], -+[ -+dnl using bundled libraries -+ dnl PCRE library definitions - see the MAJOR and MINOR values -+ dnl to see which version's configure.ac these lines come from -+ -+ dnl Provide the current PCRE version information. Do not use numbers -+ dnl with leading zeros for the minor version, as they end up in a C -+ dnl macro, and may be treated as octal constants. Stick to single -+ dnl digits for minor numbers less than 10. There are unlikely to be -+ dnl that many releases anyway. -+ -+ PCRE_MAJOR="7" -+ PCRE_MINOR="9" -+ PCRE_DATE="11-Apr-2009" -+ PCRE_VERSION="${PCRE_MAJOR}.${PCRE_MINOR}" -+ -+ dnl Default values for miscellaneous macros -+ -+ POSIX_MALLOC_THRESHOLD="-DPOSIX_MALLOC_THRESHOLD=10" -+ -+ dnl Provide versioning information for libtool shared libraries that -+ dnl are built by default on Unix systems. -+ -+ PCRE_LIB_VERSION="0:1:0" -+ PCRE_POSIXLIB_VERSION="0:0:0" -+ -+ dnl "Export" these variables for PCRE -+ AC_SUBST([HAVE_MEMMOVE]) -+ AC_SUBST([HAVE_STRERROR]) -+ AC_SUBST([PCRE_MAJOR]) -+ AC_SUBST([PCRE_MINOR]) -+ AC_SUBST([PCRE_DATE]) -+ AC_SUBST([PCRE_VERSION]) -+ AC_SUBST([PCRE_LIB_VERSION]) -+ AC_SUBST([PCRE_POSIXLIB_VERSION]) -+ AC_SUBST([POSIX_MALLOC_THRESHOLD]) -+]) - - - # Enable the purify tool: --enable-purify, sets CC and LIBTOOL ---- EMBOSS-6.6.0/emboss/Makefile.am -+++ EMBOSS-6.6.0/emboss/Makefile.am -@@ -28,15 +28,18 @@ - - AM_CPPFLAGS = -I$(top_srcdir)/ajax/acd - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ajaxdb -+AM_CPPFLAGS += -I$(top_srcdir)/ajax/core - AM_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl - AM_CPPFLAGS += -I$(top_srcdir)/ajax/graphics --AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - if !ESYSTEMLIBS -+AM_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - AM_CPPFLAGS += -I$(top_srcdir)/ajax/expat - AM_CPPFLAGS += -I$(top_srcdir)/ajax/zlib -+AM_CPPFLAGS += -I$(top_srcdir)/plplot -+else -+AM_CFLAGS += $(PLPLOT_CFLAGS) - endif - AM_CPPFLAGS += -I$(top_srcdir)/nucleus --AM_CPPFLAGS += -I$(top_srcdir)/plplot - AM_CPPFLAGS += $(AXIS2C_CPPFLAGS) - AM_CPPFLAGS += $(JAVA_CPPFLAGS) - -@@ -49,9 +52,11 @@ - if !ESYSTEMLIBS - LDADD += ../ajax/zlib/libezlib.la - LDADD += ../ajax/expat/libeexpat.la --endif - LDADD += ../ajax/pcre/libepcre.la - LDADD += ../plplot/libeplplot.la -+else -+LDADD += $(EXPAT_LIBS) $(PCRE_LIBS) $(ZLIB_LIBS) $(PLPLOT_LIBS) -+endif - LDADD += $(XLIB) - - #if PURIFY ---- EMBOSS-6.6.0/jemboss/lib/Makefile.am -+++ EMBOSS-6.6.0/jemboss/lib/Makefile.am -@@ -12,7 +12,7 @@ - jalviewApplet.jar \ - jemboss.jar - --jemboss.jar:../org/emboss/jemboss/server/JembossFile*Server.java -+jemboss.jar:$(srcdir)/../org/emboss/jemboss/server/JembossFile*Server.java - if JAVA_BUILD - $(ANT) -f ../build.xml package -Demboss.data=../emboss/data -Dname=jemboss -Djar.dir=lib -Dnotformemboss=yes; - endif ---- EMBOSS-6.6.0/m4/idxdbs.m4 -+++ EMBOSS-6.6.0/m4/idxdbs.m4 -@@ -1,17 +1,8 @@ - AC_DEFUN([CHECK_IDXDBS], - [ --AC_MSG_CHECKING(for EMBOSS pre-indexed databases) -+AC_MSG_NOTICE(checking for EMBOSS pre-indexed databases) - -- --if test -f ./emboss/index/edam.xac; then --AC_MSG_RESULT(yes) --else --AC_MSG_RESULT(no) --echo "" --echo "Pre-indexed edam, taxon + drcat databases not found." --echo "Please download them from within this directory using:" --echo " rsync -av rsync://emboss.open-bio.org/EMBOSS/ ." --echo "and then repeat the configure step." --exit 1 --fi -+AC_CHECK_FILE([$srcdir/emboss/index/edam.xac], -+ [], -+ [AC_MSG_ERROR([cannot find pre-indexed edam, taxon + drcat databases])]) - ]) ---- EMBOSS-6.6.0/Makefile.am -+++ EMBOSS-6.6.0/Makefile.am -@@ -12,8 +12,11 @@ - ONEWS \ - PROBLEMS - --SUBDIRS = \ --plplot \ -+SUBDIRS = -+if !ESYSTEMLIBS -+SUBDIRS += plplot -+endif -+SUBDIRS += \ - ajax \ - nucleus \ - emboss \ -@@ -33,5 +36,3 @@ - tar cBf - doc | ( cd $(distdir); tar xBf - ; find doc -name CVS | xargs rm -rf; ) - tar cBf - jemboss | ( cd $(distdir); tar xBf - ; find jemboss -name CVS | xargs rm -rf; find jemboss -name Makefile | xargs rm -rf; find jemboss -name .cvsignore | xargs rm -rf ) - --install-exec-hook: -- $(bindir)/embossupdate ---- EMBOSS-6.6.0/nucleus/Makefile.am -+++ EMBOSS-6.6.0/nucleus/Makefile.am -@@ -3,6 +3,7 @@ - lib_LTLIBRARIES = libnucleus.la - - libnucleus_la_CFLAGS = $(WARN_CFLAGS) $(DEVWARN_CFLAGS) $(JAVA_CFLAGS) -+libnucleus_la_LIBADD = ../ajax/core/libajax.la ../ajax/ajaxdb/libajaxdb.la ../ajax/acd/libacd.la - - if ISSHARED - if ISAIXIA64 -@@ -10,11 +11,14 @@ - endif - endif - --libnucleus_la_CPPFLAGS = -I$(top_srcdir)/plplot --libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre -+libnucleus_la_CPPFLAGS = -I$(top_srcdir)/ajax/core - if !ESYSTEMLIBS -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/plplot -+libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/pcre - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/expat - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/zlib -+else -+libnucleus_la_CFLAGS += $(PLPLOT_CFLAGS) - endif - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/graphics - libnucleus_la_CPPFLAGS += -I$(top_srcdir)/ajax/ensembl diff --git a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch deleted file mode 100644 index 15f5f967a..000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_plplot-declarations.patch +++ /dev/null @@ -1,61 +0,0 @@ ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.c -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.c -@@ -49,7 +49,7 @@ - - #define GRAPH_DEBUG 1 - --#include "plplotP.h" -+#include <plplotP.h> - - - static void GraphArray(ajuint numofpoints, -@@ -964,10 +964,10 @@ - if(!thys->ready) - { - #if GRAPH_DEBUG -- ajDebug("=g= plxsfnam ('%S', '%s')\n", txt, ext); -+ ajDebug("=g= plsfnam ('%S')\n", txt); - #endif - -- plxsfnam(ajStrGetPtr(txt), ext); -+ plsfnam(ajStrGetPtr(txt)); - ajStrAssignS(&graphBasename, txt); - ajStrAssignC(&graphExtension, ext); - if(ajStrGetCharFirst(graphExtension) == '.') -@@ -1213,10 +1213,10 @@ - void ajGraphicsSetPenwidth(float penwidth) - { - #if GRAPH_DEBUG -- ajDebug("=g= plwid(%.2f) [width]\n", penwidth); -+ ajDebug("=g= c_plwidth(%.2f) [width]\n", penwidth); - #endif - -- plwid((PLINT)penwidth); -+ c_plwidth((PLINT)penwidth); - - return; - } -@@ -1538,10 +1538,10 @@ - static void GraphSetPen(ajint colour) - { - #if GRAPH_DEBUG -- ajDebug("=g= plcol(%d '%s') [colour]\n", colour, graphColourName[colour]); -+ ajDebug("=g= plcol0(%d '%s') [colour]\n", colour, graphColourName[colour]); - #endif - -- plcol((PLINT)colour); -+ plcol0((PLINT)colour); - - return; - } ---- EMBOSS-6.6.0/ajax/graphics/ajgraph.h -+++ EMBOSS-6.6.0/ajax/graphics/ajgraph.h -@@ -32,7 +32,7 @@ - /* ========================================================================= */ - - #include "ajdefine.h" --#include "plplot.h" -+#include <plplot.h> - #include "ajgraphstruct.h" - #include "ajdefine.h" - #include "ajstr.h" diff --git a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch b/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch deleted file mode 100644 index eff10b2e6..000000000 --- a/sci-biology/emboss/files/emboss-6.6.0_qa-implicit-declarations.patch +++ /dev/null @@ -1,74 +0,0 @@ ---- EMBOSS-6.6.0/ajax/core/ajfeatread.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatread.c -@@ -45,6 +45,7 @@ - - #include <limits.h> - #include <math.h> -+#include <string.h> - #include <errno.h> - - #ifdef WIN32 ---- EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -+++ EMBOSS-6.6.0/ajax/core/ajfeatwrite.c -@@ -43,7 +43,7 @@ - - #include <limits.h> - #include <math.h> -- -+#include <string.h> - - static AjPRegexp featoutRegUfoFmt = NULL; - static AjPRegexp featoutRegUfoFile = NULL; ---- EMBOSS-6.6.0/ajax/core/ajpdbio.c -+++ EMBOSS-6.6.0/ajax/core/ajpdbio.c -@@ -37,7 +37,7 @@ - - #include <limits.h> - #include <math.h> -- -+#include <string.h> - - - ---- EMBOSS-6.6.0/ajax/core/ajreg.c -+++ EMBOSS-6.6.0/ajax/core/ajreg.c -@@ -32,6 +32,7 @@ - #include "ajlib.h" - - #include "ajreg.h" -+#include <string.h> - - - ---- EMBOSS-6.6.0/ajax/core/ajseqtype.c -+++ EMBOSS-6.6.0/ajax/core/ajseqtype.c -@@ -32,7 +32,7 @@ - #include "ajfeat.h" - #include "ajfile.h" - #include "ajreg.h" -- -+#include <string.h> - - - ---- EMBOSS-6.6.0/nucleus/embindex.c -+++ EMBOSS-6.6.0/nucleus/embindex.c -@@ -35,6 +35,7 @@ - #include "ajnam.h" - - #include <errno.h> -+#include <string.h> - - #define BTENTRYFILE ".ent" - #define KWLIMIT 12 ---- EMBOSS-6.6.0/nucleus/embword.c -+++ EMBOSS-6.6.0/nucleus/embword.c -@@ -36,7 +36,7 @@ - #include "ajutil.h" - - #include <math.h> -- -+#include <string.h> - - - diff --git a/sci-biology/emboss/metadata.xml b/sci-biology/emboss/metadata.xml deleted file mode 100644 index 3af936dc1..000000000 --- a/sci-biology/emboss/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> - <longdescription> - EMBOSS is "The European Molecular Biology Open Software Suite". - EMBOSS is a free Open Source software analysis package specially - developed for the needs of the molecular biology (e.g. EMBnet) user - community. The software automatically copes with data in a variety - of formats and even allows transparent retrieval of sequence data - from the web. Also, as extensive libraries are provided with the - package, it is a platform to allow other scientists to develop and - release software in true open source spirit. EMBOSS also integrates - a range of currently available packages and tools for sequence - analysis into a seamless whole. EMBOSS breaks the historical trend - towards commercial software packages. - </longdescription> -</pkgmetadata> diff --git a/sci-biology/epga/ChangeLog b/sci-biology/epga/ChangeLog index 1e947a08e..225a25bf2 100644 --- a/sci-biology/epga/ChangeLog +++ b/sci-biology/epga/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/epga: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> epga-9999.ebuild: Switch from git-2 to git-r3; Cleanup diff --git a/sci-biology/epga/metadata.xml b/sci-biology/epga/metadata.xml index 2bc893037..52749c688 100644 --- a/sci-biology/epga/metadata.xml +++ b/sci-biology/epga/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">bioinfomaticsCSU/EPGA</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/est2assembly/ChangeLog b/sci-biology/est2assembly/ChangeLog index 902484828..19a53e11b 100644 --- a/sci-biology/est2assembly/ChangeLog +++ b/sci-biology/est2assembly/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + est2assembly-1.08.ebuild: + fix S variable, use PV in URI + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> est2assembly-1.08.ebuild, est2assembly-9999.ebuild: Bump EAPI; drop KEYWORDS from live ebuild; fix deps diff --git a/sci-biology/est2assembly/est2assembly-1.08.ebuild b/sci-biology/est2assembly/est2assembly-1.08.ebuild index dcbcfb5e8..e9878a7f3 100644 --- a/sci-biology/est2assembly/est2assembly-1.08.ebuild +++ b/sci-biology/est2assembly/est2assembly-1.08.ebuild @@ -6,7 +6,7 @@ EAPI=5 DESCRIPTION="EST assembly and annotation pipeline for chado/gbrowse2 display" HOMEPAGE="http://code.google.com/p/est2assembly/" -SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_1.08.tar.gz" +SRC_URI="http://est2assembly.googlecode.com/files/est2assembly_${PV}.tar.gz" LICENSE="GPL-3" SLOT="0" @@ -24,3 +24,5 @@ DEPEND=" sci-biology/emboss sci-biology/bioperl" RDEPEND="${DEPEND}" + +S="${WORKDIR}"/"${PN}" diff --git a/sci-biology/est2uni/ChangeLog b/sci-biology/est2uni/ChangeLog index d35a56222..65b96e4c7 100644 --- a/sci-biology/est2uni/ChangeLog +++ b/sci-biology/est2uni/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/est2uni -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> est2uni-0.27.ebuild: + Drop keywords (php:5.3 is hardmasked) + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> est2uni-0.27.ebuild: Bump to EAPI=5 @@ -36,4 +39,3 @@ +files/9999-est_clustering.pm.patch, +files/9999-pipe_db.pm.patch, +est2uni-9999.ebuild: vim est2uni-9999.ebuild - diff --git a/sci-biology/est2uni/est2uni-0.27.ebuild b/sci-biology/est2uni/est2uni-0.27.ebuild index 7557909c2..0017c8dc6 100644 --- a/sci-biology/est2uni/est2uni-0.27.ebuild +++ b/sci-biology/est2uni/est2uni-0.27.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -17,7 +17,7 @@ SRC_URI=" SLOT="0" LICENSE="GPL-3" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" IUSE="" DEPEND="" diff --git a/sci-biology/eval/ChangeLog b/sci-biology/eval/ChangeLog index 0e9cff26a..7de843d48 100644 --- a/sci-biology/eval/ChangeLog +++ b/sci-biology/eval/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: + sci-biology/eval: fixed installation of perl-related files + + 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: + removing KEYWORDS until the perl files are installed to some other place. At + the moment I get: 'perl-module.eclass: Suspicious environment values found. + PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/eval"' + 13 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> eval-2.2.8.ebuild: fix Gentoo copyright header diff --git a/sci-biology/eval/eval-2.2.8.ebuild b/sci-biology/eval/eval-2.2.8.ebuild index 75f38c50e..c6ddde2d2 100644 --- a/sci-biology/eval/eval-2.2.8.ebuild +++ b/sci-biology/eval/eval-2.2.8.ebuild @@ -4,6 +4,9 @@ EAPI=5 +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + DESCRIPTION="Validate, compare and draw summary statistics for GTF files" HOMEPAGE="http://mblab.wustl.edu/software.html" @@ -14,7 +17,7 @@ IUSE="" SRC_URI="http://mblab.wustl.edu/software/download/"${PN}"-"${PV}".tar.gz http://mblab.wustl.edu/software/download/eval-documentation.pdf" -DEPEND="dev-lang/perl +DEPEND=" dev-lang/tk sci-biology/vcftools sci-visualization/gnuplot" @@ -25,16 +28,14 @@ src_install(){ dobin *.pl *.py dodoc "${DISTDIR}"/eval-documentation.pdf dodoc help/*.ps - insinto /usr/share/eval + insinto /usr/share/${PN} doins *.gtf - eval `perl '-V:installvendorlib'` - vendor_lib_install_dir="${installvendorlib}" - dodir ${vendor_lib_install_dir}/eval - insinto ${vendor_lib_install_dir}/eval + perl_set_version + insinto ${VENDOR_LIB} doins *.pm - echo "PERL5LIB="${vendor_lib_install_dir}"/eval" > ${S}"/99eval" - doenvd ${S}"/99eval" || die } -# the version of validate_gtf.pl bundled with eval differs a bit from -# validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf +pkg_postinst(){ + ewarn "The version of validate_gtf.pl bundled with eval differs a bit from" + ewarn "validate_gtf-1.0.pl from http://mblab.wustl.edu/software.html#validategtf" +} diff --git a/sci-biology/exomiser-bin/ChangeLog b/sci-biology/exomiser-bin/ChangeLog new file mode 100644 index 000000000..0948caa8f --- /dev/null +++ b/sci-biology/exomiser-bin/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/exomiser-bin +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*exomiser-bin-7.0.0 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +exomiser-bin-7.0.0.ebuild, +metadata.xml: + sci-biology/exomiser-bin: new package diff --git a/sci-biology/exomiser-bin/Manifest b/sci-biology/exomiser-bin/Manifest new file mode 100644 index 000000000..6e50d183b --- /dev/null +++ b/sci-biology/exomiser-bin/Manifest @@ -0,0 +1 @@ +DIST exomiser-cli-7.0.0.BETA-distribution.zip 1243391234 SHA256 524f98ef38e1cf958fcaca3bada78f52f1053905c97fd0659d92eb470474df2b SHA512 68f9e71599ab42f4500da0559ab5d1893245a2908ece245425342a9e855258de539ba440ff5c56c9c22485f646483d4b517b1cf30ba985a1ac39e6e4047a01e5 WHIRLPOOL 6eebe7b9d54af91d851d50f00229885063e8d1f6dd2ecba4624ffec5e8898aa1465f2f4043dccda1af039557ab5e4b8467d6c78a689a8b63149b5f569ff96021 diff --git a/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild new file mode 100644 index 000000000..875db0ef4 --- /dev/null +++ b/sci-biology/exomiser-bin/exomiser-bin-7.0.0.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Annotate VCF files from whole-exome sequencing (Jannovar, UCSC KnownGenes, hg19)" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/exomiser" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/exomiser-cli-${PV}.BETA-distribution.zip" +# 1.16GB ! + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/Jannovar-bin" +RDEPEND="${DEPEND}" + +pkg_postinst(){ + einfo "Please download 3.7GB file from ftp://ftp.sanger.ac.uk/pub/resources/software/exomiser/downloads/exomiser/h2_db_dumps/exomiser-${PV}.BETA.h2.db.gz" + einfo "and follow README.md" +} diff --git a/sci-biology/exomiser-bin/metadata.xml b/sci-biology/exomiser-bin/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/exomiser-bin/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/exonerate-gff3/ChangeLog b/sci-biology/exonerate-gff3/ChangeLog new file mode 100644 index 000000000..bde29ffde --- /dev/null +++ b/sci-biology/exonerate-gff3/ChangeLog @@ -0,0 +1,21 @@ +# ChangeLog for sci-biology/exonerate-gff3 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/exonerate-gff3: Add github to remote-id in metadata.xml + +*exonerate-gff3-9999 (02 Apr 2015) + + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> +exonerate-gff3-9999.ebuild, + +files/exonerate-gff3-9999-asneeded.patch, -exonerate-gff3-2.2.0-r1.ebuild, + -files/exonerate-gff3-2.2.0-asneeded.patch, metadata.xml: + sci-biology/exonerate-gff3: Move live ebuild to 9999 + +*exonerate-gff3-2.2.0-r1 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +exonerate-gff3-2.2.0-r1.ebuild, +files/exonerate-gff3-2.2.0-asneeded.patch, + +metadata.xml: + sci-biology/exonerate-gff3: an improved version of exonerate-2.2.0 with GFF3 + format output support diff --git a/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild new file mode 100644 index 000000000..46c896642 --- /dev/null +++ b/sci-biology/exonerate-gff3/exonerate-gff3-9999.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils toolchain-funcs git-r3 + +DESCRIPTION="exonerate-2.2.0 with patches to add GFF3 formatted output" +HOMEPAGE="https://github.com/hotdogee/exonerate-gff3" +SRC_URI="" +EGIT_REPO_URI="https://github.com/hotdogee/exonerate-gff3.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="utils test threads" + +REQUIRED_USE="test? ( utils )" + +# block with sci-biology/exonerate , maybe the best would be to change SRC_URI in sci-biology/exonerate +DEPEND=" + !sci-biology/exonerate + dev-libs/glib:2" +RDEPEND="${DEPEND}" + +AUTOTOOLS_IN_SOURCE_BUILD=1 + +PATCHES=( "${FILESDIR}"/${P}-asneeded.patch ) + +src_prepare() { + tc-export CC + sed \ + -e 's: -O3 -finline-functions::g' \ + -i configure.in || die + mc configure.in configure.ac + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable utils utilities) + $(use_enable threads pthreads) + --enable-largefile + --enable-glib2 + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + doman doc/man/man1/*.1 +} diff --git a/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch b/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch new file mode 100644 index 000000000..3268055cd --- /dev/null +++ b/sci-biology/exonerate-gff3/files/exonerate-gff3-9999-asneeded.patch @@ -0,0 +1,15 @@ +Fix build with --as-needed + +https://bugs.gentoo.org/268094 + +--- configure.in ++++ configure.in +@@ -289,7 +289,7 @@ + if test "$enable_pthreads" = yes; then + echo "Using PTHREADS" + CFLAGS="$CFLAGS -DUSE_PTHREADS" +- LDFLAGS="$LDFLAGS -lpthread" ++ LIBS="$LIBS -lpthread" + elif test "$enable_pthreads" = no; then + echo "Not using pthreads" + else diff --git a/sci-biology/exonerate-gff3/metadata.xml b/sci-biology/exonerate-gff3/metadata.xml new file mode 100644 index 000000000..21e8763b3 --- /dev/null +++ b/sci-biology/exonerate-gff3/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <use> + <flag name="utils">Unknown</flag> + </use> + <upstream> + <remote-id type="github">hotdogee/exonerate-gff3</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/fastqc/ChangeLog b/sci-biology/fastqc/ChangeLog index 42bae79d9..cd180e7ea 100644 --- a/sci-biology/fastqc/ChangeLog +++ b/sci-biology/fastqc/ChangeLog @@ -1,7 +1,33 @@ # ChangeLog for sci-biology/fastqc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + fastqc-0.11.3.ebuild: + more comments on the external dependencies + + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + fastqc-0.11.3.ebuild: + add dependency on jhdf5; more ebuild cleanup + +*fastqc-0.11.3 (30 May 2015) + + 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +fastqc-0.11.3.ebuild, -fastqc-0.11.2.ebuild: + sci-biology/fastqc: version bump, added perl dependency, Apache ant-building + does not work still + + 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +files/build.xml, + fastqc-0.11.2.ebuild: + added build.xml exported by author from Eclipse IDE (it doesn't work under ant + eclasses in my hands) + +*fastqc-0.11.2 (24 Feb 2015) + + 24 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +fastqc-0.11.2.ebuild, -fastqc-0.10.1.ebuild: + version bump; still missing src_compile() logic + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> fastqc-0.10.1.ebuild: clean up diff --git a/sci-biology/fastqc/Manifest b/sci-biology/fastqc/Manifest index 401fb1828..4e8207292 100644 --- a/sci-biology/fastqc/Manifest +++ b/sci-biology/fastqc/Manifest @@ -1 +1 @@ -DIST fastqc_v0.10.1_source.zip 605722 SHA256 5e7a731c9a21c6b50604db8bb43396e772a7665219ab03a5574a662c24169b88 SHA512 e344043fe9faeb02136d5df2827a1e9609752eb95f5a4b6bc4ac42f5110eb06d3ed74de5b3a2973ba6f17f79f7bb0299c2f754bcace00d8faf6ad549a3245358 WHIRLPOOL ee18a410fed681ff0a6a855f5a56fdab5417f11f59b43d1b47590e5ad40e17e7909aa25388b547379b44775560e94afa4f9890a546e5ab1836b14cdadba3dfc3 +DIST fastqc_v0.11.3_source.zip 10073593 SHA256 b62b1aea957af9051b30d306183df239b095eac4f8d281478c372b25c61fe44d SHA512 bab27d6997ad6525b7804ba9a3a54eec1cdb835d548c2840ae882334902d12eea4bbff549370669176ade76633a5f1d7dc6f7ee865a25f1a41b525764660b471 WHIRLPOOL 843039e115aa0101e687ad9fe9b40d4e658e96f6dbebe87a9f4074c1f3ea46910f3dac1a3426ec329a194a542580ca16ce5d22c348500453ba357c27f15a7f06 diff --git a/sci-biology/fastqc/fastqc-0.10.1.ebuild b/sci-biology/fastqc/fastqc-0.10.1.ebuild deleted file mode 100644 index 3e2b63954..000000000 --- a/sci-biology/fastqc/fastqc-0.10.1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 eutils - -DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" -SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="" - -DEPEND="sci-biology/picard - >=virtual/jrei-1.6" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/FastQC - -src_install(){ - dobin fastqc - - # TODO: need to compile java in uk/ac/babraham/FastQC/ - # and decide whether jbzip2-0.9.jar is a standard java lib or not - # ignore the sam-1.32.jar, that is likely library already in sci-biology/picard -} diff --git a/sci-biology/fastqc/fastqc-0.11.3.ebuild b/sci-biology/fastqc/fastqc-0.11.3.ebuild new file mode 100644 index 000000000..7c8cb9e7b --- /dev/null +++ b/sci-biology/fastqc/fastqc-0.11.3.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 eutils java-ant-2 + +DESCRIPTION="Perl-based wrapper around java apps to quality control FASTA/FASTQ sequence files" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v"${PV}"_source.zip" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="sci-biology/picard + sci-libs/jhdf5 + >=virtual/jre-1.5:*" +RDEPEND="${DEPEND} + dev-lang/perl + >=virtual/jdk-1.5:* + dev-java/ant-core" + +S="${WORKDIR}"/FastQC + +src_prepare(){ + cp "${FILESDIR}"/build.xml . || die +} + +src_compile(){ + ant || die +} + +src_install(){ + dobin fastqc run_fastqc.bat + dodoc README.txt RELEASE_NOTES.txt + + # There is no fastqc.jar. The output from the compilation is the set of + # .class files (a jar file is just a zip file full of .class files). All + # you need to copy out is the contents of the bin subdirectory, the rest of + # the download you can discard. + # + # jbzip2-0.9.jar comes from https://code.google.com/p/jbzip2 + # + # ignore the sam-1.103.jar and rely on /usr/share/picard/lib/sam.jar from sci-biology/picard + # The sam-1.103.jar library comes from + # http://sourceforge.net/projects/picard/files/sam-jdk/. Note that there is + # a newer version of this codebase at https://github.com/samtools/htsjdk but + # that FastQC is NOT yet compatible with the updated API (this will probably + # happen in a future release). This library is needed to read SAM/BAM + # format files. + # cisd-jhdf5.jar should be provided by sci-libs/jhdf5 +} diff --git a/sci-biology/fastqc/files/build.xml b/sci-biology/fastqc/files/build.xml new file mode 100644 index 000000000..c4a692096 --- /dev/null +++ b/sci-biology/fastqc/files/build.xml @@ -0,0 +1,59 @@ +<?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!-- WARNING: Eclipse auto-generated file. + Any modifications will be overwritten. + To include a user specific buildfile here, simply create one in the same + directory with the processing instruction <?eclipse.ant.import?> + as the first entry and export the buildfile again. --> +<project basedir="." default="build" name="FastQC"> + <property environment="env"/> + <property name="debuglevel" value="source,lines,vars"/> + <property name="target" value="1.5"/> + <property name="source" value="1.5"/> + <path id="FastQC.classpath"> + <pathelement location="bin"/> + <pathelement location="jbzip2-0.9.jar"/> + <pathelement location="sam-1.103.jar"/> + <pathelement location="cisd-jhdf5.jar"/> + </path> + <target name="init"> + <mkdir dir="bin"/> + <copy includeemptydirs="false" todir="bin"> + <fileset dir="."> + <exclude name="**/*.launch"/> + <exclude name="**/*.java"/> + </fileset> + </copy> + </target> + <target name="clean"> + <delete dir="bin"/> + </target> + <target depends="clean" name="cleanall"/> + <target depends="build-subprojects,build-project" name="build"/> + <target name="build-subprojects"/> + <target depends="init" name="build-project"> + <echo message="${ant.project.name}: ${ant.file}"/> + <javac debug="true" debuglevel="${debuglevel}" destdir="bin" includeantruntime="false" source="${source}" target="${target}"> + <src path="."/> + <classpath refid="FastQC.classpath"/> + </javac> + </target> + <target description="Build all projects which reference this project. Useful to propagate changes." name="build-refprojects"/> + <target description="copy Eclipse compiler jars to ant lib directory" name="init-eclipse-compiler"> + <copy todir="${ant.library.dir}"> + <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/> + </copy> + <unzip dest="${ant.library.dir}"> + <patternset includes="jdtCompilerAdapter.jar"/> + <fileset dir="${ECLIPSE_HOME}/plugins" includes="org.eclipse.jdt.core_*.jar"/> + </unzip> + </target> + <target description="compile project with Eclipse compiler" name="build-eclipse-compiler"> + <property name="build.compiler" value="org.eclipse.jdt.core.JDTCompilerAdapter"/> + <antcall target="build"/> + </target> + <target name="FastQCApplication"> + <java classname="uk.ac.babraham.FastQC.FastQCApplication" failonerror="true" fork="yes"> + <classpath refid="FastQC.classpath"/> + </java> + </target> +</project> diff --git a/sci-biology/fastx_toolkit/ChangeLog b/sci-biology/fastx_toolkit/ChangeLog index f233c5472..931fa7947 100644 --- a/sci-biology/fastx_toolkit/ChangeLog +++ b/sci-biology/fastx_toolkit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/fastx_toolkit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/fastx_toolkit: Add github to remote-id in metadata.xml + *fastx_toolkit-0.0.14 (20 Jan 2014) 20 Jan 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/fastx_toolkit/metadata.xml b/sci-biology/fastx_toolkit/metadata.xml index 897aa2e6b..bd98b5829 100644 --- a/sci-biology/fastx_toolkit/metadata.xml +++ b/sci-biology/fastx_toolkit/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="github">agordon/fastx_toolkit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/ChangeLog b/sci-biology/ffindex/ChangeLog index a711d80ab..7dfb4b433 100644 --- a/sci-biology/ffindex/ChangeLog +++ b/sci-biology/ffindex/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ffindex: Add github to remote-id in metadata.xml + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ffindex-0.9.9.3.ebuild: + sci-biology/ffindex: fix SRC_URI because TransDecoder which contains this + bundled thing has moved + *ffindex-0.9.9.3 (08 Jan 2015) 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/ffindex/Manifest b/sci-biology/ffindex/Manifest index 7f4aa956c..83f501c15 100644 --- a/sci-biology/ffindex/Manifest +++ b/sci-biology/ffindex/Manifest @@ -1 +1 @@ -DIST TransDecoder_r20140704.tar.gz 21189681 SHA256 fb53c9601c4ae9b3cd8e937f158ae3f15439115609bc7658effffa24af53517e SHA512 fa70e440c3f8b8d11da780858ff6433adf9065b126b29eb047983b17913e382c677a272881ee78be8e30867bbd447eb9bda71bd11abda5203d6a3abfb5316e90 WHIRLPOOL d603d06c8c1e84f3e721c0f5e43b2519766eaae1fc0456ece07ff43c13971706aecb24473813b7606ca885d2ef526648fc28f874200a53037b4aa6b291c4864d +DIST TransDecoder-2.0.1.tar.gz 9925281 SHA256 ce069da72c8a04e739f8c057af4f97187bf587d3f0d3db40465dfc2c89393e22 SHA512 fd12aeda089a12036e288e58eb0a3c3b9bb1f104f6821102d84ba6ddaec1a9dd32ec7937cd87129ff9814c7c8e26b6b98d27c6af8edd7ed6b5335c4878f649de WHIRLPOOL 61c6b7fe5684becdb28a3bccb113fea07889a2c4e6627e92cd27c1a90ca53f5a88504e048363a1322f1108dd6ebd5549c52aee9d438fbcfb2023390c79c126ec diff --git a/sci-biology/ffindex/ffindex-0.9.9.3.ebuild b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild index 1a9a9a18f..c3ff78e5d 100644 --- a/sci-biology/ffindex/ffindex-0.9.9.3.ebuild +++ b/sci-biology/ffindex/ffindex-0.9.9.3.ebuild @@ -6,7 +6,8 @@ EAPI=5 DESCRIPTION="Simple index/database for huge amounts of small files" HOMEPAGE="http://pubshare.genzentrum.lmu.de/scientific_computing/software/ffindex" -SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" +#SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" +SRC_URI="https://github.com/TransDecoder/TransDecoder/archive/TransDecoder.tar.gz -> TransDecoder-2.0.1.tar.gz" LICENSE="CC-BY-3.0" SLOT="0" diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 2bc893037..33de46b4c 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">TransDecoder/TransDecoder</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/freebayes/ChangeLog b/sci-biology/freebayes/ChangeLog index 9374edf38..be68896f6 100644 --- a/sci-biology/freebayes/ChangeLog +++ b/sci-biology/freebayes/ChangeLog @@ -1,7 +1,22 @@ # ChangeLog for sci-biology/freebayes -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/freebayes: Add github to remote-id in metadata.xml + + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + freebayes-9999.ebuild: + install also the vcftools binaries although it should be a separate package + + 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + freebayes-9999.ebuild: + added src_install() + + 11 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + freebayes-9999.ebuild: + ebuild cleanup; the git clone --recursive flag does not work + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> freebayes-9999.ebuild: fixed DESCRIPTION diff --git a/sci-biology/freebayes/freebayes-9999.ebuild b/sci-biology/freebayes/freebayes-9999.ebuild index 3d40b372b..88f621288 100644 --- a/sci-biology/freebayes/freebayes-9999.ebuild +++ b/sci-biology/freebayes/freebayes-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,21 +10,32 @@ inherit eutils DESCRIPTION="Bayesian gen. variant detector to find small polymorphisms: SNPs, indels, MNPs and complex events" HOMEPAGE="https://github.com/ekg/freebayes" -EGIT_REPO_URI="git://github.com/ekg/freebayes.git" -# need top checkout vcflib/ as well -# +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="git://github.com/ekg/freebayes.git" + EGIT_OPTIONS="--recursive --recurse-submodules" + KEYWORDS="" +else + EGIT_REPO_URI="git://github.com/ekg/freebayes.git" + EGIT_OPTIONS="--recursive --recurse-submodules" + EGIT_BRANCH="v0.9.21" + KEYWORDS="" +fi + # To build freebayes you must use git to also download its submodules. # Do so by downloading freebayes again using this command (note --recursive flag): # git clone --recursive git://github.com/ekg/freebayes.git -# LICENSE="MIT" SLOT="0" -KEYWORDS="" IUSE="" DEPEND="" RDEPEND="${DEPEND} sci-biology/bamtools sci-biology/samtools" + +src_install(){ + dobin bin/freebayes bin/bamleftalign + dobin vcflib/bin/* +} diff --git a/sci-biology/freebayes/metadata.xml b/sci-biology/freebayes/metadata.xml index 2bc893037..88b381109 100644 --- a/sci-biology/freebayes/metadata.xml +++ b/sci-biology/freebayes/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">ekg/freebayes</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fsl/ChangeLog b/sci-biology/fsl/ChangeLog new file mode 100644 index 000000000..086612dba --- /dev/null +++ b/sci-biology/fsl/ChangeLog @@ -0,0 +1,85 @@ +# ChangeLog for sci-biology/fsl +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 09 Apr 2015; Horea Christian <h.chr@mail.ru> + -files/fsl-5.0.4-fsldir_redux.patch: + removed 5.0.4 redux patch + + 07 Apr 2015; Horea Christian <h.chr@mail.ru> -fsl-5.0.4.ebuild, + -fsl-5.0.5.ebuild: + removed ebuilds with unavailable sources + + 07 Apr 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + added new gentoo fsl-5.0.6 source location + + 30 Mar 2015; Horea Christian <h.chr@mail.ru> + +files/fsl-5.0.8-fsldir_redux.patch, -files/fsl-5.0.8-redux.patch, + fsl-5.0.8.ebuild: + implemented 5.0.8 fsldir redux patch + + 30 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-redux.patch: + 5.0.8 redux patch by François Bissey + + 29 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: + using the 5.0.8 headers patch + + 29 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-headers.patch, + files/fsl-5.0.4-headers.patch: + reimplmented pathc fsl-5.0.4-headers + + 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: + ported changes from 5.0.6 regarding FSLDIR + + 28 Mar 2015; Horea Christian <h.chr@mail.ru> files/fsl-5.0.4-headers.patch: + hunk implemented by upstream + + 28 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.8.ebuild: + using new setup patch file for new ebuild + + 28 Mar 2015; Horea Christian <h.chr@mail.ru> +files/fsl-5.0.8-setup.patch: + new pathc by François Bissey + + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.4.ebuild, + fsl-5.0.5.ebuild, fsl-5.0.8.ebuild: + added licences to all versions + + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + added license for included gdchart + + 25 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + set the correct licences + + 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + installing fslversion + + 11 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + sed-ing before installing + + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + changed grep wrapper + + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + reformatted tcl sed calls + + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + fixed tcl location according to instructions by kiwifb + + 10 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + installing fsl.sh + + 05 Mar 2015; Horea Christian <h.chr@mail.ru> fsl-5.0.6.ebuild: + removing faulty check + + 04 Mar 2015; Horea Christian <h.chr@mail.ru> files/99fsl: + added FSLPATH + +*fsl-5.0.8 (20 Feb 2015) + + 20 Feb 2015; Horea Christian <h.chr@mail.ru> +fsl-5.0.8.ebuild: + bumped version + + 18 Oct 2013; François Bissey <francois.bissey@canterbury.ac.nz> + +files/fsl-5.0.4-headers.patch, +files/fsl-5.0.4-setup.patch, +metadata.xml, + fsl-5.0.4.ebuild: + use system package, verbose build. diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest new file mode 100644 index 000000000..c9fbe09f4 --- /dev/null +++ b/sci-biology/fsl/Manifest @@ -0,0 +1,2 @@ +DIST fsl-5.0.6-sources.tar.gz 1415430870 SHA256 af953c07dbea30190419ce1812666b60dab06ef6cd3f3641fb53aaec8604f233 SHA512 bca7d69ba0538610387b29677ad4f38c30f8e4dc58efd92ae9efe5e7498619e862f5f5a67a00dc45cd94582086dc5ed16309bdafd06b025fc689f2d7f45ff108 WHIRLPOOL b6e95c40004c5590b6c08eda702b821ab20ebdb33d95369b2edd307c34a0a30905ae47969566586458c8a2407c7e2d52a5eecb108e2a8eeb595a29d684aec0c4 +DIST fsl-5.0.8-sources.tar.gz 1420879532 SHA256 2053cc42782360b191bd9610dbbc0a56677b40796cceb4680420b93d5eddfc15 SHA512 8dedf13d633d71fa28c5dd6591fab4adda4893b76467affa6f58aee917ee3fdc83da07d8f505feb61ac2733de1bfb84f7f9ff74589756946be21cdb9f057f0f0 WHIRLPOOL 2a64245f6b4da2642237aad96270b65799f868bb7a5294f1576470173a9393296b4c26e0ddfffe2198665d068c82f6d7b64548729cfa3aff07f6809c13d57554 diff --git a/sci-biology/fsl/files/99fsl b/sci-biology/fsl/files/99fsl new file mode 100644 index 000000000..ca37941f9 --- /dev/null +++ b/sci-biology/fsl/files/99fsl @@ -0,0 +1,5 @@ +FSLOUTPUTTYPE=NIFTI_GZ +FSLMULTIFILEQUIT=TRUE +FSLTCLSH=tclsh +FSLWISH=wish +FSLDIR=/usr diff --git a/sci-biology/fsl/files/fsl-5.0.4-headers.patch b/sci-biology/fsl/files/fsl-5.0.4-headers.patch new file mode 100644 index 000000000..803151bb7 --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.4-headers.patch @@ -0,0 +1,32 @@ +--- src/avwutils/fslmaths.cc.orig 2013-10-19 00:17:44.765129309 +1300 ++++ src/avwutils/fslmaths.cc 2013-10-19 00:18:02.975157728 +1300 +@@ -71,7 +71,7 @@ + #include "newimage/newimageall.h" + #include "miscmaths/miscmaths.h" + #include "utils/fsl_isfinite.h" +-#include "libprob/libprob.h" ++#include "libprob.h" + + using namespace MISCMATHS; + using namespace NEWIMAGE; +--- src/miscvis/writepng.c.orig 2013-10-19 00:18:32.415203592 +1300 ++++ src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300 +@@ -32,6 +32,7 @@ + + #include <stdlib.h> /* for exit() prototype */ + ++#include "zlib.h" + #include "png.h" /* libpng header; includes zlib.h and setjmp.h */ + #include "writepng.h" /* typedefs, common macros, public prototypes */ + +--- src/ptx2/surfmaths.cc.orig 2013-10-19 00:19:51.595327317 +1300 ++++ src/ptx2/surfmaths.cc 2013-10-19 00:20:09.284354805 +1300 +@@ -72,7 +72,7 @@ + #include "csv_mesh.h" + #include "miscmaths/miscmaths.h" + #include "utils/fsl_isfinite.h" +-#include "libprob/libprob.h" ++#include "libprob.h" + + using namespace MISCMATHS; + diff --git a/sci-biology/fsl/files/fsl-5.0.4-setup.patch b/sci-biology/fsl/files/fsl-5.0.4-setup.patch new file mode 100644 index 000000000..0b961492a --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.4-setup.patch @@ -0,0 +1,110 @@ +--- extras/build.orig 2013-10-18 21:37:53.533939550 +1300 ++++ extras/build 2013-10-18 21:40:42.283158471 +1300 +@@ -41,7 +41,7 @@ + + errorprojs="" ; export errorprojs ; + +-PROJECTS="tcl tk zlib libpng libiconv libgd libgdc libprob libcprob newmat cprob newran cephes fftw" ++PROJECTS="libgdc libprob libcprob newmat cprob newran cephes" + + for projname in $PROJECTS; do + +--- build.orig 2013-10-18 22:24:22.312777248 +1300 ++++ build 2013-10-18 22:24:59.161835107 +1300 +@@ -11,8 +11,7 @@ + ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp"; + fi + +-echo "Building projects - see build.log file for progress..." +-./config/common/buildproj $PROJECTS > ./build.log 2>&1 +-echo "Finished build : end of log file shows ..." +-tail -10 build.log ++echo "Building projects" ++./config/common/buildproj $PROJECTS ++echo "Finished build" + +--- config/common/buildproj.orig 2013-10-18 22:28:40.683182435 +1300 ++++ config/common/buildproj 2013-10-18 22:29:09.612227825 +1300 +@@ -11,10 +11,10 @@ + fi + PROJECTS="$@" ; export PROJECTS ; + +-FSLDIR=`pwd` ++#FSLDIR=`pwd` + FSLDEVDIR=${FSLDIR} + FSLCONFDIR=${FSLDIR}/config +-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` ++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` + export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE + + buildmessages="" ; export buildmessages ; +--- config/generic/systemvars.mk.orig 2007-07-13 23:00:20.000000000 +1200 ++++ config/generic/systemvars.mk 2013-10-18 23:13:06.472693414 +1300 +@@ -4,20 +4,20 @@ + + # System dependent commands (NB: the first two are the most platform dependent) + +-INSTALL = ginstall -p +-RANLIB = ranlib ++INSTALL = install -p ++RANLIB = @@GENTOO_RANLIB@@ + + RM = /bin/rm + CP = /bin/cp + MV = /bin/mv + CHMOD = /bin/chmod + MKDIR = /bin/mkdir +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC = @@GENTOO_CC@@ ++CXX = @@GENTOO_CXX@@ + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS = + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +--- config/common/vars.mk.orig 2013-10-18 23:39:26.384029157 +1300 ++++ config/common/vars.mk 2013-10-18 23:40:49.489145387 +1300 +@@ -24,15 +24,15 @@ + USRCFLAGS = + USRCXXFLAGS = + +-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} + +-AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} + + CFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +- ${AccumulatedIncFlags} ++ ${AccumulatedIncFlags} ${USERCFLAGS} + + CXXFLAGS = ${ANSI_FLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +- ${AccumulatedIncFlags} ++ ${AccumulatedIncFlags} ${USERCXXFLAGS} + + HFILES = *.h + AFILES = *.a +--- config/common/buildproj.orig 2013-10-19 23:27:10.477238469 +1300 ++++ config/common/buildproj 2013-10-19 23:28:32.207370622 +1300 +@@ -66,7 +66,7 @@ + if [ -x fslconfig ] ; then + ./fslconfig ; + fi +- if ${MAKE} -k ${MAKEOPTIONS} ; then ++ if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then + if ${MAKE} install ; then + installok=true; + # Clean up after ourselves diff --git a/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch new file mode 100644 index 000000000..a4fff260f --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.6-fsldir_redux.patch @@ -0,0 +1,456 @@ +--- src/fast4/fast_two.cc.orig 2013-10-19 23:45:02.636971888 +1300 ++++ src/fast4/fast_two.cc 2013-10-19 23:46:45.436138299 +1300 +@@ -166,7 +166,7 @@ + string csfPriorName, grayPriorName, whitePriorName; + if(alternatePriors.unset()) + { +- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_"; ++ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_"; + csfPriorName = priorRootName+"csf"; + grayPriorName = priorRootName+"gray"; + whitePriorName = priorRootName+"white"; +@@ -215,15 +215,15 @@ + if(bapused>0) + { + char reg[1024]; +- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); ++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str()); + if(verbose.value()) + cout<<reg<<endl; + system(reg); +- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); ++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str()); + if(verbose.value()) + cout<<reg<<endl; + system(reg); +- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); ++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str()); + if(verbose.value()) + cout << reg << endl; + system(reg); +--- src/feat5/tsplot.cc.orig 2013-10-19 23:48:08.997273362 +1300 ++++ src/feat5/tsplot.cc 2013-10-19 23:50:59.376548902 +1300 +@@ -293,7 +293,7 @@ + ofstream outputFile; + int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600); + vector<double> normalisedContrasts, model, triggers; +- string fmriFileName, fslPath, featdir, vType, indexText; ++ string fmriFileName, featdir, vType, indexText; + ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4); + bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false); + bool zWeightClusters(true); +@@ -307,7 +307,6 @@ + if (argc<2) usage(""); + featdir=string(argv[1]); + fmriFileName=featdir+"/filtered_func_data"; +- fslPath=string(getenv("FSLDIR")); + + string outputName(featdir); + +@@ -725,7 +724,7 @@ + cerr << "Can't open output report file " << outputName << endl; + exit(1); + } +- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; ++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText; + if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n"; + else outputFile << "\n</BODY></HTML>\n\n"; + outputFile.close(); +@@ -740,7 +739,7 @@ + cerr << "Can't open output report file " << outputName << endl; + exit(1); + } +- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; ++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl; + outputFile.close(); + + /* now output same thing without start and end, for inclusion in feat report */ +--- src/feat5/feat_model.cc.orig 2013-10-19 23:52:13.456668655 +1300 ++++ src/feat5/feat_model.cc 2013-10-19 23:53:31.655795065 +1300 +@@ -734,7 +734,6 @@ + vector<int> G; + vector<string> titles; + float tr, mult, trmult, nltffwhm=0, maxconvwin=0; +- char fl[10000], *FSLDIR; + string fn, filename; + FONT_DATA *font_data = new FONT_DATA[1]; + +@@ -753,8 +752,6 @@ + if (argc==3) + motionparams=remmean(read_ascii_matrix(argv[2])); + +- FSLDIR=getenv("FSLDIR"); +- + fn = string(argv[1])+".fsf"; + + level = atoi(find_line(fn, "fmri(level)", fl)); +@@ -1479,7 +1476,7 @@ + writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE); + writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G); + +- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm "; ++ filename="wpng -q -overwrite "+string(argv[1])+".ppm "; + system(filename.c_str()); + + return(0); +@@ -2122,6 +2119,6 @@ + + fclose(outputfile); + +- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename; ++ filename="wpng -q -overwrite " + filename; + system(filename.c_str()); + } +--- src/first/first_utils.cc.orig 2013-10-19 23:54:30.375890034 +1300 ++++ src/first/first_utils.cc 2013-10-19 23:59:11.706344887 +1300 +@@ -1954,8 +1954,8 @@ + if (!surfaceVAout.value()) { + // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise) + volume<float> refim; +- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } +- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); } ++ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } ++ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); } + volume<float> maskvol(refim); + maskvol=0.0f; + volume4D<float> volnormals; +--- src/fnirt/fnirtfns.cpp.orig 2013-10-20 00:00:18.106452166 +1300 ++++ src/fnirt/fnirtfns.cpp 2013-10-20 00:04:56.005901533 +1300 +@@ -1203,8 +1203,7 @@ + return(string(ref_fname)); + } + else { +- const char *fsldir_ptr = getenv("FSLDIR"); +- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; ++ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; + if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname); + else return(string("")); + } +@@ -1230,9 +1229,8 @@ + NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist + eref_fname = ref_fname; + } +- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard +- const char *fsldir_ptr = getenv("FSLDIR"); +- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname; ++ catch(...) { // Didn't exist in current directory, try in .../data/standard ++ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname; + try { + cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl; + NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist +@@ -1267,8 +1265,7 @@ + if (check_exist(ecfname)) return(ecfname); + } + if (!FNIRT::path(cfname).length()) { // If no path explicitly given +- const char *fsldir_ptr = getenv("FSLDIR"); +- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; ++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; + if (check_exist(ecfname)) return(ecfname); + else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given + ecfname += string(".cnf"); +--- src/fslsurface/fslsurface_first.cc.orig 2013-10-20 00:05:35.495965454 +1300 ++++ src/fslsurface/fslsurface_first.cc 2013-10-20 00:06:54.346092913 +1300 +@@ -500,8 +500,7 @@ + + volume<float>* immni = new volume<float>(); + +- char* fsldir = getenv("FSLDIR"); +- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); ++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); + + //read_volume_hdr_only(*immni, template_name); + +@@ -699,8 +698,7 @@ + + volume<float>* immni = new volume<float>(); + +- char* fsldir = getenv("FSLDIR"); +- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm"); ++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); + + //read_volume_hdr_only(*immni, template_name); + +--- src/fslsurface/fslsurfacemaths.cpp.orig 2013-10-20 00:07:39.457165850 +1300 ++++ src/fslsurface/fslsurfacemaths.cpp 2013-10-20 00:09:28.396341998 +1300 +@@ -598,12 +598,6 @@ + + }else if (command == "-reconFromBvars"){ + cout<<"do recon "<<endl; +- char* fsldir = getenv("FSLDIR"); +- if (fsldir == NULL) +- { +- cerr<<"FSLDIR has not been set. "<<endl; +- exit(EXIT_FAILURE); +- } + //file.bvars,mni_template.nii.gz + // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; + reconSurface_from_bvars( surf, string(argv[i_arg+1])); +@@ -612,12 +606,6 @@ + + }else if (command == "-reconAllFromBvarsAndSave"){ + cout<<"do recon+save "<<argc<<" "<<i_arg<<endl; +- char* fsldir = getenv("FSLDIR"); +- if (fsldir == NULL) +- { +- cerr<<"FSLDIR has not been set. "<<endl; +- exit(EXIT_FAILURE); +- } + //file.bvars,mni_template.nii.gz + // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm"; + cout<<"recon "<< string(argv[i_arg+1])<<endl; +--- src/libvis/miscpic.h.orig 2013-10-20 00:11:03.706496109 +1300 ++++ src/libvis/miscpic.h 2013-10-20 00:12:24.515626764 +1300 +@@ -89,12 +89,7 @@ + LR_label_flag = true; + trans= -10; + edgethresh = 0.0; +- if(getenv("FSLDIR")!=0){ +- lutbase = string(getenv("FSLDIR")) + "/etc/luts/"; +- } +- else{ +- lutbase = string("/"); +- } ++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/"; + title = string(""); + cbartype = string(""); + cbarptr = NULL; +--- src/melodic/melreport.cc.orig 2013-10-20 00:13:01.475686492 +1300 ++++ src/melodic/melreport.cc 2013-10-20 00:15:02.795882687 +1300 +@@ -85,7 +85,7 @@ + + {//start IC page + IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl + << "<style type=\"text/css\">OBJECT { width: 100% }</style>" + << "<TITLE>FSL</TITLE></HEAD>" << endl + << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50 +@@ -488,7 +488,7 @@ + {//start IC2 page + IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html"); + IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl + << "<style type=\"text/css\">OBJECT { width: 100% }</style>" + << "<TITLE>FSL</TITLE></HEAD>" << endl + << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50 +@@ -666,8 +666,8 @@ + IChtml << "<HTML> " << endl + << "<TITLE>MELODIC Component " << num2str(cnum) + << "</TITLE>" << endl +- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") +- << "/doc/images/fsl-bg.jpg\">" << endl ++ << "<BODY BACKGROUND=\"file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl + << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum) + << "</H1>"<< endl; + +--- src/melodic/meloptions.cc.orig 2013-10-20 00:15:46.755953769 +1300 ++++ src/melodic/meloptions.cc 2013-10-20 00:18:26.176211442 +1300 +@@ -93,14 +93,6 @@ + explicitnums = false; + logfname = string("log.txt"); + +- // work out the path to the $FSLDIR/bin directory +- if(getenv("FSLDIR")!=0){ +- binpath = (string) getenv("FSLDIR") + "/bin/"; +- } else{ +- binpath = argv[0]; +- binpath = binpath.substr(0,binpath.length()-7); +- } +- + // parse once to establish log directory name + for(int a = options.parse_command_line(argc, argv); a < argc; a++); + +--- src/melodic/meloptions.h.orig 2013-10-20 00:19:32.176318206 +1300 ++++ src/melodic/meloptions.h 2013-10-20 00:19:53.455352701 +1300 +@@ -93,7 +93,6 @@ + ~MelodicOptions() { delete gopt; } + + string version; +- string binpath; + string logfname; + bool filtermode; + bool explicitnums; +--- src/melodic/meldata.cc.orig 2013-10-20 00:20:45.856437466 +1300 ++++ src/melodic/meldata.cc 2013-10-20 00:21:48.655538924 +1300 +@@ -921,7 +921,7 @@ + void MelodicData::est_smoothness() + { + if(Resels == 0){ +- string SM_path = opts.binpath + "smoothest"; ++ string SM_path = "smoothest"; + string Mask_fname = logger.appendDir("mask"); + + if(opts.segment.value().length()>0){ +@@ -1086,7 +1086,7 @@ + // set up all strings + string BET_outputfname = string(Mean_fname)+"_brain"; + +- string BET_path = opts.binpath + "bet"; ++ string BET_path = "bet"; + string BET_optarg = "-m -f 0.4"; // see man bet + string Mask_fname = BET_outputfname+"_mask"; + +--- src/melodic/melreport.h.orig 2013-10-20 00:22:41.816624872 +1300 ++++ src/melodic/melreport.h 2013-10-20 00:24:25.555792499 +1300 +@@ -105,20 +105,20 @@ + system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str()); + report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out); + report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" + << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" + << endl <<endl; + loghtml.setDir(report.getDir(),"log.html"); + loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" + +- (string) getenv("FSLDIR") +"/doc/fsl.css>" ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" + << "<TITLE>MELODIC report</TITLE></HEAD><BODY>" + << endl <<endl; + navigator.setDir(report.getDir(),"nav.html"); + head.setDir(report.getDir(),"head.html"); + navigator << "<link REL=stylesheet TYPE=text/css href=file:"+ +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; + head << "<link REL=stylesheet TYPE=text/css href=file:"+ +- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl; ++ "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl; + head <<"<TABLE BORDER=0><TR>" << endl + <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl + <<"<TABLE BORDER=0>"<< endl +@@ -130,8 +130,8 @@ + << "</tr></table>" << endl + << "<TD ALIGN=RIGHT>" << endl + << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl +- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR") +- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl ++ << "<IMG BORDER=0 SRC=file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl + << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl; + if(opts.guireport.value()==""){ + report <<"<OBJECT data=head.html></OBJECT>" << endl; +--- src/mm/mixture_model.cc.orig 2013-10-20 00:25:00.355848878 +1300 ++++ src/mm/mixture_model.cc 2013-10-20 00:25:32.185900186 +1300 +@@ -2224,8 +2224,8 @@ + + htmllog << "<HTML> " << endl + << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl +- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR") +- << "/doc/images/fsl-bg.jpg\">" << endl ++ << "<BODY BACKGROUND=\"file:" ++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl + << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl; + + htmllog << "<hr><p>" << endl; +--- src/siena/siena_diff.cc.orig 2013-10-20 00:26:13.215966685 +1300 ++++ src/siena/siena_diff.cc 2013-10-20 00:28:03.925145734 +1300 +@@ -107,7 +107,7 @@ + { + // {{{ vars + +-char thestring[10000], segoptions[10000], fsldir[10000]; ++char thestring[10000], segoptions[10000]; + int x_size, y_size, z_size, size, x, y, z, i, count, + seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0, + ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0; +@@ -124,8 +124,6 @@ + + string argv1(argv[1]), argv2(argv[2]); + +-sprintf(fsldir,"%s",getenv("FSLDIR")); +- + for (i = 3; i < argc; i++) { + if (!strcmp(argv[i], "-i")) + ignore_z=1; +@@ -209,26 +207,26 @@ + // }}} + // {{{ transform images and masks + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", +- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s", ++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]); + printf("%s\n",thestring); system(thestring); + +-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", +- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask", ++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + + if (edge_masking) + { +- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", +- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); ++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s", ++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]); + printf("%s\n",thestring); system(thestring); + } + +@@ -287,8 +285,8 @@ + cout << "saving image 1 to disk prior to segmentation" << endl; + save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain"); + in1.destroy(); +- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", +- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); ++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1", ++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]); + cout << thestring << endl; + system(thestring); + } +--- src/topup/topupfns.cpp.orig 2013-10-20 00:28:36.456198320 +1300 ++++ src/topup/topupfns.cpp 2013-10-20 00:29:37.905297565 +1300 +@@ -463,8 +463,7 @@ + if (TOPUP::check_exist(ecfname)) return(ecfname); + } + if (!TOPUP::path(cfname).length()) { // If no path explicitly given +- const char *fsldir_ptr = getenv("FSLDIR"); +- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname; ++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname; + if (TOPUP::check_exist(ecfname)) return(ecfname); + else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given + ecfname += string(".cnf"); +--- etc/matlab/call_fsl.m.orig 2013-10-20 23:17:58.626045346 +1300 ++++ etc/matlab/call_fsl.m 2013-10-20 23:20:06.556252150 +1300 +@@ -8,7 +8,7 @@ + % Debian/Ubuntu users should uncomment as + % indicated + +-fsldir=getenv('FSLDIR'); ++%fsldir=getenv('FSLDIR'); + + % Debian/Ubuntu - uncomment the following + %fsllibdir=sprintf('%s/%s', fsldir, 'bin'); +--- etc/js/label-div.html.orig 2013-10-20 23:22:04.906443685 +1300 ++++ etc/js/label-div.html 2013-10-20 23:23:35.006589232 +1300 +@@ -2,12 +2,12 @@ + <head> + <title>label-div</title> + <!--[if IE]> +- <script type="text/javascript" src="FSLDIR/etc/js/excanvas.js"></script> ++ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/excanvas.js"></script> + <![endif]--> +- <script type="text/javascript" src="FSLDIR/etc/js/strftime-min.js"></script> +- <script type="text/javascript" src="FSLDIR/etc/js/rgbcolor.js"></script> +- <script type="text/javascript" src="FSLDIR/etc/js/dygraph-canvas.js"></script> +- <script type="text/javascript" src="FSLDIR/etc/js/dygraph.js"></script> ++ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/strftime-min.js"></script> ++ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/rgbcolor.js"></script> ++ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph-canvas.js"></script> ++ <script type="text/javascript" src="@GENTOO_PORTAGE_EPREFIX@/etc/js/dygraph.js"></script> + <script type="text/javascript" src="PNMDATA.js"></script> + </head> + <body> diff --git a/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch new file mode 100644 index 000000000..593c1c807 --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.8-fsldir_redux.patch @@ -0,0 +1,452 @@ +diff -Naur src.orig/fast4/fast_two.cc src/fast4/fast_two.cc
+--- src.orig/fast4/fast_two.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/fast4/fast_two.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -166,7 +166,7 @@
+ string csfPriorName, grayPriorName, whitePriorName;
+ if(alternatePriors.unset())
+ {
+- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
++ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+ csfPriorName = priorRootName+"csf";
+ grayPriorName = priorRootName+"gray";
+ whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@
+ if(bapused>0)
+ {
+ char reg[1024];
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout << reg << endl;
+ system(reg);
+diff -Naur src.orig/feat5/feat_model.cc src/feat5/feat_model.cc
+--- src.orig/feat5/feat_model.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/feat5/feat_model.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -741,7 +741,7 @@
+ vector<int> G;
+ vector<string> titles;
+ float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+- char fl[10000], *FSLDIR;
++ char fl[10000];
+ string fn, filename;
+ FONT_DATA *font_data = new FONT_DATA[1];
+
+@@ -760,8 +760,6 @@
+ if (argc==3)
+ motionparams=remmean(read_ascii_matrix(argv[2]));
+
+- FSLDIR=getenv("FSLDIR");
+-
+ fn = string(argv[1])+".fsf";
+
+ level = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1491,7 +1489,7 @@
+ writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+ writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+
+- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
++ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
+ system(filename.c_str());
+
+ return(0);
+@@ -2134,6 +2132,6 @@
+
+ fclose(outputfile);
+
+- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
++ filename="wpng -q -overwrite " + filename;
+ system(filename.c_str());
+ }
+diff -Naur src.orig/feat5/tsplot.cc src/feat5/tsplot.cc
+--- src.orig/feat5/tsplot.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/feat5/tsplot.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -293,7 +293,7 @@
+ ofstream outputFile;
+ int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
+ vector<double> normalisedContrasts, model, triggers;
+- string fmriFileName, fslPath, featdir, vType, indexText;
++ string fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@
+ if (argc<2) usage("");
+ featdir=string(argv[1]);
+ fmriFileName=featdir+"/filtered_func_data";
+- fslPath=string(getenv("FSLDIR"));
+
+ string outputName(featdir);
+
+@@ -725,7 +724,7 @@
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
+ if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
+ else outputFile << "\n</BODY></HTML>\n\n";
+ outputFile.close();
+@@ -740,7 +739,7 @@
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
+ outputFile.close();
+
+ /* now output same thing without start and end, for inclusion in feat report */
+diff -Naur src.orig/first/first_utils.cc src/first/first_utils.cc
+--- src.orig/first/first_utils.cc 2015-03-30 11:54:10.482550135 +1300
++++ src/first/first_utils.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -1954,8 +1954,8 @@
+ if (!surfaceVAout.value()) {
+ // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
+ volume<float> refim;
+- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
+- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
++ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
++ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
+ volume<float> maskvol(refim);
+ maskvol=0.0f;
+ volume4D<float> volnormals;
+diff -Naur src.orig/fnirt/fnirtfns.cpp src/fnirt/fnirtfns.cpp
+--- src.orig/fnirt/fnirtfns.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/fnirt/fnirtfns.cpp 2015-03-30 11:54:18.412569892 +1300
+@@ -1203,8 +1203,7 @@
+ return(string(ref_fname));
+ }
+ else {
+- const char *fsldir_ptr = getenv("FSLDIR");
+- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ if (NEWIMAGE::fsl_imageexists(eref_fname)) return(eref_fname);
+ else return(string(""));
+ }
+@@ -1230,9 +1229,8 @@
+ NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
+ eref_fname = ref_fname;
+ }
+- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
+- const char *fsldir_ptr = getenv("FSLDIR");
+- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ catch(...) { // Didn't exist in current directory, try in .../data/standard
++ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ try {
+ cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
+ NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
+@@ -1267,8 +1265,7 @@
+ if (check_exist(ecfname)) return(ecfname);
+ }
+ if (!FNIRT::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (check_exist(ecfname)) return(ecfname);
+ else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+diff -Naur src.orig/fslsurface/fslsurface_first.cc src/fslsurface/fslsurface_first.cc
+--- src.orig/fslsurface/fslsurface_first.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/fslsurface/fslsurface_first.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -500,8 +500,7 @@
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+@@ -699,8 +698,7 @@
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+diff -Naur src.orig/fslsurface/fslsurfacemaths.cpp src/fslsurface/fslsurfacemaths.cpp
+--- src.orig/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/fslsurface/fslsurfacemaths.cpp 2015-03-30 11:54:18.412569892 +1300
+@@ -598,12 +598,6 @@
+
+ }else if (command == "-reconFromBvars"){
+ cout<<"do recon "<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ reconSurface_from_bvars( surf, string(argv[i_arg+1]));
+@@ -612,12 +606,6 @@
+
+ }else if (command == "-reconAllFromBvarsAndSave"){
+ cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ cout<<"recon "<< string(argv[i_arg+1])<<endl;
+diff -Naur src.orig/libvis/miscpic.h src/libvis/miscpic.h
+--- src.orig/libvis/miscpic.h 2015-03-30 11:54:10.482550135 +1300
++++ src/libvis/miscpic.h 2015-03-30 11:54:18.412569892 +1300
+@@ -89,12 +89,7 @@
+ LR_label_flag = true;
+ trans= -10;
+ edgethresh = 0.0;
+- if(getenv("FSLDIR")!=0){
+- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
+- }
+- else{
+- lutbase = string("/");
+- }
++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
+ title = string("");
+ cbartype = string("");
+ cbarptr = NULL;
+diff -Naur src.orig/melodic/meldata.cc src/melodic/meldata.cc
+--- src.orig/melodic/meldata.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meldata.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -971,7 +971,7 @@
+ void MelodicData::est_smoothness()
+ {
+ if(Resels == 0){
+- string SM_path = opts.binpath + "smoothest";
++ string SM_path = "smoothest";
+ string Mask_fname = logger.appendDir("mask");
+
+ if(opts.segment.value().length()>0){
+@@ -1136,7 +1136,7 @@
+ // set up all strings
+ string BET_outputfname = string(Mean_fname)+"_brain";
+
+- string BET_path = opts.binpath + "bet";
++ string BET_path = "bet";
+ string BET_optarg = "-m -f 0.4"; // see man bet
+ string Mask_fname = BET_outputfname+"_mask";
+
+diff -Naur src.orig/melodic/meloptions.cc src/melodic/meloptions.cc
+--- src.orig/melodic/meloptions.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meloptions.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -93,14 +93,6 @@
+ explicitnums = false;
+ logfname = string("log.txt");
+
+- // work out the path to the $FSLDIR/bin directory
+- if(getenv("FSLDIR")!=0){
+- binpath = (string) getenv("FSLDIR") + "/bin/";
+- } else{
+- binpath = argv[0];
+- binpath = binpath.substr(0,binpath.length()-7);
+- }
+-
+ // parse once to establish log directory name
+ for(int a = options.parse_command_line(argc, argv); a < argc; a++);
+
+diff -Naur src.orig/melodic/meloptions.h src/melodic/meloptions.h
+--- src.orig/melodic/meloptions.h 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/meloptions.h 2015-03-30 11:54:18.412569892 +1300
+@@ -93,7 +93,6 @@
+ ~MelodicOptions() { delete gopt; }
+
+ string version;
+- string binpath;
+ string logfname;
+ bool filtermode;
+ bool explicitnums;
+diff -Naur src.orig/melodic/melreport.cc src/melodic/melreport.cc
+--- src.orig/melodic/melreport.cc 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/melreport.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -84,8 +84,8 @@
+ IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
+
+ {//start IC page
+- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
+@@ -487,8 +487,8 @@
+
+ {//start IC2 page
+ IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
+- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
+@@ -666,8 +666,8 @@
+ IChtml << "<HTML> " << endl
+ << "<TITLE>MELODIC Component " << num2str(cnum)
+ << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
+ << "</H1>"<< endl;
+
+diff -Naur src.orig/melodic/melreport.h src/melodic/melreport.h
+--- src.orig/melodic/melreport.h 2015-03-30 11:54:10.502550183 +1300
++++ src/melodic/melreport.h 2015-03-30 12:11:17.995116883 +1300
+@@ -104,21 +104,21 @@
+ const time_t tmptime = time(NULL);
+ system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
+ report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
+- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ loghtml.setDir(report.getDir(),"log.html");
+- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ navigator.setDir(report.getDir(),"nav.html");
+ head.setDir(report.getDir(),"head.html");
+- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+- head << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
++ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
++ head << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head <<"<TABLE BORDER=0><TR>" << endl
+ <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
+ <<"<TABLE BORDER=0>"<< endl
+@@ -130,8 +130,8 @@
+ << "</tr></table>" << endl
+ << "<TD ALIGN=RIGHT>" << endl
+ << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
+- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
++ << "<IMG BORDER=0 SRC=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ if(opts.guireport.value()==""){
+ report <<"<OBJECT data=head.html></OBJECT>" << endl;
+diff -Naur src.orig/mm/mixture_model.cc src/mm/mixture_model.cc
+--- src.orig/mm/mixture_model.cc 2015-03-30 11:54:10.522550233 +1300
++++ src/mm/mixture_model.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -2224,8 +2224,8 @@
+
+ htmllog << "<HTML> " << endl
+ << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
+
+ htmllog << "<hr><p>" << endl;
+diff -Naur src.orig/siena/siena_diff.cc src/siena/siena_diff.cc
+--- src.orig/siena/siena_diff.cc 2015-03-30 11:54:10.482550135 +1300
++++ src/siena/siena_diff.cc 2015-03-30 11:54:18.412569892 +1300
+@@ -107,7 +107,7 @@
+ {
+ // {{{ vars
+
+-char thestring[10000], segoptions[10000], fsldir[10000];
++char thestring[10000], segoptions[10000];
+ int x_size, y_size, z_size, size, x, y, z, i, count,
+ seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
+ ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
+@@ -124,8 +124,6 @@
+
+ string argv1(argv[1]), argv2(argv[2]);
+
+-sprintf(fsldir,"%s",getenv("FSLDIR"));
+-
+ for (i = 3; i < argc; i++) {
+ if (!strcmp(argv[i], "-i"))
+ ignore_z=1;
+@@ -209,26 +207,26 @@
+ // }}}
+ // {{{ transform images and masks
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+ if (edge_masking)
+ {
+- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ }
+
+@@ -287,8 +285,8 @@
+ cout << "saving image 1 to disk prior to segmentation" << endl;
+ save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
+ in1.destroy();
+- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ cout << thestring << endl;
+ system(thestring);
+ }
+diff -Naur src.orig/topup/topupfns.cpp src/topup/topupfns.cpp
+--- src.orig/topup/topupfns.cpp 2015-03-30 11:54:10.522550233 +1300
++++ src/topup/topupfns.cpp 2015-03-30 11:54:18.412569892 +1300
+@@ -463,8 +463,7 @@
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ }
+ if (!TOPUP::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+
diff --git a/sci-biology/fsl/files/fsl-5.0.8-headers.patch b/sci-biology/fsl/files/fsl-5.0.8-headers.patch new file mode 100644 index 000000000..ab2ab3da3 --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.8-headers.patch @@ -0,0 +1,21 @@ +--- src/miscvis/writepng.c.orig 2013-10-19 00:18:32.415203592 +1300 ++++ src/miscvis/writepng.c 2013-10-19 00:19:05.414255132 +1300 +@@ -32,6 +32,7 @@ + + #include <stdlib.h> /* for exit() prototype */ + ++#include "zlib.h" + #include "png.h" /* libpng header; includes zlib.h and setjmp.h */ + #include "writepng.h" /* typedefs, common macros, public prototypes */ + +--- src/ptx2/surfmaths.cc.orig 2013-10-19 00:19:51.595327317 +1300 ++++ src/ptx2/surfmaths.cc 2013-10-19 00:20:09.284354805 +1300 +@@ -72,7 +72,7 @@ + #include "csv_mesh.h" + #include "miscmaths/miscmaths.h" + #include "utils/fsl_isfinite.h" +-#include "libprob/libprob.h" ++#include "libprob.h" + + using namespace MISCMATHS; + diff --git a/sci-biology/fsl/files/fsl-5.0.8-setup.patch b/sci-biology/fsl/files/fsl-5.0.8-setup.patch new file mode 100644 index 000000000..0cbda5d5c --- /dev/null +++ b/sci-biology/fsl/files/fsl-5.0.8-setup.patch @@ -0,0 +1,113 @@ +diff -Naur fsl.orig/build fsl/build +--- fsl.orig/build 2015-03-29 00:10:39.845936000 +1300 ++++ fsl/build 2015-03-29 00:12:37.160487000 +1300 +@@ -11,8 +11,7 @@ + ifit load_varian load_dicom misc_scripts fdt first possum sgeutils flameo oxford_asl relax qboot topup ptx2 lesions eddy dwssfp"; + fi + +-echo "Building projects - see build.log file for progress..." +-./config/common/buildproj $PROJECTS > ./build.log 2>&1 +-echo "Finished build : end of log file shows ..." +-tail -10 build.log ++echo "Building projects" ++./config/common/buildproj $PROJECTS ++echo "Finished build" + +diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj +--- fsl.orig/config/common/buildproj 2015-03-29 00:11:47.130998000 +1300 ++++ fsl/config/common/buildproj 2015-03-29 00:12:37.164319000 +1300 +@@ -11,10 +11,10 @@ + fi + PROJECTS="$@" ; export PROJECTS ; + +-FSLDIR=`pwd` ++#FSLDIR=`pwd` + FSLDEVDIR=${FSLDIR} + FSLCONFDIR=${FSLDIR}/config +-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` ++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh` + export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE + + buildmessages="" ; export buildmessages ; +@@ -66,7 +66,7 @@ + if [ -x fslconfig ] ; then + ./fslconfig ; + fi +- if ${MAKE} -k ${MAKEOPTIONS} ; then ++ if ${MAKE} ${MAKEOPTIONS} ${MAKEOPTS} ; then + if ${MAKE} install ; then + installok=true; + # Clean up after ourselves +diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk +--- fsl.orig/config/common/vars.mk 2015-03-29 00:11:47.183520000 +1300 ++++ fsl/config/common/vars.mk 2015-03-29 00:18:53.151222000 +1300 +@@ -24,15 +24,15 @@ + USRCFLAGS = + USRCXXFLAGS = + +-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS} + +-AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS} + + CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +- ${AccumulatedIncFlags} ++ ${AccumulatedIncFlags} ${USERCFLAGS} + + CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \ +- ${AccumulatedIncFlags} ++ ${AccumulatedIncFlags} ${USERCXXFLAGS} + + HFILES = *.h + AFILES = *.a +diff -Naur fsl.orig/config/generic/systemvars.mk fsl/config/generic/systemvars.mk +--- fsl.orig/config/generic/systemvars.mk 2015-03-29 00:11:47.534246000 +1300 ++++ fsl/config/generic/systemvars.mk 2015-03-29 00:12:37.162129000 +1300 +@@ -4,20 +4,20 @@ + + # System dependent commands (NB: the first two are the most platform dependent) + +-INSTALL = ginstall -p +-RANLIB = ranlib ++INSTALL = install -p ++RANLIB = @@GENTOO_RANLIB@@ + + RM = /bin/rm + CP = /bin/cp + MV = /bin/mv + CHMOD = /bin/chmod + MKDIR = /bin/mkdir +-TCLSH = ${FSLDIR}/bin/fsltclsh ++TCLSH = tclsh + + # Compiler dependent variables + +-CC = gcc +-CXX = c++ ++CC = @@GENTOO_CC@@ ++CXX = @@GENTOO_CXX@@ + CSTATICFLAGS = -static + CXXSTATICFLAGS = -static + +@@ -25,7 +25,7 @@ + + DEPENDFLAGS = -MM + +-OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS} ++OPTFLAGS = + MACHDBGFLAGS = + GNU_ANSI_FLAGS = -Wall -ansi -pedantic + SGI_ANSI_FLAGS = -ansi -fullwarn +diff -Naur fsl.orig/extras/build fsl/extras/build +--- fsl.orig/extras/build 2015-03-29 00:11:15.080236000 +1300 ++++ fsl/extras/build 2015-03-29 00:15:53.170496000 +1300 +@@ -60,7 +60,7 @@ + if [ ${BUILDICONV} -eq 1 ]; then + PROJECTS="${PROJECTS} libiconv" + fi +-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw" ++PROJECTS="libgdc libprob libcprob newmat cprob newran" + for projname in $PROJECTS; do + + if [ -d $FSLESRCDIR/$projname ] ; then diff --git a/sci-biology/fsl/fsl-5.0.6.ebuild b/sci-biology/fsl/fsl-5.0.6.ebuild new file mode 100644 index 000000000..8e5874d37 --- /dev/null +++ b/sci-biology/fsl/fsl-5.0.6.ebuild @@ -0,0 +1,130 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs prefix + +DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" +HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl" +SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}-sources.tar.gz" + +LICENSE="FSL BSD-2 newmat" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +COMMON_DEPEND="media-libs/glu + media-libs/libpng + media-libs/gd + sys-libs/zlib + dev-libs/boost + media-gfx/graphviz + " +DEPEND="${COMMON_DEPEND}" +RDEPEND="${COMMON_DEPEND} + dev-lang/tcl + dev-lang/tk + " + +S=${WORKDIR}/${PN} + +src_prepare(){ + epatch "${FILESDIR}/${PN}"-5.0.4-setup.patch + epatch "${FILESDIR}/${PN}"-5.0.4-headers.patch + epatch "${FILESDIR}/${PN}"-5.0.6-fsldir_redux.patch + + sed -i \ + -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \ + -e "s:@@GENTOO_CC@@:$(tc-getCC):" \ + -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \ + config/generic/systemvars.mk || die + + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ + etc/js/label-div.html + + makefilelist=$(find src/ -name Makefile) + + sed -i \ + -e "s:-I\${INC_BOOST}::" \ + -e "s:-I\${INC_ZLIB}::" \ + -e "s:-I\${INC_GD}::" \ + -e "s:-I\${INC_PNG}::" \ + -e "s:-L\${LIB_GD}::" \ + -e "s:-L\${LIB_PNG}::" \ + -e "s:-L\${LIB_ZLIB}::" \ + ${makefilelist} || die + + sed -i "s:\${FSLDIR}/bin/::g" \ + $(grep -rl "\${FSLDIR}/bin" src/*) \ + $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) + sed -i "s:\$FSLDIR/bin/::g" \ + $(grep -rl "\$FSLDIR/bin" src/*) \ + $(grep -rl "\$FSLDIR/bin" etc/matlab/*) + + sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ + $(grep -rl "\$FSLDIR/data" src/*) + + sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ + $(grep -rl "\${FSLDIR}/data" src/*) + + sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ + $(grep -rl "\$FSLDIR/etc" src/*) + + sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ + $(grep -rl "\${FSLDIR}/etc" src/*) + + sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\$FSLDIR/doc" src/*) + + sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\${FSLDIR}/doc" src/*) + + sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\'\${FSLDIR}\'/doc" src/*) + + sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *` +} + +src_compile() { + export FSLDIR=${WORKDIR}/${PN} + export FSLCONDIR=${WORKDIR}/${PN}/config + export FSLMACHTYPE=generic + + export USERLDFLAGS="${LDFLAGS}" + export USERCFLAGS="${CFLAGS}" + export USERCXXFLAGS="${CXXFLAGS}" + + ./build || die +} + +src_install() { + sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \ + $(grep -lI "\${FSLDIR}/tcl" bin/*) \ + $(grep -l "\${FSLDIR}/tcl" tcl/*) + sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \ + $(grep -l "\$FSLDIR/tcl" tcl/*) + + exeinto /usr/bin + doexe bin/* + + insinto /usr/share/${PN} + doins -r doc data refdoc + + insinto /usr/libexec/fsl + doins -r tcl/* + + insinto /etc/fslconf + doins etc/fslconf/fsl.sh + + insinto /etc + doins etc/fslversion + doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts + #if use matlab; then + # doins etc/matlab + #fi + + doenvd "${FILESDIR}"/99fsl + rm "${D}"/usr/bin/cluster +} diff --git a/sci-biology/fsl/fsl-5.0.8.ebuild b/sci-biology/fsl/fsl-5.0.8.ebuild new file mode 100644 index 000000000..af486a98a --- /dev/null +++ b/sci-biology/fsl/fsl-5.0.8.ebuild @@ -0,0 +1,130 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs prefix + +DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data" +HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl" +SRC_URI="http://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz" + +LICENSE="FSL BSD-2 newmat" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +COMMON_DEPEND="media-libs/glu + media-libs/libpng + media-libs/gd + sys-libs/zlib + dev-libs/boost + media-gfx/graphviz + " +DEPEND="${COMMON_DEPEND}" +RDEPEND="${COMMON_DEPEND} + dev-lang/tcl + dev-lang/tk + " + +S=${WORKDIR}/${PN} + +src_prepare(){ + epatch "${FILESDIR}/${PN}"-5.0.8-setup.patch + epatch "${FILESDIR}/${PN}"-5.0.8-headers.patch + epatch "${FILESDIR}/${PN}"-5.0.8-fsldir_redux.patch + + sed -i \ + -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \ + -e "s:@@GENTOO_CC@@:$(tc-getCC):" \ + -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \ + config/generic/systemvars.mk || die + + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \ + etc/js/label-div.html + + makefilelist=$(find src/ -name Makefile) + + sed -i \ + -e "s:-I\${INC_BOOST}::" \ + -e "s:-I\${INC_ZLIB}::" \ + -e "s:-I\${INC_GD}::" \ + -e "s:-I\${INC_PNG}::" \ + -e "s:-L\${LIB_GD}::" \ + -e "s:-L\${LIB_PNG}::" \ + -e "s:-L\${LIB_ZLIB}::" \ + ${makefilelist} || die + + sed -i "s:\${FSLDIR}/bin/::g" \ + $(grep -rl "\${FSLDIR}/bin" src/*) \ + $(grep -rl "\${FSLDIR}/bin" etc/matlab/*) + sed -i "s:\$FSLDIR/bin/::g" \ + $(grep -rl "\$FSLDIR/bin" src/*) \ + $(grep -rl "\$FSLDIR/bin" etc/matlab/*) + + sed -i "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \ + $(grep -rl "\$FSLDIR/data" src/*) + + sed -i "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \ + $(grep -rl "\${FSLDIR}/data" src/*) + + sed -i "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \ + $(grep -rl "\$FSLDIR/etc" src/*) + + sed -i "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \ + $(grep -rl "\${FSLDIR}/etc" src/*) + + sed -i "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\$FSLDIR/doc" src/*) + + sed -i "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\${FSLDIR}/doc" src/*) + + sed -i "s:\'\${FSLDIR}\'/doc:${EPREFIX}/usr/share/fsl/doc:g" \ + $(grep -rl "\'\${FSLDIR}\'/doc" src/*) + + sed -i -e "s:\$FSLDIR/etc:/etc:g" `grep -rlI \$FSLDIR/etc *` +} + +src_compile() { + export FSLDIR=${WORKDIR}/${PN} + export FSLCONDIR=${WORKDIR}/${PN}/config + export FSLMACHTYPE=generic + + export USERLDFLAGS="${LDFLAGS}" + export USERCFLAGS="${CFLAGS}" + export USERCXXFLAGS="${CXXFLAGS}" + + ./build || die +} + +src_install() { + sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \ + $(grep -lI "\${FSLDIR}/tcl" bin/*) \ + $(grep -l "\${FSLDIR}/tcl" tcl/*) + sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \ + $(grep -l "\$FSLDIR/tcl" tcl/*) + + exeinto /usr/bin + doexe bin/* + + insinto /usr/share/${PN} + doins -r doc data refdoc + + insinto /usr/libexec/fsl + doins -r tcl/* + + insinto /etc/fslconf + doins etc/fslconf/fsl.sh + + insinto /etc + doins etc/fslversion + doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts + #if use matlab; then + # doins etc/matlab + #fi + + doenvd "${FILESDIR}"/99fsl + rm "${D}"/usr/bin/cluster +} diff --git a/sci-libs/matio/metadata.xml b/sci-biology/fsl/metadata.xml index 7e65648fd..9fc2ce7bf 100644 --- a/sci-libs/matio/metadata.xml +++ b/sci-biology/fsl/metadata.xml @@ -1,9 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> - matio is an ISO C library (with a limited Fortran 90 interface) for - reading and writing Matlab MAT files. + <herd>sci-biology</herd> + <longdescription> +FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. </longdescription> </pkgmetadata> diff --git a/sci-biology/genepop/ChangeLog b/sci-biology/genepop/ChangeLog index 9eee0f120..d9ad2a573 100644 --- a/sci-biology/genepop/ChangeLog +++ b/sci-biology/genepop/ChangeLog @@ -1,11 +1,13 @@ # ChangeLog for sci-biology/genepop -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> genepop-4.2.1.ebuild: + sci-biology/genepop: Drop unnecessary *DEPEND + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -genepop-4.0.10.ebuild, +genepop-4.2.1.ebuild, metadata.xml: Punt base.eclass: version bump 26 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me - diff --git a/sci-biology/genepop/genepop-4.2.1.ebuild b/sci-biology/genepop/genepop-4.2.1.ebuild index 41647d00d..73d823434 100644 --- a/sci-biology/genepop/genepop-4.2.1.ebuild +++ b/sci-biology/genepop/genepop-4.2.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -15,9 +15,6 @@ SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="app-arch/unzip" -RDEPEND="" - S="${WORKDIR}" src_prepare() { diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog index d52eb156b..ce4b28963 100644 --- a/sci-biology/genseed/ChangeLog +++ b/sci-biology/genseed/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/genseed -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + genseed-1.0.22.ebuild: + sci-biology/genseed: some cleanup + 10 Nov 2014; Justin Lecher <jlec@gentoo.org> genseed-1.0.22.ebuild, metadata.xml: Bump to EAPI=5 @@ -15,4 +19,3 @@ 13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +genseed-1.0.22.ebuild, +metadata.xml: A seed-driven progressive assembly program genseed-1.0.22.ebuild - diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild index f87e06f57..5a1f87649 100644 --- a/sci-biology/genseed/genseed-1.0.22.ebuild +++ b/sci-biology/genseed/genseed-1.0.22.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,9 +13,6 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="" - # I am not sure whether we want to introduce yet another USE variable "phrap" - # This tools optionally uses cross_match if vector masking is required - # (sci-biology/phrap but it will be installed only by users having that licence. DEPEND=" sci-biology/cap3-bin dev-lang/perl @@ -27,3 +24,8 @@ S="${WORKDIR}" src_install() { newbin ${PN}.pl ${PN} } + +pkg_postinst(){ + einfo "Ideally install also sci-biology/phrap which provides cross_match" + einfo "It is used for vector masking" +} diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog new file mode 100644 index 000000000..c61729349 --- /dev/null +++ b/sci-biology/gffutils/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/gffutils +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/gffutils: Add github to remote-id in metadata.xml + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> gffutils-0.8.3.ebuild: + sci-biology/gffutils: Streamline ebuild + +*gffutils-0.8.3 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +gffutils-0.8.3.ebuild, + +metadata.xml: + sci-biology/gffutils: add gffutils diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest new file mode 100644 index 000000000..e59acbd00 --- /dev/null +++ b/sci-biology/gffutils/Manifest @@ -0,0 +1 @@ +DIST gffutils-0.8.3.tar.gz 1531901 SHA256 22fb404fbc2b905529583a779933dcaccec5bbcefc237c4172b4dcc53dc53d3a SHA512 98625f8838ad4dc33e85155e99bdc39acf4d260bfe68ab4210f07c7fc700824c7248311ac3d95dac70d7ef14d2221aedf77d129c5ffc964b28e35209a618022b WHIRLPOOL 830c24fa55f0fc6e9b923c9230fbb60eec5b5e23139b0405e4933f3914d2d9026303593beab9b3df92e1291419af6806a8667399d7e0a71eba21d0f1ba8cdb6b diff --git a/sci-biology/gffutils/gffutils-0.8.3.ebuild b/sci-biology/gffutils/gffutils-0.8.3.ebuild new file mode 100644 index 000000000..82fa6b41e --- /dev/null +++ b/sci-biology/gffutils/gffutils-0.8.3.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="GFF and GTF file manipulation and interconversion" +HOMEPAGE="https://pythonhosted.org/gffutils/" +SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-biology/pyfaidx[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND}" diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml new file mode 100644 index 000000000..32143ba08 --- /dev/null +++ b/sci-biology/gffutils/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">daler/gffutils</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/glean/ChangeLog b/sci-biology/glean/ChangeLog new file mode 100644 index 000000000..f9faa5ac5 --- /dev/null +++ b/sci-biology/glean/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/glean +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> glean-1.0.1.ebuild: + sci-biology/glean: Fix dependency problems due to recent mask of perl-core + packages + +*glean-1.0.1 (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +glean-1.0.1.ebuild, + +metadata.xml: + sci-biology/glean: new package diff --git a/sci-biology/glean/Manifest b/sci-biology/glean/Manifest new file mode 100644 index 000000000..ac6b8de91 --- /dev/null +++ b/sci-biology/glean/Manifest @@ -0,0 +1 @@ +DIST glean-1-0-1.tar.gz 77941 SHA256 461079d5e44f97e745db5f66ed453a1d74701081c84bc5fba942bc436d337e5f SHA512 614aadc127caca2603913088d8b43702f564db9ef489a8ecedbc90d11e819b4a4753658638dfc115da3bb5c0bde155e57c7b36728129bf93f525fc94e4cf1d58 WHIRLPOOL 99d8c413f558ac524e087e457dd32be797e4766a96886adf421dc8bf2d036091209ddba8fe7b33d30e05a375a04983c8d2816e8e046606332c0e809f4fdd3a45 diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild new file mode 100644 index 000000000..9f39cecbe --- /dev/null +++ b/sci-biology/glean/glean-1.0.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)" +HOMEPAGE="http://sourceforge.net/projects/glean-gene" +SRC_URI="http://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-1-0-1/glean-1-0-1.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="~amd64" +IUSE="graphviz" + +DEPEND="" +RDEPEND="${DEPEND} + dev-perl/yaml + virtual/perl-Storable + virtual/perl-Getopt-Long + virtual/perl-Data-Dumper + dev-perl/Module-Pluggable + dev-perl/Algorithm-Diff + sci-biology/bioperl + graphviz? ( dev-perl/GraphViz )" +# FindBin +# YAML + +S="${WORKDIR}"/glean-gene + +src_install(){ + dobin bin/* + dodoc README + perl_set_version + insinto ${VENDOR_LIB} + doins -r lib/Glean +} diff --git a/sci-biology/glean/metadata.xml b/sci-biology/glean/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/glean/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/grappa/ChangeLog b/sci-biology/grappa/ChangeLog index e27a8cc13..49ae9d71f 100644 --- a/sci-biology/grappa/ChangeLog +++ b/sci-biology/grappa/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-biology/grappa -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> grappa-2.0.ebuild: + Bump to EAPI=5 + 14 Jul 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by Pablo Nehab-Hess <natunobilis@gentoobr.org> and me - diff --git a/sci-biology/grappa/grappa-2.0.ebuild b/sci-biology/grappa/grappa-2.0.ebuild index 659fc9b01..b95b7eb35 100644 --- a/sci-biology/grappa/grappa-2.0.ebuild +++ b/sci-biology/grappa/grappa-2.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 MY_P="GRAPPA20" @@ -13,16 +13,15 @@ SRC_URI="http://www.cs.unm.edu/~moret/GRAPPA/${MY_P}.tar.gz" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="" S="${WORKDIR}/${MY_P}" src_prepare() { - sed -i -e '/CFLAGS := -mcpu/ d' -e 's/\(CFLAGS := -D${OS}\)/\1 ${CFLAGS}/' "${S}/Makefile" + sed -i -e '/CFLAGS := -mcpu/ d' -e 's/\(CFLAGS := -D${OS}\)/\1 ${CFLAGS}/' "${S}/Makefile" || die } src_install() { - dobin grappa || die + dobin grappa dosym grappa /usr/bin/invdist dosym grappa /usr/bin/distmat dodoc README diff --git a/sci-biology/hexamer/ChangeLog b/sci-biology/hexamer/ChangeLog new file mode 100644 index 000000000..7a2252f9c --- /dev/null +++ b/sci-biology/hexamer/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/hexamer +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*hexamer-19990330 (01 May 2015) + + 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +hexamer-19990330.ebuild, +metadata.xml: + sci-biology/hexamer: new package diff --git a/sci-biology/hexamer/Manifest b/sci-biology/hexamer/Manifest new file mode 100644 index 000000000..778aad15b --- /dev/null +++ b/sci-biology/hexamer/Manifest @@ -0,0 +1 @@ +DIST hexamer-19990330.tar.gz 142855 SHA256 bf4cbea551b7338c822d52e0887780085af29382ffac78618916e3e17357c337 SHA512 d5c53a43d00a16e346798129d671a12da3e1d4e0ca64d9dd6aed96e909707d5f2812a86a4df9a7621beea65573f24c8b74c94d81c17c91ba9afd3376d85b398b WHIRLPOOL 7de34b7c52c722feff692e248fb85eb61a08d2747b61c70c2e65f35e09765c95106a87c7f5aee8a8128ff28e94376b26b0b81ed01e61072beda2f6482570633b diff --git a/sci-biology/hexamer/hexamer-19990330.ebuild b/sci-biology/hexamer/hexamer-19990330.ebuild new file mode 100644 index 000000000..fda4818ce --- /dev/null +++ b/sci-biology/hexamer/hexamer-19990330.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="Predict CDS using 6mers without deriving information from base composition" +HOMEPAGE="http://www.sanger.ac.uk/resources/software" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/users/rd/hexamer.tar.gz -> hexamer-19990330.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/hexamer + +src_prepare(){ + sed -e "s#cc -g#$(tc-getCC) ${CFLAGS}#" -i Makefile || die +} + +src_install(){ + dobin hexamer hextable + dodoc README +} diff --git a/sci-biology/hexamer/metadata.xml b/sci-biology/hexamer/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/hexamer/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/igv/ChangeLog b/sci-biology/igv/ChangeLog index 8fe0e0549..243b3e9d4 100644 --- a/sci-biology/igv/ChangeLog +++ b/sci-biology/igv/ChangeLog @@ -2,6 +2,49 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/igv: Add github to remote-id in metadata.xml + +*igv-2.3.52 (11 May 2015) + + 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/2.3.52-remove-oracle.jdbc.patch, +igv-2.3.52.ebuild, igv-2.3.47.ebuild: + sci-biology/igv: added upstream patch, version bump + +*igv-2.3.47 (29 Apr 2015) + + 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.47.ebuild, + -igv-2.3.44.ebuild: + sci-biology/igv: version bump + + 21 Mar 2015; Johann Schmitz <ercpe@gentoo.org> igv-2.3.44.ebuild: + Fixed upstream bug https://github.com/broadinstitute/IGV/issues/114 as + requested by Martin Mokrejŝ (note: i've excluded the test code by passing + -Dnotests=true to ant so it may break at some point). Also improved the + ebuild by unbundling stuff we already have in portage. There are quite a + number of libraries which aren't used for compilation which may be needed at + runtime. I haven't tested the program in depth: it started at didn't throw + errors when i clicked around - everything else is way beyond my knowledge. + Improved the ebuild for sci-biology/igv + + 21 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild: + sci-biology/igv: fix inherit to git-r3 + + 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> igv-2.3.44.ebuild: + fix inherit to use git instead of previously used subversion + +*igv-2.3.44 (17 Mar 2015) + + 17 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.44.ebuild, + -igv-2.3.40.ebuild: + version bump + +*igv-2.3.40 (05 Mar 2015) + + 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +igv-2.3.40.ebuild, + -igv-2.0.35.ebuild: + updated ebuild to github URLs; version bump but does not compile for me + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -igv-2.0.32.ebuild, igv-2.0.35.ebuild, metadata.xml: sci-biology/igv: fix SLOT operators; drop KEYWORDS for live ebuilds diff --git a/sci-biology/igv/Manifest b/sci-biology/igv/Manifest new file mode 100644 index 000000000..6b83319a6 --- /dev/null +++ b/sci-biology/igv/Manifest @@ -0,0 +1,2 @@ +DIST igv-2.3.47.zip 146891756 SHA256 1a9e0f56c1dfde2bdcd3823ad196ac4e4deb983500152667e761560c34d9b91d SHA512 24eea8215db8eaa92d4562f5867d3d5cf4cdde5f0e65cd2dae63493c02a47fa27bd30765c7ce87ef4d5106dfb92106f3abca2471d077311bc1bb6de2a71d2d2c WHIRLPOOL 0dd2b6a542832d9f769ca47c7e969fd8cc7b7fdbebd57d63b4e3e8c9e80a175840255c2a7a8496415117ee58a65fa4a7f7aebfec18168223ac0232d7bd428e89 +DIST igv-2.3.52.zip 146896234 SHA256 2f3ed77e517fbb48543d02cdf68af1895846ee5c61c001f72a160695bc79812f SHA512 d93e00efa12955bf900ccbe95b7f824c3b1887e0c86d89912b31c25c2d4b8f7d0c7c749eaeb5b30904968c2b63fbe4cdad7e9c54d3abe6c5646214edef83c2d6 WHIRLPOOL a00beddad09ef8ec00a7db94c27ec391b39c8848f3501611527665908202e3727f5c64a1910527a88f6e39fa7aeca6c237ffe23cf6d852b5b206dd9c11506d28 diff --git a/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch new file mode 100644 index 000000000..7d2274833 --- /dev/null +++ b/sci-biology/igv/files/2.3.52-remove-oracle.jdbc.patch @@ -0,0 +1,21 @@ +diff --git a/src/org/broad/igv/lists/GeneListEditDialog.java b/src/org/broad/igv/lists/GeneListEditDialog.java +index f1aff7d..87d2dd1 100644 +--- a/src/org/broad/igv/lists/GeneListEditDialog.java ++++ b/src/org/broad/igv/lists/GeneListEditDialog.java +@@ -22,15 +22,12 @@ + + package org.broad.igv.lists; + +-import oracle.jdbc.proxy.annotation.Pre; +-import org.broad.igv.Globals; + import org.broad.igv.PreferenceManager; + import org.broad.igv.ui.util.MessageUtils; + + import java.awt.*; + import java.awt.event.*; + import java.io.*; +-import java.net.URLEncoder; + import java.util.ArrayList; + import java.util.Arrays; + import javax.swing.*; + diff --git a/sci-biology/igv/igv-2.0.35.ebuild b/sci-biology/igv/igv-2.0.35.ebuild deleted file mode 100644 index e5d4e933e..000000000 --- a/sci-biology/igv/igv-2.0.35.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -#ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk" -ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}" - -EANT_BUILD_TARGET="all" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_NEEDS_TOOLS="true" -WANT_ANT_TASKS="ant-apache-bcel" - -inherit subversion java-pkg-2 java-ant-2 - -DESCRIPTION="Integrative Genomics Viewer" -HOMEPAGE="http://www.broadinstitute.org/igv/" -SRC_URI="" - -LICENSE="LGPL-2.1" -SLOT="0" -IUSE="" -KEYWORDS="" - -COMMON_DEPS=" - dev-java/batik - dev-java/absolutelayout - dev-java/jama - dev-java/commons-logging - dev-java/commons-math:3 - dev-java/concurrent-util - dev-java/jcommon - dev-java/jfreechart - dev-java/hdf-java - dev-java/jlfgr - dev-java/junit:0 - dev-java/log4j - dev-db/mysql-connector-c++ - sci-biology/samtools - dev-java/swing-layout - sci-biology/vcftools" -DEPEND=">=virtual/jdk-1.6:* - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.6:* - ${COMMON_DEPS}" - -src_install() { - java-pkg_newjar igv.jar - - # probably could drop some of these below - # - # /usr/share/igv/lib/AbsoluteLayout.jar - # /usr/share/igv/lib/Jama-1.0.2.jar - # /usr/share/igv/lib/batik-awt-util.jar - # /usr/share/igv/lib/batik-bridge.jar - # /usr/share/igv/lib/batik-codec.jar - # /usr/share/igv/lib/batik-css.jar - # /usr/share/igv/lib/batik-dom.jar - # /usr/share/igv/lib/batik-ext.jar - # /usr/share/igv/lib/batik-gui-util.jar - # /usr/share/igv/lib/batik-gvt.jar - # /usr/share/igv/lib/batik-parser.jar - # /usr/share/igv/lib/batik-svg-dom.jar - # /usr/share/igv/lib/batik-svggen.jar - # /usr/share/igv/lib/batik-transcoder.jar - # /usr/share/igv/lib/batik-util.jar - # /usr/share/igv/lib/batik-xml.jar - # /usr/share/igv/lib/commons-logging-1.1.1.jar - # /usr/share/igv/lib/commons-math-1.1.jar - # /usr/share/igv/lib/concurrent.jar - # /usr/share/igv/lib/goby-io-igv.jar - # /usr/share/igv/lib/igv.jar - # /usr/share/igv/lib/jargs.jar - # /usr/share/igv/lib/jcommon-1.0.16.jar - # /usr/share/igv/lib/jfreechart-1.0.13.jar - # /usr/share/igv/lib/jhdf.jar - # /usr/share/igv/lib/jhdf5.jar - # /usr/share/igv/lib/jide-action.jar - # /usr/share/igv/lib/jide-common.jar - # /usr/share/igv/lib/jide-components.jar - # /usr/share/igv/lib/jide-dialogs.jar - # /usr/share/igv/lib/jide-dock.jar - # /usr/share/igv/lib/jide-grids.jar - # /usr/share/igv/lib/jlfgr-1_0.jar - # /usr/share/igv/lib/junit-4.5.jar - # /usr/share/igv/lib/log4j-1.2.15.jar - # /usr/share/igv/lib/mysql-connector-java-3.1.14-bin.jar - # /usr/share/igv/lib/sam-1.53.jar - # /usr/share/igv/lib/swing-layout-1.0.jar - # /usr/share/igv/lib/vcf.jar - # /usr/share/igv/lib/xml-apis-1.3.04.jar - # /usr/share/igv/lib/xml-apis-ext-1.3.04.jar - cd lib || die - rm AbsoluteLayout.jar Jama*.jar batik*.jar commons-logging*.jar commons-math*.jar concurrent*.jar jcommon*.jar jfreechart*.jar jhdf*.jar jlfgr*.jar junit*.jar log4j*.jar sam*.jar swing*.jar vcf*.jar || die - cd .. || die - - for i in lib/*.jar; do java-pkg_dojar $i; done - - java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main -} diff --git a/sci-biology/igv/igv-2.3.47.ebuild b/sci-biology/igv/igv-2.3.47.ebuild new file mode 100644 index 000000000..acdc413d1 --- /dev/null +++ b/sci-biology/igv/igv-2.3.47.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" == "9999" ] && inherit git-r3 + +if [ "$PV" == "9999" ]; then + #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk" + #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}" + EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git" + KEYWORDS="" +else + SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" + KEYWORDS="" + # binaries + # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip + # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip +fi + +DESCRIPTION="Integrative Genomics Viewer" +HOMEPAGE="http://www.broadinstitute.org/igv/" + +LICENSE="LGPL-2.1" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +COMMON_DEPS=" + dev-java/absolutelayout + dev-java/jama:0 + dev-java/commons-logging:0 + >=dev-java/commons-io-2.1:1 + dev-java/commons-math:2 + dev-java/commons-jexl:2 + dev-java/jcommon:1.0 + dev-java/jfreechart:1.0 + dev-java/jlfgr:0 + dev-java/log4j:0 + dev-java/gson:2.2.2 + dev-java/guava:17 + dev-java/swing-layout:1 + dev-java/jgrapht:0 + dev-java/junit:4" + +DEPEND=">=virtual/jdk-1.7 + app-arch/unzip + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.7 + ${COMMON_DEPS}" + +S="${WORKDIR}/IGV-${PV}" + +EANT_BUILD_TARGET="all" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_NEEDS_TOOLS="true" +EANT_EXTRA_ARGS="-Dnotests=true" + +EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," +EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4" + +java_prepare() { + mv lib oldlib || die + mkdir lib || die + + mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die + mv -v oldlib/batik* lib || die + + rm -rvf oldlib/* || die + + epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch +} + +src_install() { + java-pkg_newjar igv.jar + + for i in lib/*.jar; do java-pkg_dojar $i; done + + java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main +} diff --git a/sci-biology/igv/igv-2.3.52.ebuild b/sci-biology/igv/igv-2.3.52.ebuild new file mode 100644 index 000000000..f512b1b43 --- /dev/null +++ b/sci-biology/igv/igv-2.3.52.ebuild @@ -0,0 +1,83 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +[ "$PV" == "9999" ] && inherit git-r3 + +if [ "$PV" == "9999" ]; then + #ESVN_REPO_URI="http://igv.googlecode.com/svn/trunk" + #ESVN_REPO_URI="http://igv.googlecode.com/svn/tags/Version_${PV}" + EGIT_REPO_URI="https://github.com/broadinstitute/IGV.git" + KEYWORDS="" +else + SRC_URI="https://github.com/broadinstitute/IGV/archive/v${PV}.zip -> ${P}.zip" + KEYWORDS="" + # binaries + # http://www.broadinstitute.org/igv/projects/downloads/IGV_2.3.40.zip + # http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.3.40.zip +fi + +DESCRIPTION="Integrative Genomics Viewer" +HOMEPAGE="http://www.broadinstitute.org/igv/" + +LICENSE="LGPL-2.1" +SLOT="0" +IUSE="" +KEYWORDS="~amd64" + +COMMON_DEPS=" + dev-java/absolutelayout + dev-java/jama:0 + dev-java/commons-logging:0 + >=dev-java/commons-io-2.1:1 + dev-java/commons-math:2 + dev-java/commons-jexl:2 + dev-java/jcommon:1.0 + dev-java/jfreechart:1.0 + dev-java/jlfgr:0 + dev-java/log4j:0 + dev-java/gson:2.2.2 + dev-java/guava:17 + dev-java/swing-layout:1 + dev-java/jgrapht:0 + dev-java/junit:4" + +DEPEND=">=virtual/jdk-1.7 + app-arch/unzip + ${COMMON_DEPS}" +RDEPEND=">=virtual/jre-1.7 + ${COMMON_DEPS}" + +S="${WORKDIR}/igv-${PV}" + +EANT_BUILD_TARGET="all" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_NEEDS_TOOLS="true" +EANT_EXTRA_ARGS="-Dnotests=true" + +EANT_GENTOO_CLASSPATH="absolutelayout,jama,commons-logging,commons-math-2,commons-jexl-2,jfreechart-1.0,jlfgr,log4j,commons-io-1," +EANT_GENTOO_CLASSPATH+="gson-2.2.2,guava-17,swing-layout-1,jgrapht,junit-4" + +java_prepare() { + mv lib oldlib || die + mkdir lib || die + + mv -v oldlib/{htsjdk-1.124.jar,bcprov-debug-jdk15on-147.jar,jide-oss-3.5.5.jar,goby-io-igv__V1.0.jar,jargs.jar,mongo-java-driver-2.11.3.jar,na12878kb-utils.jar,picard-lib.jar} lib || die + mv -v oldlib/batik* lib || die + + rm -rvf oldlib/* || die + + epatch "${FILESDIR}"/"${PV}"-remove-oracle.jdbc.patch +} + +src_install() { + java-pkg_newjar igv.jar + + for i in lib/*.jar; do java-pkg_dojar $i; done + + java-pkg_dolauncher igv --jar igv.jar --main org.broad.igv.ui.Main +} diff --git a/sci-biology/igv/metadata.xml b/sci-biology/igv/metadata.xml index fc7c76942..ddebe6007 100644 --- a/sci-biology/igv/metadata.xml +++ b/sci-biology/igv/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="github">broadinstitute/IGV</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jellyfish/ChangeLog b/sci-biology/jellyfish/ChangeLog index cf2f8f7be..63efcad1d 100644 --- a/sci-biology/jellyfish/ChangeLog +++ b/sci-biology/jellyfish/ChangeLog @@ -2,6 +2,39 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 May 2015; Justin Lecher <jlec@gentoo.org> jellyfish-1.1.11.ebuild, + jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: + sci-biology/jellyfish: Correct license from HalfLICENSE to BSD as they are + identical + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-1.1.11.ebuild: + sci-biology/jellyfish: added a note + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-1.1.11.ebuild: + sci-biology/jellyfish: fixed homepage for the old version + +*jellyfish-1.1.11 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +jellyfish-1.1.11.ebuild, jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: + sci-biology/jellyfish: added older version, added HalfLICENSE to all ebuilds + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-2.1.3.ebuild, jellyfish-2.1.4.ebuild: + sci-biology/jellyfish: added missing DEPEND on virtual/pkgconfig so that the + jellyfish-2.0.pc gets installed properly + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-2.1.3.ebuild: + sci-biology/jellyfish: fix /usr/lib64/pkgconfig/jellyfish-2.0.pc + + 31 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + jellyfish-2.1.3.ebuild: + sci-biology/jellyfish: fix installation of header *.hpp files into + /usr/include/jellyfish-2.1.3/jellyfish/ broken somewhere in upstream's code + 07 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> jellyfish-2.1.3.ebuild: added a comment on old version diff --git a/sci-biology/jellyfish/Manifest b/sci-biology/jellyfish/Manifest index b5035d2e6..d8eb12660 100644 --- a/sci-biology/jellyfish/Manifest +++ b/sci-biology/jellyfish/Manifest @@ -1,2 +1,5 @@ DIST JellyfishUserGuide.pdf 142367 SHA256 6f4365f1839b0370fff50fcd25ffcf2dad4192c2ff5b8540fd929d73a8cf85c3 SHA512 a9d65be7591d4b9b275b9f76ab79806d31bf7ef36b297b67b1802a302687aa8d49d4c491c3bb9201aec58268bcfc8c703940c72991b9080bbd1bde95bbda5b8a WHIRLPOOL 1c57b1596ccfff2159bb86359f9dafac1f994b33ab38dc334827d74b8c7541728c6c8b400df54d756bfa0b98ae023fae020ccbebbb24e3eb51baccac5024a6e6 +DIST jellyfish-1.1.11.tar.gz 1067138 SHA256 496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2 SHA512 aea7373e5ffb9deba7e164425bd7d4219d9be1e48ca666ff41e70bbc77026bc581273fb5a07c47894e2b31dd1339d4f1bc1a7b0501f10a482353ecde082eed1a WHIRLPOOL d2f31e39c1d4ce4fab78abd33c62c79bf950fdfab4f5283713e67deab8e1dabc3fd1c6cf09de964a6707793426abca24c05afe0dcf5365e04ae97dda15da2040 DIST jellyfish-2.1.3.tar.gz 955773 SHA256 00530abd01c1253646f29fa4554e96fd31148ed92402940e6f357bd5cab38e9b SHA512 2b6fea6c2686de7b568988543d5a9466676eb17252ecce3243b0dc7e3c833aed02ae6570749df58c2921289db0167b39848ccd80eb3cc568cdbaa0045114b702 WHIRLPOOL 4a1e6568932db0cc4773e89e4b8f049e96ed929723ffd518ce7e0ed12bd29041d0774fba1069251a336e448dd75703a350917ffc3db5a35f2cfac828572da566 +DIST jellyfish-2.1.4.tar.gz 958038 SHA256 c4e692170d33efa9e6e4f0b134d8e257fb802832af17fdc53ac468bf8f0f29a5 SHA512 28bbaf6ed5c69caec24a09ceb2dfa99b160f3a9c2764d3f30ab205374a6f17dfc5c6d7405e75fd5161882350db160442a91568dd65ea9851e8cb74eb71f25742 WHIRLPOOL c588f4642ff0474e0565f63d2c17db03b90fa302dff9c678766e589142bc9f71a0b48e2088b24b2df15955cae85ab43aaa1ae79066113a144c8ee8bfa75594f3 +DIST jellyfish-manual-1.1.pdf 241464 SHA256 60738f790ba50baeba04de60fdc3f620fe670d3067501d472c7b42a401600c88 SHA512 b697c51af5bd85b779fea4f03772ac8e21713f906773350931a7d67adecb4268b051e766173122ad2ba9d168235f534ff6eaa070496d6318cf8a76c8690ab61c WHIRLPOOL 01b0fff7373b40b125be3b5d44bc0af62704e84e449943235cc8b8331ff73c6d5d4be4e69040d8bc54ae1e12e377cbe4fd66108b7fcee8379d69568e8809bb5c diff --git a/sci-biology/jellyfish/jellyfish-1.1.11.ebuild b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild new file mode 100644 index 000000000..4708a9b1a --- /dev/null +++ b/sci-biology/jellyfish/jellyfish-1.1.11.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="k-mer counter within reads for assemblies" +HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish" +SRC_URI="http://www.cbcb.umd.edu/software/jellyfish/jellyfish-1.1.11.tar.gz + http://www.cbcb.umd.edu/software/jellyfish/jellyfish-manual-1.1.pdf" + +# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 +# also was bundled in quorum-0.2.1 and MaSuRca-2.1.0 +# also bundled in SEECER-0.1.3 + +LICENSE="GPL-3+ BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_install(){ + default + # beware the filename say 2.0 instead of 2.1. does it matter? + sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die + mkdir -p "${D}/usr/include/${PN}" || die + mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die + rm -rf "${D}/usr/include/${P}" +} diff --git a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild index 51f683c81..6003a4863 100644 --- a/sci-biology/jellyfish/jellyfish-2.1.3.ebuild +++ b/sci-biology/jellyfish/jellyfish-2.1.3.ebuild @@ -4,17 +4,27 @@ EAPI=5 -DESCRIPTION="k-mer counter withing reads for assemblies" +DESCRIPTION="k-mer counter within reads for assemblies" HOMEPAGE="http://www.genome.umd.edu/jellyfish.html" -SRC_URI="ftp://ftp.genome.umd.edu/pub/jellyfish/jellyfish-2.1.3.tar.gz +SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 -LICENSE="GPL-3" +LICENSE="GPL-3+ BSD" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="" -RDEPEND="${DEPEND}" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_install(){ + default + # beware the filename say 2.0 instead of 2.1. does it matter? + sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die + mkdir -p "${D}/usr/include/${PN}" || die + mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die + rm -rf "${D}/usr/include/${P}" +} diff --git a/sci-biology/jellyfish/jellyfish-2.1.4.ebuild b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild new file mode 100644 index 000000000..6003a4863 --- /dev/null +++ b/sci-biology/jellyfish/jellyfish-2.1.4.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="k-mer counter within reads for assemblies" +HOMEPAGE="http://www.genome.umd.edu/jellyfish.html" +SRC_URI="ftp://ftp.genome.umd.edu/pub/${PN}/${P}.tar.gz + ftp://ftp.genome.umd.edu/pub/jellyfish/JellyfishUserGuide.pdf" + +# older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 + +LICENSE="GPL-3+ BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +src_install(){ + default + # beware the filename say 2.0 instead of 2.1. does it matter? + sed -e "s#jellyfish-${PV}#jellyfish#" -i "${D}"/usr/lib64/pkgconfig/jellyfish-2.0.pc || die + mkdir -p "${D}/usr/include/${PN}" || die + mv "${D}"/usr/include/"${P}"/"${PN}"/* "${D}/usr/include/${PN}/" || die + rm -rf "${D}/usr/include/${P}" +} diff --git a/sci-biology/kallisto/ChangeLog b/sci-biology/kallisto/ChangeLog new file mode 100644 index 000000000..6b15b362c --- /dev/null +++ b/sci-biology/kallisto/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/kallisto +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*kallisto-0.42.1 (21 May 2015) +*kallisto-9999 (21 May 2015) + + 21 May 2015; Michael Schubert <mschu.dev@gmail.com> +kallisto-0.42.1.ebuild, + +kallisto-9999.ebuild, +metadata.xml: + sci-biology/kallisto: add kallisto diff --git a/sci-biology/kallisto/Manifest b/sci-biology/kallisto/Manifest new file mode 100644 index 000000000..9994a955e --- /dev/null +++ b/sci-biology/kallisto/Manifest @@ -0,0 +1 @@ +DIST kallisto-0.42.1.tar.gz 1047963 SHA256 e620623fe36ee183cf7e1245aba8e0b7490f530c2b68c81d6e8f0c21e2c97381 SHA512 bcfec13ac9c281610486f128a72b112616823d007cccf170f1e5846f1bd206759d5b3e94c5bc26f66e458f20b04fc4ed68d0bda6a46a23636bd61483e28c21e7 WHIRLPOOL 6b2b3cc50b24534ce4e6845447f619a2b06f0d5da608f202092ef9463c6be7e7f2f812a131e6475cd5918af96034cce1613b8b74151abebb411cab0e84543cfd diff --git a/sci-biology/kallisto/kallisto-0.42.1.ebuild b/sci-biology/kallisto/kallisto-0.42.1.ebuild new file mode 100644 index 000000000..dfc4eafb5 --- /dev/null +++ b/sci-biology/kallisto/kallisto-0.42.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Near-optimal RNA-Seq quantification" +HOMEPAGE="http://pachterlab.github.io/kallisto/" +SRC_URI="https://github.com/pachterlab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="sci-libs/hdf5" +RDEPEND="${DEPEND}" diff --git a/sci-biology/kallisto/kallisto-9999.ebuild b/sci-biology/kallisto/kallisto-9999.ebuild new file mode 100644 index 000000000..cc5b26957 --- /dev/null +++ b/sci-biology/kallisto/kallisto-9999.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 cmake-utils + +DESCRIPTION="Near-optimal RNA-Seq quantification" +HOMEPAGE="http://pachterlab.github.io/kallisto/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/pachterlab/kallisto.git" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +DEPEND="sci-libs/hdf5" +RDEPEND="${DEPEND}" diff --git a/sci-biology/embassy-domalign/metadata.xml b/sci-biology/kallisto/metadata.xml index f17a827e3..b7551a6aa 100644 --- a/sci-biology/embassy-domalign/metadata.xml +++ b/sci-biology/kallisto/metadata.xml @@ -2,4 +2,8 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/khmer/ChangeLog b/sci-biology/khmer/ChangeLog index 9b61d89a2..dc085a65b 100644 --- a/sci-biology/khmer/ChangeLog +++ b/sci-biology/khmer/ChangeLog @@ -1,12 +1,15 @@ # ChangeLog for sci-biology/khmer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/khmer: Add github to remote-id in metadata.xml + *khmer-1.0.1 (15 May 2014) 15 May 2014; Justin Lecher <jlec@gentoo.org> khmer-0.8.ebuild, +khmer-1.0.1.ebuild: - Version BUmp + Version Bump 28 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> khmer-9999.ebuild: sci-biology/khmer: upstream dropped the bundled zlib/bzip2 use if it is diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml index 2bc893037..bfbb83e90 100644 --- a/sci-biology/khmer/metadata.xml +++ b/sci-biology/khmer/metadata.xml @@ -6,4 +6,8 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="pypi">khmer</remote-id> + <remote-id type="github">ged-lab/khmer</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/kmergenie/ChangeLog b/sci-biology/kmergenie/ChangeLog new file mode 100644 index 000000000..198a4ff9e --- /dev/null +++ b/sci-biology/kmergenie/ChangeLog @@ -0,0 +1,25 @@ +# ChangeLog for sci-biology/kmergenie +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + kmergenie-1.6971.ebuild: + sci-biology/kmergenie: fix installation of launcher script + +*kmergenie-1.6971 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +kmergenie-1.6971.ebuild, -kmergenie-1.6950.ebuild: + sci-biology/kmergenie: version bump + + 18 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + kmergenie-1.6950.ebuild: + install the real binary, add dependency of external python module; the DEPEND + line still needs a fix: DEPEND: Invalid atom (Invalid use dep: ''), token 1 + +*kmergenie-1.6950 (13 Mar 2015) + + 13 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +kmergenie-1.6950.ebuild, +metadata.xml: + new package; the k-mer size is set during compilation, use 'k=121 emerge + kmergenie' to set your k-mer size diff --git a/sci-biology/kmergenie/Manifest b/sci-biology/kmergenie/Manifest new file mode 100644 index 000000000..4f45385ab --- /dev/null +++ b/sci-biology/kmergenie/Manifest @@ -0,0 +1 @@ +DIST kmergenie-1.6971.tar.gz 422649 SHA256 a0a39046321f2e8cc32ca6e3538ed827ef61d568c799610d268725cffcd16ba6 SHA512 43dad36b461444023c0f730bd8097f2481e958e58db9fbe32ce6e38414438a946d3e648ec719bda63215661457ff1d3ce805631203f2ef69e3ffb8aa2075325d WHIRLPOOL 2d113ffac7d50a68335e3fc1a444700d944d854427c2ba808d7464f80c4f49a299df496b23ec0ced71f770c7a19a6831af8a94033b55d707e6b91cbab941e4d5 diff --git a/sci-biology/kmergenie/kmergenie-1.6971.ebuild b/sci-biology/kmergenie/kmergenie-1.6971.ebuild new file mode 100644 index 000000000..6081505dd --- /dev/null +++ b/sci-biology/kmergenie/kmergenie-1.6971.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +PYTHON_COMPAT=( python{2_6,2_7} ) + +DESCRIPTION="Estimate best k-mer length to be used in novo assemblies (default set during compilation is 121)" +HOMEPAGE="http://kmergenie.bx.psu.edu/" +SRC_URI="http://kmergenie.bx.psu.edu/"${P}".tar.gz" + +LICENSE="CeCILL-1.1" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +# dev-python/docopt[${PYTHON_USEDEP}] +DEPEND="dev-python/docopt + dev-lang/R" +RDEPEND="${DEPEND}" + +# Type `make` in the KmerGenie directory +# To enable larger values of k, e.g. 200, type `make clean ; make k=200`. +# +# usage: ./kmergenie reads_file + +src_prepare(){ + sed -e 's#-O4##' -i makefile || die + sed -e 's#third_party.##' -i kmergenie || die +} + +src_compile(){ + make -j 1 || die +} + +src_install(){ + dobin kmergenie specialk + dodoc README + # TODO: install also the python files + insinto /usr/share/${PN}/R + doins scripts/* +} diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/kmergenie/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/lastz/ChangeLog b/sci-biology/lastz/ChangeLog index 45c889643..eac541589 100644 --- a/sci-biology/lastz/ChangeLog +++ b/sci-biology/lastz/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/lastz -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*lastz-1.03.66 (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/lastz-1.03.66-build.patch, +lastz-1.03.66.ebuild, + -files/lastz-1.03.34-build.patch, -lastz-1.03.34.ebuild: + sci-biology/lastz: version bump + 12 Jun 2013; Justin Lecher <jlec@gentoo.org> -lastz-1.02.00.ebuild, +lastz-1.03.34.ebuild, +files/lastz-1.03.34-build.patch, metadata.xml: Version Bump; fix license; bump to EAPI=5; fix buildsystem @@ -17,4 +24,3 @@ 16 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +lastz-1.02.00.ebuild, +metadata.xml: initial ebuild - diff --git a/sci-biology/lastz/Manifest b/sci-biology/lastz/Manifest index 68cf4df31..b8f2a76b1 100644 --- a/sci-biology/lastz/Manifest +++ b/sci-biology/lastz/Manifest @@ -1 +1 @@ -DIST lastz-1.03.34.tar.gz 716550 SHA256 b831cfb7dabf85e2f9bf33a76641481ede0d18a941c3a72d57d373b018232fbf SHA512 a29d27cd718c99762397f985ad9320e9cec9b288f94b766224f904abaa6793d4557cc253e82f568223c6a256c35e357c51d29ba89a0af3c915a82f27fadaaf1f WHIRLPOOL 4f3939005aaad44042ca219138355c02b95c6e7f182d4f11ad810a27625044a29075815efefb419aa8476be6cd9cf553d0e07f8a59a0a0fc74dd2bba77f1e9bd +DIST lastz-1.03.66.tar.gz 727104 SHA256 8eb2db3fcf235065a099536f3a41323df25c6643d30b0db3a79f4b2f7430a5d0 SHA512 904c91b4f36ff94805096bd52fe3790801199739a43e5b14d06ceda06b4d38cde8f202b3492245ff5f1efc4d9070f6807fe1e19db802759fe1f23f45133e314d WHIRLPOOL 0440fd08a0a7620e094e68cff746bcbd95f0a6cf31526728f9ad2dd2697cc22ba2fda99865d83504b206d1ca986b2003b614408c0a9275889119804c702885c6 diff --git a/sci-biology/lastz/files/lastz-1.03.34-build.patch b/sci-biology/lastz/files/lastz-1.03.34-build.patch deleted file mode 100644 index bc3a8c033..000000000 --- a/sci-biology/lastz/files/lastz-1.03.34-build.patch +++ /dev/null @@ -1,43 +0,0 @@ - src/Makefile | 11 ++++++----- - 1 file changed, 6 insertions(+), 5 deletions(-) - -diff --git a/src/Makefile b/src/Makefile -index f628f3c..5bb11bf 100644 ---- a/src/Makefile -+++ b/src/Makefile -@@ -1,7 +1,7 @@ - include ../make-include.mak - include version.mak - --CC=gcc -+CC?=gcc - - # default targets - -@@ -48,7 +48,8 @@ VERSION_FLAGS= \ - -DSUBVERSION_REV="\"${SUBVERSION_REV}"\" - - --CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS} -+CFLAGS ?= -O3 ${definedForAll} -+CFLAGS += ${VERSION_FLAGS} - - - srcFiles = lastz infer_scores \ -@@ -78,13 +79,13 @@ incFiles = lastz.h infer_scores.h \ - - - lastz: $(foreach part,${srcFiles},${part}.o) -- $(CC) $(foreach part,${srcFiles},${part}.o) -lm -o $@ -+ $(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@ - - lastz_D: $(foreach part,${srcFiles},${part}_D.o) -- $(CC) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@ -+ $(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@ - - lastz_32: $(foreach part,${srcFiles},${part}_32.o) -- $(CC) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@ -+ $(CC) $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@ - - # cleanup - diff --git a/sci-biology/lastz/files/lastz-1.03.66-build.patch b/sci-biology/lastz/files/lastz-1.03.66-build.patch new file mode 100644 index 000000000..0b9a948d3 --- /dev/null +++ b/sci-biology/lastz/files/lastz-1.03.66-build.patch @@ -0,0 +1,37 @@ +--- src/Makefile.old 2015-05-02 15:07:56.169136255 +0200 ++++ src/Makefile 2015-05-02 15:10:02.249137955 +0200 +@@ -1,7 +1,7 @@ + include ../make-include.mak + include version.mak + +-CC=gcc ++CC?=gcc + + # default targets + +@@ -71,7 +71,7 @@ + -DSUBVERSION_REV="\"${SUBVERSION_REV}"\" + + +-CFLAGS = -O3 ${definedForAll} ${VERSION_FLAGS} ++CFLAGS += ${definedForAll} ${VERSION_FLAGS} + + + srcFiles = lastz infer_scores \ +@@ -101,13 +101,13 @@ + + + lastz: $(foreach part,${srcFiles},${part}.o) +- ${CC} $(foreach part,${srcFiles},${part}.o) -lm -o $@ ++ ${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}.o) -lm -o $@ + + lastz_D: $(foreach part,${srcFiles},${part}_D.o) +- ${CC} $(foreach part,${srcFiles},${part}_D.o) -lm -o $@ ++ ${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_D.o) -lm -o $@ + + lastz_32: $(foreach part,${srcFiles},${part}_32.o) +- ${CC} $(foreach part,${srcFiles},${part}_32.o) -lm -o $@ ++ ${CC} $(LDFLAGS) $(foreach part,${srcFiles},${part}_32.o) -lm -o $@ + + # cleanup + diff --git a/sci-biology/lastz/lastz-1.03.34.ebuild b/sci-biology/lastz/lastz-1.03.66.ebuild index 32364b20c..af89d9912 100644 --- a/sci-biology/lastz/lastz-1.03.34.ebuild +++ b/sci-biology/lastz/lastz-1.03.66.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-biology/lighter/ChangeLog b/sci-biology/lighter/ChangeLog new file mode 100644 index 000000000..aac7e6b24 --- /dev/null +++ b/sci-biology/lighter/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/lighter +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/lighter: Add github to remote-id in metadata.xml + +*lighter-9999 (01 May 2015) + + 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +lighter-9999.ebuild, +metadata.xml: + sci-libs/lighter: new package; contains IUSE=threads but ... does the Makefile + need a tweak for -lpthreads ? ;-). Go ahead and fix this. diff --git a/sci-biology/lighter/lighter-9999.ebuild b/sci-biology/lighter/lighter-9999.ebuild new file mode 100644 index 000000000..8e2319afa --- /dev/null +++ b/sci-biology/lighter/lighter-9999.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +[ "$PV" == "9999" ] && inherit git-r3 + +DESCRIPTION="NGS reads corrector" +HOMEPAGE="https://github.com/mourisl/Lighter" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/mourisl/Lighter.git" + KEYWORDS="" +else + SRC_URI="" + KEYWORDS="" +fi + +LICENSE="GPL-2+" +SLOT="0" +IUSE="threads" + +DEPEND="sys-libs/zlib + sci-libs/bloom" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e "s#g++#$(tc-getCC)#;s#-Wall -O3#${CXXFLAGS}#" -i Makefile || die +} + +src_install(){ + dobin lighter + dodoc README.md +} diff --git a/sci-biology/lighter/metadata.xml b/sci-biology/lighter/metadata.xml new file mode 100644 index 000000000..5a9ca59a9 --- /dev/null +++ b/sci-biology/lighter/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">mourisl/Lighter</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/MAKER/ChangeLog b/sci-biology/maker/ChangeLog index d954ed6f5..d954ed6f5 100644 --- a/sci-biology/MAKER/ChangeLog +++ b/sci-biology/maker/ChangeLog diff --git a/sci-biology/maker/Manifest b/sci-biology/maker/Manifest new file mode 100644 index 000000000..8b2a8d085 --- /dev/null +++ b/sci-biology/maker/Manifest @@ -0,0 +1 @@ +DIST maker-2.31.8.tgz 13607357 SHA256 a99c7e433638979808ea3f4bcd2b6b69f4474bd898807aba4520debd58717420 SHA512 1533888c4960a74395f4bfdd26a4f86ba33d93764b1e40094fcd2d8e7e355495464619820b0c805061f467c20d979ddf17bdb2979a7f17117c1a721032ee538d WHIRLPOOL 2df90ae76891160ed08fc3a703d3d8a982e737fa23c3f65d197bd900816588a2e8d8ec364e1122af4be289f01b5c704414487eb19ece8a8fedd9c9aac11e40e2 diff --git a/sci-biology/maker/maker-2.31.8.ebuild b/sci-biology/maker/maker-2.31.8.ebuild new file mode 100644 index 000000000..6bc8ff57a --- /dev/null +++ b/sci-biology/maker/maker-2.31.8.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils perl-module + +DESCRIPTION="A genome annotation viewer and pipeline for small eukaryota and prokaryota" +HOMEPAGE="http://www.yandell-lab.org/software/maker.html" +SRC_URI="maker-"${PV}".tgz" + +RESTRICT="fetch" + +# for academia: GPL-v2 or Artistic-2 +# for commercial: ask +LICENSE="|| ( GPL-2 Artistic-2 )" +SLOT="0" +KEYWORDS="" +IUSE="" + +# http://search.cpan.org/~rgarcia/Perl-Unsafe-Signals-0.02/ +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks.pm +# http://search.cpan.org/~rybskej/forks-0.36/lib/forks/shared.pm +# http://search.cpan.org/~dconway/IO-Prompt-0.997002/lib/IO/Prompt.pm +DEPEND="virtual/mpi + dev-perl/DBI + dev-perl/DBD-SQLite + dev-perl/File-Which + dev-perl/Bit-Vector + dev-perl/Inline-C + dev-perl/IO-All + dev-perl/libwww-perl + dev-perl/DBD-Pg + virtual/perl-Module-Build + >=sci-biology/bioperl-1.6 + sci-biology/ncbi-tools || ( sci-biology/ncbi-tools++ ) + sci-biology/snap + sci-biology/repeatmasker + sci-biology/exonerate + sci-biology/augustus" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/maker/src + +pkg_nofetch() { + einfo "Please visit ${HOMEPAGE} and obtain the file" + einfo "maker-"${PV}".tgz and place it into ${DISTDIR}" +} + +src_compile(){ + perl Build.PL || die + ./Build install || die +} diff --git a/sci-biology/maker/metadata.xml b/sci-biology/maker/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/maker/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/manatee-igs/ChangeLog b/sci-biology/manatee-igs/ChangeLog index 2c85c80cd..8a60b082e 100644 --- a/sci-biology/manatee-igs/ChangeLog +++ b/sci-biology/manatee-igs/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/manatee-igs -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> manatee-igs-2.23.1.ebuild: + sci-biology/manatee-igs: Fix dependency problems due to recent mask of perl- + core packages + 29 Aug 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> manatee-igs-2.23.1.ebuild: Both versions of manatee have same license, so rename unify the license @@ -24,4 +28,3 @@ 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +manatee-igs-2.23.1.ebuild, +metadata.xml: new package for prokaryotic genome annotation and editing - diff --git a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild index b858a9d5b..fb0fa9f2b 100644 --- a/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild +++ b/sci-biology/manatee-igs/manatee-igs-2.23.1.ebuild @@ -1,13 +1,14 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 DESCRIPTION="IGS-modified version of the genome annotation tool using Chado database schema" HOMEPAGE="http://manatee.sourceforge.net/igs" -SRC_URI="http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz - http://manatee.sourceforge.net/igs/docs/README_Linux.txt" +SRC_URI=" + http://sourceforge.net/projects/manatee/files/igs_manatee/"${PV}"/manatee-"${PV}"_linux.tgz + http://manatee.sourceforge.net/igs/docs/README_Linux.txt" LICENSE="Artistic-Manatee" SLOT="0" @@ -15,35 +16,35 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND=" - >=dev-libs/expat-1.95.8 - >=media-libs/gd-2.0.34 - virtual/perl-CGI - dev-perl/Bio-DB-Das-Chado - dev-perl/DBI - dev-perl/DBD-mysql - dev-perl/XML-Parser - dev-perl/XML-Twig - dev-perl/XML-Simple - dev-perl/XML-Writer - dev-perl/HTML-Template - dev-perl/Tree-DAG_Node - virtual/perl-File-Spec - virtual/perl-Data-Dumper - dev-perl/GD - dev-perl/GDTextUtil - dev-perl/GDGraph - virtual/perl-Storable - dev-perl/Log-Log4perl - dev-perl/Log-Cabin - dev-perl/DateManip - dev-perl/IO-Tee - dev-perl/MLDBM - dev-perl/JSON - dev-perl/JSON-Any - sci-biology/bioperl" + >=dev-libs/expat-1.95.8 + >=media-libs/gd-2.0.34 + dev-perl/CGI + dev-perl/Bio-DB-Das-Chado + dev-perl/DBI + dev-perl/DBD-mysql + dev-perl/XML-Parser + dev-perl/XML-Twig + dev-perl/XML-Simple + dev-perl/XML-Writer + dev-perl/HTML-Template + dev-perl/Tree-DAG_Node + virtual/perl-File-Spec + virtual/perl-Data-Dumper + dev-perl/GD + dev-perl/GDTextUtil + dev-perl/GDGraph + virtual/perl-Storable + dev-perl/Log-Log4perl + dev-perl/Log-Cabin + dev-perl/DateManip + dev-perl/IO-Tee + dev-perl/MLDBM + dev-perl/JSON + dev-perl/JSON-Any + sci-biology/bioperl" RDEPEND="${DEPEND} - >=dev-db/mysql-5.0 - >=www-servers/apache-2.2" + >=dev-db/mysql-5.0 + >=www-servers/apache-2.2" S="${WORKDIR}"/manatee-"${PV}"_linux diff --git a/sci-biology/metaseq/ChangeLog b/sci-biology/metaseq/ChangeLog new file mode 100644 index 000000000..058230ae6 --- /dev/null +++ b/sci-biology/metaseq/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/metaseq +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/metaseq: Add github to remote-id in metadata.xml + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> metaseq-0.5.3.ebuild: + sci-biology/metaseq: Streamline ebuild + +*metaseq-0.5.3 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, + +metaseq-0.5.3.ebuild: + sci-biology/metaseq: add metaseq diff --git a/sci-biology/metaseq/Manifest b/sci-biology/metaseq/Manifest new file mode 100644 index 000000000..933c9b385 --- /dev/null +++ b/sci-biology/metaseq/Manifest @@ -0,0 +1 @@ +DIST metaseq-0.5.3.tar.gz 5233997 SHA256 28d55b7f584100c2c7a47e761a13490bf3a4f19721adc991d767a4e707a3de14 SHA512 18e9aa7260d076c0332674dd99e189964f49a5af689858905f43b8ef4168923c50cc9a42ce53cd0865329663d76863c95eb1c4fb125c62b2e03026bd6f0bccac WHIRLPOOL 9d3257a7f1d88f914a2397d6f189955fce95788a59edc27fa5a7dfe9c5ee9c55dcb4b60a3ee0b432f776dc3edcd6c725591cedf839c691d578e128a6c006eb53 diff --git a/sci-biology/metaseq/metadata.xml b/sci-biology/metaseq/metadata.xml new file mode 100644 index 000000000..8174cbd9e --- /dev/null +++ b/sci-biology/metaseq/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">daler/metaseq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/metaseq/metaseq-0.5.3.ebuild b/sci-biology/metaseq/metaseq-0.5.3.ebuild new file mode 100644 index 000000000..c75c4d807 --- /dev/null +++ b/sci-biology/metaseq/metaseq-0.5.3.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data" +HOMEPAGE="http://pythonhosted.org/metaseq/" +SRC_URI="https://github.com/daler/metaseq/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + sci-biology/bx-python[${PYTHON_USEDEP}] + sci-biology/gffutils[${PYTHON_USEDEP}] + sci-biology/pysam[${PYTHON_USEDEP}] + sci-biology/pybedtools[${PYTHON_USEDEP}] + sci-biology/samtools[${PYTHON_USEDEP}] + sci-libs/scipy[${PYTHON_USEDEP}] + " +DEPEND="${RDEPEND}" diff --git a/sci-biology/minced/ChangeLog b/sci-biology/minced/ChangeLog new file mode 100644 index 000000000..8f2fcc345 --- /dev/null +++ b/sci-biology/minced/ChangeLog @@ -0,0 +1,16 @@ +# ChangeLog for sci-biology/minced +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/minced: Add github to remote-id in metadata.xml + + 29 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> minced-9999.ebuild: + sci-biology/minced: fixed the launcher + +*minced-9999 (27 Apr 2015) + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +minced-9999.ebuild: + sci-biology/minced: new package; the /usr/bin/minced wrapper for the + minced.jar does not work diff --git a/sci-biology/minced/metadata.xml b/sci-biology/minced/metadata.xml new file mode 100644 index 000000000..193c48204 --- /dev/null +++ b/sci-biology/minced/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">ctSkennerton/minced/tree/master</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/minced/minced-9999.ebuild b/sci-biology/minced/minced-9999.ebuild new file mode 100644 index 000000000..05e06f141 --- /dev/null +++ b/sci-biology/minced/minced-9999.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 java-pkg-2 + +DESCRIPTION="Short Palindromic Repeat finder tool (for CRISPRs)" +HOMEPAGE="https://github.com/ctSkennerton/minced/tree/master" +EGIT_REPO_URI="https://github.com/ctSkennerton/minced.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND=">=virtual/jdk-1.7" +RDEPEND=">=virtual/jre-1.7" + +src_compile(){ + emake +} + +src_install(){ + java-pkg_dojar minced.jar + java-pkg_dolauncher + dodoc README +} diff --git a/sci-biology/mip-scaffolder/ChangeLog b/sci-biology/mip-scaffolder/ChangeLog index b9261e60b..1574e9243 100644 --- a/sci-biology/mip-scaffolder/ChangeLog +++ b/sci-biology/mip-scaffolder/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + mip-scaffolder-0.6.ebuild: + sci-biology/mip-scaffolder: respect CXXFLAGS although the Makefile speaks + about CFLAGS + 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mip-scaffolder-0.6.ebuild: fixed LICENSE diff --git a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild index 0bcf6d786..967ecc652 100644 --- a/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild +++ b/sci-biology/mip-scaffolder/mip-scaffolder-0.6.ebuild @@ -22,7 +22,7 @@ RDEPEND="${DEPEND}" src_prepare(){ sed -e 's:/home/user/lp-solve/:/usr/include/lpsolve/:; s:/home/user/lemon/:/usr/include/lemon:; s:/home/user/mip-scaffolder-0.6/:/usr/bin:' -i Makefile - find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CFLAGS}:" -i $f; done + find . -name Makefile | while read f; do sed -e "s:CC=g++:CC=$(tc-getCXX):; s:CFLAGS=-Wall -g -O9:CFLAGS=${CXXFLAGS}:" -i $f; done sed -e 's:$(LPSOLVEROOT)/liblpsolve55.a:-llpsolve55:' -i split-scaffold/Makefile } diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog index b5f200eea..8e61af53c 100644 --- a/sci-biology/mira/ChangeLog +++ b/sci-biology/mira/ChangeLog @@ -1,57 +1,133 @@ # ChangeLog for sci-biology/mira -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/ChangeLog,v 1.31 2015/04/07 14:33:30 jlec Exp $ -*mira-4.0.1 (12 Apr 2014) + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mira: Updating remote-id in metadata.xml - 12 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +mira-4.0.1.ebuild: - sci-biology/mira-4.0.1: bump to current recommended bugfix release + 25 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-4.0.2.ebuild, + +files/mira-4.0.2-cout.patch: + Build fix for newer gcc, #537564 - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.4.0.1.ebuild, - -mira-3.4.1.1.ebuild, -mira-3.9.9.ebuild, -mira-3.9.15.ebuild, - -mira-4.0_rc2.ebuild, mira-4.0_rc4.ebuild: - Drop old; punt base.eclass +*mira-4.0.2 (23 Jan 2015) - 12 Nov 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mira-3.4.0.1.ebuild, mira-3.4.1.1.ebuild, mira-3.9.9.ebuild, - mira-3.9.15.ebuild, mira-4.0_rc2.ebuild, +mira-4.0_rc4.ebuild: - Added 4.0_rc4 release candidate. Removing the sed hack redirecting autoconf - to config/m4/ instead of m4/ because upstream accepted that source tree - layout change in _rc3 already. + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> +mira-4.0.2.ebuild: + Version Bump, thanks Martin Mokrejš for the work + 23 Jan 2015; Justin Lecher <jlec@gentoo.org> mira-3.9.18.ebuild: + Add workaroung for m4 dir location, #536172 - 01 Oct 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - mira-4.0_rc2.ebuild: - Improve ebuild to use MY_PV. + 14 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1.ebuild: + Drop old - 25 Sep 2013; Justin Lecher <jlec@gentoo.org> mira-4.0_rc2.ebuild, - metadata.xml: - Fix m4 macrodir location + 14 Jan 2014; Agostino Sarubbo <ago@gentoo.org> mira-3.9.18.ebuild: + Stable for x86, wrt bug #497218 -*mira-3.9.15 (30 Apr 2013) + 12 Jan 2014; Pacho Ramos <pacho@gentoo.org> mira-3.9.18.ebuild: + amd64 stable, bug #497218 - 30 Apr 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mira-3.9.15.ebuild: - sci-biology/mira-3.9.15: bump to current besta version mira-3.9.15.ebuild + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild: + Punt base.eclass -*mira-3.4.1.1 (22 Feb 2013) -*mira-3.9.9 (22 Feb 2013) + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r1.ebuild, + -mira-3.4.0.2.ebuild: + Drop old - 22 Feb 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/mira-3.4.0.2-boost-1.50.patch, +mira-3.4.1.1.ebuild, - +mira-3.9.9.ebuild: - sci-biology/mira: current stable and development version bumps +*mira-3.9.18 (07 Jul 2013) - 22 May 2012; Justin Lecher <jlec@gentoo.org> -mira-3.2.1-r2.ebuild, - -mira-3.2.1.17-r1.ebuild, -mira-3.2.1.20.ebuild, mira-3.4.0.1.ebuild: - Add missing eutils.eclass, bump to EAPI=4, remove usage of base.eclass; drop - old + 07 Jul 2013; Justin Lecher <jlec@gentoo.org> +mira-3.9.18.ebuild: + Version Bump; fixed compilation with dev-libs/boost-1.53.0 and some libtool + versions, #450322; thanks Martin Mokrejs for all his work -*mira-3.4.0.1 (08 Dec 2011) + 11 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly - 08 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +mira-3.4.0.1.ebuild, +files/mira-3.4.0.1-asneeded.patch: - version bump and dropped the expat patch for --as-needed CFLAGS as upstream - fixed that in a different way, the still applicable part of the patch is - however provided under files/ but is just a cosmetic change (hence not really - needed) +*mira-3.4.0.2 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + mira-3.2.1-r1.ebuild, +mira-3.4.0.2.ebuild, + +files/mira-3.4.0.2-boost-1.50.patch: + Version Bump, #377807 + +*mira-3.2.1-r1 (07 Nov 2012) + + 07 Nov 2012; Justin Lecher <jlec@gentoo.org> mira-3.2.1.ebuild, + +mira-3.2.1-r1.ebuild, +files/mira-3.2.1-boost-1.50.patch: + Fix for boost >1.50, #425468 + + 08 Jul 2012; Justin Lecher <jlec@gentoo.org> -mira-3.0.5.ebuild, + -mira-3.2.0.ebuild: + Drop old + + 25 Jun 2012; Jeff Horelick <jdhore@gentoo.org> mira-3.2.1.ebuild: + marked x86 per bug 418439 + + 24 Jun 2012; Agostino Sarubbo <ago@gentoo.org> mira-3.2.1.ebuild: + Stable for amd64, wrt bug #418439 + + 23 Jun 2012; Kacper Kowalik <xarthisius.kk@gmail.com> mira-3.2.1.ebuild: + Don't install docs that are no longer there, thanks to David Abbott for the + patch + +*mira-3.2.1 (21 May 2011) + + 21 May 2011; Andrey Kislyuk <weaver@gentoo.org> +mira-3.2.1.ebuild: + Version bump and fix bug 367921 + + 11 Feb 2011; Markos Chandras <hwoarang@gentoo.org> mira-3.2.0.ebuild: + Stable on amd64 wrt bug #353568 + + 07 Feb 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> mira-3.2.0.ebuild: + x86 stable wrt bug #353568 + + 17 Oct 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.2.0.ebuild: + Remove doc USE flag and dependency, workaround for bug 340419 + +*mira-3.2.0 (26 Sep 2010) + + 26 Sep 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.0.ebuild, + -mira-3.0.3.ebuild, +mira-3.2.0.ebuild: + Version bump, drop old + + 28 Jun 2010; Justin Lecher <jlec@gentoo.org> mira-3.0.0.ebuild, + mira-3.0.3.ebuild, mira-3.0.5.ebuild: + Prepared for prefix, #325929 + +*mira-3.0.5 (05 May 2010) + + 05 May 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.5.ebuild: + Version bump + +*mira-3.0.3 (18 Mar 2010) + + 18 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.2.ebuild, + +mira-3.0.3.ebuild: + Hotfix from upstream + +*mira-3.0.2 (10 Mar 2010) + + 10 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> -mira-3.0.1.ebuild, + +mira-3.0.2.ebuild: + Hotfix from upstream + +*mira-3.0.1 (06 Mar 2010) + + 06 Mar 2010; Andrey Kislyuk <weaver@gentoo.org> +mira-3.0.1.ebuild: + Version bump (bugfix release) + + 25 Feb 2010; Samuli Suominen <ssuominen@gentoo.org> mira-3.0.0.ebuild, + +files/mira-3.0.0-asneeded.patch: + Fix ax_lib_expat.m4 macro to not use LDFLAGS for passing libraries wrt + #305547 by Kacper Kowalik. + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + add eautoreconf + + 03 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> mira-3.0.0.ebuild: + Install 3rd party files + +*mira-3.0.0 (02 Feb 2010) + + 02 Feb 2010; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +mira-3.0.0.ebuild: + New package, ebuild written by me diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest index 98cb65231..a095295dd 100644 --- a/sci-biology/mira/Manifest +++ b/sci-biology/mira/Manifest @@ -1,3 +1,2 @@ -DIST mira-4.0.2.tar.bz2 10368046 SHA256 a32cb2b21e0968a5536446287c895fe9e03d11d78957554e355c1080b7b92a80 SHA512 a7f9845de207cefb87ffa652f4f6b9b85735ef22eeb29b456e4d946ba1675e7dd2c78abb2da56f11fddcb699f5c0700a08ce298196ce1a8e586a758a8d3bdc7e WHIRLPOOL d038472f9b129e97883f59c471df51f07315ee38eda5a9e804cdd2d33988306162b1bb1dde2cb7fd510c82be5734240dfd69364d39865a47af439762c7154747 -DIST mira-4.0rc4.tar.bz2 10418692 SHA256 5149e25462625be98a18945921e17bb3c9bef110d820af295c7473a44acf09b4 SHA512 9ada6abaf36993e8738cd8fbe7ec710e0672335afc83902fd962fe9c0c430dae80df64f272bfbb1b4d132cb080e93ed791eaf8a7652b22e5e6e816466fe3eb5b WHIRLPOOL f2d605f2ad7985f60038ed93d4c1d45b6b60c97552588ac1daae449f8ee503691c0ef79d52df75bd9241cdc888a107df2801d31c9e6c9b8e3c6f3c561910c09f +DIST mira-4.9.5.tar.bz2 10444005 SHA256 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8 WHIRLPOOL be0abe4213ecbe40534bee65dba390ac3695d3763123ad93c4a32bbcded15aa2f99ef93304b8e4cdc65728f0859e2748ad828826919bf7e4fc6b8499bccbdf9c DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2 diff --git a/sci-biology/mira/files/libtool.m4.patch b/sci-biology/mira/files/libtool.m4.patch deleted file mode 100644 index 9cfaeef09..000000000 --- a/sci-biology/mira/files/libtool.m4.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- config/m4/libtool.m4.ori 2011-06-22 12:28:14.000000000 +0200 -+++ config/m4/libtool.m4 2011-06-22 12:28:39.000000000 +0200 -@@ -88,10 +88,6 @@ - # This can be used to rebuild libtool when needed - LIBTOOL_DEPS="$ltmain" - --# Always use our own libtool. --LIBTOOL='$(SHELL) $(top_builddir)/libtool' --AC_SUBST(LIBTOOL)dnl -- - _LT_SETUP - - # Only expand once: diff --git a/sci-biology/mira/files/mira-3.0.0-asneeded.patch b/sci-biology/mira/files/mira-3.0.0-asneeded.patch deleted file mode 100644 index 9bbd267cf..000000000 --- a/sci-biology/mira/files/mira-3.0.0-asneeded.patch +++ /dev/null @@ -1,56 +0,0 @@ -http://bugs.gentoo.org/show_bug.cgi?id=305547 - ---- config/m4/ax_lib_expat.m4 -+++ config/m4/ax_lib_expat.m4 -@@ -96,6 +99,7 @@ - - EXPAT_CFLAGS="" - EXPAT_LDFLAGS="" -+ EXPAT_LIBS="" - EXPAT_VERSION="" - - dnl -@@ -105,7 +109,8 @@ - - if test -n "$expat_prefix"; then - expat_include_dir="$expat_prefix/include" -- expat_lib_flags="-L$expat_prefix/lib -lexpat" -+ expat_lib_flags="-L$expat_prefix/lib" -+ expat_libs="-lexpat" - run_expat_test="yes" - elif test "$expat_requested" = "yes"; then - if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then -@@ -126,6 +131,8 @@ - saved_LDFLAGS="$LDFLAGS" - LDFLAGS="$LDFLAGS $expat_lib_flags" - -+ saved_LIBS="$LIBS" -+ LIBS="$LIBS $expat_libs" - dnl - dnl Check Expat headers - dnl -@@ -171,7 +178,8 @@ - ]] - )], - [ - EXPAT_LDFLAGS="$expat_lib_flags" -+ EXPAT_LIBS="$expat_libs" - expat_lib_found="yes" - AC_MSG_RESULT([found]) - ], -@@ -185,6 +193,7 @@ - - CPPFLAGS="$saved_CPPFLAGS" - LDFLAGS="$saved_LDFLAGS" -+ LIBS="$saved_LIBS" - fi - - AC_MSG_CHECKING([for Expat XML Parser]) -@@ -194,6 +203,7 @@ - - AC_SUBST([EXPAT_CFLAGS]) - AC_SUBST([EXPAT_LDFLAGS]) -+ AC_SUBST([EXPAT_LIBS]) - - HAVE_EXPAT="yes" - else diff --git a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch b/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch deleted file mode 100644 index 418432376..000000000 --- a/sci-biology/mira/files/mira-3.4.0.1-asneeded.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- config/m4/ax_lib_expat.m4.ori 2011-12-08 01:59:42.000000000 +0100 -+++ config/m4/ax_lib_expat.m4 2011-12-08 02:00:08.000000000 +0100 -@@ -108,7 +108,8 @@ - - if test -n "$expat_prefix"; then - expat_include_dir="$expat_prefix/include" -- expat_lib_flags="-L$expat_prefix/lib -lexpat" -+ expat_lib_flags="-L$expat_prefix/lib" -+ expat_libs="-lexpat" - run_expat_test="yes" - elif test "$expat_requested" = "yes"; then - if test -n "$expat_include_dir" -a -n "$expat_lib_flags"; then -@@ -129,6 +130,8 @@ - saved_LDFLAGS="$LDFLAGS" - LIBS="$LDFLAGS $expat_lib_flags" - -+ saved_LIBS="$LIBS" -+ LIBS="$LIBS $expat_libs" - dnl - dnl Check Expat headers - dnl -@@ -188,6 +191,7 @@ - - CPPFLAGS="$saved_CPPFLAGS" - LDFLAGS="$saved_LDFLAGS" -+ LIBS="$saved_LIBS" - fi - - AC_MSG_CHECKING([for Expat XML Parser]) diff --git a/sci-biology/mira/files/mira-4.9.5-cout.patch b/sci-biology/mira/files/mira-4.9.5-cout.patch new file mode 100644 index 000000000..14feb0284 --- /dev/null +++ b/sci-biology/mira/files/mira-4.9.5-cout.patch @@ -0,0 +1,16 @@ + src/progs/quirks.C | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/progs/quirks.C b/src/progs/quirks.C +index 47e5ee8..060b6f3 100644 +--- a/src/progs/quirks.C ++++ b/src/progs/quirks.C +@@ -25,6 +25,8 @@ + + #include <boost/filesystem.hpp> + ++#include <iostream> ++ + // make the "tcmalloc: large alloc" messages from TCMallom disappear + // by setting the reporting environment variable to a very large value + // see: http://groups.google.com/group/google-perftools/browse_thread/thread/24a003fc35f3d470?pli=1 diff --git a/sci-biology/mira/files/mira_left_clip.readpool.C.patch b/sci-biology/mira/files/mira_left_clip.readpool.C.patch deleted file mode 100644 index 12977dd7c..000000000 --- a/sci-biology/mira/files/mira_left_clip.readpool.C.patch +++ /dev/null @@ -1,36 +0,0 @@ -*** src/mira/readpool.C.ori 2010-11-21 11:42:29.000000000 -0600 ---- src/mira/readpool.C 2011-01-13 10:20:38.000000000 -0600 -*************** -*** 1751,1757 **** - break; - } - case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : { -! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())); - break; - } - case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : { ---- 1751,1757 ---- - break; - } - case NCBIInfoXML::NCBIXML_CLIP_QUALITY_LEFT : { -! REP_thepool[idoffound].setLQClipoff(atoi(ECD->c_str())-1); - break; - } - case NCBIInfoXML::NCBIXML_CLIP_QUALITY_RIGHT : { -*************** -*** 1759,1765 **** - break; - } - case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : { -! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())); - break; - } - case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : { ---- 1759,1765 ---- - break; - } - case NCBIInfoXML::NCBIXML_CLIP_VECTOR_LEFT : { -! REP_thepool[idoffound].setLSClipoff(atoi(ECD->c_str())-1); - break; - } - case NCBIInfoXML::NCBIXML_CLIP_VECTOR_RIGHT : { diff --git a/sci-biology/mira/metadata.xml b/sci-biology/mira/metadata.xml index 2bc893037..a2c7c1a0a 100644 --- a/sci-biology/mira/metadata.xml +++ b/sci-biology/mira/metadata.xml @@ -2,8 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <upstream> + <remote-id type="sourceforge">mira-assembler</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mira/mira-4.0_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild deleted file mode 100644 index f9c38faeb..000000000 --- a/sci-biology/mira/mira-4.0_rc4.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -MIRA_3RDPARTY_PV="06-07-2012" -MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat) - -inherit autotools eutils multilib - -DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" -HOMEPAGE="http://www.chevreux.org/projects_mira.html" -SRC_URI=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 - mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" -# http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 -# mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" - -S="${WORKDIR}"/"${PN}"-"${MY_PV}" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos" -IUSE="doc" - -CDEPEND=" - dev-libs/boost - dev-util/google-perftools" -DEPEND="${CDEPEND} - app-editors/vim-core - dev-libs/expat" -RDEPEND="${CDEPEND}" - -#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED -# THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) -DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) - -src_prepare() { - find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die - epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch - - sed \ - -e "s:-O[23]::g" \ - -e "s:-funroll-loops::g" \ - -i configure.ac || die - - eautoreconf -} - -src_configure() { - econf \ - --with-boost="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \ - --with-boost-thread=boost_thread-mt -} - -#src_compile() { -# base_src_compile -# # TODO: resolve docbook incompatibility for building docs -# if use doc; then emake -C doc clean docs || die; fi -#} - -src_install() { - default - dodoc ${DOCS[@]} - - dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl} - dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta} -} - -pkg_postinst() { - einfo "Documentation is no longer built, you can find it at:" - einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html" -} diff --git a/sci-biology/mira/mira-4.0.2.ebuild b/sci-biology/mira/mira-4.9.5.ebuild index f9c38faeb..e643b5b79 100644 --- a/sci-biology/mira/mira-4.0.2.ebuild +++ b/sci-biology/mira/mira-4.9.5.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-4.0.2.ebuild,v 1.2 2015/01/25 17:04:35 jlec Exp $ EAPI=5 @@ -12,8 +12,9 @@ inherit autotools eutils multilib DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina" HOMEPAGE="http://www.chevreux.org/projects_mira.html" SRC_URI=" - http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 + http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2 mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" +# http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2 # http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2 # mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2" @@ -36,10 +37,12 @@ RDEPEND="${CDEPEND}" # THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf ) DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS ) +# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1 src_prepare() { find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die epatch \ - "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch + "${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \ + "${FILESDIR}"/${P}-cout.patch sed \ -e "s:-O[23]::g" \ diff --git a/sci-biology/mrbayes/ChangeLog b/sci-biology/mrbayes/ChangeLog deleted file mode 100644 index ca36e0f92..000000000 --- a/sci-biology/mrbayes/ChangeLog +++ /dev/null @@ -1,94 +0,0 @@ -# ChangeLog for sci-biology/mrbayes -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/mrbayes/ChangeLog,v 1.19 2008/06/11 18:10:48 ken69267 Exp $ - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild: - sci-biology/mrbayes: fix SLOT operators - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild, - metadata.xml: - Bump EAPI - - 25 Jun 2011; Justin Lecher <jlec@gentoo.org> mrbayes-3.1.2-r1.ebuild, - metadata.xml: - RDEPEND is not explicitly assigned -> fixed - - 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - mrbayes-3.1.2-r1.ebuild: - QA fixes - - 05 Jun 2009; Justin Bronder <jsbronder@gentoo.org> mrbayes-3.1.2-r1.ebuild: - +sci-biology/mrbayes/files/mb_readline_312.patch, - +sci-biology/mrbayes/metadata.xml: - Add an mpi.eclass version of mrbayes. - - 11 Jun 2008; Kenneth Prugh <ken69267@gentoo.org> mrbayes-3.1.2.ebuild: - amd64 stable, bug #213362 - - 17 Mar 2008; Donnie Berkholz <dberkholz@gentoo.org>; mrbayes-3.1.2.ebuild: - (#213362) Keyword ~amd64. - - 25 Mar 2007; Danny van Dyk <kugelfang@gentoo.org> mrbayes-3.1.2.ebuild: - QA: Cleaned up whitespaces. Removed redundant src_compile(). - - 06 Jan 2007; Danny van Dyk <kugelfang@gentoo.org> -mrbayes-3.1.1.ebuild: - QA: Removed unused versions. - - 03 Nov 2006; Fabian Groffen <grobian@gentoo.org> mrbayes-3.1.1.ebuild, - mrbayes-3.1.2.ebuild: - Dropped ppc-macos, see you in prefix. - - 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Stepping down from maintaining this package. - - 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> mrbayes-3.1.1.ebuild, - mrbayes-3.1.2.ebuild: - Removed amd64 keywords because of bad pointer arithmetics causing segfaults - in the sumt function on all 64 bit architectures (see bug #143094). - - 09 Jul 2006; Donnie Berkholz <dberkholz@gentoo.org>; mrbayes-3.1.2.ebuild: - x86 stable. - -*mrbayes-3.1.2 (03 Feb 2006) - - 03 Feb 2006; Olivier Fisette <ribosome@gentoo.org> - +files/mb_readline_312.patch, +mrbayes-3.1.2.ebuild: - New version. Added readline support. Thanks to Paul van der Mark for his - work on this ebuild. - - 09 Jan 2006; Homer Parker <hparker@gentoo.org> mrbayes-3.1.1.ebuild: - Marked ~amd64. - - 09 Oct 2005; Olivier Fisette <ribosome@gentoo.org> -mrbayes-3.0.ebuild: - Pruning old version. - - 08 Oct 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.1.1.ebuild: - Stable ppc-macos, Bug 108333 - - 08 Oct 2005; Paul Varner <fuzzyray@gentoo.org> mrbayes-3.1.1.ebuild: - Stable on x86. Bug# 108333 - -*mrbayes-3.1.1 (14 Aug 2005) - - 14 Aug 2005; Olivier Fisette <ribosome@gentoo.org> metadata.xml, - +mrbayes-3.1.1.ebuild: - New version. Added MPI support. - - 20 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.0.ebuild: - Stable x86 and ppc-macos - - 09 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> mrbayes-3.0.ebuild: - Restricted fetching because of the license. Verified with GNU lawyers - -*mrbayes-3.0 (02 Feb 2005) - - 02 Feb 2005; Lina Pezzella <j4rg0n@gentoo.org> +metadata.xml, +mrbayes-3.0.ebuild: - Moved from sci-biology/MrBayes to sci-biology/mrbayes. - -*MrBayes-3.0 (30 Jan 2005) - - 30 Jan 2005; Olivier Fisette <ribosome@gentoo.org> MrBayes-3.0.ebuild: - Check for "sed" exit code. - - 19 Jan 2005; Lina Pezzella <j4rg0n@gentoo.org> : - Initial commit diff --git a/sci-biology/mrbayes/Manifest b/sci-biology/mrbayes/Manifest deleted file mode 100644 index 537b716e2..000000000 --- a/sci-biology/mrbayes/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mrbayes-3.1.2.tar.gz 545968 SHA256 c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 diff --git a/sci-biology/mrbayes/files/mb_readline_312.patch b/sci-biology/mrbayes/files/mb_readline_312.patch deleted file mode 100644 index 2f8bab1e7..000000000 --- a/sci-biology/mrbayes/files/mb_readline_312.patch +++ /dev/null @@ -1,37 +0,0 @@ -Index: Makefile -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/Makefile,v -retrieving revision 3.23 -retrieving revision 3.24 -diff -U2 -r3.23 -r3.24 ---- Makefile 22 Dec 2005 16:13:06 -0000 3.23 -+++ Makefile 3 Jan 2006 16:43:13 -0000 3.24 -@@ -50,4 +50,5 @@ - ifeq ($(strip $(USEREADLINE)),yes) - CFLAGS += -DUSE_READLINE -+# CFLAGS += -DCOMPLETIONMATCHES - LIBS += -lncurses -lreadline - endif -Index: bayes.c -=================================================================== -RCS file: /cvsroot/mrbayes/mrbayes/bayes.c,v -retrieving revision 3.39 -retrieving revision 3.40 -diff -U2 -r3.39 -r3.40 ---- bayes.c 23 Dec 2005 16:26:28 -0000 3.39 -+++ bayes.c 3 Jan 2006 16:43:13 -0000 3.40 -@@ -382,9 +382,11 @@ - char **readline_completion(const char *text, int start, int stop) { - char **matches = (char **) NULL; -- -+ -+#ifdef COMPLETIONMATCHES - if(start == 0) -- matches = rl_completion_matches (text, command_generator); -+ matches = rl_completion_matches (text, command_generator); -+#endif - -- return (matches); -+ return (matches); - } - #endif diff --git a/sci-biology/mrbayes/metadata.xml b/sci-biology/mrbayes/metadata.xml deleted file mode 100644 index 9b0503f3a..000000000 --- a/sci-biology/mrbayes/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> - <longdescription> -MrBayes is a program for the Bayesian estimation of phylogeny. -Bayesian inference of phylogeny is based upon a quantity called the -posterior probability distribution of trees, which is the probability of a -tree conditioned on the observations. The conditioning is accomplished using -Bayes's theorem. The posterior probability distribution of trees is -impossible to calculate analytically; instead, MrBayes uses a simulation -technique called Markov chain Monte Carlo (or MCMC) to approximate the -posterior probabilities of trees. -</longdescription> -</pkgmetadata> diff --git a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild b/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild deleted file mode 100644 index 9ead9a633..000000000 --- a/sci-biology/mrbayes/mrbayes-3.1.2-r1.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils mpi toolchain-funcs - -DESCRIPTION="Bayesian Inference of Phylogeny" -HOMEPAGE="http://mrbayes.csit.fsu.edu/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86" -IUSE="mpi readline" - -DEPEND=" - mpi? ( $(mpi_pkg_deplist) ) - readline? ( sys-libs/readline:0 )" -RDEPEND="${DEPEND}" - -src_prepare() { - sed \ - -e "s:OPTFLAGS ?= -O3:CFLAGS = ${CFLAGS}:" \ - -e "s:CC = gcc:CC = $(tc-getCC):" \ - -e "s:CC = mpicc:CC = $(mpi_pkg_cc):" \ - -e "s:LDFLAGS =:LDFLAGS ?=:" \ - -i Makefile || die "Patching CC/CFLAGS." - if use mpi; then - sed -e "s:MPI ?= no:MPI=yes:" -i Makefile || die "Patching MPI support." - fi - if ! use readline; then - sed -e "s:USEREADLINE ?= yes:USEREADLINE=no:" \ - -i Makefile || die "Patching readline support." - else - # Only needed for OSX with an old (4.x) version of - # libreadline, but it doesn't hurt for other distributions. - epatch "${FILESDIR}"/mb_readline_312.patch - fi -} - -src_compile() { - mpi_pkg_set_env - emake -} - -src_install() { - mpi_dobin mb -} diff --git a/sci-biology/mrfast/ChangeLog b/sci-biology/mrfast/ChangeLog index f5dd75faf..d621fb810 100644 --- a/sci-biology/mrfast/ChangeLog +++ b/sci-biology/mrfast/ChangeLog @@ -1,9 +1,11 @@ # ChangeLog for sci-biology/mrfast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mrfast: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrfast-2.1.0.3.ebuild, +mrfast-2.6.0.1.ebuild, -files/mrfast-2.1.0.3-disc_buffer_overflow.patch, metadata.xml: Version Bump; punt base.eclass - diff --git a/sci-biology/mrfast/metadata.xml b/sci-biology/mrfast/metadata.xml index fc7c76942..dec6e9f34 100644 --- a/sci-biology/mrfast/metadata.xml +++ b/sci-biology/mrfast/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mrfast</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mrsfast/ChangeLog b/sci-biology/mrsfast/ChangeLog index b0aea7fdb..49579cc44 100644 --- a/sci-biology/mrsfast/ChangeLog +++ b/sci-biology/mrsfast/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-biology/mrsfast -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/mrsfast: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> -mrsfast-2.3.0.2.ebuild, +mrsfast-2.6.0.4.ebuild, metadata.xml: Version Bump; punt base.eclass - diff --git a/sci-biology/mrsfast/metadata.xml b/sci-biology/mrsfast/metadata.xml index fc7c76942..1ad193e4c 100644 --- a/sci-biology/mrsfast/metadata.xml +++ b/sci-biology/mrsfast/metadata.xml @@ -6,4 +6,7 @@ <name>Andrey Kislyuk</name> </maintainer> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">mrsfast</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ChangeLog b/sci-biology/ncbi-tools++/ChangeLog index 44abaa213..0267684f7 100644 --- a/sci-biology/ncbi-tools++/ChangeLog +++ b/sci-biology/ncbi-tools++/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 11 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/ncbi-tools++-12.0.0-bdb6.patch, ncbi-tools++-12.0.0.ebuild: + sci-biology/ncbi-tools++: added upstream patch to compile against sys- + libs/db-6.0.30 + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ncbi-tools++-12.0.0.ebuild: + sci-biology/ncbi-tools++: re-added KEYWORDS + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ncbi-tools++-12.0.0.ebuild: sci-biology/ncbi-tools++: fix SLOT operators; correct python deps diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch new file mode 100644 index 000000000..9589481d4 --- /dev/null +++ b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch @@ -0,0 +1,114 @@ +Index: include/db/bdb/bdb_file.hpp +=================================================================== +--- include/db/bdb/bdb_file.hpp (revision 470126) ++++ include/db/bdb/bdb_file.hpp (working copy) +@@ -660,6 +660,9 @@ + void x_ConstructKeyBuf(); + void x_ConstructDataBuf(); + ++ static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t* locp); ++ + private: + auto_ptr<CBDB_BufferManager> m_KeyBuf; + auto_ptr<CBDB_BufferManager> m_DataBuf; +Index: src/db/bdb/bdb_blob.cpp +=================================================================== +--- src/db/bdb/bdb_blob.cpp (revision 470126) ++++ src/db/bdb/bdb_blob.cpp (working copy) +@@ -583,12 +583,31 @@ + return m_DBT_Data->size; + } + ++#if DB_VERSION_MAJOR >= 6 ++extern "C" { ++ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, ++ size_t*); ++ int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++ { return BDB_Uint4Compare(db, dbt1, dbt2); } ++ int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t*) ++ { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); } ++} ++#endif ++ + void CBDB_LobFile::SetCmp(DB*) + { ++#if DB_VERSION_MAJOR >= 6 ++ BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6; ++ if (IsByteSwapped()) { ++ func = BDB_ByteSwap_Uint4Compare_V6; ++ } ++#else + BDB_CompareFunction func = BDB_Uint4Compare; + if (IsByteSwapped()) { + func = BDB_ByteSwap_Uint4Compare; + } ++#endif + + _ASSERT(func); + int ret = m_DB->set_bt_compare(m_DB, func); +Index: src/db/bdb/bdb_file.cpp +=================================================================== +--- src/db/bdb/bdb_file.cpp (revision 470126) ++++ src/db/bdb/bdb_file.cpp (working copy) +@@ -1535,12 +1535,27 @@ + } + + ++#if DB_VERSION_MAJOR >= 6 ++int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++{ ++ const CBDB_BufferManager* key_buf ++ = static_cast<const CBDB_BufferManager*>(db->app_private); ++ _ASSERT(key_buf); ++ return (key_buf->GetCompareFunction())(db, dbt1, dbt2); ++} ++#endif ++ ++ + void CBDB_File::SetCmp(DB* db) + { + _ASSERT(m_DB_Type == eBtree); ++#if DB_VERSION_MAJOR >= 6 ++ int ret = db->set_bt_compare(db, x_CompareShim); ++#else + BDB_CompareFunction func = m_KeyBuf->GetCompareFunction(); + _ASSERT(func); + int ret = db->set_bt_compare(db, func); ++#endif + BDB_CHECK(ret, 0); + + if (m_PrefixCompress) { +@@ -2056,12 +2071,31 @@ + BindKey("id", &IdKey); + } + ++#if DB_VERSION_MAJOR >= 6 ++extern "C" { ++ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, ++ size_t*); ++ int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) ++ { return BDB_Int4Compare(db, dbt1, dbt2); } ++ int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, ++ size_t*) ++ { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); } ++} ++#endif ++ + void CBDB_IdFile::SetCmp(DB* /* db */) + { ++#if DB_VERSION_MAJOR >= 6 ++ BDB_CompareFunction_V6 func = BDB_Int4Compare_V6; ++ if (IsByteSwapped()) { ++ func = BDB_ByteSwap_Int4Compare_V6; ++ } ++#else + BDB_CompareFunction func = BDB_Int4Compare; + if (IsByteSwapped()) { + func = BDB_ByteSwap_Int4Compare; + } ++#endif + + _ASSERT(func); + int ret = m_DB->set_bt_compare(m_DB, func); diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index b2933a43a..2948c7402 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -14,6 +14,7 @@ MY_PV="12_0_0" MY_P="ncbi_cxx--${MY_PV}" #ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz +# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" HOMEPAGE="http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=toolkit" SRC_URI=" @@ -31,7 +32,7 @@ IUSE=" glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python sablotron sqlite sqlite3 tiff xerces xalan xml xpm xslt X" #KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -KEYWORDS="" +KEYWORDS="~amd64" REQUIRED_USE="${PYTHON_REQUIRED_USE}" @@ -119,6 +120,7 @@ src_prepare() { "${FILESDIR}"/${P}-configure.patch "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch "${FILESDIR}"/${P}-fix-install.patch + "${FILESDIR}"/${P}-bdb6.patch ) # "${FILESDIR}"/${P}-as-needed.patch # "${FILESDIR}"/${P}-fix-creaders-linking.patch diff --git a/sci-biology/ngs_backbone/ChangeLog b/sci-biology/ngs_backbone/ChangeLog index 231e15327..463e8e57c 100644 --- a/sci-biology/ngs_backbone/ChangeLog +++ b/sci-biology/ngs_backbone/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/ngs_backbone -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + ngs_backbone-9999.ebuild: + added PYTHON_USEDEP + 12 Sep 2014; Christoph Junghans <ottxor@gentoo.org> ngs_backbone-9999.ebuild: drop ~x86 as deps are missing diff --git a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild index 7defc7335..b2de33478 100644 --- a/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild +++ b/sci-biology/ngs_backbone/ngs_backbone-9999.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 @@ -26,21 +26,21 @@ IUSE="" DEPEND="" RDEPEND="${DEPEND} - sci-biology/biopython - sci-biology/samtools + sci-biology/biopython[${PYTHON_USEDEP}] + sci-biology/samtools[${PYTHON_USEDEP}] sci-biology/picard sci-biology/mira sci-biology/bwa sci-biology/gatk - sci-biology/pysam + sci-biology/pysam[${PYTHON_USEDEP}] sci-biology/estscan sci-biology/ncbi-tools sci-biology/lucy sci-biology/gmap sci-biology/emboss - dev-python/matplotlib - dev-python/psubprocess - dev-python/configobj" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/psubprocess[${PYTHON_USEDEP}] + dev-python/configobj[${PYTHON_USEDEP}]" # ( blast2GO || b2g4pipe ) # sci-biology/sputnik # sci-biology/gsnap diff --git a/sci-biology/ngsview/ChangeLog b/sci-biology/ngsview/ChangeLog index 231f7fe5a..bdd09d059 100644 --- a/sci-biology/ngsview/ChangeLog +++ b/sci-biology/ngsview/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ngsview: Updating remote-id in metadata.xml + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/ngsview: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> ngsview-0.91.ebuild: sci-biology/ngsview: fix SLOT operators diff --git a/sci-biology/ngsview/metadata.xml b/sci-biology/ngsview/metadata.xml index 2bc893037..11f9c4b13 100644 --- a/sci-biology/ngsview/metadata.xml +++ b/sci-biology/ngsview/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="sourceforge">ngsview</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pairagon/ChangeLog b/sci-biology/pairagon/ChangeLog new file mode 100644 index 000000000..2f0d713f4 --- /dev/null +++ b/sci-biology/pairagon/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for sci-biology/pairagon +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild: + sci-biology/pairagon: fixed installation of perl-related files + + 19 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> pairagon-1.1.ebuild: + removing KEYWORDS until the perl files are installed to some other place. At + the moment I get: 'perl-module.eclass: Suspicious environment values found. + PERL5LIB="/usr/lib64/perl5/vendor_perl/5.18.2/pairagon"' + +*pairagon-1.1 (05 Mar 2015) + + 05 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +pairagon-1.1.ebuild: + new package diff --git a/sci-biology/pairagon/Manifest b/sci-biology/pairagon/Manifest new file mode 100644 index 000000000..3c7bc9b31 --- /dev/null +++ b/sci-biology/pairagon/Manifest @@ -0,0 +1 @@ +DIST pairagon_.tar 1198080 SHA256 c84ae663ac39e7aad10bd524115da3f89503583e8579066843b4db0aeaa6cf9c SHA512 1043c4cb66bd361cb9c0bf866706c480f2a5098b7d655117f6ee349e2256a86cc4362bda16d8f7f4d1ef0486709d82d06403d990f29402eae7b8eea28fdbc643 WHIRLPOOL 312e77494d464c29e5381ed6c6ba689564006799bbc436b86931a63d1263e1eb01667f118c8ea28030646b862256aa905db1d40926191dcdc8734755e61107a7 diff --git a/sci-biology/pairagon/metadata.xml b/sci-biology/pairagon/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/pairagon/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/pairagon/pairagon-1.1.ebuild b/sci-biology/pairagon/pairagon-1.1.ebuild new file mode 100644 index 000000000..6d78d0a1e --- /dev/null +++ b/sci-biology/pairagon/pairagon-1.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="HMM-based cDNA to genome aligner" +HOMEPAGE="http://mblab.wustl.edu/software.html" +SRC_URI="http://mblab.wustl.edu/software/download/pairagon_.tar" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="dev-lang/perl" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/pairagon + +src_prepare(){ + sed -e 's:src/get-glib-flags.sh:#src/get-glib-flags.sh:; s:-Wall -Werror::' -i Makefile +} + +src_compile(){ + emake pairagon-linux +} + +src_install(){ + # emake DESTDIR="${D}"/usr install + dobin bin/* + dodoc README + perl_set_version + insinto /usr/share/pairagon + doins parameters/* + insinto ${VENDOR_LIB} + doins lib/perl5/Alignment.pm +} diff --git a/sci-biology/pb-honey/ChangeLog b/sci-biology/pb-honey/ChangeLog index f5e93dc50..e8c26e906 100644 --- a/sci-biology/pb-honey/ChangeLog +++ b/sci-biology/pb-honey/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + pb-honey-14.1.15.ebuild: + added PYTHON_USEDEP + 10 Jan 2015; Justin Lecher <jlec@gentoo.org> pb-honey-14.1.15.ebuild: Fix license; add missing [] - diff --git a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild index 0c3bfef60..1d9176592 100644 --- a/sci-biology/pb-honey/pb-honey-14.1.15.ebuild +++ b/sci-biology/pb-honey/pb-honey-14.1.15.ebuild @@ -18,7 +18,7 @@ KEYWORDS="" IUSE="" DEPEND=" - sci-biology/samtools + sci-biology/samtools[${PYTHON_USEDEP}] sci-biology/blasr sci-biology/pysam[${PYTHON_USEDEP}] dev-python/h5py[${PYTHON_USEDEP}] diff --git a/sci-biology/perlprimer/ChangeLog b/sci-biology/perlprimer/ChangeLog index 123306dd1..f3b587a57 100644 --- a/sci-biology/perlprimer/ChangeLog +++ b/sci-biology/perlprimer/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/perlprimer -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/perlprimer: Updating remote-id in metadata.xml + 10 Nov 2014; Justin Lecher <jlec@gentoo.org> -perlprimer-1.1.17.ebuild, +perlprimer-1.1.21.ebuild, metadata.xml: Bump to EAPI=5; Version Bump @@ -14,4 +17,3 @@ cleaned up ebuild Added ~x86 as requested in bug 231230 removed redundant database - diff --git a/sci-biology/perlprimer/metadata.xml b/sci-biology/perlprimer/metadata.xml index f17a827e3..4d85fe0a5 100644 --- a/sci-biology/perlprimer/metadata.xml +++ b/sci-biology/perlprimer/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">perlprimer</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/phusion/ChangeLog b/sci-biology/phusion/ChangeLog new file mode 100644 index 000000000..b82964513 --- /dev/null +++ b/sci-biology/phusion/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/phusion +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*phusion-2.1c (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +phusion-2.1c.ebuild: + sci-biology/phusion: clarified missing LICENSE, have asked upstream for + clarification diff --git a/sci-biology/phusion/Manifest b/sci-biology/phusion/Manifest new file mode 100644 index 000000000..ded1cc97c --- /dev/null +++ b/sci-biology/phusion/Manifest @@ -0,0 +1 @@ +DIST phusion_pipeline_v2.1c.tar.gz 12029104 SHA256 d6cd98d9194faf91c3b497c569529f0b0af8b2fa7bf083d24a5c946fd2804457 SHA512 b5ed5b2b893fa3d4cdbb6ae96acf515894b1df65ba2536f3a47829f383eca1e157f1b7b117e0d1bf0f763328e8bc2ffddac9a570dbec757c057040c3fb66a765 WHIRLPOOL 76d21eb6ab558395ac7b18043b4e4e31d1b2a6f02779f09fcbc2e2591a304738af5ab9abe042d3a982f73fd04cf32c1125d8798f3e04ab6fb67fcaa7c2b6e642 diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/phusion/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild new file mode 100644 index 000000000..14fde04dc --- /dev/null +++ b/sci-biology/phusion/phusion-2.1c.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/phusion/phusion_pipeline_v2.1c.tar.gz" + +LICENSE="all-rights-reserved" # temporarily placed value +# from http://genome.cshlp.org/content/13/1/81.full +# Availability +# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors. +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="app-shells/tcsh" +RDEPEND="${DEPEND} + sci-biology/phrap + dev-lang/perl" + +# contains bundled ssaha +# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq + +S="${WORKDIR}"/"phusion_pipeline_v2.1c" + +src_prepare(){ + cp -pf /usr/bin/phrap src/phrap/phrap.manylong || die +} + +src_compile(){ + tcsh install.csh || csh install.csh || die +} + +src_install(){ + dobin bin/* + dodoc README.1st releaseNote_v2.1c doc/* +} diff --git a/sci-biology/plinkseq/ChangeLog b/sci-biology/plinkseq/ChangeLog new file mode 100644 index 000000000..10c843e63 --- /dev/null +++ b/sci-biology/plinkseq/ChangeLog @@ -0,0 +1,13 @@ +# ChangeLog for sci-biology/plinkseq +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + plinkseq-0.10.ebuild: + reported a file collision to upstream + +*plinkseq-0.10 (10 May 2015) + + 10 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +plinkseq-0.10.ebuild: + sci-biology/plinkseq: new package diff --git a/sci-biology/plinkseq/Manifest b/sci-biology/plinkseq/Manifest new file mode 100644 index 000000000..36abf40f7 --- /dev/null +++ b/sci-biology/plinkseq/Manifest @@ -0,0 +1 @@ +DIST plinkseq-0.10.tgz 6090698 SHA256 e9d4705acf8b22eddba0c48cf502e3bd4236f3b60b010f39f94deecf37e94b58 SHA512 b8fa0a0b42a5f67612b1549d1f2fbed67333abb57ef024d4be683cd326e53a8ef08c6c0acae8ed3195fad619c8aea9005e315f937d76cd990a7ffff1d808af41 WHIRLPOOL 4e2df6ea70da185c57fe9fd87c536d54c90e932a5ea8956c8294ea643de2cddaae24f69b4eeaef1f9c8931c8e5e43a14ebf56897e223b963c4c8a2ffbeda83bd diff --git a/sci-biology/plinkseq/metadata.xml b/sci-biology/plinkseq/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/plinkseq/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/plinkseq/plinkseq-0.10.ebuild b/sci-biology/plinkseq/plinkseq-0.10.ebuild new file mode 100644 index 000000000..22f917b10 --- /dev/null +++ b/sci-biology/plinkseq/plinkseq-0.10.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs + +DESCRIPTION="C/C++ library for working with human genetic variation data" +HOMEPAGE="http://atgu.mgh.harvard.edu/plinkseq" +SRC_URI="http://psychgen.u.hpc.mssm.edu/plinkseq_downloads/plinkseq-src-latest.tgz -> ${P}.tgz" +# https://bitbucket.org/statgen/plinkseq.git +# http://pngu.mgh.harvard.edu/~purcell/plink/download.shtml + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="sys-libs/zlib" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e "s/gcc/$(tc-getCC)/g;s/g++/$(tc-getCXX)/g;s/-O3/${CFLAGS}/g" -i config_defs.Makefile || die + sed -e "s/= -static/=/g" -i config_defs.Makefile || die +} + +src_install(){ + cd build/execs || die + # TODO: avoid file collision with sci-biology/fsl + # https://bitbucket.org/statgen/plinkseq/issue/9/rename-mm-filename-to-plinkseq_mm + dobin gcol browser pseq behead mm smp tab2vcf mongoose pdas +} diff --git a/sci-biology/polyphen/ChangeLog b/sci-biology/polyphen/ChangeLog new file mode 100644 index 000000000..da1810a1c --- /dev/null +++ b/sci-biology/polyphen/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/polyphen +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*polyphen-2.2.2 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +polyphen-2.2.2.ebuild: + sci-biology/polyphen: package skeleton diff --git a/sci-biology/polyphen/Manifest b/sci-biology/polyphen/Manifest new file mode 100644 index 000000000..60d0df7bb --- /dev/null +++ b/sci-biology/polyphen/Manifest @@ -0,0 +1 @@ +DIST polyphen-2.2.2r405b.tar.gz 2189910 SHA256 25415a0dcc1149968d116fe5ffc8663c939bc4533a9fb660431a12a7ca4b4859 SHA512 0dfcce2bc1670416520149cc5d8544fd59a1586ac41bf96eb90d0425fdc60b19503acef196793b72cfaa9a7165d2d97c4868a7383eb7d7f17ec4b63cb92447d9 WHIRLPOOL be6b649536bb993eff5674ac09c2e2ad8ef3ea0d6e7d1eb72dd084167e103e8697530a0ee47cda7098bf97989937e55ef87de86da027d894f0c571f25e62ff50 diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/polyphen/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild new file mode 100644 index 000000000..3f602cfb7 --- /dev/null +++ b/sci-biology/polyphen/polyphen-2.2.2.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Predict effect of aminoacid substitution on human protein function" +HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start" +SRC_URI="http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-2.2.2r405b.tar.gz" + +LICENSE="polyphen" # for non-commercial use only +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +# 3.7GB +# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2 + +# 2.4GB +# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2 + +# 895MB +# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2 + diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog new file mode 100644 index 000000000..a5e4045b3 --- /dev/null +++ b/sci-biology/prokka/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/prokka +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: + sci-biology/prokka: require either of ncbi-tools++ or ncbi-blast+ + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild: + sci-biology/prokka: more DEPs recorded + +*prokka-1.11 (05 May 2015) + + 05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +prokka-1.11.ebuild: + sci-biology/prokka: new package diff --git a/sci-biology/prokka/Manifest b/sci-biology/prokka/Manifest new file mode 100644 index 000000000..0ce314c87 --- /dev/null +++ b/sci-biology/prokka/Manifest @@ -0,0 +1 @@ +DIST prokka-1.11.tar.gz 359226217 SHA256 ee18146c768fe6ac8e6c9e28bb35f686a5b79d5d5362c4b7665f6a33978101ae SHA512 7b35d340ca07685886ff9ef97f0d40a28f05bc378a407a0349b06c8be9df005c4030b205a93985ec691fac4b6442a607f8723f3ca8f2066704f15b8667476034 WHIRLPOOL 075807739662e9a8c450f1706923ba2bd230b50dd342524e4d54de29e08ad526934c16271715451f2cc1766a5e79efdf614a902c8cc9830bc24ef287dafaa839 diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/prokka/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild new file mode 100644 index 000000000..9e0e86c7e --- /dev/null +++ b/sci-biology/prokka/prokka-1.11.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Prokaryotic whole genome annotation pipeline" +HOMEPAGE="http://www.bioinformatics.net.au/software.prokka.shtml" +SRC_URI="http://www.vicbioinformatics.com/prokka-"${PV}".tar.gz" +# 360MB + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sys-process/parallel + sci-biology/bioperl + sci-biology/prodigal + sci-biology/ncbi-tools++ || ( sci-biology/ncbi-blast+ ) + sci-biology/hmmer + sci-biology/infernal + sci-biology/exonerate + sci-biology/barrnap" +# sci-biology/minced +# >=sci-biolohy/hmmer-3.1 +# Aragorn +# >=RNAmmer-1.2 +# >=HMMmmer-2.0 (that is not sci-biology/hmmer) +# SignalP >= 3.0 +# sequin +# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz diff --git a/sci-biology/psychopy/ChangeLog b/sci-biology/psychopy/ChangeLog index 49cc4a4a9..a180e47c8 100644 --- a/sci-biology/psychopy/ChangeLog +++ b/sci-biology/psychopy/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Apr 2015; Justin Lecher <jlec@gentoo.org> psychopy-1.78.00.ebuild: + sci-biology/psychopy: Drop eselect dependency + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> -psychopy-1.75.01.ebuild, -psychopy-1.77.02.ebuild, psychopy-1.78.00.ebuild, psychopy-9999.ebuild: sci-biology/psychopy: fix SLOT operators diff --git a/sci-biology/psychopy/psychopy-1.78.00.ebuild b/sci-biology/psychopy/psychopy-1.78.00.ebuild index 864a1d312..8de257bb1 100644 --- a/sci-biology/psychopy/psychopy-1.78.00.ebuild +++ b/sci-biology/psychopy/psychopy-1.78.00.ebuild @@ -32,7 +32,7 @@ RDEPEND=" dev-python/pygame[${PYTHON_USEDEP}] " -DEPEND="app-admin/eselect +DEPEND=" app-arch/unzip dev-python/setuptools[${PYTHON_USEDEP}] test? ( ${RDEPEND} ) diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog new file mode 100644 index 000000000..2fb878ae1 --- /dev/null +++ b/sci-biology/pybedtools/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/pybedtools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/pybedtools: Add github to remote-id in metadata.xml + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild: + sci-biology/pybedtools: Streamline ebuild + +*pybedtools-0.6.9 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, + +pybedtools-0.6.9.ebuild: + sci-biology/pybedtools: add pybedtools diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest new file mode 100644 index 000000000..fe26335b1 --- /dev/null +++ b/sci-biology/pybedtools/Manifest @@ -0,0 +1 @@ +DIST pybedtools-0.6.9.tar.gz 18738115 SHA256 2639e80917999e76572017fd93757e8d7ceb384f0b92647ccfdd23a0d60def7c SHA512 64d54145899db947499b706310941980c75b515cb8d88f67708153b625d782e62021826b9615dd4fe225f4435d9c9d4aa8583538109308625f703883599aeb79 WHIRLPOOL e3dcc61f3c395068929c69f8419891aa792e3725b7709527cb471677d15f81c91ba3f56a385063324f475600aef7d54992a1ca1911e4210f7005b344dd63ce84 diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml new file mode 100644 index 000000000..3352804f1 --- /dev/null +++ b/sci-biology/pybedtools/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">daler/pybedtools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild new file mode 100644 index 000000000..1ab30c9cd --- /dev/null +++ b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working" +HOMEPAGE="http://pythonhosted.org/pybedtools/" +SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND="sci-biology/bedtools" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}]" diff --git a/sci-biology/pybrain/pybrain-9999.ebuild b/sci-biology/pybrain/pybrain-9999.ebuild index 677a65e98..cda7882a9 100644 --- a/sci-biology/pybrain/pybrain-9999.ebuild +++ b/sci-biology/pybrain/pybrain-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/sci-biology/pyfaidx/ChangeLog b/sci-biology/pyfaidx/ChangeLog new file mode 100644 index 000000000..98ad3f4c2 --- /dev/null +++ b/sci-biology/pyfaidx/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-biology/pyfaidx +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> pyfaidx-0.3.8.ebuild: + sci-biology/pyfaidx: Streamline ebuild + +*pyfaidx-0.3.8 (12 Apr 2015) + + 12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml, + +pyfaidx-0.3.8.ebuild: + sci-biology/pyfaidx: add pyfaidx diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest new file mode 100644 index 000000000..e7b0e57bd --- /dev/null +++ b/sci-biology/pyfaidx/Manifest @@ -0,0 +1 @@ +DIST pyfaidx-0.3.8.tar.gz 18156 SHA256 1927a332d2aa06fc50f343ecdc5abf6c3ce77937b258411b59ab7ad6c2a12c16 SHA512 78b82f150f4371bfc98fb50936358dd2b728ce85011bdb8d06ebde5994572983153ffbbfc7ae56dae2a0e15d480ce6f85d5abc93235feafa3c0ee1bff4437614 WHIRLPOOL b0ecb39263cf1f521cf002499eea5e266a66de4684288d2eb7364c896e20d429d66e5f03e7ba2e482f719336708cd3cd82dd6093719b6af4e302fbdf7d856709 diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml new file mode 100644 index 000000000..44913ccb4 --- /dev/null +++ b/sci-biology/pyfaidx/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="pypi">pyfaidx</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/pyfaidx/pyfaidx-0.3.8.ebuild b/sci-biology/pyfaidx/pyfaidx-0.3.8.ebuild new file mode 100644 index 000000000..5a1e84686 --- /dev/null +++ b/sci-biology/pyfaidx/pyfaidx-0.3.8.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Efficient pythonic random access to fasta subsequences" +HOMEPAGE="https://pypi.python.org/pypi/pyfaidx" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" diff --git a/sci-biology/pysam/ChangeLog b/sci-biology/pysam/ChangeLog new file mode 100644 index 000000000..e48ec44da --- /dev/null +++ b/sci-biology/pysam/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/pysam +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 04 May 2015; Marius Brehler <marbre@linux.sungazer.de> pysam-0.7.5.ebuild: + Fix deps + + 04 May 2015; Marius Brehler <marbre@linux.sungazer.de> pysam-0.6-r2.ebuild: + Drop keywords due to broken deps + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + pysam-0.6-r2.ebuild, pysam-0.7.5.ebuild: + added PYTHON_USEDEP + +*pysam-0.6-r2 (30 Apr 2015) +*pysam-0.7.5 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +pysam-0.6-r2.ebuild, +pysam-0.7.5.ebuild: + sci-biology/pysam: version bump; noted samtools dependencies as mentioned in + download page accessible from https://code.google.com/p/pysam/downloads/list ; + also added PYTHON_COMPAT for python3 diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest new file mode 100644 index 000000000..48d0aab5f --- /dev/null +++ b/sci-biology/pysam/Manifest @@ -0,0 +1,2 @@ +DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2 +DIST pysam-0.7.5.tar.gz 1466667 SHA256 fa85900ead3d1c2c9ce24f28d2b1843c0a8ffb761cd21d440049e29eca2e2453 SHA512 ce609c65eef1188186c28cb8ea1bad73608d738c47089a5ef3a22a14e7bba5acd8f8b6a3fd67935cf1dc9fb57927205ad0f009dc0122b12c1866955ada01198c WHIRLPOOL c9a4488fb8f6fbd2aa74081f5b286befbab980e8544036956e83d82b3f4f9238c6f0138f094b090b30e18b3eb25c36ce4f6cadf65d6e80195091de6d7995f19d diff --git a/sci-biology/embassy-emnu/metadata.xml b/sci-biology/pysam/metadata.xml index f17a827e3..49afc3c3d 100644 --- a/sci-biology/embassy-emnu/metadata.xml +++ b/sci-biology/pysam/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="google-code">pysam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pysam/pysam-0.6-r2.ebuild b/sci-biology/pysam/pysam-0.6-r2.ebuild new file mode 100644 index 000000000..ee8603949 --- /dev/null +++ b/sci-biology/pysam/pysam-0.6-r2.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/pysam/pysam-0.6-r1.ebuild,v 1.2 2015/04/13 06:22:56 jlec Exp $ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam" +SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + <=sci-biology/samtools-0.1.18[${PYTHON_USEDEP}]" + +python_compile() { + python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" + distutils-r1_python_compile +} diff --git a/sci-biology/pysam/pysam-0.7.5.ebuild b/sci-biology/pysam/pysam-0.7.5.ebuild new file mode 100644 index 000000000..c5163822b --- /dev/null +++ b/sci-biology/pysam/pysam-0.7.5.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/pysam/pysam-0.6-r1.ebuild,v 1.2 2015/04/13 06:22:56 jlec Exp $ + +EAPI="5" + +PYTHON_COMPAT=( python2_7 ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE="http://code.google.com/p/pysam http://pypi.python.org/pypi/pysam" +SRC_URI="http://${PN}.googlecode.com/files/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="dev-python/setuptools[${PYTHON_USEDEP}] + <=sci-biology/samtools-0.1.19-r2[${PYTHON_USEDEP}]" + +python_compile() { + python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" + distutils-r1_python_compile +} diff --git a/sci-biology/quorum/ChangeLog b/sci-biology/quorum/ChangeLog new file mode 100644 index 000000000..e7b52a907 --- /dev/null +++ b/sci-biology/quorum/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/quorum +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quorum-0.2.1.ebuild, + quorum-1.0.0.ebuild: + sci-biology/quorum: avoid full path on linker commandline + /usr/lib64/libjellyfish-2.0.so + +*quorum-0.2.1 (30 Apr 2015) +*quorum-1.0.0 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +quorum-0.2.1.ebuild, +quorum-1.0.0.ebuild: + sci-biology/quorum: new package diff --git a/sci-biology/quorum/Manifest b/sci-biology/quorum/Manifest new file mode 100644 index 000000000..be7384485 --- /dev/null +++ b/sci-biology/quorum/Manifest @@ -0,0 +1,2 @@ +DIST quorum-0.2.1.tar.gz 369756 SHA256 d9287fd2f23894c779f8cd087ba09aea9a6b550e9937533131dcd7fde108b543 SHA512 137d867dc0b8b8d6d1fdc8de1de955f512b3da5d78f6d489b6c3bb8130e4b2a702830afe271e3d98894dfa8dead1a2b87bab348e3d513468a85bef40dd0fe07e WHIRLPOOL 99bd79ab20a508be1cfd0b1bd83f357329304c79dbf7785abc45c4790cc8fed36e38c94b7a4b643d29e3a76bcc06b8c049c31e70066dc00ab7a34ac3ee642df2 +DIST quorum-1.0.0.tar.gz 618414 SHA256 ec11af84ab3887b1cb0a526d9ab295e8cde6fe2cbba3060147da9fa2f12a518d SHA512 6a7ab569ef97a89a325dbda0c4c4ba2ccba0305cf53d7aaf7b823ca79aa56547372a5d23e65ce1aa6a520a3f5b8550908a9d1d1ece79ad259599c43364158937 WHIRLPOOL c95e8b4f060d2ef9fa5632baf4cb9d02fa904036ba418e45c74715e04db27decb46876d2a62a70baa0fe3b700eecec1fc39f21c69b456e3c7320b7be06a6c59b diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/quorum/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild b/sci-biology/quorum/quorum-0.2.1.ebuild new file mode 100644 index 000000000..d2a540ac9 --- /dev/null +++ b/sci-biology/quorum/quorum-0.2.1.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Illumina reads error corrector" +HOMEPAGE="http://www.genome.umd.edu/quorum.html" +SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="=sci-biology/jellyfish-1.1.11" +RDEPEND="${DEPEND}" + +src_configure(){ + econf --enable-relative-paths --with-relative-jf-path +} diff --git a/sci-biology/quorum/quorum-1.0.0.ebuild b/sci-biology/quorum/quorum-1.0.0.ebuild new file mode 100644 index 000000000..6870eedac --- /dev/null +++ b/sci-biology/quorum/quorum-1.0.0.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Illumina reads error corrector" +HOMEPAGE="http://www.genome.umd.edu/quorum.html" +SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="=sci-biology/jellyfish-2.1.4" +RDEPEND="${DEPEND}" + +src_configure(){ + econf --enable-relative-paths --with-relative-jf-path +} diff --git a/sci-biology/reptile/ChangeLog b/sci-biology/reptile/ChangeLog new file mode 100644 index 000000000..bf348f8ef --- /dev/null +++ b/sci-biology/reptile/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/reptile +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*reptile-1.1 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +reptile-1.1.ebuild: + sci-biology/reptile: new package diff --git a/sci-biology/reptile/Manifest b/sci-biology/reptile/Manifest new file mode 100644 index 000000000..4e1ed40f6 --- /dev/null +++ b/sci-biology/reptile/Manifest @@ -0,0 +1 @@ +DIST reptile-v1.1.zip 79227 SHA256 400e30238599bc64320e1fd5c0b37a517a55e242458afc334bbf2f7dea5eb781 SHA512 ca397671d16e718926f61f8671920cff06f0ec458c63987361dc4c1b8b0742ee94759b22786ab3c8176238078a0d571d5b33edf805b176d8967a331a505c6d0e WHIRLPOOL 4b3342b9f1c3391c47c8ad761406d9cf81122df8231778243d81e2f377cce58c25d6cfee108e11ab69459cd51aff1121fa02dfce99419d14225f1d30a2ded062 diff --git a/sci-biology/reptile/metadata.xml b/sci-biology/reptile/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/reptile/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/reptile/reptile-1.1.ebuild b/sci-biology/reptile/reptile-1.1.ebuild new file mode 100644 index 000000000..fd6ec7741 --- /dev/null +++ b/sci-biology/reptile/reptile-1.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Illumina read corrector" +HOMEPAGE="http://aluru-sun.ece.iastate.edu/doku.php?id=reptile" +SRC_URI="http://aluru-sun.ece.iastate.edu/lib/exe/fetch.php?media=source:reptile-v${PV}.zip -> "${PN}"-v"${PV}".zip" + +LICENSE="LGPL-3 GPL-3 Boost-1.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + dev-lang/perl" + +S="${WORKDIR}"/"${PN}"-v"${PV}" + +src_prepare(){ + sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i src/makefile || die + sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/reptile_merger/makefile || die + sed -e 's#-Wall -O3#$(CXXFLAGS)#' -i utils/seq-analy/makefile || die +} + +src_compile(){ + cd src || die + emake all + cd ../utils/reptile_merger || die + emake all + cd ../seq-analy || die + emake all +} + +src_install(){ + newbin src/reptile-v1.1 reptile + dobin utils/reptile_merger/reptile_merger + dobin utils/fastq-converter-v2.0.pl +} diff --git a/sci-biology/ruffus/ruffus-9999.ebuild b/sci-biology/ruffus/ruffus-9999.ebuild index b75b96135..e5a3b10ce 100644 --- a/sci-biology/ruffus/ruffus-9999.ebuild +++ b/sci-biology/ruffus/ruffus-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/sci-biology/rum/ChangeLog b/sci-biology/rum/ChangeLog new file mode 100644 index 000000000..62ff2bf3c --- /dev/null +++ b/sci-biology/rum/ChangeLog @@ -0,0 +1,15 @@ +# ChangeLog for sci-biology/rum +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> rum-2.0.5.5.ebuild: + sci-biology/rum: Use perl virtuals, add missing die; use PN for tarball + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/rum: Add github to remote-id in metadata.xml + +*rum-2.0.5.5 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +rum-2.0.5.5.ebuild: + sci-biology/rum: new package diff --git a/sci-biology/rum/Manifest b/sci-biology/rum/Manifest new file mode 100644 index 000000000..7ef715410 --- /dev/null +++ b/sci-biology/rum/Manifest @@ -0,0 +1 @@ +DIST rum-2.0.5.5.tar.gz 5420665 SHA256 077fdee93f70d3d7cec05ddac22f07b22759f22c1fb63f927769beed2cd0670c SHA512 7a6600e7d98fa4649a281b161eaaaa2fbfd337b7b26b0d054e23974aa555a383d476b5464183b259812330c4e00a36be44a5efe210950e2ad24ab867375cb9be WHIRLPOOL ebcd634341016a46c098bc4708f93b51fa46f79dd367162711a965d3167f734f640d55f8415062e513f776149f645de7933b7f681614f3b38c1a3ec1a35d2585 diff --git a/sci-biology/rum/metadata.xml b/sci-biology/rum/metadata.xml new file mode 100644 index 000000000..e6b052fa8 --- /dev/null +++ b/sci-biology/rum/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">itmat/rum/wiki</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/rum/rum-2.0.5.5.ebuild b/sci-biology/rum/rum-2.0.5.5.ebuild new file mode 100644 index 000000000..3411f20f4 --- /dev/null +++ b/sci-biology/rum/rum-2.0.5.5.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit perl-module eutils + +DESCRIPTION="RNA-Seq Unified Mapper (digital normalization)" +HOMEPAGE="https://github.com/itmat/rum/wiki" +SRC_URI="https://github.com/itmat/rum/archive/v2.0.5_05.tar.gz -> ${P}.tar.gz" + +# stable +#EGIT_REPO_URI="https://github.com/PGFI/rum/tags" + +# dev +#EGIT_REPO_URI="https://github.com/PGFI/rum" + +LICENSE="UPennState" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-perl/Log-Log4perl + virtual/perl-autodie" +RDEPEND="${DEPEND} + sci-biology/seqclean + sci-biology/blat + sci-biology/bowtie + sci-biology/seqclean" + +S="${WORKDIR}/${PN}-2.0.5_05" + +src_install(){ + default + rm "${ED}"/usr/lib64/perl5/vendor_perl/*/RUM/{bowtie,blat,mdust} ]] die +} diff --git a/sci-biology/sabre/ChangeLog b/sci-biology/sabre/ChangeLog index fb47d2375..a43393aaa 100644 --- a/sci-biology/sabre/ChangeLog +++ b/sci-biology/sabre/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sabre: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sabre-9999.ebuild: Switch from git-2 to git-r3; Cleanup diff --git a/sci-biology/sabre/metadata.xml b/sci-biology/sabre/metadata.xml index 2bc893037..dfc808149 100644 --- a/sci-biology/sabre/metadata.xml +++ b/sci-biology/sabre/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">najoshi/sabre</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/salmon/ChangeLog b/sci-biology/salmon/ChangeLog new file mode 100644 index 000000000..5b870c43c --- /dev/null +++ b/sci-biology/salmon/ChangeLog @@ -0,0 +1,22 @@ +# ChangeLog for sci-biology/salmon +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/salmon: Add github to remote-id in metadata.xml + + 23 May 2015; Michael Schubert <mschu.dev@gmail.com> + files/salmon-0.3.2-no-boost-static.patch: + sci-biology/salmon: clean patch + + 21 May 2015; Michael Schubert <mschu.dev@gmail.com> salmon-0.3.2.ebuild, + salmon-9999.ebuild: + sci-biology/salmon: streamline ebuild + +*salmon-0.3.2 (21 May 2015) +*salmon-9999 (21 May 2015) + + 21 May 2015; Michael Schubert <mschu.dev@gmail.com> + +files/salmon-0.3.2-no-boost-static.patch, +metadata.xml, + +salmon-0.3.2.ebuild, +salmon-9999.ebuild: + sci-biology/salmon: add salmon diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest new file mode 100644 index 000000000..cef7a9cd2 --- /dev/null +++ b/sci-biology/salmon/Manifest @@ -0,0 +1 @@ +DIST salmon-0.3.2.tar.gz 1674131 SHA256 e0c957f0bc612e1fd7d7c4383758396042b68ea08aeae024cadb5d63e6dd9cf2 SHA512 d9db133d8fb009a4b23251bce209a869644eb6139e0e4b9133f947999e0be4c30039f5cb8617dc4b73977cd690837abb407549a619ef82e6bb82577ff082becf WHIRLPOOL e2f8f636547c93fbf3fade454754352537bc5a9fce668b0989ca58f5f5b9ca8f2454077af5dfc948f0acf9c6c2a6bdd6995d481dc08fd0f3db938639435afc0f diff --git a/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch new file mode 100644 index 000000000..edc09e711 --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.3.2-no-boost-static.patch @@ -0,0 +1,20 @@ +Do not force static and multithreaded boost libs, use what is available + +Patch by Michael Schubert + +--- CMakeLists.txt ++++ CMakeLists.txt +@@ -162,13 +162,6 @@ if ( DEFINED CUSTOM_BOOST_PATH ) + set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) + endif ( DEFINED CUSTOM_BOOST_PATH ) + +-## +-# We want static, multithreaded boost libraries +-## +-set (Boost_USE_STATIC_LIBS ON) +-set (Boost_USE_MULTITHREADED ON) +-#set (Boost_USE_STATIC_RUNTIME OFF) +- + find_package (ZLIB) + if (NOT ZLIB_FOUND) + message (FATAL_ERROR "zlib must be installed before configuration & building can proceed") diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml new file mode 100644 index 000000000..c72510b68 --- /dev/null +++ b/sci-biology/salmon/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">COMBINE-lab/salmon</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/salmon/salmon-0.3.2.ebuild b/sci-biology/salmon/salmon-0.3.2.ebuild new file mode 100644 index 000000000..0a6409e49 --- /dev/null +++ b/sci-biology/salmon/salmon-0.3.2.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" +HOMEPAGE="https://github.com/COMBINE-lab/salmon" +SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch ) diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild new file mode 100644 index 000000000..5e80cc22b --- /dev/null +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit git-r3 cmake-utils + +DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" +HOMEPAGE="https://github.com/COMBINE-lab/salmon" +SRC_URI="" +EGIT_REPO_URI="https://github.com/COMBINE-lab/salmon.git" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +PATCHES=( "${FILESDIR}"/${PN}-0.3.2-no-boost-static.patch ) diff --git a/sci-biology/samtools/ChangeLog b/sci-biology/samtools/ChangeLog new file mode 100644 index 000000000..f5eaa814a --- /dev/null +++ b/sci-biology/samtools/ChangeLog @@ -0,0 +1,20 @@ +# ChangeLog for sci-biology/samtools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/samtools: Updating remote-id in metadata.xml + +*samtools-1.0-r2 (11 May 2015) +*samtools-1.1-r1 (11 May 2015) +*samtools-1.2-r1 (11 May 2015) + + 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/samtools-1.0-buildsystem.patch, +files/samtools-1.0-rmdup.patch, + +files/samtools-1.1-buildsystem.patch, +files/samtools-1.1-rmdup.patch, + +files/samtools-1.2-buildsystem.patch, +files/samtools-1.2-rmdup.patch, + +metadata.xml, +samtools-1.0-r2.ebuild, +samtools-1.1-r1.ebuild, + +samtools-1.2-r1.ebuild: + sci-biology/samtools: fix core dump on 'samtools rmdup' by adding + bam_get_library() from an upstream patch from + https://github.com/samtools/samtools/issues/138 diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest new file mode 100644 index 000000000..867b5820b --- /dev/null +++ b/sci-biology/samtools/Manifest @@ -0,0 +1,3 @@ +DIST samtools-1.0.tar.bz2 4459669 SHA256 7340b843663c3f54a902a06f2f73c68198f3a62d29a2ed20671139957f7fd7c0 SHA512 5b80995c522d08b06a4c559f60a5e200d9085be7f44c3c9618db91e3de85e36c1473e42715eae8175520d7da3df8245bafa82e625d2fc08e0197adb395851693 WHIRLPOOL 2aa0f8639da9b0b828ca7296969e5c600b0e5452ad3231b914e4a7be418700906a4d695c928eaf837b643255567ec82cfadf0b53007e0f1e3a956856f6c4c832 +DIST samtools-1.1.tar.bz2 4495373 SHA256 c24d26c303153d72b5bf3cc11f72c6c375a4ca1140cc485648c8c5473414b7f8 SHA512 a5552a6c8c4b0808b725b39ddb2fafa36c4f6623bfc7f84faadae7690223e4eec8d722af09c77145796ad9b3f01e04115dd0207207ccfafbb52ffc22d5fc09f0 WHIRLPOOL ed3131b2a8d8b4dab40b53d35a9b00b657670a949dc1597c91fbcd00392c1c1715a85a1d1e49bf0c73ae082738ccfb13d2c6809dbbeba17ff3028f6023ebc449 +DIST samtools-1.2.tar.bz2 4547126 SHA256 420e7a4a107fe37619b9d300b6379452eb8eb04a4a9b65c3ec69de82ccc26daa SHA512 4849c3274e732267516b63799f5430c5415d575d46eddf6b704dac51053281094b03b90dd9f5367bcd14c22fb0fb1bd6a412f7d4225f7be5f5385437c5d2101d WHIRLPOOL 273185764a807365a20c381769f987ef02d14ae8e20a3a7fd5af4344769c5fab68d7155523e8c0c8c3cc86092898c2c8454cce8f1560d415bc2b41549cdf04f4 diff --git a/sci-biology/samtools/files/samtools-1.0-buildsystem.patch b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch new file mode 100644 index 000000000..53a8b66f9 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.0-buildsystem.patch @@ -0,0 +1,59 @@ + Makefile | 26 ++++++++++++++++++-------- + 1 file changed, 18 insertions(+), 8 deletions(-) + +diff --git a/Makefile b/Makefile +index ae59abf..0d2788c 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++bindir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,14 +117,22 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) $(HTSLIB) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h diff --git a/sci-biology/samtools/files/samtools-1.0-rmdup.patch b/sci-biology/samtools/files/samtools-1.0-rmdup.patch new file mode 100644 index 000000000..023b5d73d --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.0-rmdup.patch @@ -0,0 +1,47 @@ +From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 +From: kirkmcclure <kirkmcclure@users.noreply.github.com> +Date: Mon, 23 Mar 2015 05:35:00 -0800 +Subject: [PATCH] Update bam.c + + For issue #138 - Samtools view -l no longer works. +Implement bam_get_library() +--- + bam.c | 23 ++++++++++++----------- + 1 file changed, 12 insertions(+), 11 deletions(-) + +diff --git a/bam.c b/bam.c +index f909b7e..864d3f0 100644 +--- a/bam.c ++++ b/bam.c +@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) + return 1; + } + +-// FIXME: we should also check the LB tag associated with each alignment + const char *bam_get_library(bam_header_t *h, const bam1_t *b) + { +-#if 0 +- const uint8_t *rg; +- if (h->dict == 0) h->dict = sam_header_parse2(h->text); +- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); +- rg = bam_aux_get(b, "RG"); +- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); +-#else +- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); +- abort(); +-#endif ++ const uint8_t *rg = 0; ++ const uint8_t *pLibName, *pDict; ++ if ( b != 0 && h != 0 ) { ++ if ( (rg = bam_aux_get(b, "RG") ) != 0 ++ && (pDict = sam_header_parse2(h->text)) != 0 ) { ++ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); ++ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { ++ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); ++ } ++ } ++ } ++ return 0; + } + + int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) diff --git a/sci-biology/samtools/files/samtools-1.1-buildsystem.patch b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch new file mode 100644 index 000000000..b9ae77de6 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.1-buildsystem.patch @@ -0,0 +1,153 @@ + Makefile | 76 ++++++++++++++++++++++++++++++++++++---------------------------- + 1 file changed, 43 insertions(+), 33 deletions(-) + +diff --git a/Makefile b/Makefile +index 43cefc3..743dd07 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,63 +117,71 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h + bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) + bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) ++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) + sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sample_h = sample.h $(HTSDIR)/htslib/kstring.h ++sample_h = sample.h + + bam.o: bam.c $(bam_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h ++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h + bam2bcf_indel.o: bam2bcf_indel.c bam2bcf.h + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h + bam_aux.o: bam_aux.c + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h ++bam_import.o: bam_import.c $(bam_h) ++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) ++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) + bam_mate.o: bam_mate.c $(bam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kaln.h kprobaln.h + bam_pileup.o: bam_pileup.c $(sam_h) + bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) ++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) +-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h +-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h +-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) ++bam_rmdup.o: bam_rmdup.c $(sam_h) ++bam_rmdupse.o: bam_rmdupse.c $(sam_h) ++bam_sort.o: bam_sort.c $(htslib_sam_h) + bam_stat.o: bam_stat.c $(bam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(bam_h) version.h samtools.h +-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h +-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) +-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h ++errmod.o: errmod.c errmod.h + kaln.o: kaln.c kaln.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h ++phase.o: phase.c $(htslib_sam_h) errmod.h + sam.o: sam.c $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h +-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h +-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h +-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) ++sam_header.o: sam_header.c sam_header.h ++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h ++sample.o: sample.c $(sample_h) ++stats_isize.o: stats_isize.c stats_isize.h ++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) + + + # test programs +@@ -179,8 +189,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_pretty_header + test/merge/test_rtrans_build +@@ -253,10 +263,10 @@ misc/md5sum-lite: misc/md5sum-lite.o + misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz + +-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h ++misc/ace2sam.o: misc/ace2sam.c + misc/md5.o: misc/md5.c misc/md5.h +-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h +-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h ++misc/md5fa.o: misc/md5fa.c misc/md5.h ++misc/wgsim.o: misc/wgsim.c + + misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/files/samtools-1.1-rmdup.patch b/sci-biology/samtools/files/samtools-1.1-rmdup.patch new file mode 100644 index 000000000..023b5d73d --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.1-rmdup.patch @@ -0,0 +1,47 @@ +From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 +From: kirkmcclure <kirkmcclure@users.noreply.github.com> +Date: Mon, 23 Mar 2015 05:35:00 -0800 +Subject: [PATCH] Update bam.c + + For issue #138 - Samtools view -l no longer works. +Implement bam_get_library() +--- + bam.c | 23 ++++++++++++----------- + 1 file changed, 12 insertions(+), 11 deletions(-) + +diff --git a/bam.c b/bam.c +index f909b7e..864d3f0 100644 +--- a/bam.c ++++ b/bam.c +@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) + return 1; + } + +-// FIXME: we should also check the LB tag associated with each alignment + const char *bam_get_library(bam_header_t *h, const bam1_t *b) + { +-#if 0 +- const uint8_t *rg; +- if (h->dict == 0) h->dict = sam_header_parse2(h->text); +- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); +- rg = bam_aux_get(b, "RG"); +- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); +-#else +- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); +- abort(); +-#endif ++ const uint8_t *rg = 0; ++ const uint8_t *pLibName, *pDict; ++ if ( b != 0 && h != 0 ) { ++ if ( (rg = bam_aux_get(b, "RG") ) != 0 ++ && (pDict = sam_header_parse2(h->text)) != 0 ) { ++ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); ++ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { ++ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); ++ } ++ } ++ } ++ return 0; + } + + int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) diff --git a/sci-biology/samtools/files/samtools-1.2-buildsystem.patch b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch new file mode 100644 index 000000000..2343b2245 --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.2-buildsystem.patch @@ -0,0 +1,193 @@ + Makefile | 94 +++++++++++++++++++++++++++++++++++----------------------------- + 1 file changed, 52 insertions(+), 42 deletions(-) + +diff --git a/Makefile b/Makefile +index e368cee..9054526 100644 +--- a/Makefile ++++ b/Makefile +@@ -21,11 +21,12 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-CPPFLAGS = $(DFLAGS) $(INCLUDES) +-CFLAGS = -g -Wall -O2 +-LDFLAGS = +-LDLIBS = ++CC ?= gcc ++CPPFLAGS += $(DFLAGS) $(INCLUDES) ++CFLAGS ?= -g -Wall -O2 ++LDFLAGS += ++LDLIBS += ++BAMLIB ?= libbam.a + DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o +@@ -42,6 +43,7 @@ LIBCURSES= -lcurses # -lXCurses + prefix = /usr/local + exec_prefix = $(prefix) + bindir = $(exec_prefix)/bin ++libdir = $(exec_prefix)/lib + mandir = $(prefix)/share/man + man1dir = $(mandir)/man1 + +@@ -115,62 +117,70 @@ version.h: + .c.o: + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ $< + ++$(LOBJS): ++ $(CC) $(CFLAGS) $(CPPFLAGS) -fPIC -c -o $@ $< + +-lib:libbam.a ++ ++lib:libbam.a libbam.so.1.0 + + libbam.a:$(LOBJS) + $(AR) -csru $@ $(LOBJS) + +-samtools: $(AOBJS) libbam.a $(HTSLIB) +- $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz ++libbam.so.1.0:$(LOBJS) ++ $(CC) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB) -lz ++ ln -sf $@ libbam.so.0 ++ ln -sf $@ libbam.so ++ ++samtools: $(AOBJS) lib ++ $(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) $(BAMLIB) $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz + + bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h) + bam2bcf_h = bam2bcf.h $(htslib_vcf_h) errmod.h + bam_lpileup_h = bam_lpileup.h $(htslib_sam_h) + bam_plbuf_h = bam_plbuf.h $(htslib_sam_h) +-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(HTSDIR)/htslib/khash.h $(bam_lpileup_h) ++bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(bam_lpileup_h) + sam_h = sam.h $(htslib_sam_h) $(bam_h) +-sample_h = sample.h $(HTSDIR)/htslib/kstring.h ++sample_h = sample.h + + bam.o: bam.c $(bam_h) sam_header.h +-bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kfunc.h $(bam2bcf_h) errmod.h ++bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(bam2bcf_h) errmod.h + bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h + bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h + bam_aux.o: bam_aux.c + bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(bam_h) + bam_color.o: bam_color.c $(bam_h) +-bam_import.o: bam_import.c $(HTSDIR)/htslib/kstring.h $(bam_h) $(HTSDIR)/htslib/kseq.h +-bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(HTSDIR)/htslib/khash.h +-bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(HTSDIR)/htslib/ksort.h ++bam_import.o: bam_import.c $(bam_h) ++bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) ++bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) + bam_mate.o: bam_mate.c $(bam_h) + bam_md.o: bam_md.c $(htslib_faidx_h) $(sam_h) kprobaln.h + bam_pileup.o: bam_pileup.c $(sam_h) + bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h) +-bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash_str2int.h sam_header.h samtools.h $(bam2bcf_h) $(sample_h) ++bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) sam_header.h samtools.h $(bam2bcf_h) $(sample_h) + bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(bam_h) +-bam_rmdup.o: bam_rmdup.c $(sam_h) $(HTSDIR)/htslib/khash.h +-bam_rmdupse.o: bam_rmdupse.c $(sam_h) $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h +-bam_sort.o: bam_sort.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/klist.h $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) ++bam_rmdup.o: bam_rmdup.c $(sam_h) ++bam_rmdupse.o: bam_rmdupse.c $(sam_h) ++bam_sort.o: bam_sort.c $(htslib_sam_h) + bam_stat.o: bam_stat.c $(bam_h) samtools.h + bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) + bam_tview_curses.o: bam_tview_curses.c $(bam_tview_h) + bam_tview_html.o: bam_tview_html.c $(bam_tview_h) + bam_flags.o: bam_flags.c $(sam_h) +-bamshuf.o: bamshuf.c $(htslib_sam_h) $(HTSDIR)/htslib/ksort.h samtools.h ++bamshuf.o: bamshuf.c $(htslib_sam_h) samtools.h + bamtk.o: bamtk.c $(htslib_hts_h) version.h samtools.h +-bedcov.o: bedcov.c $(HTSDIR)/htslib/kstring.h $(htslib_sam_h) $(HTSDIR)/htslib/kseq.h +-bedidx.o: bedidx.c $(HTSDIR)/htslib/ksort.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h ++bedcov.o: bedcov.c $(htslib_sam_h) ++bedidx.o: bedidx.c + cut_target.o: cut_target.c $(bam_h) errmod.h $(htslib_faidx_h) +-errmod.o: errmod.c errmod.h $(HTSDIR)/htslib/ksort.h ++errmod.o: errmod.c errmod.h + kprobaln.o: kprobaln.c kprobaln.h + padding.o: padding.c sam_header.h $(sam_h) $(bam_h) $(htslib_faidx_h) +-phase.o: phase.c $(htslib_sam_h) errmod.h $(HTSDIR)/htslib/kseq.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/ksort.h ++phase.o: phase.c $(htslib_sam_h) errmod.h + sam.o: sam.c $(htslib_faidx_h) $(sam_h) +-sam_header.o: sam_header.c sam_header.h $(HTSDIR)/htslib/khash.h +-sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/khash.h samtools.h +-sample.o: sample.c $(sample_h) $(HTSDIR)/htslib/khash.h +-stats_isize.o: stats_isize.c stats_isize.h $(HTSDIR)/htslib/khash.h +-stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib/khash.h $(HTSDIR)/htslib/khash_str2int.h $(htslib_faidx_h) ++sam_header.o: sam_header.c sam_header.h ++sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) samtools.h ++sample.o: sample.c $(sample_h) ++stats_isize.o: stats_isize.c stats_isize.h ++stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(htslib_faidx_h) + + + # test programs +@@ -178,8 +188,8 @@ stats.o: stats.c $(sam_h) sam_header.h samtools.h stats_isize.h $(HTSDIR)/htslib + # For tests that might use it, set $REF_PATH explicitly to use only reference + # areas within the test suite (or set it to ':' to use no reference areas). + # (regression.sh sets $REF_PATH to a subdirectory itself.) +-check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) +- REF_PATH=: test/test.pl --exec bgzip=$(BGZIP) ++check test: samtools $(BUILT_TEST_PROGRAMS) ++ REF_PATH=: test/test.pl --exec bgzip=bgzip + test/merge/test_bam_translate test/merge/test_bam_translate.tmp + test/merge/test_pretty_header + test/merge/test_rtrans_build +@@ -191,31 +201,31 @@ check test: samtools $(BGZIP) $(BUILT_TEST_PROGRAMS) + test/split/test_parse_args + + +-test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o $(HTSLIB) ++test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_pretty_header: test/merge/test_pretty_header.o $(HTSLIB) ++test/merge/test_pretty_header: test/merge/test_pretty_header.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_pretty_header.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_rtrans_build: test/merge/test_rtrans_build.o $(HTSLIB) ++test/merge/test_rtrans_build: test/merge/test_rtrans_build.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o $(HTSLIB) $(LDLIBS) -lz + +-test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o $(HTSLIB) ++test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o + $(CC) -pthread $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_count_rg: test/split/test_count_rg.o test/test.o $(HTSLIB) ++test/split/test_count_rg: test/split/test_count_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o $(HTSLIB) ++test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o $(HTSLIB) ++test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/split/test_parse_args: test/split/test_parse_args.o test/test.o $(HTSLIB) ++test/split/test_parse_args: test/split/test_parse_args.o test/test.o + $(CC) -pthread $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o $(HTSLIB) $(LDLIBS) -lz + +-test/vcf-miniview: test/vcf-miniview.o $(HTSLIB) ++test/vcf-miniview: test/vcf-miniview.o + $(CC) -pthread $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB) $(LDLIBS) -lz + + test_test_h = test/test.h $(htslib_sam_h) +@@ -252,10 +262,10 @@ misc/md5sum-lite: misc/md5sum-lite.o + misc/wgsim: misc/wgsim.o + $(CC) $(LDFLAGS) -o $@ misc/wgsim.o $(LDLIBS) -lm -lz + +-misc/ace2sam.o: misc/ace2sam.c $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h ++misc/ace2sam.o: misc/ace2sam.c + misc/md5.o: misc/md5.c misc/md5.h +-misc/md5fa.o: misc/md5fa.c misc/md5.h $(HTSDIR)/htslib/kseq.h +-misc/wgsim.o: misc/wgsim.c $(HTSDIR)/htslib/kseq.h ++misc/md5fa.o: misc/md5fa.c misc/md5.h ++misc/wgsim.o: misc/wgsim.c + + misc/maq2sam-short.o: misc/maq2sam.c + $(CC) $(CFLAGS) $(CPPFLAGS) -c -o $@ misc/maq2sam.c diff --git a/sci-biology/samtools/files/samtools-1.2-rmdup.patch b/sci-biology/samtools/files/samtools-1.2-rmdup.patch new file mode 100644 index 000000000..023b5d73d --- /dev/null +++ b/sci-biology/samtools/files/samtools-1.2-rmdup.patch @@ -0,0 +1,47 @@ +From 05fb5c2e17576b1d0ea5a0b8203b9eba236f2455 Mon Sep 17 00:00:00 2001 +From: kirkmcclure <kirkmcclure@users.noreply.github.com> +Date: Mon, 23 Mar 2015 05:35:00 -0800 +Subject: [PATCH] Update bam.c + + For issue #138 - Samtools view -l no longer works. +Implement bam_get_library() +--- + bam.c | 23 ++++++++++++----------- + 1 file changed, 12 insertions(+), 11 deletions(-) + +diff --git a/bam.c b/bam.c +index f909b7e..864d3f0 100644 +--- a/bam.c ++++ b/bam.c +@@ -61,19 +61,20 @@ int bam_validate1(const bam_header_t *header, const bam1_t *b) + return 1; + } + +-// FIXME: we should also check the LB tag associated with each alignment + const char *bam_get_library(bam_header_t *h, const bam1_t *b) + { +-#if 0 +- const uint8_t *rg; +- if (h->dict == 0) h->dict = sam_header_parse2(h->text); +- if (h->rg2lib == 0) h->rg2lib = sam_header2tbl(h->dict, "RG", "ID", "LB"); +- rg = bam_aux_get(b, "RG"); +- return (rg == 0)? 0 : sam_tbl_get(h->rg2lib, (const char*)(rg + 1)); +-#else +- fprintf(stderr, "Samtools-htslib-API: bam_get_library() not yet implemented\n"); +- abort(); +-#endif ++ const uint8_t *rg = 0; ++ const uint8_t *pLibName, *pDict; ++ if ( b != 0 && h != 0 ) { ++ if ( (rg = bam_aux_get(b, "RG") ) != 0 ++ && (pDict = sam_header_parse2(h->text)) != 0 ) { ++ pLibName = sam_header2tbl(pDict, "RG", "ID", "LB"); ++ if ( pLibName && strlen( (char*)pLibName ) > 0 ) { ++ return sam_tbl_get((void*)pLibName, (const char*)(rg + 1)); ++ } ++ } ++ } ++ return 0; + } + + int bam_fetch(bamFile fp, const bam_index_t *idx, int tid, int beg, int end, void *data, bam_fetch_f func) diff --git a/sci-biology/embassy-domsearch/metadata.xml b/sci-biology/samtools/metadata.xml index f17a827e3..74dc02bc9 100644 --- a/sci-biology/embassy-domsearch/metadata.xml +++ b/sci-biology/samtools/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="sourceforge">samtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/samtools/samtools-1.0-r2.ebuild b/sci-biology/samtools/samtools-1.0-r2.ebuild new file mode 100644 index 000000000..de23c2220 --- /dev/null +++ b/sci-biology/samtools/samtools-1.0-r2.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.0-r1.ebuild,v 1.1 2014/09/25 15:20:53 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + sci-libs/htslib" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-1.0 -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + epatch "${FILESDIR}"/${P}-rmdup.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.1-r1.ebuild b/sci-biology/samtools/samtools-1.1-r1.ebuild new file mode 100644 index 000000000..04211ba9e --- /dev/null +++ b/sci-biology/samtools/samtools-1.1-r1.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.1.ebuild,v 1.1 2015/01/06 12:57:48 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + ~sci-libs/htslib-${PV}" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-* -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + epatch "${FILESDIR}"/${P}-rmdup.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/samtools/samtools-1.2-r1.ebuild b/sci-biology/samtools/samtools-1.2-r1.ebuild new file mode 100644 index 000000000..fdf5806a7 --- /dev/null +++ b/sci-biology/samtools/samtools-1.2-r1.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/samtools/samtools-1.2.ebuild,v 1.2 2015/02/28 10:51:24 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils multilib python-r1 toolchain-funcs + +DESCRIPTION="Utilities for SAM (Sequence Alignment/Map), a format for large nucleotide sequence alignments" +HOMEPAGE="http://www.htslib.org/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="examples" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +CDEPEND=" + sys-libs/ncurses + >=sci-libs/htslib-${PV}" + +RDEPEND="${CDEPEND} + dev-lang/lua + dev-lang/perl" +DEPEND="${CDEPEND} + virtual/pkgconfig" + +src_prepare() { + find htslib-* -delete || die + + sed -i 's~/software/bin/python~/usr/bin/env python~' "${S}"/misc/varfilter.py || die + + epatch "${FILESDIR}"/${P}-buildsystem.patch + epatch "${FILESDIR}"/${P}-rmdup.patch + + tc-export CC AR + + sed \ + -e '/htslib.mk/d' \ + -i Makefile || die + +} + +src_compile() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + emake "${mymakeargs[@]}" +} + +src_test() { + local mymakeargs=( + LIBCURSES="$($(tc-getPKG_CONFIG) --libs ncurses)" + HTSDIR="${EPREFIX}/usr/include" + HTSLIB=$($(tc-getPKG_CONFIG) --libs htslib) + BAMLIB="libbam.so" + ) + LD_LIBRARY_PATH="${S}" emake "${mymakeargs[@]}" test +} + +src_install() { + dobin samtools $(find misc -type f -executable) + + python_replicate_script "${ED}"/usr/bin/varfilter.py + dolib.so libbam.so* + + insinto /usr/include/bam + doins *.h + + doman ${PN}.1 + dodoc AUTHORS NEWS README + + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi +} diff --git a/sci-biology/scaffold_builder/ChangeLog b/sci-biology/scaffold_builder/ChangeLog index 5663f61d2..0db66bf40 100644 --- a/sci-biology/scaffold_builder/ChangeLog +++ b/sci-biology/scaffold_builder/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + scaffold_builder-20131122.ebuild: + sci-biology/scaffold_builder: set proper LICENSE to the one mentioned in the + http://www.scfbm.org/content/pdf/1751-0473-8-23.pdf article and also in the + COPYING.txt file in the distribution .zip file + + 26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + scaffold_builder-20131122.ebuild: + sci-biology/scaffold_builder: noted RDEPEND, added second HOMEPAGE + *scaffold_builder-20131122 (30 Jan 2015) 30 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild index dc14a4d91..40110cc89 100644 --- a/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild +++ b/sci-biology/scaffold_builder/scaffold_builder-20131122.ebuild @@ -7,19 +7,21 @@ EAPI=5 S="${WORKDIR}" DESCRIPTION="Combine FASTA contigs from a de novo assembly into scaffolds using a reference assembly" -HOMEPAGE="http://sourceforge.net/projects/scaffold-b/" +HOMEPAGE="http://sourceforge.net/projects/scaffold-b + http://edwards.sdsu.edu/scaffold_builder" SRC_URI="http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2.1.zip http://sourceforge.net/projects/scaffold-b/files/scaffold_builder_v2_help.doc http://downloads.sourceforge.net/project/scaffold-b/Manual_v2.1.pdf" #http://www.scfbm.org/content/8/1/23 -LICENSE="CC-BY-2.0" +LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" IUSE="" DEPEND="" RDEPEND="${DEPEND} + sci-biology/mummer dev-lang/python" src_install(){ diff --git a/sci-biology/screed/ChangeLog b/sci-biology/screed/ChangeLog index 28c056131..66b9d3432 100644 --- a/sci-biology/screed/ChangeLog +++ b/sci-biology/screed/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/screed -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/screed: Add github to remote-id in metadata.xml + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> screed-0.7.1.ebuild: removed empty line diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml index f17a827e3..a773552b0 100644 --- a/sci-biology/screed/metadata.xml +++ b/sci-biology/screed/metadata.xml @@ -2,4 +2,8 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <upstream> + <remote-id type="pypi">screed</remote-id> + <remote-id type="github">ged-lab/screed</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/scythe/ChangeLog b/sci-biology/scythe/ChangeLog index 679d1b148..d577319ad 100644 --- a/sci-biology/scythe/ChangeLog +++ b/sci-biology/scythe/ChangeLog @@ -1,10 +1,12 @@ # ChangeLog for sci-biology/scythe -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/scythe: Add github to remote-id in metadata.xml + *scythe-0.992 (24 Mar 2014) 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +scythe-0.992.ebuild, +metadata.xml: bundled Makefile forces -O3, wrong version number, but works - diff --git a/sci-biology/scythe/metadata.xml b/sci-biology/scythe/metadata.xml index 2bc893037..540814e51 100644 --- a/sci-biology/scythe/metadata.xml +++ b/sci-biology/scythe/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">vsbuffalo/scythe</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/seqclean/ChangeLog b/sci-biology/seqclean/ChangeLog index b03c585ea..f7c664a62 100644 --- a/sci-biology/seqclean/ChangeLog +++ b/sci-biology/seqclean/ChangeLog @@ -1,10 +1,17 @@ # ChangeLog for sci-biology/seqclean -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + seqclean-110625.ebuild: + sci-biology/seqclean: bump EAPI + + 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + seqclean-110625.ebuild: + sci-biology/seqclean: fix language + *seqclean-110625 (25 Jun 2011) 25 Jun 2011; Justin Lecher <jlec@gentoo.org> -seqclean-0.1.ebuild, +seqclean-110625.ebuild, +files/seqclean-110625-build.patch: Cleaned ebuild - diff --git a/sci-biology/seqclean/seqclean-110625.ebuild b/sci-biology/seqclean/seqclean-110625.ebuild index 1078c0c1f..1de8c7256 100644 --- a/sci-biology/seqclean/seqclean-110625.ebuild +++ b/sci-biology/seqclean/seqclean-110625.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit eutils toolchain-funcs @@ -48,7 +48,7 @@ src_install() { dobin ${i}/${i} done - einfo "Optionally, you might want to download UniVec from NCBI if you do not have your own" + einfo "Optionally, you may want to download UniVec from NCBI if you do not have your own" einfo "fasta file with vector sequences you want to remove from sequencing" einfo "reads. See http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html" } diff --git a/sci-biology/seqtools/ChangeLog b/sci-biology/seqtools/ChangeLog new file mode 100644 index 000000000..27ab135ea --- /dev/null +++ b/sci-biology/seqtools/ChangeLog @@ -0,0 +1,17 @@ +# ChangeLog for sci-biology/seqtools +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*seqtools-4.34.5 (12 May 2015) + + 12 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +seqtools-4.34.5.ebuild, -seqtools-4.34.1.ebuild: + sci-biology/seqtools: upstream fixed dependency issues so that MAKEOPTS=-j5 + works; version bump + +*seqtools-4.34.1 (09 May 2015) + + 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +seqtools-4.34.1.ebuild: + sci-biology/seqtools: new package, said to be derived from AceDB (watch for + file collisions?) diff --git a/sci-biology/seqtools/Manifest b/sci-biology/seqtools/Manifest new file mode 100644 index 000000000..5d579cde9 --- /dev/null +++ b/sci-biology/seqtools/Manifest @@ -0,0 +1 @@ +DIST seqtools-4.34.5.tar.gz 5591057 SHA256 7677c61852db459137d541857314110f1a4450fb0f41d6d865d110e26d41e4d2 SHA512 9f4a521434e10fd1715f0b3ab228b955bf701fb355780a03a6912826a1bf3ad84ad0ead29a5d9abeb073a5ed045df92ec7b3e754570062c7baf9f4f7c82f0ce9 WHIRLPOOL 99e0c8e6412ab35bc7ba3f8eabee070945f10271f20abbb260ddeaf7bbf1b41d9d54e47fe6828553fcfd6b0eb8a01236994ff3c587a9d4854304f25a1d21e0c1 diff --git a/sci-biology/seqtools/metadata.xml b/sci-biology/seqtools/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/seqtools/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/seqtools/seqtools-4.34.5.ebuild b/sci-biology/seqtools/seqtools-4.34.5.ebuild new file mode 100644 index 000000000..4e1c12d72 --- /dev/null +++ b/sci-biology/seqtools/seqtools-4.34.5.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Display alignments and GFF files, matrix dot plots (blixem, dotter, belvu)" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/seqtools" +SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/${PN}/PRODUCTION/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND=" + sys-libs/readline:* + net-misc/curl:* + dev-db/sqlite:* + dev-libs/glib:2 + x11-libs/gtk+:2" +RDEPEND="${DEPEND}" diff --git a/sci-biology/sga/ChangeLog b/sci-biology/sga/ChangeLog index 1408f942d..af6716396 100644 --- a/sci-biology/sga/ChangeLog +++ b/sci-biology/sga/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sga: Add github to remote-id in metadata.xml + 09 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> sga-9999.ebuild: Switch from git-2 to git-r3; Cleanup; Add missing die @@ -10,4 +13,3 @@ 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sga-9999.ebuild, +metadata.xml: new package; forces its own optimization flags but works fine - diff --git a/sci-biology/sga/metadata.xml b/sci-biology/sga/metadata.xml index 4e873d87d..5ac32df20 100644 --- a/sci-biology/sga/metadata.xml +++ b/sci-biology/sga/metadata.xml @@ -6,7 +6,10 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> -<use> - <flag name='jemalloc'>Use <pkg>dev-libs/jemalloc</pkg></flag> -</use> + <use> + <flag name="jemalloc">Use <pkg>dev-libs/jemalloc</pkg></flag> + </use> + <upstream> + <remote-id type="github">jts/sga</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sgp2/ChangeLog b/sci-biology/sgp2/ChangeLog index 4175f8384..3f1498953 100644 --- a/sci-biology/sgp2/ChangeLog +++ b/sci-biology/sgp2/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/sgp2 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sgp2-1.1.ebuild: + sci-biology/sgp2: add dobin() call + *sgp2-1.1 (17 Jun 2014) 17 Jun 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/sgp2/sgp2-1.1.ebuild b/sci-biology/sgp2/sgp2-1.1.ebuild index cd6becfeb..b398dc522 100644 --- a/sci-biology/sgp2/sgp2-1.1.ebuild +++ b/sci-biology/sgp2/sgp2-1.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -29,6 +29,7 @@ src_prepare() { } src_install() { + dobin bin/sgp2 bin/parseblast insinto /usr/share/"${PN}" doins -r param samples } diff --git a/sci-biology/sickle/ChangeLog b/sci-biology/sickle/ChangeLog index 443ff95fa..060cfa220 100644 --- a/sci-biology/sickle/ChangeLog +++ b/sci-biology/sickle/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/sickle: Add github to remote-id in metadata.xml + +*sickle-1.33 (09 Mar 2015) + + 09 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +sickle-1.33.ebuild, + sickle-9999.ebuild: + respect CC and CFLAGS; added an ebuild for latest release tarball, works + 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> sickle-9999.ebuild: correct package description diff --git a/sci-biology/sickle/Manifest b/sci-biology/sickle/Manifest new file mode 100644 index 000000000..570d99efb --- /dev/null +++ b/sci-biology/sickle/Manifest @@ -0,0 +1 @@ +DIST v1.33.tar.gz 631275 SHA256 eab271d25dc799e2ce67c25626128f8f8ed65e3cd68e799479bba20964624734 SHA512 94d9794861655c9d8688a4c71757ba93166f167ae529c5661998d287b93c6ccc9755d9e3db8d481bbd5dca4cf047f6266880a5fc1f8099e597bc857954404dcb WHIRLPOOL f54f911ddb58596c88aa2963a235a6c77f4b84d2c86f594329763c582763ffd7ccc86b28bf3d0126b9d8cd693c1a6cf1be05aa82d9521e5977b6ef0d01547a25 diff --git a/sci-biology/sickle/metadata.xml b/sci-biology/sickle/metadata.xml index 2bc893037..74adcee63 100644 --- a/sci-biology/sickle/metadata.xml +++ b/sci-biology/sickle/metadata.xml @@ -6,4 +6,7 @@ <email>mmokrejs@fold.natur.cuni.cz</email> <name>Martin Mokrejs</name> </maintainer> + <upstream> + <remote-id type="github">najoshi/sickle</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sickle/sickle-1.33.ebuild b/sci-biology/sickle/sickle-1.33.ebuild new file mode 100644 index 000000000..2288aeaeb --- /dev/null +++ b/sci-biology/sickle/sickle-1.33.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils eutils toolchain-funcs + +[ "$PV" == "9999" ] && inherit git-r3 + +DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa" +HOMEPAGE="https://github.com/najoshi/sickle" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/najoshi/sickle" + KEYWORDS="" +else + SRC_URI="https://github.com/najoshi/sickle/archive/v"${PV}".tar.gz" + KEYWORDS="~amd64" +fi + +LICENSE="MIT" +SLOT="0" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sys-libs/zlib" + +src_prepare(){ + sed -e "s#-pedantic#-pedantic ${CFLAGS}#;s#gcc#"$(tc-getCC)"#" -i Makefile || die +} + +src_install(){ + dobin sickle + dodoc README.md +} diff --git a/sci-biology/sickle/sickle-9999.ebuild b/sci-biology/sickle/sickle-9999.ebuild index 022474e57..2288aeaeb 100644 --- a/sci-biology/sickle/sickle-9999.ebuild +++ b/sci-biology/sickle/sickle-9999.ebuild @@ -4,21 +4,32 @@ EAPI=5 -inherit eutils git-r3 +inherit eutils eutils toolchain-funcs + +[ "$PV" == "9999" ] && inherit git-r3 DESCRIPTION="Windowed adaptive quality-based trimming tool for FASTQ data from Illumina/Solexa" HOMEPAGE="https://github.com/najoshi/sickle" -EGIT_REPO_URI="https://github.com/najoshi/sickle" +if [ "$PV" == "9999" ]; then + EGIT_REPO_URI="https://github.com/najoshi/sickle" + KEYWORDS="" +else + SRC_URI="https://github.com/najoshi/sickle/archive/v"${PV}".tar.gz" + KEYWORDS="~amd64" +fi LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64" IUSE="" DEPEND="" RDEPEND="${DEPEND} sys-libs/zlib" +src_prepare(){ + sed -e "s#-pedantic#-pedantic ${CFLAGS}#;s#gcc#"$(tc-getCC)"#" -i Makefile || die +} + src_install(){ dobin sickle dodoc README.md diff --git a/sci-biology/signalp/ChangeLog b/sci-biology/signalp/ChangeLog index 7321c88eb..f5136c095 100644 --- a/sci-biology/signalp/ChangeLog +++ b/sci-biology/signalp/ChangeLog @@ -1,11 +1,13 @@ # ChangeLog for sci-biology/signalp -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> signalp-3.0.ebuild: + Bump to EAPI=5 + 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> signalp-3.0.ebuild: QA fixes 01 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package sci-biology/signalp, ebuild written by me - diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild index d91a964ef..f463c6716 100644 --- a/sci-biology/signalp/signalp-3.0.ebuild +++ b/sci-biology/signalp/signalp-3.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences" HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/" @@ -32,7 +32,7 @@ src_prepare() { } src_install() { - dobin signalp || die + dobin signalp insinto /opt/${P} doins -r bin hmm how mod syn* test exeinto /opt/${P}/bin diff --git a/sci-biology/skewer-bin/ChangeLog b/sci-biology/skewer-bin/ChangeLog index a00543cda..a94eb4ddc 100644 --- a/sci-biology/skewer-bin/ChangeLog +++ b/sci-biology/skewer-bin/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/skewer-bin -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + skewer-bin-0.1.104.ebuild: + sci-biology/skewer: fix typo + *skewer-bin-0.1.104 (23 Mar 2014) 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, diff --git a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild index 23afc2e54..615ec1195 100644 --- a/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild +++ b/sci-biology/skewer-bin/skewer-bin-0.1.104.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -21,5 +21,5 @@ RDEPEND="${DEPEND} src_install() { cp "${DISTDIR}"/skewer-* skewer || die dobin *.pl || die - dobin skewer || die "Failed to install clview binary" + dobin skewer || die "Failed to install skewer binary" } diff --git a/sci-biology/snap/ChangeLog b/sci-biology/snap/ChangeLog new file mode 100644 index 000000000..68ed8bc29 --- /dev/null +++ b/sci-biology/snap/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-biology/snap +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*snap-20131129 (30 Mar 2015) + + 30 Mar 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +snap-20131129.ebuild: + sci-biology/snap: new package diff --git a/sci-biology/snap/Manifest b/sci-biology/snap/Manifest new file mode 100644 index 000000000..3d7ad61cf --- /dev/null +++ b/sci-biology/snap/Manifest @@ -0,0 +1 @@ +DIST snap-2013-11-29.tar.gz 703047 SHA256 e2a236392d718376356fa743aa49a987aeacd660c6979cee67121e23aeffc66a SHA512 162c39701d72fe6bb6e9941178593c9c0aeffb6fb197f7a456cdaea63d0beb4b2f03919f3659151250d571eeafffd4aee275224bb8cbf22ee1a48a92f4866d7a WHIRLPOOL 5207fbd779a1f53ae5b08a02811868067a4abd0052e8adea732c59af79e04bcda90270ee83e62883664c3e242dfc63561a83e9f4f8f3c12e53ecc265038f4b91 diff --git a/sci-biology/snap/metadata.xml b/sci-biology/snap/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/snap/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snap/snap-20131129.ebuild b/sci-biology/snap/snap-20131129.ebuild new file mode 100644 index 000000000..6592102b9 --- /dev/null +++ b/sci-biology/snap/snap-20131129.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs + +DESCRIPTION="HMM-based prokaryotic and eukaryotic gene prediction tool" +HOMEPAGE="http://korflab.ucdavis.edu/software.html" +SRC_URI="http://korflab.ucdavis.edu/Software/snap-2013-11-29.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +S="${WORKDIR}"/snap + +src_prepare(){ + sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Zoe/Makefile || die + sed -e "s#CC=\"gcc.*#CC=$(tc-getCC)#" -i Makefile || die +} + +src_install(){ + echo "ZOE=/usr/share/snap/HMM" > 99snap || die + doenvd 99snap + insinto /usr/share/snap/HMM + doins HMM/[a-zA-Z]*.hmm + dobin snap fathom forge *.pl + dodoc 00README +} diff --git a/sci-biology/snphylo/ChangeLog b/sci-biology/snphylo/ChangeLog new file mode 100644 index 000000000..a04d6e32d --- /dev/null +++ b/sci-biology/snphylo/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/snphylo +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*snphylo-20140701 (11 May 2015) + + 11 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +snphylo-20140701.ebuild: + sci-biology/snphylo: new package, needs some R packages and we have to avoid + the interactive setup.sh step diff --git a/sci-biology/snphylo/Manifest b/sci-biology/snphylo/Manifest new file mode 100644 index 000000000..4c31433c0 --- /dev/null +++ b/sci-biology/snphylo/Manifest @@ -0,0 +1 @@ +DIST snphylo-20140701.tar.gz 19522 SHA256 adea6dde1a4f1edbbe053cf97618528d2fa8409847fc5865327861cc601619aa SHA512 575c97caf01126dea194007494c783de69653b468964c8f0a004a93c8b33deefd9d79a0e02841814bcceda69bed29fd3343ca492c7f71b46c55139acf4f0a3c6 WHIRLPOOL 6a1667a8cec6e92135135321275e6929e286b1dfe18f661a6ca85cdf75d9f200de194aa7fa94b7dc1e974e7ca29c9e0a2e11cca3af8e158ca6a6b659c8b0b8f3 diff --git a/sci-biology/snphylo/metadata.xml b/sci-biology/snphylo/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-biology/snphylo/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snphylo/snphylo-20140701.ebuild b/sci-biology/snphylo/snphylo-20140701.ebuild new file mode 100644 index 000000000..9734989d3 --- /dev/null +++ b/sci-biology/snphylo/snphylo-20140701.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Pipeline to generate phylogenetic tree from SNP data" +HOMEPAGE="http://chibba.pgml.uga.edu/snphylo" +SRC_URI="http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz -> ${P}.tar.gz" +# http://github.com/thlee/SNPhylo +# http://www.biomedcentral.com/1471-2164/15/162 + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/fastdnaml + sci-biology/muscle + sci-biology/phylip" +# http://chibba.pgml.uga.edu/snphylo/install_on_linux.html +# R packages (phangorn, gdsfmt, SNPRelate and getopt) +# $ apt-get -y install r-base-dev r-cran-getopt r-cran-rgl + +S="${WORKDIR}"/"${PN}" + +src_compile(){ + bash setup.sh || die +} + +src_install(){ + dobin snphylo.sh +} diff --git a/sci-biology/spm/ChangeLog b/sci-biology/spm/ChangeLog new file mode 100644 index 000000000..3ee22afe8 --- /dev/null +++ b/sci-biology/spm/ChangeLog @@ -0,0 +1,29 @@ +# ChangeLog for sci-biology/spm +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 11 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: + installing into octave M subdirectory + + 10 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: + installing ALL the things + + 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: + typo + + 04 Mar 2015; Horea Christian <h.chr@mail.ru> spm-12.ebuild: + fixed doins path + +*spm-12 (04 Mar 2015) + + 04 Mar 2015; Horea Christian <h.chr@mail.ru> +spm-12.ebuild, + spm-8.ebuild: + removed slots, added new version + + 17 Feb 2015; Horea Christian <h.chr@mail.ru> -spm-8.ebuild.orig, + spm-8.ebuild: + added quotation marks, removed ori file + + 17 Feb 2015; Horea Christian <h.chr@mail.ru> +metadata.xml, + +spm-8.ebuild.orig, spm-8.ebuild: + added metadata diff --git a/sci-biology/spm/Manifest b/sci-biology/spm/Manifest new file mode 100644 index 000000000..828ddc825 --- /dev/null +++ b/sci-biology/spm/Manifest @@ -0,0 +1,2 @@ +DIST spm12.zip 93842449 SHA256 ca0679a2d416e4212c66dc0c9ca9729601c75a9baf22cc68bfa72e7cca999eb4 SHA512 d09267360c3d67ae0b462f47c9b4445c4970524c60cf80e96afc035087e2212050ab7422957525aeb67f6853dd9ba3b9ee5cfe2e26afcec2e1ea7bc2f5828e4b WHIRLPOOL 3378b6518b0f9f4b251f2412936b08ed6023053e7e24566f1d02acf8361079b3994de1f2f7b13f32f8c90b4399773ea225f7c0ddf78c907982c47e167fec6786 +DIST spm8.zip 92048821 SHA256 43f952eb11435454510ba8ca4111ded28c845455d03a7f420ec492dbeb12a499 SHA512 da942841bbac74461950639648aeb4f8aef1c6229f3b30a47713c158bf9751dcec0d825b7d6349c03eab1ee91467f86e0c504c761ac1094343718a373effb451 WHIRLPOOL 07c5bec3f48271f40f182e2cc0b2cc65ffe2657be9fe46c6e98d68d40da902b38f773a65dea9915600f903b251813bf5447bc1bf5ca313c9d502bb6914c9a8f6 diff --git a/dev-lua/cmsgpack/metadata.xml b/sci-biology/spm/metadata.xml index 897aa2e6b..897aa2e6b 100644 --- a/dev-lua/cmsgpack/metadata.xml +++ b/sci-biology/spm/metadata.xml diff --git a/sci-biology/spm/spm-12.ebuild b/sci-biology/spm/spm-12.ebuild new file mode 100644 index 000000000..adb2a678d --- /dev/null +++ b/sci-biology/spm/spm-12.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab" +HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/" +SRC_URI="http://www.fil.ion.ucl.ac.uk/spm/download/restricted/eldorado/${PN}${PV}.zip" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=">=sci-mathematics/octave-3.8 + " + +DEPEND="${RDEPEND} + app-arch/unzip + " + +S="${WORKDIR}/${PN}${PV}/src" + +src_prepare() { + emake distclean PLATFORM=octave +} + +src_compile() { + emake -j1 PLATFORM=octave +} + +src_install() { + emake install PLATFORM=octave + insinto "$(octave-config --m-site-dir)/${P}" + doins -r "${WORKDIR}/${PN}${PV}"/* +} diff --git a/sci-biology/spm/spm-8.ebuild b/sci-biology/spm/spm-8.ebuild new file mode 100644 index 000000000..60885ae52 --- /dev/null +++ b/sci-biology/spm/spm-8.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +DESCRIPTION="Analysis of brain imaging data sequences for Octave or Matlab" +HOMEPAGE="http://www.fil.ion.ucl.ac.uk/spm/" +SRC_URI="http://www.fil.ion.ucl.ac.uk/spm/download/restricted/idyll/${PN}${PV}.zip" + +LICENSE="GPL-2+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=">=sci-mathematics/octave-3.6.4 + " + +DEPEND="${RDEPEND} + app-arch/unzip + " + +S="${WORKDIR}/${PN}${PV}" + +src_prepare() { + echo "MEXOPTS += -v" >> src/Makefile.var + emake -C src distclean PLATFORM=octave + emake -C src toolbox-distclean PLATFORM=octave +} + +src_compile() { + emake -C src -j1 PLATFORM=octave + emake -C src toolbox PLATFORM=octave +} + +src_install() { + emake -C src -j1 install PLATFORM=octave + emake -C src -j1 toolbox-install PLATFORM=octave + insinto $(octave-config --m-site-dir) + doins -r "${S}"/*.m +} diff --git a/sci-biology/stacks/ChangeLog b/sci-biology/stacks/ChangeLog index c842760da..5730b3d14 100644 --- a/sci-biology/stacks/ChangeLog +++ b/sci-biology/stacks/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/stacks -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild: + sci-biology/stacks: commented out sys-cluster/openmpi DEPENDency + + 27 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> stacks-1.16.ebuild: + sci-biology/stacks: SRC_URI cleanup + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> stacks-1.16.ebuild: clean up diff --git a/sci-biology/stacks/stacks-1.16.ebuild b/sci-biology/stacks/stacks-1.16.ebuild index d8a94109a..36b15739e 100644 --- a/sci-biology/stacks/stacks-1.16.ebuild +++ b/sci-biology/stacks/stacks-1.16.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,14 +10,15 @@ inherit flag-o-matic eutils perl-module webapp DESCRIPTION="Analyze Restriction enzyme data, draw gen. maps, population genomics (RAD-seq Illumina sequencing)" HOMEPAGE="http://creskolab.uoregon.edu/stacks" -SRC_URI="http://creskolab.uoregon.edu/stacks/source/stacks-1.16.tar.gz" +SRC_URI="http://creskolab.uoregon.edu/stacks/source/${P}.tar.gz" LICENSE="GPL-3" # SLOT="0" # webapp ebuilds do not set SLOT KEYWORDS="" IUSE="" -DEPEND="sys-cluster/openmpi +# sys-cluster/openmpi +DEPEND=" dev-cpp/sparsehash sci-biology/samtools sci-biology/bamtools" diff --git a/sci-biology/staden/ChangeLog b/sci-biology/staden/ChangeLog index 1b635edeb..e874d2958 100644 --- a/sci-biology/staden/ChangeLog +++ b/sci-biology/staden/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-biology/staden -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + staden-2.0.0_beta9.ebuild, staden-9999.ebuild: + sci-biology/staden: added SLOT operator + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + staden-2.0.0_beta9.ebuild, staden-9999.ebuild: + added PYTHON_USEDEP + 24 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> staden-9999.ebuild: sci-biology/staden: fix ESVN_REPO_URI to include trailing 'src/' so that we do not have to change ''. Thanks to Justin Lercher for the patch. diff --git a/sci-biology/staden/staden-2.0.0_beta9.ebuild b/sci-biology/staden/staden-2.0.0_beta9.ebuild index 90dd7ef90..152ee6ca7 100644 --- a/sci-biology/staden/staden-2.0.0_beta9.ebuild +++ b/sci-biology/staden/staden-2.0.0_beta9.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -28,7 +28,7 @@ IUSE="curl debug fortran png tcl tk X zlib" # DEPEND=" app-arch/xz-utils - dev-lang/tk + dev-lang/tk:* dev-tcltk/tklib media-libs/libpng:0 sci-biology/samtools diff --git a/sci-biology/staden/staden-9999.ebuild b/sci-biology/staden/staden-9999.ebuild index 2c1d490c1..af64ca007 100644 --- a/sci-biology/staden/staden-9999.ebuild +++ b/sci-biology/staden/staden-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -27,7 +27,7 @@ IUSE="curl debug fortran png tcl tk X zlib" # DEPEND=" app-arch/xz-utils - dev-lang/tk + dev-lang/tk:* dev-tcltk/tklib media-libs/libpng:0 sci-biology/samtools diff --git a/sci-biology/swissknife/ChangeLog b/sci-biology/swissknife/ChangeLog index d679425a5..ecb4b87ae 100644 --- a/sci-biology/swissknife/ChangeLog +++ b/sci-biology/swissknife/ChangeLog @@ -1,8 +1,11 @@ # ChangeLog for sci-biology/swissknife -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> swissknife-1.70.ebuild: + sci-biology/swissknife: Fix dependency problems due to recent mask of perl- + core packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> -swissknife-1.67.ebuild, +swissknife-1.70.ebuild, metadata.xml: - Version BUmp; Bump to EAPI=5 - + Version Bump; Bump to EAPI=5 diff --git a/sci-biology/swissknife/swissknife-1.70.ebuild b/sci-biology/swissknife/swissknife-1.70.ebuild index 3955e7420..102865637 100644 --- a/sci-biology/swissknife/swissknife-1.70.ebuild +++ b/sci-biology/swissknife/swissknife-1.70.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -14,7 +14,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="virtual/perl-Module-Build" +DEPEND="dev-perl/Module-Build" RDEPEND="${DEPEND} >=dev-lang/perl-5.002:=" #dev-perl/Carp diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog index 7128ae0d2..686447588 100644 --- a/sci-biology/tablet-bin/ChangeLog +++ b/sci-biology/tablet-bin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/tablet-bin -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*tablet-bin-1.14.10.21 (15 Mar 2015) + + 15 Mar 2015; Ted Tanberry <ted.tanberry@gmail.com> + +tablet-bin-1.14.10.21.ebuild, + -tablet-bin-1.13.12.17.ebuild, -tablet-bin-1.14.04.10.ebuild: + Version bump, update SRC_URI, remove dead ebuilds + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> tablet-bin-1.14.04.10.ebuild: clean up diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index 7c1877c79..fbb7986d1 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,3 +1,2 @@ DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664 -DIST tablet-bin-1.13.12.17.sh 34395356 SHA256 fab481dd2a19e1c25142c41e75c483eeac36cc6793921a2643d9472f0aecbd2b SHA512 6fee28fd68ac4dde777dc7b873735e165d19bec47997a49185f21eecaaf2f38ca019b5af30ff18177ed69ad01eb8a797ef8b892631780ad548bf8fdf3ceb2f0b WHIRLPOOL 274e3849096179707af5ad36001ba060b5c5be068350454553997a120ec5c5f33b347ea26f3f9bd356bb7191b1c1e07199a6f6c0073e5b7edb7bf953d46c0974 -DIST tablet-bin-1.14.04.10.sh 36267340 SHA256 d716eab1c4f8f7de099bed6b10a7346fcc2340cf69e527e5af33f521fad00b97 SHA512 9ef7f3332171f66bee6cfceb46dae56170fc744709bc34ebcd6abf201b8d4dd9f6a3e21b61ec341297b66c1b2527970cd15715d1b87f9b864ac97aae4f994ac9 WHIRLPOOL 0369d8bd46ce3ce5bd4da66f23d21a47dcdb74bfa54ff7748fd1ae28180c3ec300eb1e02caeeb8f7090e908fe3984bd14845d9a4e5c099e76bd67ee562759124 +DIST tablet-bin-1.14.10.21.sh 44245815 SHA256 3e949fdb3610bce2c5e3db932cacdc6848d46a67240769ac136d790f789dd294 SHA512 2ded1c11e98232a82d34b813903bf52606c245f34a6eab0392e90947ea03885e4010ecfb784d60260a81356d08c38e4be5d3050e3d98b2565c4ad6b98b960c86 WHIRLPOOL 318dca0899b25b3acd64cbb92d5400983020477c721b379ebb219ac2e54c597408d7822ef9102c844a1e4fb0d4d7dd639869def11efa075b9be07f844dc47ac6 diff --git a/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild deleted file mode 100644 index 7b7d0013a..000000000 --- a/sci-biology/tablet-bin/tablet-bin-1.13.12.17.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit java-pkg-2 python-r1 - -DESCRIPTION="Viewer of next generation sequence assemblies and alignments." -HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" -SRC_URI=" - x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) - amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. - -LICENSE="Tablet" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS}" -RDEPEND="${DEPEND} - virtual/jre" - -S="${WORKDIR}" - -src_unpack() { - local file - for file in ${A}; do - cp "${DISTDIR}"/${file} "${WORKDIR}" || die - done -} - -src_install() { - # In theory it seems this binary package could be installed through ant - # instead of the install4j package which is not easy to be forced - # non-interactive. The below approach via install4j is not ideal but works. - sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed" - - # the intallation script somehow does not pickup - # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore - # we place the file rather directly into the place where it should reside. - # In the file you can read details how the variables were mangled. For - # example, the trick with sys.symlinkDir in the response.varfile is to - # disable the installation process to symlink from /usr/local/bin/table to - # /opt/Tablet/tablet. That was logged in that file with the following line: - # - # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: - # Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] - # - # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile - dodir /opt/Tablet/.install4j - cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die - - # make sure we force java to point a to $HOME which is inside our sanbox - # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome - # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed \ - -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \ - -i "${WORKDIR}"/${P}.sh || die - sh \ - "${WORKDIR}"/${P}.sh \ - -q -overwrite \ - -varfile="${DISTDIR}"/response.varfile \ - --destination="${ED}"/opt/Tablet \ - -dir "${ED}"/opt/Tablet || die - - rm -rf "${ED}"/opt/Tablet/jre || die - - python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py - - echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet - doenvd 99Tablet || die -} diff --git a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild index d13ad0ce0..680756318 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.14.04.10.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.14.10.21.ebuild @@ -1,19 +1,19 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit java-pkg-2 python-r1 DESCRIPTION="Viewer of next generation sequence assemblies and alignments." -HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" +HOMEPAGE="http://ics.hutton.ac.uk/tablet/" SRC_URI=" - x86? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) - amd64? ( http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" + x86? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh ) + amd64? ( http://bioinf.hutton.ac.uk/tablet/installers/tablet_linux_x64_$(replace_all_version_separators _).sh -> ${P}.sh ) + http://bioinf.hutton.ac.uk/tablet/additional/coveragestats.py" # Upstream says regarding source code unavailability: # Tablet uses a modified version of the BSD License which has been edited to diff --git a/sci-biology/tgicl/ChangeLog b/sci-biology/tgicl/ChangeLog index 683f68c53..76e65851e 100644 --- a/sci-biology/tgicl/ChangeLog +++ b/sci-biology/tgicl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/tgicl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 15 Jun 2015; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild: + sci-biology/tgicl: Fix dependency problems due to recent mask of perl-core + packages + 24 Sep 2014; Justin Lecher <jlec@gentoo.org> tgicl-2.1.ebuild, metadata.xml: Bump to EAPI=5 - diff --git a/sci-biology/tgicl/tgicl-2.1.ebuild b/sci-biology/tgicl/tgicl-2.1.ebuild index 0c920ea5d..67bb99d46 100644 --- a/sci-biology/tgicl/tgicl-2.1.ebuild +++ b/sci-biology/tgicl/tgicl-2.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -16,7 +16,7 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND=" - virtual/perl-Module-Build + dev-perl/Module-Build sci-biology/cap3-bin sci-biology/ncbi-tools sci-biology/cdbfasta diff --git a/sci-biology/tmhmm/ChangeLog b/sci-biology/tmhmm/ChangeLog index 8ab8d4d00..ac2c4a879 100644 --- a/sci-biology/tmhmm/ChangeLog +++ b/sci-biology/tmhmm/ChangeLog @@ -1,11 +1,13 @@ # ChangeLog for sci-biology/tmhmm -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> tmhmm-2.0c.ebuild: + Bump to EAPI=5 and cleanup + 27 Jun 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> tmhmm-2.0c.ebuild, -tmhmm: QA fixes 21 Aug 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me - diff --git a/sci-biology/tmhmm/tmhmm-2.0c.ebuild b/sci-biology/tmhmm/tmhmm-2.0c.ebuild index 7c4e7a674..4fab9e67d 100644 --- a/sci-biology/tmhmm/tmhmm-2.0c.ebuild +++ b/sci-biology/tmhmm/tmhmm-2.0c.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 DESCRIPTION="Prediction of transmembrane helices in proteins" HOMEPAGE="http://www.cbs.dtu.dk/services/TMHMM/" @@ -10,12 +10,8 @@ SRC_URI="${P}.Linux.tar.gz" LICENSE="tmhmm" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="" - RESTRICT="fetch" S="TMHMM${PV}" @@ -32,9 +28,9 @@ src_prepare() { src_install() { exeinto /opt/${PN}/bin - doexe bin/* || die + doexe bin/* insinto /opt/${PN}/lib - doins lib/* || die + doins lib/* dosym /opt/${PN}/bin/tmhmm /usr/bin/tmhmm dodoc README TMHMM2.0.html } diff --git a/sci-biology/tophat/ChangeLog b/sci-biology/tophat/ChangeLog new file mode 100644 index 000000000..84e8313d9 --- /dev/null +++ b/sci-biology/tophat/ChangeLog @@ -0,0 +1,84 @@ +# ChangeLog for sci-biology/tophat +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/ChangeLog,v 1.14 2015/04/07 14:35:24 jlec Exp $ + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: + added PYTHON_USEDEP + + 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + tophat-2.0.12.ebuild, tophat-2.0.13.ebuild, tophat-2.0.14.ebuild: + sci-biology/tophat: recorded depependencies; dropped KEYWORDS until we have + slotted samtools (or multiple static binaries with version appended to + filename), link tophat_reporter against -lsam-0.1.18 and similarly adjust + tophat_reporter + + 28 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + tophat-2.0.14.ebuild: + sci-biology/tophat: try to introduce all-recursive target to make upstream + 'make all' call happy + + 17 Oct 2014; Sergey Popov <pinkbyte@gentoo.org> tophat-1.0.12.ebuild: + Non-maintainer commit: fix building, approved by Justin Lecher + +*tophat-2.0.9 (06 Mar 2014) + + 06 Mar 2014; Justin Lecher <jlec@gentoo.org> +tophat-2.0.9.ebuild, + +files/tophat-2.0.9-flags.patch: + Version Bump, #502532; thanks José María Fernández González for the new + ebuild + +*tophat-2.0.8 (13 Mar 2013) + + 13 Mar 2013; Justin Lecher <jlec@gentoo.org> +tophat-2.0.8.ebuild, + +files/tophat-2.0.8-flags.patch: + Version Bump; unbundle sci-biology/seqan + + 12 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: + Drop Andrey as maintainer so that bugs get assigned to sci-biology directly + +*tophat-2.0.2 (19 Jul 2012) + + 19 Jul 2012; Justin Lecher <jlec@gentoo.org> tophat-2.0.0.ebuild, + +tophat-2.0.2.ebuild, +files/tophat-2.0.2-flags.patch, metadata.xml: + Version Bump; do parallel builds; handle debug build + + 25 Apr 2012; Justin Lecher <jlec@gentoo.org> tophat-1.0.12.ebuild, + tophat-1.4.1.ebuild, tophat-2.0.0.ebuild: + Drop unnessecary die + +*tophat-2.0.0 (15 Apr 2012) + + 15 Apr 2012; Andrey Kislyuk <weaver@gentoo.org> -tophat-1.3.3.ebuild, + +tophat-2.0.0.ebuild: + version bump + +*tophat-1.4.1 (04 Feb 2012) +*tophat-1.3.3 (04 Feb 2012) + + 04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> -tophat-1.3.2.ebuild, + +tophat-1.3.3.ebuild, +tophat-1.4.1.ebuild: + version bump + + 04 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> tophat-1.3.2.ebuild: + filter as-needed + +*tophat-1.3.2 (26 Sep 2011) + + 26 Sep 2011; Andrey Kislyuk <weaver@gentoo.org> +tophat-1.3.2.ebuild: + Version bump + + 05 Apr 2010; Pawel Hajdan jr <phajdan.jr@gentoo.org> tophat-1.0.12.ebuild: + x86 stable wrt bug #311829 + + 29 Mar 2010; Pacho Ramos <pacho@gentoo.org> tophat-1.0.12.ebuild: + amd64 stable, bug 311829 + + 07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> tophat-1.0.12.ebuild: + Fix x86 compile issue. Thanks to Fabian Groffen. + +*tophat-1.0.12 (07 Dec 2009) + + 07 Dec 2009; Andrey Kislyuk <weaver@gentoo.org> +metadata.xml, + +tophat-1.0.12.ebuild: + Import from Science overlay and version bump. Thanks to Philippe Veber. diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest new file mode 100644 index 000000000..0361b69de --- /dev/null +++ b/sci-biology/tophat/Manifest @@ -0,0 +1,3 @@ +DIST tophat-2.0.12.tar.gz 1767329 SHA256 ce97d9f3c6d6c0dd256744498b5209a9260ca3118a8e5210d9404fae890a4d74 SHA512 c2eae628cb1d0a19793708df710a10e04663e3dae12725f93faf17d1784360239a82a7fd9cee6e3d9b7156fe74b9612b71a97de540c9ba0ff9a61005a14c4b3b WHIRLPOOL a2582c7ec91fd589e0e8854b65250eaafe567241fad0023b788359e1d67b3cbf024ddf3a3543974bf43e13b13420ea37186a85d1b55059ea1cfd87915e4d39c0 +DIST tophat-2.0.13.tar.gz 1998819 SHA256 acbe8f1a47131053d4b766df117c9f83458fdc5df6a500d7488e4c6cef51e512 SHA512 1fd38f4e866997f82209892111c976d29dc9e1055ba8fc65ee3ea2436a4d9673a73985dcac73519c7f8abc719bda20366aa84a36e8dea4a9b7d135c1b94afb89 WHIRLPOOL bf4dc17c5d508194c85dc73c73d66a390e95484db14ca282c5be5ca6ab55e2c7edfd9861ff6f0daba4344089a25e47372ceaf2d4ea269d27dc6808f4e0b637b0 +DIST tophat-2.0.14.tar.gz 2013476 SHA256 547c5c9d127cbf7d61bc73c4251ff98a07d57e59b3718666a18b58acfb8fcfbf SHA512 fcdf7c8ad298284acabeac3bc96c7f08e74927d3c6e38fa93914a0bba470ba495cc5920ef0c22efcd652788e484162c0632c6d3574f3d90ba15fe8690feb0ec8 WHIRLPOOL ca2bcc89553160480b5594cfb755701d3b72ee8c8c7629b8b6091a9849bd910423a699dd7750f7ee654fa15c216538bfa0786ecdc14855eb73e39a30029ca00e diff --git a/sci-biology/tophat/files/tophat-2.0.9-flags.patch b/sci-biology/tophat/files/tophat-2.0.9-flags.patch new file mode 100644 index 000000000..af89e7208 --- /dev/null +++ b/sci-biology/tophat/files/tophat-2.0.9-flags.patch @@ -0,0 +1,109 @@ + configure.ac | 3 ++- + src/Makefile.am | 50 +++++++++++++++++++++++++------------------------- + 2 files changed, 27 insertions(+), 26 deletions(-) + +diff --git a/configure.ac b/configure.ac +index 75e9218..98b05d2 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -68,7 +68,8 @@ AC_CANONICAL_HOST + # set CFLAGS and CXXFLAGS + #user_CFLAGS="${CXXFLAGS}" + user_CFLAGS=${CFLAGS} +-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++#generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized" ++generic_CFLAGS="" + ext_CFLAGS="" + debug_CFLAGS="" + user_LDFLAGS="$LDFLAGS" +diff --git a/src/Makefile.am b/src/Makefile.am +index dde692e..ebb9fcd 100644 +--- a/src/Makefile.am ++++ b/src/Makefile.am +@@ -545,10 +545,10 @@ CLEANFILES = \ + tophat2 + + tophat2: tophat2.in +- sed -e 's|__PREFIX__|$(prefix)|' tophat2.in > tophat2 ++ sed -e 's|__PREFIX__|$(prefix)|' $(top_srcdir)/src/tophat2.in > tophat2 + + tophat: tophat.py +- sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat ++ sed -e 's|__VERSION__|$(VERSION)|' $(top_srcdir)/src/tophat.py > tophat + + #SUFFIXES = .py + #.py: +@@ -617,49 +617,49 @@ libgc_a_SOURCES = \ + #-- program sources + + prep_reads_SOURCES = prep_reads.cpp +-prep_reads_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-prep_reads_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++prep_reads_LDADD = libtophat.a $(BAM_LIB) ++prep_reads_LDFLAGS = $(BAM_LDFLAGS) + + segment_juncs_SOURCES = segment_juncs.cpp +-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-segment_juncs_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++segment_juncs_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++segment_juncs_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + long_spanning_reads_SOURCES = long_spanning_reads.cpp +-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-long_spanning_reads_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++long_spanning_reads_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++long_spanning_reads_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + gtf_juncs_SOURCES = gtf_juncs.cpp +-gtf_juncs_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_juncs_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_juncs_LDFLAGS = $(BAM_LDFLAGS) + + juncs_db_SOURCES = juncs_db.cpp +-juncs_db_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-juncs_db_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++juncs_db_LDADD = libtophat.a $(BAM_LIB) ++juncs_db_LDFLAGS = $(BAM_LDFLAGS) + + tophat_reports_SOURCES = tophat_reports.cpp +-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) +-tophat_reports_LDFLAGS = $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) ++tophat_reports_LDADD = libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB) ++tophat_reports_LDFLAGS = $(BOOST_LDFLAGS) $(BAM_LDFLAGS) + + fix_map_ordering_SOURCES = fix_map_ordering.cpp +-fix_map_ordering_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-fix_map_ordering_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++fix_map_ordering_LDADD = libtophat.a $(BAM_LIB) ++fix_map_ordering_LDFLAGS = $(BAM_LDFLAGS) + + bam2fastx_SOURCES = bam2fastx.cpp +-bam2fastx_LDADD = $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam2fastx_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam2fastx_LDADD = libgc.a $(BAM_LIB) ++bam2fastx_LDFLAGS = $(BAM_LDFLAGS) + + bam_merge_SOURCES = bam_merge.cpp +-bam_merge_LDADD = $(top_builddir)/src/libtophat.a $(top_builddir)/src/libgc.a $(BAM_LIB) +-bam_merge_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++bam_merge_LDADD = libtophat.a libgc.a $(BAM_LIB) ++bam_merge_LDFLAGS = $(BAM_LDFLAGS) + + sam_juncs_SOURCES = sam_juncs.cpp +-sam_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BAM_LIB) +-sam_juncs_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++sam_juncs_LDADD = libtophat.a $(BAM_LIB) ++sam_juncs_LDFLAGS = $(BAM_LDFLAGS) + + map2gtf_SOURCES = map2gtf.cpp +-map2gtf_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-map2gtf_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++map2gtf_LDADD = libtophat.a libgc.a $(BAM_LIB) ++map2gtf_LDFLAGS = $(BAM_LDFLAGS) + + gtf_to_fasta_SOURCES = GTFToFasta.cpp FastaTools.cpp +-gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB) +-gtf_to_fasta_LDFLAGS = $(LDFLAGS) $(BAM_LDFLAGS) ++gtf_to_fasta_LDADD = libtophat.a libgc.a $(BAM_LIB) ++gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) diff --git a/sci-biology/embassy-esim4/metadata.xml b/sci-biology/tophat/metadata.xml index f17a827e3..36cf4a138 100644 --- a/sci-biology/embassy-esim4/metadata.xml +++ b/sci-biology/tophat/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> + <use> + <flag name="bam">Compile support for the BAM format</flag> + </use> </pkgmetadata> diff --git a/sci-biology/tophat/tophat-2.0.12.ebuild b/sci-biology/tophat/tophat-2.0.12.ebuild new file mode 100644 index 000000000..f818f1cbf --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.12.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2" +HOMEPAGE="http://ccb.jhu.edu/software/tophat" +# https://github.com/infphilo/tophat +# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="dev-libs/boost" +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +# boost and seqan is needed for tophat_reporter + +# tophat.py calls +# samtools_0.1.18 view -h - +# samtools_0.1.18 sort +# samtools_0.1.18 merge -f -h -u -Q --sam-header +RDEPEND="${DEPEND} + >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}] + <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}] + >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )" + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* src/Makefile* || die + sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die + #rm -rf src/SeqAn* || die + eautoreconf + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* src/Makefile* || die +} + +src_install() { + # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?) + sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +} diff --git a/sci-biology/tophat/tophat-2.0.13.ebuild b/sci-biology/tophat/tophat-2.0.13.ebuild new file mode 100644 index 000000000..c24d230d3 --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.13.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2" +HOMEPAGE="http://ccb.jhu.edu/software/tophat" +# https://github.com/infphilo/tophat +# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="dev-libs/boost" +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +# boost and seqan is needed for tophat_reporter + +# tophat.py calls +# samtools_0.1.18 view -h - +# samtools_0.1.18 sort +# samtools_0.1.18 merge -f -h -u -Q --sam-header +RDEPEND="${DEPEND} + >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}] + <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}] + >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )" + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die + sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die + # rm -rf src/SeqAn* || die + eautoreconf + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + cd ../"${P}"_build/src || die + ln -s ../"${P}"/src/SeqAn-1.3 . || die + ln -s ../../"${P}"/src/samtools-0.1.18 . || die + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die +} + +src_install() { + # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?) + sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +} diff --git a/sci-biology/tophat/tophat-2.0.14.ebuild b/sci-biology/tophat/tophat-2.0.14.ebuild new file mode 100644 index 000000000..579641f6e --- /dev/null +++ b/sci-biology/tophat/tophat-2.0.14.ebuild @@ -0,0 +1,64 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/tophat/tophat-2.0.9.ebuild,v 1.1 2014/03/06 09:46:50 jlec Exp $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=yes +PYTHON_COMPAT=( python2_7 ) + +inherit autotools-utils python-single-r1 + +DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie/bowtie2" +HOMEPAGE="http://ccb.jhu.edu/software/tophat" +# https://github.com/infphilo/tophat +# http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.14.tar.gz +SRC_URI="http://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz" + +LICENSE="Artistic" +SLOT="0" +KEYWORDS="" +IUSE="debug" + +DEPEND="dev-libs/boost" +# sci-biology/seqan provides binaries and headers but there are no *.so files so no need for a runtime dependency +# boost and seqan is needed for tophat_reporter + +# tophat.py calls +# samtools_0.1.18 view -h - +# samtools_0.1.18 sort +# samtools_0.1.18 merge -f -h -u -Q --sam-header +RDEPEND="${DEPEND} + >=sci-biology/samtools-0.1.17[${PYTHON_USEDEP}] + <=sci-biology/samtools-0.1.19[${PYTHON_USEDEP}] + >=sci-biology/bowtie-0.12.9 || ( >=sci-biology/bowtie-2.0.5 <=sci-biology/bowtie-2.2.3 )" + +# see https://aur.archlinux.org/packages/tophat/ about linking issues + +# PATCHES=( "${FILESDIR}"/${P}-flags.patch ) + +src_prepare() { + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i configure* Makefile* || die + sed -e "s#./SeqAn-1.3#"${S}"/src/SeqAn-1.3#g" -i configure* || die + eautoreconf + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-optim + $(use_enable debug) + ) + autotools-utils_src_configure + cd ../"${P}"_build/src || die + ln -s ../../"${P}"/src/SeqAn-1.3 . || die + ln -s ../../"${P}"/src/samtools-0.1.18 . || die + sed -e "s#./samtools-0.1.18#"${S}"/src/samtools-0.1.18#g" -i Makefile* || die +} + +src_install() { + # introduce empty all-recursive: target in tophat-2.0.14_build/src/Makefile (BUG: does not replace?) + sed -e "s#^all: all-am#all: all-am\nall-recursive: all#g" -i src/Makefile* || die + autotools-utils_src_install + python_fix_shebang "${ED}"/usr/bin/tophat +} diff --git a/sci-biology/transdecoder/ChangeLog b/sci-biology/transdecoder/ChangeLog deleted file mode 100644 index 87a58f901..000000000 --- a/sci-biology/transdecoder/ChangeLog +++ /dev/null @@ -1,25 +0,0 @@ -# ChangeLog for sci-biology/transdecoder -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 15 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - drop hmmer-3 dependency, it is an optional dependency only - - 10 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - transdecoder-20140704.ebuild: - install *.pm into PERL5LIB/TransDecoder and pass that via env.d - - 09 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +files/TransDecoder.patch, +files/pfam_runner.pl.patch, - transdecoder-20140704.ebuild: - sci-biology/transdecoder: added patches so that we use PATH to loclate - binaries and not in a local subdirectory named 'util', drop sys- - cluster/openmpi requirement, it does not link against it all all, this is a - bunch of perl and shell scripts - -*transdecoder-20140704 (08 Jan 2015) - - 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, - +transdecoder-20140704.ebuild: - sci-biology/transdecoder: new package diff --git a/sci-biology/transdecoder/Manifest b/sci-biology/transdecoder/Manifest deleted file mode 100644 index 7f4aa956c..000000000 --- a/sci-biology/transdecoder/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST TransDecoder_r20140704.tar.gz 21189681 SHA256 fb53c9601c4ae9b3cd8e937f158ae3f15439115609bc7658effffa24af53517e SHA512 fa70e440c3f8b8d11da780858ff6433adf9065b126b29eb047983b17913e382c677a272881ee78be8e30867bbd447eb9bda71bd11abda5203d6a3abfb5316e90 WHIRLPOOL d603d06c8c1e84f3e721c0f5e43b2519766eaae1fc0456ece07ff43c13971706aecb24473813b7606ca885d2ef526648fc28f874200a53037b4aa6b291c4864d diff --git a/sci-biology/transdecoder/transdecoder-20140704.ebuild b/sci-biology/transdecoder/transdecoder-20140704.ebuild deleted file mode 100644 index c8af8967b..000000000 --- a/sci-biology/transdecoder/transdecoder-20140704.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit perl-module - -DESCRIPTION="Extract ORF/CDS regions from FASTA sequences" -HOMEPAGE="http://sourceforge.net/projects/transdecoder/" -SRC_URI="http://downloads.sourceforge.net/project/transdecoder/TransDecoder_r20140704.tar.gz" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND="sci-biology/hmmer - sci-biology/cd-hit - sci-biology/parafly - sci-biology/ffindex" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/TransDecoder_r20140704 - -src_prepare(){ - rm -rf 3rd_party - mv Makefile Makefile.old - epatch "${FILESDIR}"/TransDecoder.patch - epatch "${FILESDIR}"/pfam_runner.pl.patch -} - -# avoid fetching 1.5TB "${S}"/pfam/Pfam-AB.hmm.bin, see -# "Re: [Transdecoder-users] Announcement: Transdecoder release r20140704" thread in archives -# -# you cna get it from http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin - -src_install(){ - dobin TransDecoder *.pl util/*.pl util/*.sh - eval `perl '-V:installvendorlib'` - vendor_lib_install_dir="${installvendorlib}" - dodir ${vendor_lib_install_dir}/TransDecoder - insinto ${vendor_lib_install_dir}/TransDecoder - doins PerlLib/*.pm - echo "PERL5LIB="${vendor_lib_install_dir}"/TransDecoder" > ${S}"/99TransDecoder" - doenvd ${S}"/99TransDecoder" || die - - einfo "Fetch on your own:" - einfo "wget --mirror -nH -nd http://downloads.sourceforge.net/project/transdecoder/Pfam-AB.hmm.bin" - einfo "hmmpress Pfam-AB.hmm.bin" -} diff --git a/sci-biology/trf/trf-4.07b.ebuild b/sci-biology/trf/trf-4.07b.ebuild index 649d201e5..5f913986d 100644 --- a/sci-biology/trf/trf-4.07b.ebuild +++ b/sci-biology/trf/trf-4.07b.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/trf/trf-4.04.ebuild,v 1.6 2014/04/17 21:08:54 ulm Exp $ +# $Header: $ EAPI=4 diff --git a/sci-biology/trim_galore/ChangeLog b/sci-biology/trim_galore/ChangeLog index 3dba9316b..6cb3dfe21 100644 --- a/sci-biology/trim_galore/ChangeLog +++ b/sci-biology/trim_galore/ChangeLog @@ -1,7 +1,20 @@ # ChangeLog for sci-biology/trim_galore -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*trim_galore-0.4.0 (30 May 2015) + + 30 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +trim_galore-0.4.0.ebuild, -trim_galore-0.3.7.ebuild: + sci-biology/trim_galore: version bump; ajusted S variable to match current + upstream's packaging habit; still needs fastqc package to be finished + +*trim_galore-0.3.7 (24 Feb 2015) + + 24 Feb 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +trim_galore-0.3.7.ebuild, -trim_galore-0.3.3.ebuild: + version bump; installs the simple perl script and PDF doc files + *trim_galore-0.3.3 (23 Mar 2014) 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest index d2a6a47c2..3f46bbb6e 100644 --- a/sci-biology/trim_galore/Manifest +++ b/sci-biology/trim_galore/Manifest @@ -1 +1 @@ -DIST trim_galore_v0.3.3.zip 1236911 SHA256 7af792c846cac17b8d2890017173159b397a04674427a62b68da34a1e441cd1e SHA512 5a582f27adf23f6d1f367df016b3770f39d3d120ceb6e07774c68462d457ec58e2eb99bb8d87f293195a5dfdb0e98ca839985b1bd0bf1ef8e43dc48d8cb6d73b WHIRLPOOL 59fea62fcac1776e9e9a4a0693c82d3e8045b727eb3b87f5f55406e48a4092a3e99fd597e13b2acb28388bd37591db9176fa49679a2db27913e31b3db8162804 +DIST trim_galore_v0.4.0.zip 1271343 SHA256 b7146c4a3c541910925ab4b490b754c467d4641bfd53e304884d837f95e859ba SHA512 71a742fe0f5d851f46bd21c3da2fdea5f6b048462179fb4784e49e7fd82fca51a521eda97f18844f6edbcf7e222189cef995c05d0433139b931dc8a351ce2924 WHIRLPOOL 40b40ff3032632083e7c2ce876eb116a05896b0500e981120b32acc93063499bc520aac4d7059fb6e8fa67ffdf0c5736f13717a3522dfa5e4099114b3a16d752 diff --git a/sci-biology/trim_galore/trim_galore-0.3.3.ebuild b/sci-biology/trim_galore/trim_galore-0.4.0.ebuild index 258ee3849..f27f48a3e 100644 --- a/sci-biology/trim_galore/trim_galore-0.3.3.ebuild +++ b/sci-biology/trim_galore/trim_galore-0.4.0.ebuild @@ -1,13 +1,12 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -DESCRIPTION="Wrapper around Cutadapt and FastQC to consistently apply quality and adapter trimming" -HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/" -SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v0.3.3.zip" - +DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming" +HOMEPAGE="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore" +SRC_URI="http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/trim_galore_v${PV}.zip" LICENSE="GPL-3" SLOT="0" KEYWORDS="" @@ -15,6 +14,14 @@ IUSE="" DEPEND="" RDEPEND=" + dev-lang/perl sci-biology/cutadapt sci-biology/fastqc ${DEPEND}" + +S="${WORKDIR}" + +src_install(){ + dobin trim_galore + dodoc *.pdf +} diff --git a/sci-biology/trinityrnaseq/ChangeLog b/sci-biology/trinityrnaseq/ChangeLog new file mode 100644 index 000000000..c8d81e0c1 --- /dev/null +++ b/sci-biology/trinityrnaseq/ChangeLog @@ -0,0 +1,31 @@ +# ChangeLog for sci-biology/trinityrnaseq +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-biology/trinityrnaseq: Add github to remote-id in metadata.xml + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + trinityrnaseq-2.0.6.ebuild: + sci-biology/trinityrnaseq: added missing quotes + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + trinityrnaseq-2.0.6.ebuild: + sci-biology/trinityrnaseq: added a note and removed broken symlink upon + installation + +*trinityrnaseq-2.0.6 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +trinityrnaseq-2.0.6.ebuild, -files/r3590_chmod.patch, -files/sort.patch, + -trinityrnaseq-20140413.ebuild: + sci-biology/trinityrnaseq: version bump; dropped patches because target file + is gone; ideally should depend on <sci-biology/samtools-1.1 but lets see what + are the real requirements + +*trinityrnaseq-20140413 (30 Apr 2015) + + 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +files/r3590_chmod.patch, +files/sort.patch, +metadata.xml, + +trinityrnaseq-20140413.ebuild: + sci-biology/trinityrnaseq: new package (with last release on sourceforge) diff --git a/sci-biology/trinityrnaseq/Manifest b/sci-biology/trinityrnaseq/Manifest new file mode 100644 index 000000000..654ee86b6 --- /dev/null +++ b/sci-biology/trinityrnaseq/Manifest @@ -0,0 +1 @@ +DIST trinityrnaseq-2.0.6.tar.gz 158619106 SHA256 e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1 SHA512 459461db38e42d0b77b9cb84b1ecc4ccb03bbe0fe6e970915d5df58e8c98368a07fab7a157679b0d4247b729b49966b1f3927abee11059e5e3a3406e8e598d45 WHIRLPOOL 040926ab4d1a157c340cf5886bc4cf2846e8756d84c39a1f8673b5ba59dd57b39f075b0fc915deff05dd50655b0e8f0c1b8fe3b6ceb0e0a4b2aec618bef58470 diff --git a/sci-biology/trinityrnaseq/metadata.xml b/sci-biology/trinityrnaseq/metadata.xml new file mode 100644 index 000000000..5fa67e941 --- /dev/null +++ b/sci-biology/trinityrnaseq/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <upstream> + <remote-id type="github">trinityrnaseq/trinityrnaseq</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild new file mode 100644 index 000000000..6169bfb10 --- /dev/null +++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.0.6.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +# Butterfly should not require any special compilation, as its written in Java and already provided as portable precompiled software ... +# There is bundled jellyfish-1.1.11 source tree + +DESCRIPTION="Transcriptome assembler for RNA-seq reads" +HOMEPAGE="http://trinityrnaseq.github.io/" +SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD-BroadInstitute" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND} + sci-biology/parafly + =sci-biology/jellyfish-2.1.4 + sci-biology/samtools + dev-perl/IO-All" +# ReleaseNotes mentions that <sci-biology/samtools-1.1 is needed +# version of bundled jellyfish is 2.1.4 + +# optionally install https://github.com/HpcGridRunner/HpcGridRunner/releases + +#src_compile(){ +# emake all +# emake plugins # bundled copies of TransDecoder, trimmomatic, fastool, parafly +#} + +src_install(){ + perl_set_version + dobin Trinity util/*.pl trinity-plugins/GAL_0.2.1/fasta_tool + # should become a new package depending on dev-perl/IO-All + dobin trinity-plugins/fstrozzi-Fastool-7c3e034f05/fastool + dodoc trinity-plugins/fstrozzi-Fastool-7c3e034f05/README.md + # + insinto /usr/share/"${PN}"/util + rm -f util/fasta_tool + doins -r util/* + # + dobin Inchworm/bin/* + cd Chrysalis + dobin MakeDepend checkLock BreakTransByPairs Chrysalis GraphFromFasta IsoformAugment JoinTransByPairs QuantifyGraph ReadsToTranscripts RunButterfly TranscriptomeFromVaryK analysis/ReadsToComponents.pl + cd "${S}" || die + insinto "${VENDOR_LIB}/${PN}" + doins util/misc/PerlLib/*.pm PerlLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/KmerGraphLib + doins PerlLib/KmerGraphLib/*.pm + insinto "${VENDOR_LIB}/${PN}"/CDNA + doins PerlLib/CDNA/*.pm + insinto "${VENDOR_LIB}/${PN}"/HPC + doins PerlLib/HPC/*.pm + insinto "${VENDOR_LIB}/${PN}"/Simulate + doins PerlLib/Simulate/*.pm + insinto "${VENDOR_LIB}/${PN}"/CanvasXpress + doins PerlLib/CanvasXpress/*.pm + chmod a+rx -R "${ED}/${VENDOR_LIB}/${PN}" +} diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog index fedf86e90..a37738407 100644 --- a/sci-biology/twinscan/ChangeLog +++ b/sci-biology/twinscan/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/twinscan -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*twinscan-4.1.2-r1 (02 May 2015) + + 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +twinscan-4.1.2-r1.ebuild, -twinscan-4.1.2.ebuild: + sci-biology/twinscan: lots of tweaks to install process, install perl modules, + more perl scripts, noted optional external dependencies + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild, metadata.xml: Bump to EAPI=5 and fix license @@ -15,4 +22,3 @@ 17 Apr 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, bug 154939, ebuild written by me - diff --git a/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild new file mode 100644 index 000000000..11500ca38 --- /dev/null +++ b/sci-biology/twinscan/twinscan-4.1.2-r1.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PERL_EXPORT_PHASE_FUNCTIONS=no +inherit perl-module eutils toolchain-funcs + +DESCRIPTION="iscan (aka twinscan and N-SCAN) and wrapper around Pairagon: A gene structure prediction pipeline" +HOMEPAGE="http://mblab.wustl.edu/software/twinscan" +SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" + +LICENSE="all-rights-reserved" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +DEPEND="dev-libs/glib:2" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/N-SCAN" + +src_prepare() { + sed "1 a use lib '/usr/share/${PN}/lib/perl5';" -i "${S}"/bin/*.pl || die + sed '/my $blast_param/ s/#//' -i "${S}/bin/runTwinscan2.pl" || die + tc-export CC AR RANLIB + + sed \ + -e 's:ar :$(AR) :g' \ + -e 's:ranlib :$(RANLIB) :g' \ + -e 's: -o : $(LDFLAGS) -o :g' \ + -i Makefile || die + + sed \ + -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ + -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ + -i Makefile.include || die +} + +src_install() { + dobin bin/iscan bin/zoe2gtf bin/*.pl src/*.pl + dolib lib/libzoe.a + insinto /usr/share/${PN} + doins -r parameters + insinto /usr/share/${PN}/src + doins src/*.zhmm + perl_set_version + insinto ${VENDOR_LIB}/${PN} + doins lib/perl5/*.pm + echo "TWINSCAN=/usr" > "${S}"/99${PN} + doenvd "${S}"/99${PN} + rm -rf examples/tmp + dodoc examples/* README* src/doc/*.txt +} + +pkg_postinst(){ + einfo "Pairagon acts on output from either: sci-biology/gmap sci-biology/blat." + einfo "It also works on blastn output from WU-BLAST (not provided in Gentoo)." + einfo "It also calls blastz (seems superseded by LASTZ) and genscan++ (not provided in Gentoo)." + einfo "For some reason we have pslCDnaFilter provided only by sci-biology/ucsc-genome-browser" +} diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild b/sci-biology/twinscan/twinscan-4.1.2.ebuild deleted file mode 100644 index 4667c0e36..000000000 --- a/sci-biology/twinscan/twinscan-4.1.2.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit toolchain-funcs - -DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline" -HOMEPAGE="http://mblab.wustl.edu/software/twinscan" -SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" - -LICENSE="all-rights-reserved" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -DEPEND="dev-libs/glib:2" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/N-SCAN" - -src_prepare() { - sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl || die - sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die - tc-export CC AR RANLIB - - sed \ - -e 's:ar :$(AR) :g' \ - -e 's:ranlib :$(RANLIB) :g' \ - -e 's: -o : $(LDFLAGS) -o :g' \ - -i Makefile || die - - sed \ - -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ - -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ - -i Makefile.include || die -} - -src_install() { - dobin "${S}/bin/iscan" "${S}"/bin/*.pl || die - insinto /usr/share/${PN} - doins -r "${S}/parameters" || die - doins -r "${S}/lib" || die - echo "TWINSCAN=/usr" > "${S}"/99${PN} - doenvd "${S}"/99${PN} || die - rm -rf examples/tmp - dodoc examples/* README* -} diff --git a/sci-biology/ucsc-genome-browser/Manifest b/sci-biology/ucsc-genome-browser/Manifest deleted file mode 100644 index 3cf6c6051..000000000 --- a/sci-biology/ucsc-genome-browser/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST jksrc.v260.zip 59090224 SHA256 ec28dad706f69a02f8d8fb56b9e3010f5e23b7880d717e58d9bb8d1e258fe7d1 SHA512 48aa964ab3ae456ab7e7ddc5d73b91774bd4892f21f1498578a5de38d3a07e4684778ddb1ac1ae389d5bbb3586f9b8506ca3697acca1f6777b85d343cf5d9485 WHIRLPOOL 669b0f342a97f84164b32707a3b2bb51f64219168beceb8f9d46211749351b2c65b21ffe830f82620e7112a332e88ca271d4327739d8f93afbe14e399e45e248 diff --git a/sci-biology/ucsc-genome-browser/metadata.xml b/sci-biology/ucsc-genome-browser/metadata.xml deleted file mode 100644 index 18137f66a..000000000 --- a/sci-biology/ucsc-genome-browser/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> - <use> - <flag name="server">Install genome browser Web application. If this flag is off, only libraries and utilities from the suite are installed.</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild b/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild deleted file mode 100644 index ae00dd8df..000000000 --- a/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild +++ /dev/null @@ -1,106 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/ucsc-genome-browser/ucsc-genome-browser-260.ebuild,v 1.1 2011/12/27 09:39:04 jlec Exp $ - -EAPI=4 - -inherit toolchain-funcs flag-o-matic webapp - -DESCRIPTION="The UCSC genome browser suite, also known as Jim Kent's library and GoldenPath" -HOMEPAGE="http://genome.ucsc.edu/" -SRC_URI="http://hgdownload.cse.ucsc.edu/admin/jksrc.v${PV}.zip" - -LICENSE="blat" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="+mysql +server +static-libs" - -REQUIRED_USE="server? ( mysql )" - -WEBAPP_MANUAL_SLOT="yes" - -DEPEND=" - app-arch/unzip - !<sci-biology/ucsc-genome-browser-223 - mysql? ( virtual/mysql ) - server? ( virtual/httpd-cgi )" # TODO: test with other webservers -RDEPEND="${DEPEND}" - -S="${WORKDIR}/kent" - -src_prepare() { - use server && webapp_src_preinst - sed \ - -e 's/-Werror//' \ - -e "/COPT/s:=.*$:=${LDFLAGS}:g" \ - -e "s/CC=gcc/CC=$(tc-getCC) ${CFLAGS}/" \ - -e 's:${CC} ${COPT} ${CFLAGS}:${CC} ${CFLAGS}:g' \ - -i src/inc/common.mk src/hg/lib/makefile || die - find -name makefile -or -name cgi_build_rules.mk \ - | xargs sed -i \ - -e 's/-${USER}//g' \ - -e 's/-$(USER)//g' \ - -e 's:-O2::g' \ - -e 's:-ggdb::g' \ - -e 's:-pipe::g' || die - sed \ - -e 's:${DISTDIR}${BINDIR}:${BINDIR}:g' \ - -i src/hg/genePredToMafFrames/makefile || die -} - -src_compile() { - export MACHTYPE=${MACHTYPE/-*/} \ - BINDIR="${WORKDIR}/destdir/opt/${PN}/bin" \ - SCRIPTS="${WORKDIR}/destdir/opt/${PN}/cluster/scripts" \ - ENCODE_PIPELINE_BIN="${WORKDIR}/destdir/opt/${PN}/cluster/data/encode/pipeline/bin" \ - PATH="${BINDIR}:${PATH}" \ - STRIP="echo 'skipping strip' " - - export MYSQLLIBS="none" MYSQLINC="none" DOCUMENTROOT="none" CGI_BIN="none" - - use mysql && export MYSQLLIBS="-L${EROOT}usr/$(get_libdir)/mysql/ -lmysqlclient -lz -lssl" \ - MYSQLINC="${ROOT}usr/include/mysql" - - use server && export DOCUMENTROOT="${WORKDIR}/destdir/${MY_HTDOCSDIR}" \ - CGI_BIN="${WORKDIR}/destdir/${MY_HTDOCSDIR}/cgi-bin" - - mkdir -p "$BINDIR" "$SCRIPTS" "$ENCODE_PIPELINE_BIN" || die - use server && mkdir -p "$CGI_BIN" "$DOCUMENTROOT" - - emake -C src clean - emake -C src/lib - emake -C src/jkOwnLib - emake -C src/utils/stringify - emake -C src blatSuite - if use mysql; then - emake -j1 -C src/hg utils - emake -j1 -C src utils - emake -C src libs userApps - if use server; then - emake -j1 -C src/hg - emake -j1 -C src - fi - fi -} - -src_install() { - use server && webapp_src_preinst - cp -ad "${WORKDIR}"/destdir/* "${D}" || die - use static-libs && dolib.a src/lib/${MACHTYPE/-*/}/*.a - echo "PATH=${EPREFIX}/opt/${PN}/bin" > "${S}/98${PN}" - doenvd "${S}/98${PN}" - - use server && webapp_postinst_txt en src/product/README.QuickStart - use server && webapp_src_install - - insinto "/usr/include/${PN}" - doins src/inc/*.h - insinto "/usr/share/${PN}" - doins -r src/product - keepdir "/usr/share/doc/${PF}" - find -name 'README*' -or -name '*.doc' | grep -v test | cpio -padv "${ED}/usr/share/doc/${PF}" || die -} - -pkg_postinst() { - use server && webapp_pkg_postinst -} diff --git a/sci-biology/ugene/ChangeLog b/sci-biology/ugene/ChangeLog index e7a8604a2..53c008c5d 100644 --- a/sci-biology/ugene/ChangeLog +++ b/sci-biology/ugene/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*ugene-1.16.1 (09 May 2015) + + 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +ugene-1.16.1.ebuild: + sci-biology/ugene: version bump + 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> ugene-1.13.3.ebuild.ebuild: Convert sse2 to cpu_flags_x86_sse2 diff --git a/sci-biology/ugene/Manifest b/sci-biology/ugene/Manifest index 0ea7da6f4..e5d29d6b5 100644 --- a/sci-biology/ugene/Manifest +++ b/sci-biology/ugene/Manifest @@ -1 +1,2 @@ DIST ugene-1.13.3.tar.gz 19098687 SHA256 043a6b3c6dcb9cb872bf2cd335e40a479ae62d333099e6cbe7ddd3663abda611 SHA512 6ae3645d25e37ee40d0e383dca1c6e0c05f388d3486326be24f5ecea9d7c8a2e1f82c302c21567339e47cd4d0fe404bfe1ada00fb7c7d2e5fc8e790e2d7c582b WHIRLPOOL 1b774e6e1e7c17de6c766bd3d97a024abee65e0a6061530e9e466f3597500c7f027ec91582363409576bda89316cbe7b01c784588844d8735f65dd2d4181b435 +DIST ugene-1.16.1.tar.gz 20462247 SHA256 5d7dbbe0d2364ad72b947c53bb91cfa4b80eb2e8a1bd061149ce3354858c3074 SHA512 04a18f35c2884d77693efb710995c284c5e87a5634b21e089b885c78e05fee2f5afd8749d527f6a3bef57f96d13c7e58c7f96e50f72d3215d0bd89b824943d4f WHIRLPOOL e0c150a1d1799fa3e08ce58a56f47ca7530285020dbcd30576d63973fbf4c0a37b1e5e4319a4986f99bd5e099fa8307adc55a156784243ec57f3298abc3716d0 diff --git a/sci-biology/ugene/ugene-1.16.1.ebuild b/sci-biology/ugene/ugene-1.16.1.ebuild new file mode 100644 index 000000000..9d6e4fb2e --- /dev/null +++ b/sci-biology/ugene/ugene-1.16.1.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit qt4-r2 + +DESCRIPTION="A free open-source cross-platform bioinformatics software" +HOMEPAGE="http://ugene.unipro.ru" +SRC_URI="http://${PN}.unipro.ru/downloads/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +IUSE="cpu_flags_x86_sse2" + +DEPEND=" + dev-qt/qtgui:4" +RDEPEND="${DEPEND}" + +LANGS="cs en ru zh" + +src_configure() { + local CONFIG_OPTS + if use amd64; then + CONFIG_OPTS+=( CONFIG+="x64" ) + elif use ppc; then + CONFIG_OPTS+=( CONFIG+="ppc" ) + fi + + use cpu_flags_x86_sse2 && CONFIG_OPTS+=( use_sse2 ) + + eqmake4 $CONFIG_OPTS || die +} diff --git a/sci-biology/wgs-assembler/ChangeLog b/sci-biology/wgs-assembler/ChangeLog new file mode 100644 index 000000000..d52282e88 --- /dev/null +++ b/sci-biology/wgs-assembler/ChangeLog @@ -0,0 +1,19 @@ +# ChangeLog for sci-biology/wgs-assembler +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wgs-assembler-8.3_rc2 (25 May 2015) + + 25 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +wgs-assembler-8.3_rc2.ebuild, -wgs-assembler-8.3_rc1.ebuild: + version bump + +*wgs-assembler-8.2 (18 Apr 2015) +*wgs-assembler-8.3_rc1 (18 Apr 2015) + + 18 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +wgs-assembler-8.2.ebuild, +wgs-assembler-8.3_rc1.ebuild: + sci-biology/wgs-assembler: version bumps; did not check if the LDFLAGS part of + the v7.0 patch should be carried over; CFLAGS seems are already handled + properly by current code; 8.3rc1 dies at: install: cannot stat 'Linux- + amd64/bin/TIGR': No such file or directory diff --git a/sci-biology/wgs-assembler/Manifest b/sci-biology/wgs-assembler/Manifest new file mode 100644 index 000000000..c8a83d2a4 --- /dev/null +++ b/sci-biology/wgs-assembler/Manifest @@ -0,0 +1,2 @@ +DIST wgs-8.2.tar.bz2 21179974 SHA256 6ee026031928a27e9dde2343c174e9d027bfca84a2207309113a07f81888b88e SHA512 375baabf5df453f14d757c614771a15c32b2450beee82fae55b5db75c19a689a731e2e9653ee7acf835e82daa6ef7cc565ef0e40811ff742db1fc50142c1ec4b WHIRLPOOL 51d202acdbdc97268ceec235e9a8faf60a994cfbab8bc0b7151115fabdb893562ca5847a880b7b6bdd8d1857f40bef52d38754194bad807329af18ada6b40e4f +DIST wgs-8.3rc2.tar.bz2 24603412 SHA256 6ba1711ebe56629b670be87ae040ac948057474b3959666a88f0862c6a40f27b SHA512 10646ce59c3d557b744287b63f8f0ff494fd6919c61974389b9a3870a03b19067d58ba3f545afbc1e1dfda85cac76ea0e84474911442ae2097660cc6ea73fc44 WHIRLPOOL d3a5356839c6242b3deb2184963d7afd072c67d92590de8902cfeefd2fe564db3a0510677c9a9203a39be4bc4bf7861fbaf3ff9990e640b9965514b64b335ce1 diff --git a/sci-biology/embassy-clustalomega/metadata.xml b/sci-biology/wgs-assembler/metadata.xml index f17a827e3..f17a827e3 100644 --- a/sci-biology/embassy-clustalomega/metadata.xml +++ b/sci-biology/wgs-assembler/metadata.xml diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild new file mode 100644 index 000000000..c9e564120 --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-8.2.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ + +EAPI=5 + +PYTHON_DEPEND=2 + +inherit eutils python toolchain-funcs + +DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="mirror://sourceforge/${PN}/wgs-${PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${PV}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + # epatch \ + # "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install + emake -C src -j1 SITE_NAME=LOCAL +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/"${MY_S}"/bin/* + insinto /usr/"$(get_libdir)/${PN}" + use static-libs && doins kmer/"${MY_S}"/lib/* + + insinto /usr/include/"${PN}" + doins kmer/"${MY_S}"/include/* + + insinto /usr/share/"${PN}"/lib + doins -r "${MY_S}"/bin/TIGR + rm -rf "${MY_S}"/bin/TIGR || die + dobin "${MY_S}"/bin/* + use static-libs && dolib.a "${MY_S}"/lib/* + dodoc README + + # avoid file collision + rm -f "${D}"/usr/bin/jellyfish +} diff --git a/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild new file mode 100644 index 000000000..22a765bdd --- /dev/null +++ b/sci-biology/wgs-assembler/wgs-assembler-8.3_rc2.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wgs-assembler/wgs-assembler-7.0-r1.ebuild,v 1.3 2012/11/13 19:19:00 nativemad Exp $ + +EAPI=5 + +PYTHON_DEPEND=2 + +inherit eutils python toolchain-funcs + +MY_PV="${PV/_}" # convert from _rc2 to rc2 + +DESCRIPTION="De novo whole-genome shotgun DNA sequence assembler also known as Celera Assembler and CABOG" +HOMEPAGE="http://sourceforge.net/projects/wgs-assembler/" +SRC_URI="http://sourceforge.net/projects/wgs-assembler/files/wgs-assembler/wgs-8.3/wgs-${MY_PV}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="static-libs" + +DEPEND=" + x11-libs/libXt + !x11-terms/terminator" +RDEPEND="${DEPEND} + app-shells/tcsh + dev-perl/Log-Log4perl" + +S="${WORKDIR}/wgs-${MY_PV}" + +pkg_setup() { + python_set_active_version 2 + python_pkg_setup +} + +src_prepare() { + # epatch \ + # "${FILESDIR}"/${P}-build.patch + tc-export CC CXX +} + +src_configure() { + cd "${S}/kmer" + ./configure.sh || die +} + +src_compile() { + # not really an install target + emake -C kmer -j1 install + emake -C src -j1 SITE_NAME=LOCAL +} + +src_install() { + OSTYPE=$(uname) + MACHTYPE=$(uname -m) + MACHTYPE=${MACHTYPE/x86_64/amd64} + MY_S="${OSTYPE}-${MACHTYPE}" + sed -i 's|#!/usr/local/bin/|#!/usr/bin/env |' $(find $MY_S -type f) || die + + sed -i '/sub getBinDirectory ()/ a return "/usr/bin";' ${MY_S}/bin/runCA* || die + sed -i '/sub getBinDirectoryShellCode ()/ a return "bin=/usr/bin\n";' ${MY_S}/bin/runCA* || die + sed -i '1 a use lib "/usr/share/'${PN}'/lib";' $(find $MY_S -name '*.p*') || die + + dobin kmer/"${MY_S}"/bin/* + insinto /usr/$(get_libdir)/"${PN}" + use static-libs && doins kmer/"${MY_S}"/lib/* + + insinto /usr/include/"${PN}" + doins kmer/"${MY_S}"/include/* + + insinto /usr/share/${PN}/lib + doins -r "${MY_S}"/bin/TIGR + rm -rf "${MY_S}"/bin/TIGR || die + dobin "${MY_S}"/bin/* + use static-libs && dolib.a ${MY_S}/lib/* + dodoc README + + # avoid file collision + rm -f "${D}"/usr/bin/jellyfish +} diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog new file mode 100644 index 000000000..7bbe62926 --- /dev/null +++ b/sci-biology/wise/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/wise +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*wise-2.4.1 (09 May 2015) + + 09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml, + +wise-2.4.1.ebuild: + sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the + former patches need to be updated as well diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest new file mode 100644 index 000000000..3480f82a0 --- /dev/null +++ b/sci-biology/wise/Manifest @@ -0,0 +1 @@ +DIST wise2.4.1.tar.gz 3193910 SHA256 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1 SHA512 aca14bf4fb1ab6070847cfd857d5b3c518695a020fc85b67e1f34b69b5cdb7b28b68c5779eca9af84679d56ca98f7caf1f8c2596ff02b5dd304cd9235aeb2f61 WHIRLPOOL e410abb35b126319b406c06c305076ca15fa677b1a67df617116e809297d06011a2353c869d2a9dbbedd3bec3b8fcc0bbbc8bd0c7ad0fcd9704f6b2f5f77d1ee diff --git a/sci-biology/embassy-domainatrix/metadata.xml b/sci-biology/wise/metadata.xml index f17a827e3..f17a827e3 100644 --- a/sci-biology/embassy-domainatrix/metadata.xml +++ b/sci-biology/wise/metadata.xml diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild new file mode 100644 index 000000000..d7d88b668 --- /dev/null +++ b/sci-biology/wise/wise-2.4.1.ebuild @@ -0,0 +1,74 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.4.0_alpha.ebuild,v 1.6 2015/04/19 10:02:55 ago Exp $ + +EAPI=5 + +inherit eutils toolchain-funcs versionator + +DESCRIPTION="Genewise, promoterwise: align protein HMMs to DNA for CDS predictions" +HOMEPAGE="http://www.ebi.ac.uk/~birney/wise2" +SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).tar.gz" +#SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="" +IUSE="doc static-libs" + +RDEPEND="~sci-biology/hmmer-2.3.2" +DEPEND=" + ${RDEPEND} + app-shells/tcsh + dev-lang/perl + virtual/latex-base" + +S="${WORKDIR}"/${PN}$(delete_version_separator 3) + +#src_prepare() { +# epatch \ +# "${FILESDIR}"/${P}-glibc-2.10.patch \ +# "${FILESDIR}"/${P}-cflags.patch +# cd "${S}"/docs || die +# cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die +# cat wise2api.tex temp.tex apiend.tex > api.tex || die +# epatch "${FILESDIR}"/${PN}-api.tex.patch +#} + +src_compile() { + emake \ + -C src \ + CC="$(tc-getCC)" \ + all + if use doc; then + cd "${S}"/docs || die + for i in api appendix dynamite wise2 wise3arch; do + latex ${i} || die + latex ${i} || die + dvips ${i}.dvi -o || die + done + fi +} + +src_test() { + cd "${S}"/src || die + WISECONFIGDIR="${S}/wisecfg" emake test +} + +src_install() { + dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb + use static-libs && \ + dolib.a \ + "${S}"/src/base/libwisebase.a \ + "${S}"/src/dynlibsrc/libdyna.a \ + "${S}"/src/models/libmodel.a + + insinto /usr/share/${PN} + doins -r "${S}"/wisecfg + + if use doc; then + insinto /usr/share/doc/${PF} + doins "${S}"/docs/*.ps + fi + newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file" +} diff --git a/sci-chemistry/GromacsWrapper/ChangeLog b/sci-chemistry/GromacsWrapper/ChangeLog index 7e3d83cec..eba252f5a 100644 --- a/sci-chemistry/GromacsWrapper/ChangeLog +++ b/sci-chemistry/GromacsWrapper/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/GromacsWrapper -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/GromacsWrapper: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> GromacsWrapper-9999.ebuild: Switch from git-2 to git-r3 diff --git a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild index c510eabd7..022399655 100644 --- a/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild +++ b/sci-chemistry/GromacsWrapper/GromacsWrapper-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) if [[ $PV = *9999* ]]; then scm_eclass=git-r3 diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml index 13ef0bf5a..43390c986 100644 --- a/sci-chemistry/GromacsWrapper/metadata.xml +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">orbeckst/GromacsWrapper</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/avogadro2/ChangeLog b/sci-chemistry/avogadro2/ChangeLog index e2e10ecd5..13b6e53f0 100644 --- a/sci-chemistry/avogadro2/ChangeLog +++ b/sci-chemistry/avogadro2/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/avogadro2 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/avogadro2: Updating remote-id in metadata.xml + 16 Jan 2014; Justin Lecher <jlec@gentoo.org> avogadro2-0.7.2.ebuild: fix USE deps; don't install license file @@ -10,4 +13,3 @@ 16 Jan 2014; Justin Lecher <jlec@gentoo.org> +avogadro2-0.7.2.ebuild, +metadata.xml: New package, written by me - diff --git a/sci-chemistry/avogadro2/metadata.xml b/sci-chemistry/avogadro2/metadata.xml index 807ce86d3..9a5ff7dd0 100644 --- a/sci-chemistry/avogadro2/metadata.xml +++ b/sci-chemistry/avogadro2/metadata.xml @@ -8,4 +8,7 @@ <use> <flag name="rpc">Enable RPC server</flag> </use> + <upstream> + <remote-id type="sourceforge">avogadro</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/ball/ball-9999.ebuild b/sci-chemistry/ball/ball-9999.ebuild index e39865cab..91e59e9bc 100644 --- a/sci-chemistry/ball/ball-9999.ebuild +++ b/sci-chemistry/ball/ball-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils git-r3 python-single-r1 diff --git a/sci-chemistry/burrow-owl/ChangeLog b/sci-chemistry/burrow-owl/ChangeLog index c6289f3f0..6e36684f8 100644 --- a/sci-chemistry/burrow-owl/ChangeLog +++ b/sci-chemistry/burrow-owl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/burrow-owl -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/burrow-owl: Updating remote-id in metadata.xml + 28 Dec 2013; Justin Lecher <jlec@gentoo.org> burrow-owl-9999.ebuild, metadata.xml: Bump to git-r3.eclass and virtualx.eclass @@ -66,4 +69,3 @@ +metadata.xml: moved from dberkholz overlay to sci. fix for glibc-2.10.1 and gcc-4.4 - diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml index 51fdedab1..9849d77b1 100644 --- a/sci-chemistry/burrow-owl/metadata.xml +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">burrow-owl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild index 916bbb2a3..9cde1fbf3 100644 --- a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild +++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-single-r1 toolchain-funcs diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild index 24554b77f..0db0c7a4d 100644 --- a/sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild +++ b/sci-chemistry/chemBuild/chemBuild-1.0.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-single-r1 toolchain-funcs diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild index 24554b77f..0db0c7a4d 100644 --- a/sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild +++ b/sci-chemistry/chemBuild/chemBuild-1.0.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-single-r1 toolchain-funcs diff --git a/sci-chemistry/cnsface/ChangeLog b/sci-chemistry/cnsface/ChangeLog index 91fb75e01..5026f9466 100644 --- a/sci-chemistry/cnsface/ChangeLog +++ b/sci-chemistry/cnsface/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/cnsface -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/cnsface: Updating remote-id in metadata.xml + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> cnsface-0.0.12.ebuild, metadata.xml: Bump to EAPI5 and distutils-r1.eclass @@ -11,4 +14,3 @@ 01 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/0.0.12-binary.patch, +cnsface-0.0.12.ebuild, +metadata.xml: New addition - diff --git a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild index a8da2cb05..a9c69c7dd 100644 --- a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild +++ b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml index 9ac9ffdb3..07ea2e9d8 100644 --- a/sci-chemistry/cnsface/metadata.xml +++ b/sci-chemistry/cnsface/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> + <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">cnsface</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/cpmgfit/ChangeLog b/sci-chemistry/cpmgfit/ChangeLog index 9ada1a258..a2f40c52b 100644 --- a/sci-chemistry/cpmgfit/ChangeLog +++ b/sci-chemistry/cpmgfit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/cpmgfit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 Mar 2015; Justin Lecher <jlec@gentoo.org> cpmgfit-1.43.ebuild: + sci-chemistry/cpmgfit: Fix for new gcc slotting + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> cpmgfit-1.43.ebuild: Drop all KEYWORDS due to broken revdeps @@ -10,4 +13,3 @@ 03 Jul 2014; Justin Lecher <jlec@gentoo.org> +cpmgfit-1.43.ebuild, +metadata.xml: New package written by me - diff --git a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild index 3a35bef0d..0ba9268bd 100644 --- a/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild +++ b/sci-chemistry/cpmgfit/cpmgfit-1.43.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -17,7 +17,7 @@ IUSE="examples" RDEPEND=" sci-libs/blas-reference - sys-devel/gcc:4.1" + =sys-devel/gcc-4.1*" DEPEND="dev-util/patchelf" S="${WORKDIR}"/linux diff --git a/sci-chemistry/curvefit/ChangeLog b/sci-chemistry/curvefit/ChangeLog index 88972cd0b..f19c1661d 100644 --- a/sci-chemistry/curvefit/ChangeLog +++ b/sci-chemistry/curvefit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/curvefit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 Mar 2015; Justin Lecher <jlec@gentoo.org> curvefit-1.40.ebuild: + sci-chemistry/curvefit: Fix for new gcc slotting + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> curvefit-1.40.ebuild: Drop all KEYWORDS due to broken revdeps @@ -32,4 +35,3 @@ 14 Sep 2012; Justin Lecher <jlec@gentoo.org> +curvefit-1.40.ebuild, +metadata.xml: New addition - diff --git a/sci-chemistry/curvefit/curvefit-1.40.ebuild b/sci-chemistry/curvefit/curvefit-1.40.ebuild index 8ac1975ac..2bfb1b54b 100644 --- a/sci-chemistry/curvefit/curvefit-1.40.ebuild +++ b/sci-chemistry/curvefit/curvefit-1.40.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -17,7 +17,7 @@ IUSE="examples" RDEPEND=" sci-libs/blas-reference - sys-devel/gcc:4.1" + =sys-devel/gcc-4.1*" DEPEND="dev-util/patchelf" S="${WORKDIR}"/linux diff --git a/sci-chemistry/dl_poly/ChangeLog b/sci-chemistry/dl_poly/ChangeLog index 139ec77ec..587f55668 100644 --- a/sci-chemistry/dl_poly/ChangeLog +++ b/sci-chemistry/dl_poly/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/dl_poly -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> dl_poly-4.05.ebuild: + clean up + 18 Dec 2013; Christoph Junghans <ottxor@gentoo.org> dl_poly-1.9.ebuild, dl_poly-4.05.ebuild: fixed install name diff --git a/sci-chemistry/dl_poly/dl_poly-4.05.ebuild b/sci-chemistry/dl_poly/dl_poly-4.05.ebuild index a646090c4..cb77f4a2e 100644 --- a/sci-chemistry/dl_poly/dl_poly-4.05.ebuild +++ b/sci-chemistry/dl_poly/dl_poly-4.05.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -31,8 +31,7 @@ src_prepare() { } src_compile() { - # -I/usr/$(get_libdir) is needed to find mpi.mod - emake -j1 FC="mpif77 -c" FCFLAGS="${FFLAGS} -I${EPREFIX}/usr/$(get_libdir)" LD="mpif77 -o" LDFLAGS="${LDFLAGS}" EXE="${PN}" master + emake -j1 FC="mpif77 -c" FCFLAGS="${FFLAGS}" LD="mpif77 -o" LDFLAGS="${LDFLAGS}" EXE="${PN}" master } src_install() { diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog index 5860bfe0a..d4a2d1010 100644 --- a/sci-chemistry/freeon/ChangeLog +++ b/sci-chemistry/freeon/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/freeon -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Apr 2015; Nicolas Bock <nicolasbock@gentoo.org> freeon-9999.ebuild: + sci-chemistry/freeon: Updated live ebuild. + 22 Dec 2014; Nicolas Bock <nicolasbock@gentoo.org> freeon-9999.ebuild: sci-chemistry/freeon-9999: Add proper prefix flags to configure. diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild index 28e6d1788..b9d957e05 100644 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=1 FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit autotools-utils fortran-2 git-r3 python-any-r1 @@ -14,6 +14,7 @@ DESCRIPTION="An experimental suite of programs for linear scaling quantum chemis HOMEPAGE="http://www.freeon.org" SRC_URI="" EGIT_REPO_URI="https://github.com/FreeON/freeon.git" +EGIT_BRANCH="master" LICENSE="GPL-3" SLOT="live" diff --git a/sci-chemistry/gromacs/ChangeLog b/sci-chemistry/gromacs/ChangeLog index 5acf30f6d..1e2a646c0 100644 --- a/sci-chemistry/gromacs/ChangeLog +++ b/sci-chemistry/gromacs/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Mar 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild, + metadata.xml: + removed openmm build + 31 Jan 2015; Christoph Junghans <ottxor@gentoo.org> gromacs-4.6.9999.ebuild, gromacs-5.0.9999.ebuild, gromacs-9999.ebuild, metadata.xml: Switch to CPU_FLAGS_X86 (bug #538268) diff --git a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild index e8ac17c31..3b8475ab4 100644 --- a/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-4.6.9999.ebuild @@ -44,7 +44,7 @@ HOMEPAGE="http://www.gromacs.org/" # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmm openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" +IUSE="X blas cuda doc -double-precision +fftw gsl lapack mkl mpi +offensive openmp +single-precision test +threads zsh-completion ${ACCE_IUSE}" CDEPEND=" X? ( @@ -58,11 +58,7 @@ CDEPEND=" gsl? ( sci-libs/gsl ) lapack? ( virtual/lapack ) mkl? ( sci-libs/mkl ) - mpi? ( virtual/mpi ) - openmm? ( - >=dev-util/nvidia-cuda-toolkit-4.2.9-r1 - sci-libs/openmm[cuda,opencl] - )" + mpi? ( virtual/mpi )" DEPEND="${CDEPEND} virtual/pkgconfig ${LIVE_DEPEND} @@ -72,7 +68,6 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) - openmm? ( single-precision ) mkl? ( !blas !fftw !lapack )" DOCS=( AUTHORS README ) @@ -191,15 +186,6 @@ src_configure() { "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")" -DGMX_BINARY_SUFFIX="${suffix}" -DGMX_LIBS_SUFFIX="${suffix}" ) BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure - if [[ ${x} = float ]] && use openmm; then - einfo "Configuring for openmm build" - mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_MPI=OFF - -DGMX_THREAD_MPI=OFF -DGMX_GPU=OFF -DGMX_OPENMM=ON - -DOpenMM_PLUGIN_DIR="${EPREFIX}/usr/$(get_libdir)/plugins" - -DGMX_BINARY_SUFFIX="_openmm" -DGMX_LIBS_SUFFIX="_openmm" ) - BUILD_DIR="${WORKDIR}/${P}_openmm" \ - OPENMM_ROOT_DIR="${EPREFIX}/usr" cmake-utils_src_configure - fi use mpi || continue einfo "Configuring for ${x} precision with mpi" mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF @@ -214,11 +200,6 @@ src_compile() { einfo "Compiling for ${x} precision" BUILD_DIR="${WORKDIR}/${P}_${x}"\ cmake-utils_src_compile - if [[ ${x} = float ]] && use openmm; then - einfo "Compiling for openmm build" - BUILD_DIR="${WORKDIR}/${P}_openmm"\ - cmake-utils_src_compile mdrun - fi use mpi || continue einfo "Compiling for ${x} precision with mpi" BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\ @@ -237,10 +218,6 @@ src_install() { for x in ${GMX_DIRS}; do BUILD_DIR="${WORKDIR}/${P}_${x}" \ cmake-utils_src_install - if [[ ${x} = float ]] && use openmm; then - BUILD_DIR="${WORKDIR}/${P}_openmm" \ - DESTDIR="${D}" cmake-utils_src_make install-mdrun - fi #manual can only be build after gromacs was installed once in image if use doc && [[ $PV = *9999* && ! -d ${WORKDIR}/manual_build ]]; then mycmakeargs=( -DGMXBIN="${ED}"/usr/bin -DGMXSRC="${WORKDIR}/${P}" ) diff --git a/sci-chemistry/gromacs/metadata.xml b/sci-chemistry/gromacs/metadata.xml index 8a5c7453f..30ce22ad1 100644 --- a/sci-chemistry/gromacs/metadata.xml +++ b/sci-chemistry/gromacs/metadata.xml @@ -15,7 +15,6 @@ <flag name="make-symlinks">Create symbolic links for pre-5.0 binary names</flag> <!-- acceleration optimization flags --> <flag name="offensive">Enable gromacs partly offensive quotes</flag> - <flag name="openmm">Add acceleration through <pkg>sci-libs/openmm</pkg></flag> <flag name="mkl">Use <pkg>sci-libs/mkl</pkg> for fft, blas, lapack routines</flag> </use> </pkgmetadata> diff --git a/sci-chemistry/mage/ChangeLog b/sci-chemistry/mage/ChangeLog index 4459827f3..38a7e7b73 100644 --- a/sci-chemistry/mage/ChangeLog +++ b/sci-chemistry/mage/ChangeLog @@ -1,6 +1,10 @@ # ChangeLog for sci-chemistry/mage -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/probe/ChangeLog,v 1.5 2006/09/20 05:09:00 dberkholz Exp $ +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + mage-6.44.060606.ebuild: + Bump to EAPI=5 *mage-6.44.060606 (02 Dec 2009) @@ -28,4 +32,3 @@ 04 Jun 2006; Donnie Berkholz <dberkholz@gentoo.org>; +metadata.xml, +probe-2.11.050121.ebuild: New program that evaluates atomic packing within or between molecules. - diff --git a/sci-chemistry/mage/Manifest b/sci-chemistry/mage/Manifest index 5bcae5fc9..588fdd9d3 100644 --- a/sci-chemistry/mage/Manifest +++ b/sci-chemistry/mage/Manifest @@ -1 +1 @@ -DIST mage.6.44.060606.src.tgz 726357 SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 +DIST mage.6.44.060606.src.tgz 726357 SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 SHA512 dceb63cc9806690539d0838079c2b57d6e62164049ca178d158e9c7eae759988c28d7e911942fd50f1ea880e61b2e9d7a38cc64bc5c229a4e5d442357c1f9227 WHIRLPOOL 30954a3a314c91acfce89eeffd37ae4600db76b602216c98a0d4f808a8e39b702a6076bcbb7d6c93a3fccfa58135942392cd6dd78e5b1dc5dd88bcb95415e452 diff --git a/sci-chemistry/mage/mage-6.44.060606.ebuild b/sci-chemistry/mage/mage-6.44.060606.ebuild index 355b23411..acd4577ac 100644 --- a/sci-chemistry/mage/mage-6.44.060606.ebuild +++ b/sci-chemistry/mage/mage-6.44.060606.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 inherit eutils toolchain-funcs @@ -15,7 +15,6 @@ SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/mage/${MY_P}.src.tg LICENSE="richardson" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86" -IUSE="" RDEPEND="sci-chemistry/prekin" DEPEND="${RDEPEND}" @@ -29,10 +28,9 @@ src_prepare() { src_compile() { emake \ CC="$(tc-getCC)" \ - dynamic \ - || die "make failed" + dynamic } src_install() { - dobin "${S}"/mage || die "dobin failed" + dobin "${S}"/mage } diff --git a/sci-chemistry/mdsctk/ChangeLog b/sci-chemistry/mdsctk/ChangeLog index 7fd81d3fc..a3307e9d0 100644 --- a/sci-chemistry/mdsctk/ChangeLog +++ b/sci-chemistry/mdsctk/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mdsctk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/mdsctk: Add github to remote-id in metadata.xml + + 08 Mar 2015; Justin Lecher <jlec@gentoo.org> mdsctk-1.2.0.ebuild, + metadata.xml: + fix SLOT operator; drop KEYWORDS as deps are missing + 14 Dec 2013; Christoph Junghans <ottxor@gentoo.org> mdsctk-1.2.0.ebuild: fixed install diff --git a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild index 8af615e02..5bb80460a 100644 --- a/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild +++ b/sci-chemistry/mdsctk/mdsctk-1.2.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -12,13 +12,13 @@ SRC_URI="https://github.com/douradopalmares/${PN}/archive/${PV}.tar.gz -> ${P}.t LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~amd64-linux" +KEYWORDS="" IUSE="examples R" DEPEND=" =sci-chemistry/gromacs-4.6*:= sci-libs/gsl - sys-libs/db[cxx] + sys-libs/db:=[cxx] virtual/blas virtual/lapack sci-libs/arpack diff --git a/sci-chemistry/mdsctk/metadata.xml b/sci-chemistry/mdsctk/metadata.xml index 390953747..d9fa95a3a 100644 --- a/sci-chemistry/mdsctk/metadata.xml +++ b/sci-chemistry/mdsctk/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> - <use> - <flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag> - </use> + <herd>sci-chemistry</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <use> + <flag name="R">Install <pkg>dev-lang/R</pkg> scripts as well</flag> + </use> + <upstream> + <remote-id type="github">douradopalmares/mdsctk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/mgltools-autodocktools/ChangeLog b/sci-chemistry/mgltools-autodocktools/ChangeLog index a0207894e..ba4ce9520 100644 --- a/sci-chemistry/mgltools-autodocktools/ChangeLog +++ b/sci-chemistry/mgltools-autodocktools/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-chemistry/mgltools-autodocktools -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-autodocktools-1.5.6.ebuild: + sci-chemistry/mgltools-autodocktools: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-autodocktools-1.5.6.ebuild: + sci-chemistry/mgltools-autodocktools: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> mgltools-autodocktools-1.5.6.ebuild: Add missing python use dep, move to virtual/python-imaging @@ -89,4 +98,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-autodocktools-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild b/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild index 8bf261800..d460d4400 100644 --- a/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild +++ b/sci-chemistry/mgltools-autodocktools/mgltools-autodocktools-1.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" inherit distutils-r1 eutils @@ -12,8 +12,6 @@ inherit distutils-r1 eutils MY_PN="AutoDockTools" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- AutoDockTools" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -24,7 +22,6 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=" - virtual/python-imaging[tk,${PYTHON_USEDEP}] dev-python/zsi[${PYTHON_USEDEP}] sci-chemistry/autodock sci-chemistry/mgltools-dejavu[${PYTHON_USEDEP}] @@ -36,7 +33,9 @@ RDEPEND=" sci-chemistry/mgltools-pybabel[${PYTHON_USEDEP}] sci-chemistry/mgltools-pyglf[${PYTHON_USEDEP}] sci-chemistry/mgltools-support[${PYTHON_USEDEP}] - sci-chemistry/mgltools-viewer-framework[${PYTHON_USEDEP}]" + sci-chemistry/mgltools-viewer-framework[${PYTHON_USEDEP}] + virtual/python-imaging[tk,${PYTHON_USEDEP}] +" DEPEND="${RDEPEND} dev-lang/swig" @@ -45,8 +44,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( AutoDockTools/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { @@ -64,5 +63,5 @@ python_install_all() { distutils-r1_python_install_all sed '1s:^.*$:#!/usr/bin/python:g' -i AutoDockTools/bin/runAdt || die - dobin AutoDockTools/bin/runAdt + python_foreach_impl python_doscript AutoDockTools/bin/runAdt } diff --git a/sci-chemistry/mgltools-bhtree/ChangeLog b/sci-chemistry/mgltools-bhtree/ChangeLog index 4726ae7dc..faa8eca8a 100644 --- a/sci-chemistry/mgltools-bhtree/ChangeLog +++ b/sci-chemistry/mgltools-bhtree/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-bhtree -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-bhtree-1.5.6.ebuild: + sci-chemistry/mgltools-bhtree: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-bhtree-1.5.6.ebuild: + sci-chemistry/mgltools-bhtree: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-bhtree-1.5.4-r1.ebuild, mgltools-bhtree-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-bhtree-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild b/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild index a36f764bf..5a44a49d7 100644 --- a/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild +++ b/sci-chemistry/mgltools-bhtree/mgltools-bhtree-1.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" inherit distutils-r1 eutils @@ -12,8 +12,6 @@ inherit distutils-r1 eutils MY_PN="bhtree" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- bhtree" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -23,15 +21,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-cadd/ChangeLog b/sci-chemistry/mgltools-cadd/ChangeLog index bffe9d5bb..73c8e6f56 100644 --- a/sci-chemistry/mgltools-cadd/ChangeLog +++ b/sci-chemistry/mgltools-cadd/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-cadd -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-cadd-1.5.6.ebuild: + sci-chemistry/mgltools-cadd: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-cadd-1.5.6.ebuild: + sci-chemistry/mgltools-cadd: Drop PYTHON_MODNAME and support for python2_6 + 14 Apr 2013; Justin Lecher <jlec@gentoo.org> mgltools-cadd-1.5.6.ebuild: Correct license @@ -31,4 +37,3 @@ 08 Jan 2012; Justin Lecher <jlec@gentoo.org> +mgltools-cadd-1.5.6_rc2.ebuild, +metadata.xml: Version Bump, #373679 - diff --git a/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild b/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild index 47f8abd40..0f1f1a3fc 100644 --- a/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild +++ b/sci-chemistry/mgltools-cadd/mgltools-cadd-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="CADD" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- CADD" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-cmolkit/ChangeLog b/sci-chemistry/mgltools-cmolkit/ChangeLog index 8c23ec67a..400875334 100644 --- a/sci-chemistry/mgltools-cmolkit/ChangeLog +++ b/sci-chemistry/mgltools-cmolkit/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-cmolkit -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-cmolkit-1.5.6.ebuild: + sci-chemistry/mgltools-cmolkit: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-cmolkit-1.5.6.ebuild: + sci-chemistry/mgltools-cmolkit: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-cmolkit-1.5.4-r1.ebuild, mgltools-cmolkit-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-cmolkit-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild b/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild index 6e5aed6ad..06f55b026 100644 --- a/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild +++ b/sci-chemistry/mgltools-cmolkit/mgltools-cmolkit-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="cMolKit" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- cMolKit" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-dejavu/ChangeLog b/sci-chemistry/mgltools-dejavu/ChangeLog index ca71dd1fd..fac9608ca 100644 --- a/sci-chemistry/mgltools-dejavu/ChangeLog +++ b/sci-chemistry/mgltools-dejavu/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-dejavu -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-dejavu-1.5.6-r1.ebuild: + sci-chemistry/mgltools-dejavu: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> -mgltools-dejavu-1.5.6.ebuild, + mgltools-dejavu-1.5.6-r1.ebuild: + sci-chemistry/mgltools-dejavu: Drop PYTHON_MODNAME and support for python2_6 + *mgltools-dejavu-1.5.6-r1 (11 Nov 2014) 11 Nov 2014; Justin Lecher <jlec@gentoo.org> @@ -56,4 +63,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-dejavu-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild b/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild index 07a346f6c..ecb637d43 100644 --- a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild +++ b/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6-r1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" inherit distutils-r1 eutils @@ -12,8 +12,6 @@ inherit distutils-r1 eutils MY_PN="DejaVu" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- DejaVu" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -34,8 +32,8 @@ DOCS=( DejaVu/RELNOTES ) PATCHES=( "${FILESDIR}"/${P}-pil.patch ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild b/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild deleted file mode 100644 index 0e8d5f52d..000000000 --- a/sci-chemistry/mgltools-dejavu/mgltools-dejavu-1.5.6.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) -PYTHON_REQ_USE="tk" - -inherit distutils-r1 eutils - -MY_PN="DejaVu" -MY_P="${MY_PN}-${PV/_rc3/}" - -PYTHON_MODNAME="${MY_PN}" - -DESCRIPTION="MGLTools Plugin -- DejaVu" -HOMEPAGE="http://mgltools.scripps.edu" -SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" - -LICENSE="MGLTOOLS MPL-1.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND} - dev-lang/swig" - -S="${WORKDIR}"/${MY_P} - -DOCS=( DejaVu/RELNOTES ) - -src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz -} - -python_prepare_all() { - ecvs_clean - find "${S}" -name LICENSE -type f -delete || die - - sed \ - -e 's:^.*CVS:#&1:g' \ - -e 's:^.*LICENSE:#&1:g' \ - -i "${S}"/MANIFEST.in || die - distutils-r1_python_prepare_all -} diff --git a/sci-chemistry/mgltools-geomutils/ChangeLog b/sci-chemistry/mgltools-geomutils/ChangeLog index 0a85510ff..15c90597b 100644 --- a/sci-chemistry/mgltools-geomutils/ChangeLog +++ b/sci-chemistry/mgltools-geomutils/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-geomutils -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-geomutils-1.5.6.ebuild: + sci-chemistry/mgltools-geomutils: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-geomutils-1.5.6.ebuild: + sci-chemistry/mgltools-geomutils: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-geomutils-1.5.4-r1.ebuild, mgltools-geomutils-1.5.6.ebuild: Drop old @@ -51,4 +58,3 @@ +files/1.5.4-gcc4.3.patch, +mgltools-geomutils-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild b/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild index 5e221fb68..66eb7c492 100644 --- a/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild +++ b/sci-chemistry/mgltools-geomutils/mgltools-geomutils-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="geomutils" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- geomutils" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-gle/ChangeLog b/sci-chemistry/mgltools-gle/ChangeLog index f74eae337..235229175 100644 --- a/sci-chemistry/mgltools-gle/ChangeLog +++ b/sci-chemistry/mgltools-gle/ChangeLog @@ -1,7 +1,17 @@ # ChangeLog for sci-chemistry/mgltools-gle -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-gle-1.5.6.ebuild: + sci-chemistry/mgltools-gle: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/mgltools-gle-1.5.6-swig.patch, mgltools-gle-1.5.6.ebuild: + sci-chemistry/mgltools-gle: Add fix for newer swig + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-gle-1.5.6.ebuild: + sci-chemistry/mgltools-gle: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-gle-1.5.4-r1.ebuild, mgltools-gle-1.5.6.ebuild: Drop old @@ -53,4 +63,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-gle-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch b/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch new file mode 100644 index 000000000..4b632df88 --- /dev/null +++ b/sci-chemistry/mgltools-gle/files/mgltools-gle-1.5.6-swig.patch @@ -0,0 +1,43 @@ + gle-1.5.6/gle/gle.i | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/gle-1.5.6/gle/gle.i b/gle-1.5.6/gle/gle.i +index bc48694..76170f1 100644 +--- a/gle-1.5.6/gle/gle.i ++++ b/gle-1.5.6/gle/gle.i +@@ -149,7 +149,7 @@ glePolyCone_c4f (int npoints, /* numpoints in poly-line */ + gleColor4f color_array[1], /* colors at polyline verts */ + gleDouble radius_array[1]); /* cone radii at polyline verts */ + +-#typemaps for Numeric arrays ++/* typemaps for Numeric arrays */ + DOUBLE_ARRAY2D( contour, [1][2], ncp ) + %apply double ARRAY2D[ANY][ANY] { double cont_normal[1][2] }; + %apply double VECTOR_NULL[ANY] { double up[3] }; +@@ -172,7 +172,7 @@ gleExtrusion_c4f (int ncp, /* number of contour points */ + gleDouble point_array[1][3], /* polyline vertices */ + gleColor4f color_array[1]); /* colors at polyline verts */ + +-#typemaps for Numeric arrays ++/* typemaps for Numeric arrays */ + %apply double VECTOR[ANY] { double twist_array[1] }; + + /* extrude 2D contour, specifying local rotations (twists) */ +@@ -195,7 +195,7 @@ gleTwistExtrusion_c4f (int ncp, /* number of contour points */ + gleDouble twist_array[1]); /* countour twists (in degrees) */ + + +-#typemaps for Numeric arrays ++/* typemaps for Numeric arrays */ + %apply double ARRAY3D_NULL[ANY][ANY][ANY] { double xform_array[1][2][3] }; + + /* extrude 2D contour, specifying local affine tranformations */ +@@ -218,7 +218,7 @@ gleSuperExtrusion_c4f (int ncp, /* number of contour points */ + gleColor4f color_array[1], /* color at polyline verts */ + gleDouble xform_array[1][2][3]); /* 2D contour xforms */ + +-#typemaps for Numeric arrays ++/* typemaps for Numeric arrays */ + %apply double ARRAY2D_NULL[ANY][ANY] { double startXform[2][3] }; + %apply double ARRAY2D_NULL[ANY][ANY] { double dXformdTheta[2][3] }; + diff --git a/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild b/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild index bac4ce538..946368652 100644 --- a/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild +++ b/sci-chemistry/mgltools-gle/mgltools-gle-1.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" inherit distutils-r1 eutils @@ -12,8 +12,6 @@ inherit distutils-r1 eutils MY_PN="gle" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- gle" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -30,11 +28,12 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { + local PATCHES=( "${FILESDIR}"/${P}-swig.patch ) ecvs_clean find "${S}" -name LICENSE -type f -delete || die diff --git a/sci-chemistry/mgltools-mglutil/ChangeLog b/sci-chemistry/mgltools-mglutil/ChangeLog index a809a94a7..8ff5b57d7 100644 --- a/sci-chemistry/mgltools-mglutil/ChangeLog +++ b/sci-chemistry/mgltools-mglutil/ChangeLog @@ -1,7 +1,20 @@ # ChangeLog for sci-chemistry/mgltools-mglutil -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mgltools-mglutil-1.5.6-r1 (25 Mar 2015) + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + +files/mgltools-mglutil-1.5.6-tcltk86.patch, + +mgltools-mglutil-1.5.6-r1.ebuild, -mgltools-mglutil-1.5.6.ebuild: + sci-chemistry/mgltools-mglutil: Add backport for tcltk8.6 + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-mglutil-1.5.6.ebuild: + sci-chemistry/mgltools-mglutil: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-mglutil-1.5.6.ebuild: + sci-chemistry/mgltools-mglutil: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-mglutil-1.5.4-r1.ebuild, mgltools-mglutil-1.5.6.ebuild: Drop old @@ -50,4 +63,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-mglutil-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch b/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch new file mode 100644 index 000000000..dc926cf83 --- /dev/null +++ b/sci-chemistry/mgltools-mglutil/files/mgltools-mglutil-1.5.6-tcltk86.patch @@ -0,0 +1,104 @@ +Index: mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/thumbwheel.py +=================================================================== +--- mglutil-1.5.7~rc1+cvs.20150324.orig/mglutil/gui/BasicWidgets/Tk/thumbwheel.py ++++ mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/thumbwheel.py +@@ -88,7 +88,8 @@ + # checkkeywords(kw) + + Tkinter.Frame.__init__(self, master) +- Tkinter.Pack.config(self, side='left', anchor='w') ++ #Tkinter.Pack.config(self, side='left', anchor='w') ++ Tkinter.Pack.config(master, side='left', anchor='w') + + #FIXME: nblines are not dynamically computed + self.nblines = 30 +Index: mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py +=================================================================== +--- mglutil-1.5.7~rc1+cvs.20150324.orig/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py ++++ mglutil-1.5.7~rc1+cvs.20150324/mglutil/gui/BasicWidgets/Tk/vector3DGUI.py +@@ -86,7 +86,7 @@ + [ 0.25 , 0.25 , 0.93541437, 0. ], + [ 0. , 0. , 0. , 1. ]],'f') + self.viewingMat = Numeric.transpose(self.viewingMatInv) +- self.createCanvas(master, size) ++ self.createCanvas(self, size) + self.createEntries(self.frame) + Tkinter.Widget.bind(self.canvas, "<ButtonPress-1>", self.mouseDown) + Tkinter.Widget.bind(self.canvas, "<ButtonRelease-1>", self.mouseUp) +@@ -357,19 +357,22 @@ + + def createEntries(self, master): + self.f = Tkinter.Frame(master) +- self.f.grid(column=3, rowspan=3) ++ self.f.pack(side='top', expand=1) ++ self.f.grid = Tkinter.Frame(self.f) ++ self.f.grid.pack(side='top', expand=1) ++ self.f.grid.grid(column=3, rowspan=3) + + def fX(): self.vector = [1.,0.,0.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector) + def fY(): self.vector = [0.,1.,0.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector) + def fZ(): self.vector = [0.,0.,1.]; self.setEntries(); self.callbacks.CallCallbacks(self.vector) +- lX = Tkinter.Button(master=self.f, text='x', command=fX) +- lY = Tkinter.Button(master=self.f, text='y', command=fY) +- lZ = Tkinter.Button(master=self.f, text='z', command=fZ) ++ lX = Tkinter.Button(master=self.f.grid, text='x', command=fX) ++ lY = Tkinter.Button(master=self.f.grid, text='y', command=fY) ++ lZ = Tkinter.Button(master=self.f.grid, text='z', command=fZ) + lX.grid(row=0, column=0) + lY.grid(row=1, column=0) + lZ.grid(row=2, column=0) + +- self.thumbx = ThumbWheel(master=self.f, width=50, ++ self.thumbx = ThumbWheel(master=self.f.grid, width=50, + height=20, labcfg={'text':'X:','side':'left'}, + wheelPad=2, oneTurn=.1, min=-1, max=1, + showLabel=0, precision=5, type=float) +@@ -378,7 +381,7 @@ + self.thumbx.canvas.unbind("<Button-3>") + self.thumbx.grid(row=0, column=1) + +- self.thumby = ThumbWheel(master=self.f, width=50, ++ self.thumby = ThumbWheel(master=self.f.grid, width=50, + height=20, labcfg={'text':'Y:','side':'left'}, + wheelPad=2, oneTurn=.1, min=-1, max=1, + showLabel=0, precision=5, type=float) +@@ -387,7 +390,7 @@ + self.thumby.canvas.unbind("<Button-3>") + self.thumby.grid(row=1, column=1) + +- self.thumbz = ThumbWheel(master=self.f, width=50, ++ self.thumbz = ThumbWheel(master=self.f.grid, width=50, + height=20, labcfg={'text':'Z:','side':'left'}, + wheelPad=2, oneTurn=.1, min=-1, max=1, + showLabel=0, precision=5, type=float) +@@ -397,19 +400,19 @@ + self.thumbz.grid(row=2, column=1) + + self.entryXTk = Tkinter.StringVar() +- self.entryX = Tkinter.Entry(master=self.f, textvariable=self.entryXTk, ++ self.entryX = Tkinter.Entry(master=self.f.grid, textvariable=self.entryXTk, + width=8) + self.entryX.bind('<Return>', self.entryX_cb) + self.entryX.grid(row=0, column=2) + + self.entryYTk = Tkinter.StringVar() +- self.entryY = Tkinter.Entry(master=self.f, textvariable=self.entryYTk, ++ self.entryY = Tkinter.Entry(master=self.f.grid, textvariable=self.entryYTk, + width=8) + self.entryY.bind('<Return>', self.entryY_cb) + self.entryY.grid(row=1, column=2) + + self.entryZTk = Tkinter.StringVar() +- self.entryZ = Tkinter.Entry(master=self.f, textvariable=self.entryZTk, ++ self.entryZ = Tkinter.Entry(master=self.f.grid, textvariable=self.entryZTk, + width=8) + self.entryZ.bind('<Return>', self.entryZ_cb) + self.entryZ.grid(row=2, column=2) +@@ -420,7 +423,6 @@ + + self.entryV.bind('<Return>', self.entryV_cb) + +- self.f.pack(side='top', expand=1) + + self.entryV.pack() + diff --git a/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild b/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6-r1.ebuild index 6c49892a9..1c70a67d4 100644 --- a/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6.ebuild +++ b/sci-chemistry/mgltools-mglutil/mgltools-mglutil-1.5.6-r1.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="mglutil" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- mglutil" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,12 +29,15 @@ S="${WORKDIR}"/${MY_P} DOCS=( mglutil/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { - local PATCHES=( "${FILESDIR}"/1.5.4-python.patch ) + local PATCHES=( + "${FILESDIR}"/1.5.4-python.patch + "${FILESDIR}"/${P}-tcltk86.patch + ) ecvs_clean find "${S}" -name LICENSE -type f -delete || die diff --git a/sci-chemistry/mgltools-molkit/ChangeLog b/sci-chemistry/mgltools-molkit/ChangeLog index aa978e4d4..fc3ad35dc 100644 --- a/sci-chemistry/mgltools-molkit/ChangeLog +++ b/sci-chemistry/mgltools-molkit/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-molkit -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-molkit-1.5.6.ebuild: + sci-chemistry/mgltools-molkit: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-molkit-1.5.6.ebuild: + sci-chemistry/mgltools-molkit: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-molkit-1.5.4-r1.ebuild, mgltools-molkit-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-molkit-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild b/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild index 29b1fd000..bab98713c 100644 --- a/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild +++ b/sci-chemistry/mgltools-molkit/mgltools-molkit-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="MolKit" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- MolKit" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( MolKit/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-networkeditor/ChangeLog b/sci-chemistry/mgltools-networkeditor/ChangeLog index ef4b065f9..cc5fa3d6d 100644 --- a/sci-chemistry/mgltools-networkeditor/ChangeLog +++ b/sci-chemistry/mgltools-networkeditor/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-chemistry/mgltools-networkeditor -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-networkeditor-1.5.6.ebuild: + sci-chemistry/mgltools-networkeditor: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-networkeditor-1.5.6.ebuild: + sci-chemistry/mgltools-networkeditor: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-networkeditor-1.5.4-r1.ebuild, mgltools-networkeditor-1.5.6.ebuild: Drop old @@ -54,4 +63,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-networkeditor-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild b/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild index 9daf6bd4c..5257d33d6 100644 --- a/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild +++ b/sci-chemistry/mgltools-networkeditor/mgltools-networkeditor-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="NetworkEditor" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- NetworkEditor" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( NetworkEditor/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-opengltk/ChangeLog b/sci-chemistry/mgltools-opengltk/ChangeLog index 8691b28f9..eab603f25 100644 --- a/sci-chemistry/mgltools-opengltk/ChangeLog +++ b/sci-chemistry/mgltools-opengltk/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-opengltk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-opengltk-1.5.6.ebuild: + sci-chemistry/mgltools-opengltk: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-opengltk-1.5.6.ebuild: + sci-chemistry/mgltools-opengltk: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-opengltk-1.5.4-r2.ebuild, mgltools-opengltk-1.5.6.ebuild: Drop old @@ -68,4 +74,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-opengltk-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild b/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild index bbcb0addd..0f7753ad6 100644 --- a/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild +++ b/sci-chemistry/mgltools-opengltk/mgltools-opengltk-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils prefix MY_PN="opengltk" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- opengltk" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -23,10 +21,10 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=" - dev-lang/tk - dev-python/numpy + dev-lang/tk:0 + dev-python/numpy[${PYTHON_USEDEP}] dev-tcltk/tkdnd - dev-tcltk/togl + dev-tcltk/togl:0 media-libs/glew virtual/opengl" DEPEND="${RDEPEND} @@ -35,8 +33,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-pmv/ChangeLog b/sci-chemistry/mgltools-pmv/ChangeLog index 5621b7dd7..5e1e651c4 100644 --- a/sci-chemistry/mgltools-pmv/ChangeLog +++ b/sci-chemistry/mgltools-pmv/ChangeLog @@ -1,7 +1,22 @@ # ChangeLog for sci-chemistry/mgltools-pmv -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pmv-1.5.6.ebuild: + sci-chemistry/mgltools-pmv: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pmv-1.5.6.ebuild: + sci-chemistry/mgltools-pmv: Drop PYTHON_MODNAME and support for python2_6 + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pmv-1.5.6.ebuild: + sci-chemistry/mgltools-pmv: Add missing dep + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pmv-1.5.6.ebuild: + sci-chemistry/mgltools-pmv: Add missing dep + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pmv-1.5.6.ebuild: + sci-chemistry/mgltools-pmv: Drop PYTHON_MODNAME + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-pmv-1.5.4-r1.ebuild, mgltools-pmv-1.5.6.ebuild: Drop old @@ -53,4 +68,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-pmv-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild b/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild index cf7c0ee41..a01b7e941 100644 --- a/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild +++ b/sci-chemistry/mgltools-pmv/mgltools-pmv-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="Pmv" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- Pmv" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,7 +20,14 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="" +RDEPEND=" + sci-chemistry/mgltools-dejavu[${PYTHON_USEDEP}] + sci-chemistry/mgltools-mglutil[${PYTHON_USEDEP}] + sci-chemistry/mgltools-molkit[${PYTHON_USEDEP}] + sci-chemistry/mgltools-opengltk[${PYTHON_USEDEP}] + sci-chemistry/mgltools-pybabel[${PYTHON_USEDEP}] + sci-chemistry/mgltools-support[${PYTHON_USEDEP}] + " DEPEND="${RDEPEND} dev-lang/swig" @@ -31,8 +36,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( Pmv/RELNOTES Pmv/doc ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-pyautodock/ChangeLog b/sci-chemistry/mgltools-pyautodock/ChangeLog index cc486b0da..2268280e2 100644 --- a/sci-chemistry/mgltools-pyautodock/ChangeLog +++ b/sci-chemistry/mgltools-pyautodock/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-pyautodock -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pyautodock-1.5.6.ebuild: + sci-chemistry/mgltools-pyautodock: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pyautodock-1.5.6.ebuild: + sci-chemistry/mgltools-pyautodock: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-pyautodock-1.5.4-r1.ebuild, mgltools-pyautodock-1.5.6.ebuild: Drop old @@ -51,4 +58,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-pyautodock-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild b/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild index 1b87efb52..ad601bbfe 100644 --- a/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild +++ b/sci-chemistry/mgltools-pyautodock/mgltools-pyautodock-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="PyAutoDock" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- PyAutoDock" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-pybabel/ChangeLog b/sci-chemistry/mgltools-pybabel/ChangeLog index 539007bb9..2b961575e 100644 --- a/sci-chemistry/mgltools-pybabel/ChangeLog +++ b/sci-chemistry/mgltools-pybabel/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-pybabel -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pybabel-1.5.6.ebuild: + sci-chemistry/mgltools-pybabel: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pybabel-1.5.6.ebuild: + sci-chemistry/mgltools-pybabel: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-pybabel-1.5.4-r1.ebuild, mgltools-pybabel-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-pybabel-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild b/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild index 85f8495d5..ba9a4685f 100644 --- a/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild +++ b/sci-chemistry/mgltools-pybabel/mgltools-pybabel-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="PyBabel" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- PyBabel" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( PyBabel/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-pyglf/ChangeLog b/sci-chemistry/mgltools-pyglf/ChangeLog index fa456a467..dc0e429dc 100644 --- a/sci-chemistry/mgltools-pyglf/ChangeLog +++ b/sci-chemistry/mgltools-pyglf/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-pyglf -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pyglf-1.5.6.ebuild: + sci-chemistry/mgltools-pyglf: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-pyglf-1.5.6.ebuild: + sci-chemistry/mgltools-pyglf: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-pyglf-1.5.4-r1.ebuild, mgltools-pyglf-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-pyglf-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild b/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild index 685d8a02f..144115d24 100644 --- a/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild +++ b/sci-chemistry/mgltools-pyglf/mgltools-pyglf-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="pyglf" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- pyglf" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-qslimlib/ChangeLog b/sci-chemistry/mgltools-qslimlib/ChangeLog index 76ddf87d1..f3f9113d4 100644 --- a/sci-chemistry/mgltools-qslimlib/ChangeLog +++ b/sci-chemistry/mgltools-qslimlib/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-qslimlib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-qslimlib-1.5.6.ebuild: + sci-chemistry/mgltools-qslimlib: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-qslimlib-1.5.6.ebuild: + sci-chemistry/mgltools-qslimlib: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-qslimlib-1.5.4-r1.ebuild, mgltools-qslimlib-1.5.6.ebuild: Drop old @@ -54,4 +60,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +files/1.5.4-gcc4.3.patch, +mgltools-qslimlib-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild b/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild index 55ced2b10..880383a95 100644 --- a/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild +++ b/sci-chemistry/mgltools-qslimlib/mgltools-qslimlib-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="QSlimLib" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- QSlimLib" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-scenario2/ChangeLog b/sci-chemistry/mgltools-scenario2/ChangeLog index a56b2915d..54968bf01 100644 --- a/sci-chemistry/mgltools-scenario2/ChangeLog +++ b/sci-chemistry/mgltools-scenario2/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-scenario2 -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-scenario2-1.5.6.ebuild: + sci-chemistry/mgltools-scenario2: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-scenario2-1.5.6.ebuild: + sci-chemistry/mgltools-scenario2: Drop PYTHON_MODNAME and support for + python2_6 + 14 Apr 2013; Justin Lecher <jlec@gentoo.org> mgltools-scenario2-1.5.6.ebuild: Correct license @@ -49,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-scenario-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild b/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild index 440859324..2e1f8a1ff 100644 --- a/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild +++ b/sci-chemistry/mgltools-scenario2/mgltools-scenario2-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="Scenario2" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- Scenario2" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -23,16 +21,17 @@ KEYWORDS="~amd64 ~x86" IUSE="" RDEPEND=" - dev-python/simpy - dev-python/pmw[${PYTHON_USEDEP}]" + dev-python/simpy[${PYTHON_USEDEP}] + virtual/pmw[${PYTHON_USEDEP}] + " DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-sff/ChangeLog b/sci-chemistry/mgltools-sff/ChangeLog index ea586c669..36a527d35 100644 --- a/sci-chemistry/mgltools-sff/ChangeLog +++ b/sci-chemistry/mgltools-sff/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-sff -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-sff-1.5.6.ebuild: + sci-chemistry/mgltools-sff: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-sff-1.5.6.ebuild: + sci-chemistry/mgltools-sff: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-sff-1.5.4-r1.ebuild, mgltools-sff-1.5.6.ebuild: Drop old @@ -49,4 +55,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-sff-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild b/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild index ee22cc89a..7e9a49751 100644 --- a/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild +++ b/sci-chemistry/mgltools-sff/mgltools-sff-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="sff" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- sff" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-support/ChangeLog b/sci-chemistry/mgltools-support/ChangeLog index 9fe772d84..29e6649e1 100644 --- a/sci-chemistry/mgltools-support/ChangeLog +++ b/sci-chemistry/mgltools-support/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-support -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-support-1.5.6.ebuild: + sci-chemistry/mgltools-support: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-support-1.5.6.ebuild: + sci-chemistry/mgltools-support: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-support-1.5.4-r1.ebuild, mgltools-support-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-support-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild b/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild index b591d590f..ff3edead2 100644 --- a/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild +++ b/sci-chemistry/mgltools-support/mgltools-support-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="Support" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- Support" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-symserv/ChangeLog b/sci-chemistry/mgltools-symserv/ChangeLog index 13649aa06..2268944d9 100644 --- a/sci-chemistry/mgltools-symserv/ChangeLog +++ b/sci-chemistry/mgltools-symserv/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-symserv -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-symserv-1.5.6.ebuild: + sci-chemistry/mgltools-symserv: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-symserv-1.5.6.ebuild: + sci-chemistry/mgltools-symserv: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-symserv-1.5.4-r1.ebuild, mgltools-symserv-1.5.6.ebuild: Drop old @@ -48,4 +54,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-symserv-1.5.4.ebuild, +metadata.xml: Initial setup - diff --git a/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild b/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild index 3d4aa6ac5..d170158a7 100644 --- a/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild +++ b/sci-chemistry/mgltools-symserv/mgltools-symserv-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="symserv" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- symserv" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-utpackages/ChangeLog b/sci-chemistry/mgltools-utpackages/ChangeLog index d4325cc5e..5b532d76b 100644 --- a/sci-chemistry/mgltools-utpackages/ChangeLog +++ b/sci-chemistry/mgltools-utpackages/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-utpackages -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-utpackages-1.5.6.ebuild: + sci-chemistry/mgltools-utpackages: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-utpackages-1.5.6.ebuild: + sci-chemistry/mgltools-utpackages: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-utpackages-1.5.4-r1.ebuild, mgltools-utpackages-1.5.6.ebuild: Drop old @@ -56,4 +63,3 @@ +files/1.5.4-gcc4.3.patch, +mgltools-utpackages-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild b/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild index dc644958b..24ab26e22 100644 --- a/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild +++ b/sci-chemistry/mgltools-utpackages/mgltools-utpackages-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="UTpackages" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- UTpackages" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/numpy" +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-viewer-framework/ChangeLog b/sci-chemistry/mgltools-viewer-framework/ChangeLog index 230f8e9f9..2f52b60d1 100644 --- a/sci-chemistry/mgltools-viewer-framework/ChangeLog +++ b/sci-chemistry/mgltools-viewer-framework/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-chemistry/mgltools-viewer-framework -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-viewer-framework-1.5.6.ebuild: + sci-chemistry/mgltools-viewer-framework: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-viewer-framework-1.5.6.ebuild: + sci-chemistry/mgltools-viewer-framework: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-viewer-framework-1.5.4-r2.ebuild, mgltools-viewer-framework-1.5.6.ebuild: @@ -63,4 +72,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-viewer-framework-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild b/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild index c96a1787c..259b5bee6 100644 --- a/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild +++ b/sci-chemistry/mgltools-viewer-framework/mgltools-viewer-framework-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="ViewerFramework" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- ViewerFramework" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( ViewerFramework/RELNOTES ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-vision/ChangeLog b/sci-chemistry/mgltools-vision/ChangeLog index a1e92d46b..193cea8f8 100644 --- a/sci-chemistry/mgltools-vision/ChangeLog +++ b/sci-chemistry/mgltools-vision/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-vision -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-vision-1.5.6.ebuild: + sci-chemistry/mgltools-vision: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-vision-1.5.6.ebuild: + sci-chemistry/mgltools-vision: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-vision-1.5.4-r1.ebuild, mgltools-vision-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-vision-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild b/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild index 719d42b2e..d4530f8d7 100644 --- a/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild +++ b/sci-chemistry/mgltools-vision/mgltools-vision-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="Vision" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- Vision" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,7 +20,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/matplotlib[tk]" +RDEPEND="dev-python/matplotlib[tk,${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( Vision/FAQ.txt ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-visionlib/ChangeLog b/sci-chemistry/mgltools-visionlib/ChangeLog index ac7a8714c..21abdc97a 100644 --- a/sci-chemistry/mgltools-visionlib/ChangeLog +++ b/sci-chemistry/mgltools-visionlib/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/mgltools-visionlib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-visionlib-1.5.6.ebuild: + sci-chemistry/mgltools-visionlib: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-visionlib-1.5.6.ebuild: + sci-chemistry/mgltools-visionlib: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-visionlib-1.5.4-r1.ebuild, mgltools-visionlib-1.5.6.ebuild: Drop old @@ -50,4 +57,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-visionlib-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild b/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild index 1a80b256c..be66b23d1 100644 --- a/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild +++ b/sci-chemistry/mgltools-visionlib/mgltools-visionlib-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="VisionLibraries" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- VisionLibraries" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -29,8 +27,8 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-volume/ChangeLog b/sci-chemistry/mgltools-volume/ChangeLog index 4cf8384d8..570ec6904 100644 --- a/sci-chemistry/mgltools-volume/ChangeLog +++ b/sci-chemistry/mgltools-volume/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/mgltools-volume -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-volume-1.5.6.ebuild: + sci-chemistry/mgltools-volume: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-volume-1.5.6.ebuild: + sci-chemistry/mgltools-volume: Drop PYTHON_MODNAME and support for python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-volume-1.5.4-r1.ebuild, mgltools-volume-1.5.6.ebuild: Drop old @@ -50,4 +56,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-volume-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild b/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild index 89751fd1e..24f55deb7 100644 --- a/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild +++ b/sci-chemistry/mgltools-volume/mgltools-volume-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="Volume" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- Volume" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -31,8 +29,8 @@ S="${WORKDIR}"/${MY_P} DOCS=( Volume/RELNOTES Volume/README Volume/TODO ) src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools-webservices/ChangeLog b/sci-chemistry/mgltools-webservices/ChangeLog index d48d14696..fc59a49be 100644 --- a/sci-chemistry/mgltools-webservices/ChangeLog +++ b/sci-chemistry/mgltools-webservices/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-chemistry/mgltools-webservices -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-webservices-1.5.6.ebuild: + sci-chemistry/mgltools-webservices: Add missing die + + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> + mgltools-webservices-1.5.6.ebuild: + sci-chemistry/mgltools-webservices: Drop PYTHON_MODNAME and support for + python2_6 + 10 Jun 2013; Justin Lecher <jlec@gentoo.org> -mgltools-webservices-1.5.4-r2.ebuild, mgltools-webservices-1.5.6.ebuild: Drop old @@ -54,4 +63,3 @@ 17 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-WebServices-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild b/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild index 555eaebfe..a22280d57 100644 --- a/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild +++ b/sci-chemistry/mgltools-webservices/mgltools-webservices-1.5.6.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 eutils MY_PN="WebServices" MY_P="${MY_PN}-${PV/_rc3/}" -PYTHON_MODNAME="${MY_PN}" - DESCRIPTION="MGLTools Plugin -- WebServices" HOMEPAGE="http://mgltools.scripps.edu" SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" @@ -22,15 +20,15 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -RDEPEND="dev-python/zsi" +RDEPEND="dev-python/zsi[${PYTHON_USEDEP}]" DEPEND="${RDEPEND} dev-lang/swig" S="${WORKDIR}"/${MY_P} src_unpack() { - tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz - tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz + tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die + tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz || die } python_prepare_all() { diff --git a/sci-chemistry/mgltools/ChangeLog b/sci-chemistry/mgltools/ChangeLog index cb0f756ff..a93f84e46 100644 --- a/sci-chemistry/mgltools/ChangeLog +++ b/sci-chemistry/mgltools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/mgltools -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 Mar 2015; Justin Lecher <jlec@gentoo.org> mgltools-1.5.6.ebuild: + sci-chemistry/mgltools: Drop PYTHON_MODNAME and support for python2_6 + 14 Nov 2013; Justin Lecher <jlec@gentoo.org> mgltools-1.5.6.ebuild: Remove unnecessary CVS folder prior to installation @@ -65,4 +68,3 @@ 18 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> +mgltools-1.5.4.ebuild, +metadata.xml: Initial checkin - diff --git a/sci-chemistry/mgltools/mgltools-1.5.6.ebuild b/sci-chemistry/mgltools/mgltools-1.5.6.ebuild index cf9569ccb..516b630ab 100644 --- a/sci-chemistry/mgltools/mgltools-1.5.6.ebuild +++ b/sci-chemistry/mgltools/mgltools-1.5.6.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils python-r1 @@ -32,12 +32,13 @@ done RDEPEND="${PLUG_DEP} ${PYTHON_DEPS} - dev-lang/tk - sci-libs/msms - dev-python/pmw[${PYTHON_USEDEP}] + dev-lang/tk:0 + dev-python/numpy[${PYTHON_USEDEP}] dev-python/simpy[${PYTHON_USEDEP}] + sci-libs/msms virtual/python-imaging[tk,${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}]" + virtual/pmw[${PYTHON_USEDEP}] +" DEPEND="${RDEPEND}" src_install() { diff --git a/sci-chemistry/modelfree/ChangeLog b/sci-chemistry/modelfree/ChangeLog index dea500009..b70932c7e 100644 --- a/sci-chemistry/modelfree/ChangeLog +++ b/sci-chemistry/modelfree/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/modelfree -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 Mar 2015; Justin Lecher <jlec@gentoo.org> modelfree-4.20.ebuild: + sci-chemistry/modelfree: Fix for new gcc slotting + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> modelfree-4.20.ebuild: Drop all KEYWORDS due to broken revdeps @@ -35,4 +38,3 @@ 09 Feb 2012; Justin Lecher <jlec@gentoo.org> Manifest: Add this nasty binary package - diff --git a/sci-chemistry/modelfree/modelfree-4.20.ebuild b/sci-chemistry/modelfree/modelfree-4.20.ebuild index 9dbce615e..e848dc355 100644 --- a/sci-chemistry/modelfree/modelfree-4.20.ebuild +++ b/sci-chemistry/modelfree/modelfree-4.20.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -17,7 +17,7 @@ IUSE="doc examples" RDEPEND=" sci-libs/blas-reference - sys-devel/gcc:4.1" + =sys-devel/gcc-4.1*" DEPEND="dev-util/patchelf" S="${WORKDIR}" diff --git a/sci-chemistry/modeller/modeller-9.12-r3.ebuild b/sci-chemistry/modeller/modeller-9.12-r3.ebuild index 47251c86e..0ae04b5be 100644 --- a/sci-chemistry/modeller/modeller-9.12-r3.ebuild +++ b/sci-chemistry/modeller/modeller-9.12-r3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) PYTHON_COMPAT=( python{2_6,2_7} ) inherit distutils-r1 eutils multilib versionator diff --git a/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild b/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild index 0faad4a35..5ca38640f 100644 --- a/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild +++ b/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog index 6070df8a1..329425ea6 100644 --- a/sci-chemistry/nmrpipe/ChangeLog +++ b/sci-chemistry/nmrpipe/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/nmrpipe -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> + nmrpipe-8.1.2013.218.23.09-r1.ebuild: + sci-chemistry/nmrpipe: Drop emul package support + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> nmrpipe-8.1.2013.218.23.09-r1.ebuild: Drop all KEYWORDS due to broken revdeps diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild index 402cda36c..938dc8dd2 100644 --- a/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild +++ b/sci-chemistry/nmrpipe/nmrpipe-8.1.2013.218.23.09-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -47,14 +47,7 @@ RDEPEND="${DEPEND} sys-libs/ncurses x11-apps/xset || ( x11-libs/xview x11-libs/xview-bin ) - || ( - ( - x11-libs/libX11[abi_x86_32(-)] - ) - ( - app-emulation/emul-linux-x86-xlibs[-abi_x86_32(-)] - ) - ) + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] prefix? ( dev-util/patchelf )" S="${WORKDIR}" diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog index 9b16e0014..8b67f4305 100644 --- a/sci-chemistry/nwchem/ChangeLog +++ b/sci-chemistry/nwchem/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*nwchem-6.5_p26243-r7 (02 Mar 2015) + + 02 Mar 2015; Honza Macháček <Hloupy.Honza@centrum.cz> + -nwchem-6.5_p26243-r6.ebuild, +nwchem-6.5_p26243-r7.ebuild: + 2 more upstream patches added (Hnd_rys and Tddft_grad) + *nwchem-6.5_p26243-r6 (16 Feb 2015) 16 Feb 2015; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest index 73d4d6267..b86a88dd1 100644 --- a/sci-chemistry/nwchem/Manifest +++ b/sci-chemistry/nwchem/Manifest @@ -3,6 +3,7 @@ DIST Dmapp_inc.patch.gz 234 SHA256 58e25a87d9a2844eaaae542ffa244c55c1075b040b720 DIST Elpa_syncs.patch.gz 554 SHA256 ce5c45cf83d84e0a95266e667808e6e40df82e649db3b9faeb556f1e3724b8df SHA512 c6b6a11dbd40ec4ccd8e230cfd33f2667122c05572deb693ee5c516f0a7dfdefcca0bae8aef518b9cd88ce0a1aec413d3518cf29d14c0f91afdd3024ef9fd506 WHIRLPOOL 21c78a2041f5bd25475b4589c9bbef47aa98a18e7a313cea127530f21cff9f54bdecdd2b53e02e4fd991bb6f19a3399df527af2d289284070dde133aab2ca952 DIST Hbar.patch.gz 458 SHA256 6058010a77bc7d0bf7468dde49d7905863f2550b282abee4cceef901481272a7 SHA512 595d5250dd3d462e9d2e0b385a3b41ac828da0792e19606b0365f27b47c839e81ff16cdae590f91f48fa0ac52a4dfcee1c4929bd9054651ee27f9e7c3bf54dbc WHIRLPOOL 691ecac56d8ef8bfd377df40429e484d232b82ee28c0b546bb379d6120e00b54c408f55ccc3340e612759d1e4d72f2933f0ec40d3655ae94be03f9db3e925124 DIST Hnd_giaxyz_noinline.patch.gz 368 SHA256 4e89a383ebd0cc87b3de03133f4a0537de799e1ae938f82a6460632e324aeeb1 SHA512 a798412821e35fb3be28ff2df59ce578506635532b08f0f247bae39c85f1c0c912e5205f201f94407d9e3360e66bfb98119596bacc693165fc2b6924800c283c WHIRLPOOL f424a9773dfc45f8f6597dd5162bb10283e3b1e38b12b557089b925fa45aae02c0e988eb0785a1c7cbb5f6883df8767042e195037cc50f6a29e6cb033e5ff342 +DIST Hnd_rys.patch.gz 1585 SHA256 e52eee4df9149cce039b4b1d8047d51a5f47373fe03b57c6d0f44ca23b33c06e SHA512 5e95ec72e1b1e17b324d43f3cc68003b5724295e3cad03a9ab8c58636d43ad62ab1cc42e90a5f386854bfeb02b8327ee0f6632c5bd532320e3f34080628b8d84 WHIRLPOOL 6e8eaadb3c9312e247e5c06a34848311f5921622b448c32de67e1ee2d258fcc82eff75434d8392c0fe794e6261b08736a4bea7c569a00f969575c0d87e16f7ae DIST Ifort15_fpp_offload.patch.gz 1326 SHA256 907d86049b085bc4c2b9cb2e2554fba94e54e0cb2e380f9d4c5c6ea483c16915 SHA512 fd5559b334fd14006ef984157e22c7fb5297cad7bb29d5696dfe6eb458ba6822b3c2972b8e83e87375091dac4dc18863dd4a817e8b1a64f720de6af99d34aa19 WHIRLPOOL e9a09b91a9ecc0f186bc53bb345bd35d9a0cbb8e145eb95c69a523d55b633ff38a3791b8b106d9855b09381cf400e72bb36be11af37e337928b9fa2f3e8b9917 DIST Makefile_gcc4x.patch.gz 1493 SHA256 c548c64eab196ef7aabd473379ec56c879c5a6e9e9a4d31c6503279a72094839 SHA512 35d46f78da48519ccf21b8853bfc32b958419a600ef7897135f52bc8f7dcfe733883f6600cfd88e75a8c68c3fe9fb0f6302493889df7fbc84f1dd7be29929136 WHIRLPOOL 70b7431fb11f8da971de52a4cba985548da1fa388859cf784016fc646e49d00cedf2918c9a7c47f29239b514220f47837bddff6aaa3762c5afd2c69a68bb18cb DIST Nwchem-6.3.revision2-src.2013-10-17.tar.gz 112262489 SHA256 6a6adf068d559be1ab1bf0addc6b8aa65dbb746b8716a913f5f1bb2eb16f1718 SHA512 28b812b62bba464e6a9c76ccae17145b42ab92c460cc4372bfb6e5d48db0b618d06e778bd2f4787ffcb2d95e60e869af60739181b2f334430592764b41e5f988 WHIRLPOOL 75d4053711fcd1f69c9b3813ed00fe492aa918e75c11c60a7fb67b202bd0dfe410e80d4c7f5423ef76f4a8472db809bd91c4218159087255b495908b4be32b4b @@ -10,6 +11,7 @@ DIST Nwchem-6.5.revision26243-src.2014-09-10.tar.gz 131069464 SHA256 9af6d7d7424 DIST Parallelmpi.patch.gz 216 SHA256 d30de8a7027bd5ea7672ad1fa63711a3cfc5cb118f878bc5308a142319d31420 SHA512 21d9020f77814056d3690dca71783e635a4eb951785cf12addc1ff4082b582c82399eb3c3f4f01892d5249fc30a8de1a9a18c1bf37841957bfc924d579f8f7ea WHIRLPOOL 12ac85104503ad5a14b2b67cf727ac8cd16d19311a1100e8aee612bdf1dcacc8e606b3be10c464daaf3681f22b141fd31019cfc5ed84ed5e89e33b2985c89554 DIST Print1e.patch.gz 463 SHA256 59c4d96c9da4b7fb08dee2a89afcbc6ac603c141d48cf3a16e41a92dc2a539e5 SHA512 c53105fb01bb307f7483e55adcd920a4c538cb8634af2c3fa0a13ae1899060603d67fc19392c53ae7499bef48434d667ce690ce66a50dd084bc0583fbe1d95d9 WHIRLPOOL b7562de186a0211ff97c3d378319580578fc7faa7e72ece190c852673a10101207ff779a29781559de2ac5bb373c87639c97ae4465e4a3c84e504958148d231f DIST Tcenxtask.patch.gz 1556 SHA256 6b3f713024fec9a41bd7738e3cd6d31731d17a3b59a02d9a484e0a2408fcb9ca SHA512 9e11a2566c20b07a458cbd0ebe58e006b3ef04831625f3b88e38d20570945ff5138c18f148491bf890f8431699af3c180d948fe6677acf82d557c44e9a7384b5 WHIRLPOOL 8d0923a1789845be126e569a4a17703e2fda4aed9a9d2e9472d62968c9c40c38af8c40f35033bd4d644077da5ae8218c38d8ddfa82ef6313d67bfd6a5888f249 +DIST Tddft_grad.patch.gz 1301 SHA256 73028f7e1d5cae1f3b1e31d30accbaec519a073696d96110ebba02cb6735ba9f SHA512 5b047f9bbd42cf5b02e651a43b65a4be95208139a75fe959267a9445fd84c8a47667d7dde24a7c02aa380a9d0d40b7dd74a4ad1051657f8bf582aa1345d45632 WHIRLPOOL 425a804dd0d3f3533a456206188a86b3ae4296508379cd6cb75938050022fd5a728a26da2c3beb20087ed7c5ebe55e8cf0eb48cdba982954806737f88aa0ec80 DIST Texas_iorb.patch.gz 378 SHA256 0caab84a2b9628a65232c24364c45ab29dd8637b0b29b15e1d089005eda20745 SHA512 9dc89172999606245e899a884aac073ebd40a102ba6e4164b0e548ad6cc3b37d5744b70896309c2e53871694aeb63b231b90b12e32c019ec84547b2b12e9c2f2 WHIRLPOOL 50ae525f445b4091174171fd69152a967ac48ed9ad1d0a70a9e034de27bed78ca5c7f83d9ef042ad2d19ec3b8c342cb18ee0c9d931a9d34878aa5f7779ed9702 DIST Util_md_sockets.patch.gz 324 SHA256 843d0d9152a3d3735557a8710ae8c6a260732a2b8e0d9ed823bbd430efff44ee SHA512 743ae8d7cdbe6612a26a10ce845003abab08c1704956940bccf249d00c1d07cf169cfb3cf648c209d5c1dc564abfeddeb8d216259f463c0d564f617c099f5e82 WHIRLPOOL cedf1d8253fb085bb6851effe25e230965cc6690441c865344f10d01e2966687753375fa3e69475378ec495c3ba85d4539417e07f2e61597060730e9f63b8f0d DIST Xlmpoles_ifort15.patch.gz 256 SHA256 ae957064165afe8abcfeb580146b59b8ca680a7a5f528402047b3f8672c1e131 SHA512 f770263a22d5f680c92d52a521ddbd748633dcdf125fe75f353d70d4557fe4c8f0c25ad07e05d8452124f78523552bb87446bff10532cfccc5bc2ce941aac855 WHIRLPOOL f97940620e05d8439119e78c2ba46ea5ebae33c16b69e6bb334cf19156573a21cf0a2c8271bc76ebf3c3e27b9b0d43239d5884fccac004b7ce4a80ac5a6f5e42 diff --git a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild b/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild index a14e8f91c..64a6a2f52 100644 --- a/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild +++ b/sci-chemistry/nwchem/nwchem-6.3_p2-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs diff --git a/sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild index 118d6a52d..d689417a1 100644 --- a/sci-chemistry/nwchem/nwchem-6.5_p26243-r6.ebuild +++ b/sci-chemistry/nwchem/nwchem-6.5_p26243-r7.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs @@ -25,7 +25,9 @@ SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV%_p*}.revision${PV#*_p}-src. http://www.nwchem-sw.org/images/Ifort15_fpp_offload.patch.gz http://www.nwchem-sw.org/images/Texas_iorb.patch.gz http://www.nwchem-sw.org/images/Dmapp_inc.patch.gz - http://www.nwchem-sw.org/images/Print1e.patch.gz" + http://www.nwchem-sw.org/images/Print1e.patch.gz + http://www.nwchem-sw.org/images/Hnd_rys.patch.gz + http://www.nwchem-sw.org/images/Tddft_grad.patch.gz" LICENSE="ECL-2.0" SLOT="0" @@ -111,7 +113,7 @@ src_unpack() { src_prepare() { pushd "${S}"/src - for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb Dmapp_inc Print1e + for p in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs Xlmpoles_ifort15 Ifort15_fpp_offload Texas_iorb Dmapp_inc Print1e Hnd_rys Tddft_grad do epatch "${WORKDIR}"/"${p}.patch" done cd NWints/hondo diff --git a/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild b/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild index 3a6c09005..615d0379f 100644 --- a/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild +++ b/sci-chemistry/openbabel-python/openbabel-python-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) inherit cmake-utils eutils git-r3 multilib python-r1 diff --git a/sci-chemistry/pesto/pesto-9999.ebuild b/sci-chemistry/pesto/pesto-9999.ebuild index 50a39917d..788365c62 100644 --- a/sci-chemistry/pesto/pesto-9999.ebuild +++ b/sci-chemistry/pesto/pesto-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 flag-o-matic fortran-2 mercurial toolchain-funcs diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.8.2.1309.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.8.2.1309.ebuild index 07737df46..3be483d54 100644 --- a/sci-chemistry/phenix-bin/phenix-bin-1.8.2.1309.ebuild +++ b/sci-chemistry/phenix-bin/phenix-bin-1.8.2.1309.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit python-single-r1 versionator diff --git a/sci-chemistry/phenix-bin/phenix-bin-1.8.4.1496.ebuild b/sci-chemistry/phenix-bin/phenix-bin-1.8.4.1496.ebuild index 9219d5e6c..277160561 100644 --- a/sci-chemistry/phenix-bin/phenix-bin-1.8.4.1496.ebuild +++ b/sci-chemistry/phenix-bin/phenix-bin-1.8.4.1496.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) WX_GTK_VER=2.8 diff --git a/sci-chemistry/pymol-plugins-psico/ChangeLog b/sci-chemistry/pymol-plugins-psico/ChangeLog index 00cfae7b4..dd34ca921 100644 --- a/sci-chemistry/pymol-plugins-psico/ChangeLog +++ b/sci-chemistry/pymol-plugins-psico/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/pymol-plugins-psico -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/pymol-plugins-psico: Add github to remote-id in metadata.xml + 14 Nov 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild: bump to git-r3 eclass @@ -17,4 +20,3 @@ 21 Mar 2012; Justin Lecher <jlec@gentoo.org> +pymol-plugins-psico-9999.ebuild, +metadata.xml: New addition, written by me, #408995 - diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml index ae9ec7c5f..3eff7c70c 100644 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ b/sci-chemistry/pymol-plugins-psico/metadata.xml @@ -5,4 +5,7 @@ <maintainer> <email>jlec@gentoo.org</email> </maintainer> + <upstream> + <remote-id type="github">speleo3/pymol-psico</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild index 7c59b346a..98f499c36 100644 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild +++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog index 2f4a8434c..656aa2529 100644 --- a/sci-chemistry/pymol/ChangeLog +++ b/sci-chemistry/pymol/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-chemistry/pymol -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Mar 2015; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild: + sci-chemistry/pymol: Move to virtual/pmw + + 14 Mar 2015; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild: + sci-chemistry/pymol: Fix for latest HEAD; fix SLOT operators + 05 Nov 2014; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild, -files/pymol-9999-listing.patch, -files/pymol-9999-options.patch, -files/pymol-9999-tk8.6.patch: @@ -371,4 +377,3 @@ +sci-chemistry/pymol/files/nosplash-gentoo.patch, +sci-chemistry/pymol/metadata.xml: Initial checkin of pymol to sci-overlay - diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild index 56c62a80d..ab58ffe9a 100644 --- a/sci-chemistry/pymol/pymol-9999.ebuild +++ b/sci-chemistry/pymol/pymol-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -7,7 +7,7 @@ EAPI=5 PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" -inherit distutils-r1 fdo-mime subversion versionator +inherit distutils-r1 fdo-mime flag-o-matic subversion versionator DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="http://www.pymol.org/" @@ -21,14 +21,14 @@ IUSE="apbs web" DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pmw[${PYTHON_USEDEP}] dev-python/pyopengl[${PYTHON_USEDEP}] + media-libs/freeglut media-libs/freetype:2 media-libs/glew - media-libs/libpng + media-libs/libpng:0= media-video/mpeg-tools sys-libs/zlib - media-libs/freeglut + virtual/pmw[${PYTHON_USEDEP}] apbs? ( sci-chemistry/apbs[${PYTHON_USEDEP}] sci-chemistry/pdb2pqr[${PYTHON_USEDEP}] @@ -54,6 +54,8 @@ python_prepare_all() { -e '/ext_comp_args/s:\[.*\]:[]:g' \ -i setup.py || die + append-cxxflags -std=c++0x + distutils-r1_python_prepare_all } diff --git a/sci-chemistry/pyquante/ChangeLog b/sci-chemistry/pyquante/ChangeLog index f854df533..a44c5e8fa 100644 --- a/sci-chemistry/pyquante/ChangeLog +++ b/sci-chemistry/pyquante/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/pyquante -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-chemistry/pyquante: Updating remote-id in metadata.xml + *pyquante-1.6.4 (07 Dec 2013) 07 Dec 2013; Nicolas Bock <nicolasbock@gmail.com> +pyquante-1.6.4.ebuild: diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml index 51fdedab1..12ca64b3a 100644 --- a/sci-chemistry/pyquante/metadata.xml +++ b/sci-chemistry/pyquante/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> + <upstream> + <remote-id type="sourceforge">pyquante</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild index 6e106b1e0..ad49ccdff 100644 --- a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild +++ b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-chemistry/pyquante/pyquante-1.6.4.ebuild b/sci-chemistry/pyquante/pyquante-1.6.4.ebuild index 6e106b1e0..ad49ccdff 100644 --- a/sci-chemistry/pyquante/pyquante-1.6.4.ebuild +++ b/sci-chemistry/pyquante/pyquante-1.6.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild index e012c653a..14da0c747 100644 --- a/sci-chemistry/smmp/smmp-3.0.5.ebuild +++ b/sci-chemistry/smmp/smmp-3.0.5.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils fortran-2 python-r1 toolchain-funcs diff --git a/sci-chemistry/specView/ChangeLog b/sci-chemistry/specView/ChangeLog index 7ce8a0409..d5c601059 100644 --- a/sci-chemistry/specView/ChangeLog +++ b/sci-chemistry/specView/ChangeLog @@ -5,12 +5,12 @@ *specView-1.0.4 (25 Apr 2014) 25 Apr 2014; Justin Lecher <jlec@gentoo.org> +specView-1.0.4.ebuild: - Version BUmp + Version Bump *specView-1.0.3_p2 (26 Mar 2014) 26 Mar 2014; Justin Lecher <jlec@gentoo.org> +specView-1.0.3_p2.ebuild: - Version BUmp + Version Bump 08 Jan 2014; Justin Lecher <jlec@gentoo.org> specView-1.0.3.ebuild: Fix double prefix diff --git a/sci-chemistry/specView/specView-1.0.2.ebuild b/sci-chemistry/specView/specView-1.0.2.ebuild index df30e7b8a..c1c87eafa 100644 --- a/sci-chemistry/specView/specView-1.0.2.ebuild +++ b/sci-chemistry/specView/specView-1.0.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit multilib python-single-r1 toolchain-funcs diff --git a/sci-chemistry/specView/specView-1.0.3.ebuild b/sci-chemistry/specView/specView-1.0.3.ebuild index ebf074924..77a96e964 100644 --- a/sci-chemistry/specView/specView-1.0.3.ebuild +++ b/sci-chemistry/specView/specView-1.0.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit multilib python-single-r1 toolchain-funcs diff --git a/sci-chemistry/specView/specView-1.0.3_p2.ebuild b/sci-chemistry/specView/specView-1.0.3_p2.ebuild index 279a8fc60..169f1beee 100644 --- a/sci-chemistry/specView/specView-1.0.3_p2.ebuild +++ b/sci-chemistry/specView/specView-1.0.3_p2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit multilib python-single-r1 toolchain-funcs diff --git a/sci-chemistry/specView/specView-1.0.4.ebuild b/sci-chemistry/specView/specView-1.0.4.ebuild index 762bdc97a..82d2a668d 100644 --- a/sci-chemistry/specView/specView-1.0.4.ebuild +++ b/sci-chemistry/specView/specView-1.0.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit flag-o-matic multilib python-single-r1 toolchain-funcs diff --git a/sci-chemistry/unio/ChangeLog b/sci-chemistry/unio/ChangeLog index dedf80d89..45ac72c5d 100644 --- a/sci-chemistry/unio/ChangeLog +++ b/sci-chemistry/unio/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/unio -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> unio-2.0.3-r1.ebuild: + sci-chemistry/unio: Drop emul package support + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> unio-2.0.3-r1.ebuild: Drop all KEYWORDS due to broken revdeps diff --git a/sci-chemistry/unio/unio-2.0.3-r1.ebuild b/sci-chemistry/unio/unio-2.0.3-r1.ebuild index 94617754e..1104689b0 100644 --- a/sci-chemistry/unio/unio-2.0.3-r1.ebuild +++ b/sci-chemistry/unio/unio-2.0.3-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -18,13 +18,8 @@ IUSE="" RDEPEND=" app-shells/ksh - || ( - ( - x11-libs/libX11[abi_x86_32(-)] - x11-libs/libXext[abi_x86_32(-)] - ) - app-emulation/emul-linux-x86-xlibs[-abi_x86_32(-)] - )" + >=x11-libs/libX11-1.6.2[abi_x86_32(-)] + >=x11-libs/libXext-1.3.2[abi_x86_32(-)]" DEPEND="" S="${WORKDIR}/UNIO_10" diff --git a/sci-chemistry/xplor-nih/ChangeLog b/sci-chemistry/xplor-nih/ChangeLog index e635dd662..e5e80148d 100644 --- a/sci-chemistry/xplor-nih/ChangeLog +++ b/sci-chemistry/xplor-nih/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Mar 2015; Justin Lecher <jlec@gentoo.org> xplor-nih-2.38.ebuild: + sci-chemistry/xplor-nih: Add missing deps + *xplor-nih-2.38 (10 Feb 2015) 10 Feb 2015; Justin Lecher <jlec@gentoo.org> +metadata.xml, diff --git a/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild b/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild index f8f0bb747..c36e385fd 100644 --- a/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild +++ b/sci-chemistry/xplor-nih/xplor-nih-2.38.ebuild @@ -22,7 +22,10 @@ IUSE="" REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RDEPEND="${PYTHON_DEPS}" +RDEPEND="${PYTHON_DEPS} + dev-lang/tcl:8.5 + dev-lang/tk:8.5 +" DEPEND="${RDEPEND}" RESTRICT="fetch" diff --git a/sci-electronics/player/ChangeLog b/sci-electronics/player/ChangeLog index f6e4fa099..95f7f30b5 100644 --- a/sci-electronics/player/ChangeLog +++ b/sci-electronics/player/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-electronics/player -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/player: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> player-2.0.4.ebuild: Fix deps diff --git a/sci-electronics/player/metadata.xml b/sci-electronics/player/metadata.xml index 50de93857..822054cc9 100644 --- a/sci-electronics/player/metadata.xml +++ b/sci-electronics/player/metadata.xml @@ -8,4 +8,7 @@ <flag name="openssl">Automatically generated description for openssl</flag> <flag name="festival">Automatically generated description for festival</flag> </use> + <upstream> + <remote-id type="sourceforge">playerstage</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-electronics/player/player-2.0.4.ebuild b/sci-electronics/player/player-2.0.4.ebuild index 2c9f7120a..bcce27202 100644 --- a/sci-electronics/player/player-2.0.4.ebuild +++ b/sci-electronics/player/player-2.0.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils java-pkg-opt-2 python-single-r1 diff --git a/sci-electronics/stage/ChangeLog b/sci-electronics/stage/ChangeLog index d03723fcd..64514c649 100644 --- a/sci-electronics/stage/ChangeLog +++ b/sci-electronics/stage/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-electronics/stage -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/stage: Updating remote-id in metadata.xml + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> stage-2.0.3.ebuild: + Bump to EAPI=5 + 07 Mar 2011; Justin Lecher <jlec@gentoo.org> stage-2.0.3.ebuild: Correct Slots for gtk 3 introduction to tree diff --git a/sci-electronics/stage/Manifest b/sci-electronics/stage/Manifest index 729e06304..a1f4cb210 100644 --- a/sci-electronics/stage/Manifest +++ b/sci-electronics/stage/Manifest @@ -1 +1 @@ -DIST stage-2.0.3.tar.bz2 451664 SHA256 7a9619f5ef633d18a11900da1e59e807547180fce4420bb9e9b4c681ddbe6c83 +DIST stage-2.0.3.tar.bz2 451664 SHA256 7a9619f5ef633d18a11900da1e59e807547180fce4420bb9e9b4c681ddbe6c83 SHA512 1126b923dce49a8ea278fba39e3af87cf79273102e7349ec5418e421853f39dbc0512e71246b503bc34d96d424512f327a501ff5c1a22ba80c585ccf07f63de3 WHIRLPOOL 555ecfcdda19a069a8e12eb916d991badc3b09130c9038efda7a242d0084fd7221d675683df45ca386abe85b75aafb07f7ecdd83328bc1591e9982fae08d0c5e diff --git a/sci-electronics/stage/metadata.xml b/sci-electronics/stage/metadata.xml index 53ae7d77c..6c801c492 100644 --- a/sci-electronics/stage/metadata.xml +++ b/sci-electronics/stage/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-electronics</herd> + <herd>sci-electronics</herd> + <upstream> + <remote-id type="sourceforge">playerstage</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-electronics/stage/stage-2.0.3.ebuild b/sci-electronics/stage/stage-2.0.3.ebuild index 9ed0b530c..b293697f6 100644 --- a/sci-electronics/stage/stage-2.0.3.ebuild +++ b/sci-electronics/stage/stage-2.0.3.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 inherit autotools eutils @@ -37,25 +37,25 @@ src_configure() { } src_compile() { - emake || die "emake failed" + emake if use doc; then pushd docsrc doxygen -u stage.dox || die "doxygen failed" - touch header.html - emake "doc" || die "emake doc failed" + touch header.html || die + emake "doc" popd fi } src_install() { - emake DESTDIR="${D}" install || die "emake install failed" + emake DESTDIR="${D}" install if use doc; then pushd docsrc - emake DESTDIR="${D}" "doc-install" || die "emake doc-install failed" + emake DESTDIR="${D}" "doc-install" popd fi - dodoc AUTHORS ChangeLog NEWS README || die + dodoc AUTHORS ChangeLog NEWS README } diff --git a/sci-electronics/tnt/ChangeLog b/sci-electronics/tnt/ChangeLog index 24b19c3df..d70be2df2 100644 --- a/sci-electronics/tnt/ChangeLog +++ b/sci-electronics/tnt/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-electronics/tnt -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-electronics/tnt: Updating remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> tnt-1.2.2.ebuild, +files/tnt-1.2.2-autotools.patch, metadata.xml: Punt base.eclass diff --git a/sci-electronics/tnt/metadata.xml b/sci-electronics/tnt/metadata.xml index ce0e016bb..87d1cd2b1 100644 --- a/sci-electronics/tnt/metadata.xml +++ b/sci-electronics/tnt/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-electronics</herd> + <upstream> + <remote-id type="sourceforge">mmtl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/cdat-lite/ChangeLog b/sci-geosciences/cdat-lite/ChangeLog deleted file mode 100644 index 242e26723..000000000 --- a/sci-geosciences/cdat-lite/ChangeLog +++ /dev/null @@ -1,26 +0,0 @@ -# ChangeLog for sci-geosciences/cdat-lite -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 04 Dec 2013; Justin Lecher <jlec@gentoo.org> cdat-lite-5.2.ebuild, - cdat-lite-6.0_rc2.ebuild, metadata.xml: - Bump to distutils-r1 eclass - -*cdat-lite-6.0_rc2 (16 Jul 2011) - - 16 Jul 2011; Tim Cera <tim@cerazone.net> +cdat-lite-6.0_rc2.ebuild: - Version bump. - - 29 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/5.2-impl-dec.patch, - cdat-lite-5.2.ebuild, +files/5.2-shared-lib.patch: - Python ABI fixes, implicit declaration fixes - - 24 Apr 2010; Tim Cera <tim@cerazone.net> cdat-lite-5.2.ebuild: - Updated to latest style for Python ebuilds. - -*cdat-lite-5.2 (24 Jan 2010) - - 24 Jan 2010; Tim Cera <tim@cerazone.net> +cdat-lite-5.2.ebuild, - +metadata.xml: - Initial ebuild. - diff --git a/sci-geosciences/cdat-lite/Manifest b/sci-geosciences/cdat-lite/Manifest deleted file mode 100644 index a8e187dde..000000000 --- a/sci-geosciences/cdat-lite/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cdat_lite-5.2.tar.gz 3454154 SHA256 72e851d61d9f8be5d744b346ccbb16a757809f723e332ed09703bfaeb8c84bd7 SHA512 84ddd0f75bda999cea15c1dfa25c11e1cc1f94b163821e43ffdf18a0cf58e7561a7d771180dd32a01a5e70cfb4e8db25b12252f9b50276a6bb54602366efe758 WHIRLPOOL c52e908a14296ef519713976336d5bd402848e06f6f333288e862811133d91fd01be0096e413236d192efd7aa8804640ecf4782c3f3d9d408003e6645e396f14 -DIST cdat_lite-6.0rc2.tar.gz 3563402 SHA256 6cbfdf9b47fdbc189ca7d2819dafb6cf958116e0f6077b325c375a0ddfab2a95 diff --git a/sci-geosciences/cdat-lite/cdat-lite-5.2.ebuild b/sci-geosciences/cdat-lite/cdat-lite-5.2.ebuild deleted file mode 100644 index f7e252d5b..000000000 --- a/sci-geosciences/cdat-lite/cdat-lite-5.2.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 toolchain-funcs - -MY_P=${P/-/_} - -DESCRIPTION="Large suite of open source tools for the management and analysis of climate data" -HOMEPAGE="http://proj.badc.rl.ac.uk/cedaservices/wiki/CdatLite" -SRC_URI="http://ndg.nerc.ac.uk/dist/${MY_P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -COMMON_DEPEND=" - >=sci-libs/netcdf-4.0.1 - >=sci-libs/hdf5-1.6.4" -DEPEND="${COMMON_DEPEND} - dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND="${COMMON_DEPEND} - !sci-biology/ncbi-tools" - -S="${WORKDIR}"/${MY_P} - -PATCHES=( - "${FILESDIR}"/${PV}-shared-lib.patch - "${FILESDIR}"/${PV}-impl-dec.patch - ) - -python_prepare_all() { - find "${S}" -type l -exec rm '{}' \; - tc-export CC - sed \ - -e 's:libhdf5.a:libhdf5.so:g' \ - -i setup_util.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-geosciences/cdat-lite/cdat-lite-6.0_rc2.ebuild b/sci-geosciences/cdat-lite/cdat-lite-6.0_rc2.ebuild deleted file mode 100644 index 004e5c1ec..000000000 --- a/sci-geosciences/cdat-lite/cdat-lite-6.0_rc2.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 toolchain-funcs - -MY_P=${P/-/_} -MY_P=${MY_P/_rc/rc} - -DESCRIPTION="Large suite of open source tools for the management and analysis of climate data" -HOMEPAGE="http://proj.badc.rl.ac.uk/cedaservices/wiki/CdatLite" -SRC_URI="http://ndg.nerc.ac.uk/dist/${MY_P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -COMMON_DEPEND=" - >=sci-libs/netcdf-4.0.1 - >=sci-libs/hdf5-1.6.4" -DEPEND="${COMMON_DEPEND} - dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND="${COMMON_DEPEND} - !sci-biology/ncbi-tools" - -S="${WORKDIR}/${MY_P}" - -python_prepare_all() { - find "${S}" -type l -exec rm '{}' \; - tc-export CC - sed \ - -e 's:libhdf5.a:libhdf5.so:g' \ - -i setup_util.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-geosciences/cdat-lite/files/5.2-impl-dec.patch b/sci-geosciences/cdat-lite/files/5.2-impl-dec.patch deleted file mode 100644 index 866ae72c3..000000000 --- a/sci-geosciences/cdat-lite/files/5.2-impl-dec.patch +++ /dev/null @@ -1,60 +0,0 @@ -diff --git a/Packages/cdms2/Src/bindex.c b/Packages/cdms2/Src/bindex.c -index 9a91a3b..d8e6e4d 100644 ---- a/Packages/cdms2/Src/bindex.c -+++ b/Packages/cdms2/Src/bindex.c -@@ -2,6 +2,7 @@ - with data on non-rectilinear grids. - */ - #include <math.h> -+#include <stdio.h> - /* NBINI, NBINJ should match definition in bindex.bindexHorizontalGrid */ - #define NBINI 720 /* number of bins in the i (longitude) direction */ - #define NBINJ 360 /* number of bins in the j (latitude) direction */ -diff --git a/libcdms/src/cdunif/cdunifnc.c b/libcdms/src/cdunif/cdunifnc.c -index 75f2b2f..8af93e1 100644 ---- a/libcdms/src/cdunif/cdunifnc.c -+++ b/libcdms/src/cdunif/cdunifnc.c -@@ -28,6 +28,7 @@ - - #ifdef netcdf - #include <stdlib.h> -+#include <string.h> - #include "netcdf.h" - #include "cdunifint.h" - -diff --git a/libcdms/src/cdunif/gaddes.c b/libcdms/src/cdunif/gaddes.c -index aac8152..0dcd634 100644 ---- a/libcdms/src/cdunif/gaddes.c -+++ b/libcdms/src/cdunif/gaddes.c -@@ -20,6 +20,7 @@ - #include <stdio.h> - #include <math.h> - #include <ctype.h> -+#include <string.h> - #ifndef __APPLE__ - #include <malloc.h> - #endif -diff --git a/libcdms/src/cdunif/gaio.c b/libcdms/src/cdunif/gaio.c -index c64ae83..21b61f8 100644 ---- a/libcdms/src/cdunif/gaio.c -+++ b/libcdms/src/cdunif/gaio.c -@@ -4,6 +4,7 @@ - - #include <math.h> - #include <stdio.h> -+#include <string.h> - #ifndef __APPLE__ - #include <malloc.h> - #endif -diff --git a/libcdms/src/db_util/cdRegTrfm.c b/libcdms/src/db_util/cdRegTrfm.c -index cd88441..97d0185 100644 ---- a/libcdms/src/db_util/cdRegTrfm.c -+++ b/libcdms/src/db_util/cdRegTrfm.c -@@ -32,6 +32,7 @@ - */ - - #include <stdio.h> -+#include <string.h> - #include <cdmsint.h> - #include <isdb.h> - /* copy CDMS geom to NEONS ngeom */ diff --git a/sci-geosciences/cdat-lite/files/5.2-shared-lib.patch b/sci-geosciences/cdat-lite/files/5.2-shared-lib.patch deleted file mode 100644 index 81bec96a6..000000000 --- a/sci-geosciences/cdat-lite/files/5.2-shared-lib.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/setup_util.py b/setup_util.py -index 1eea295..e17342a 100644 ---- a/setup_util.py -+++ b/setup_util.py -@@ -116,7 +116,7 @@ def check_ifnetcdf4(netcdf4_incdir): - - netcdf_incdir, netcdf_libdir = DepFinder('NetCDF', 'NETCDF_HOME', - includefile='netcdf.h', -- libfile='libnetcdf.a').find() -+ libfile='libnetcdf.so').find() - # If using NetCDF4 find the HDF5 libraries - if check_ifnetcdf4(netcdf_incdir): - print 'NetCDF4 detected. Including HDF libraries' diff --git a/sci-geosciences/cdat-lite/metadata.xml b/sci-geosciences/cdat-lite/metadata.xml deleted file mode 100644 index 50f2b52a9..000000000 --- a/sci-geosciences/cdat-lite/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -CDAT-Lite is a large suite of open source tools for the management and analysis of climate data. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/congen/ChangeLog b/sci-geosciences/congen/ChangeLog deleted file mode 100644 index 04daa7cc6..000000000 --- a/sci-geosciences/congen/ChangeLog +++ /dev/null @@ -1,11 +0,0 @@ -# ChangeLog for sci-geosciences/congen -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 12 Nov 2014; Justin Lecher <jlec@gentoo.org> congen-1.6.ebuild, metadata.xml: - Bump to EAPI=5 - - 23 Aug 2008; Tim Cera <tim@cerazone.net> +congen-1.6.ebuild, - +metadata.xml: - Initial ebuild. - diff --git a/sci-geosciences/congen/Manifest b/sci-geosciences/congen/Manifest deleted file mode 100644 index 43b44ab3e..000000000 --- a/sci-geosciences/congen/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST congen-1.6.tar.bz2 243967 SHA256 162f7563fdf13a307745eaa4261df5bd46f74bbc29cfdadefbe8af1f6bb641b3 diff --git a/sci-geosciences/congen/congen-1.6.ebuild b/sci-geosciences/congen/congen-1.6.ebuild deleted file mode 100644 index afdb0c9a9..000000000 --- a/sci-geosciences/congen/congen-1.6.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Generate the speeds, equilibrium arguments, and node factors of tidal constituents" -HOMEPAGE="http://www.flaterco.com/xtide/files.html" -SRC_URI="ftp://ftp.flaterco.com/xtide/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=">=sci-geosciences/libtcd-2.2.3" -RDEPEND="${DEPEND}" diff --git a/sci-geosciences/congen/metadata.xml b/sci-geosciences/congen/metadata.xml deleted file mode 100644 index 5f27678c1..000000000 --- a/sci-geosciences/congen/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> -</pkgmetadata> diff --git a/sci-geosciences/harmonics-dwf-free-noncomm/ChangeLog b/sci-geosciences/harmonics-dwf-free-noncomm/ChangeLog deleted file mode 100644 index 114669307..000000000 --- a/sci-geosciences/harmonics-dwf-free-noncomm/ChangeLog +++ /dev/null @@ -1,48 +0,0 @@ -# ChangeLog for sci-geosciences/harmonics-dwf-free-noncomm -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> - harmonics-dwf-free-noncomm-20110410-r1.ebuild, metadata.xml: - Bump to EAPI=5 - -*harmonics-dwf-free-noncomm-20110410-r1 (13 Dec 2011) - - 13 Dec 2011; Tim Cera <tim@cerazone.net> - -harmonics-dwf-free-noncomm-20110410.ebuild, - +harmonics-dwf-free-noncomm-20110410-r1.ebuild: - Changed location of tidal constituent database (tcd) file to - /usr/share/harmonics - -*harmonics-dwf-free-noncomm-20110410 (23 Nov 2011) - - 23 Nov 2011; Tim Cera <tim@cerazone.net> - -harmonics-dwf-free-noncomm-20100529.ebuild, - +harmonics-dwf-free-noncomm-20110410.ebuild: - Version bump and now creates a /etc/env.d/50xtide_harm file that contains the - HFILE_PATH environment variable pointing to all installed tidal constituent - databases. - -*harmonics-dwf-free-noncomm-20100529 (19 Nov 2010) - - 19 Nov 2010; Tim Cera <tim@cerazone.net> - -harmonics-dwf-free-noncomm-20071228.ebuild, - -harmonics-dwf-free-noncomm-20081228.ebuild, - +harmonics-dwf-free-noncomm-20100529.ebuild: - Version bump. - -*harmonics-dwf-free-noncomm-20081228 (12 Jun 2009) - - 12 Jun 2009; Tim Cera <tim@cerazone.net> - +harmonics-dwf-free-noncomm-20081228.ebuild: - sci-geosciences/harmonics-dwf-free-noncomm: Version bump to 20081228. - Minor changes. - - 06 Jul 2008; Tim Cera <tim@cerazone.net> - harmonics-dwf-free-noncomm-20071228.ebuild: - Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214873#c4 - - 16 May 2008; Tim Cera <tim@cerazone.net> - +harmonics-dwf-free-noncomm-20071228.ebuild, +metadata.xml: - Initial import. - diff --git a/sci-geosciences/harmonics-dwf-free-noncomm/Manifest b/sci-geosciences/harmonics-dwf-free-noncomm/Manifest deleted file mode 100644 index 2fc99df39..000000000 --- a/sci-geosciences/harmonics-dwf-free-noncomm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST harmonics-dwf-20110410-nonfree.tar.bz2 308042 SHA256 31b58f73cf5e15496e4279e5a8ba480c2cc1190bc29524a21a634efde9839952 diff --git a/sci-geosciences/harmonics-dwf-free-noncomm/harmonics-dwf-free-noncomm-20110410-r1.ebuild b/sci-geosciences/harmonics-dwf-free-noncomm/harmonics-dwf-free-noncomm-20110410-r1.ebuild deleted file mode 100644 index e56ee8678..000000000 --- a/sci-geosciences/harmonics-dwf-free-noncomm/harmonics-dwf-free-noncomm-20110410-r1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -MY_P="${P/-free-noncomm-/-}" -DESCRIPTION="Tidal harmonics database for libtcd" -HOMEPAGE="http://www.flaterco.com/xtide/" -# Even though the SRC_URI is labeled nonfree, the data is actually available for -# any non-commercial use. -SRC_URI="ftp://ftp.flaterco.com/xtide/${MY_P}-nonfree.tar.bz2" - -LICENSE="free-noncomm" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -src_install() { - insinto /usr/share/harmonics - doins "${WORKDIR}/${MY_P}"-nonfree.tcd -} diff --git a/sci-geosciences/harmonics-dwf-free-noncomm/metadata.xml b/sci-geosciences/harmonics-dwf-free-noncomm/metadata.xml deleted file mode 100644 index 8005b9ff2..000000000 --- a/sci-geosciences/harmonics-dwf-free-noncomm/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -Tidal harmonics database for libtcd. Free to use for any non-commercial -purpose. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/harmonics-dwf-free/ChangeLog b/sci-geosciences/harmonics-dwf-free/ChangeLog deleted file mode 100644 index e4a9577b4..000000000 --- a/sci-geosciences/harmonics-dwf-free/ChangeLog +++ /dev/null @@ -1,50 +0,0 @@ -# ChangeLog for sci-geosciences/harmonics-dwf-free -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 10 Nov 2014; Justin Lecher <jlec@gentoo.org> - -harmonics-dwf-free-20110410-r1.ebuild, harmonics-dwf-free-20120302.ebuild, - metadata.xml: - Bump to EAPI=5 - - 17 Jun 2012; Tim Cera <tim@cerazone.net> harmonics-dwf-free-20120302.ebuild: - sci-geosciences/harmonics-dwf-20120302: Fixed problem where "S" directory - wasn't found. - -*harmonics-dwf-free-20120302 (16 Jun 2012) - - 16 Jun 2012; Tim Cera <tim@cerazone.net> +harmonics-dwf-free-20120302.ebuild: - Version bump. - -*harmonics-dwf-free-20110410-r1 (13 Dec 2011) - - 13 Dec 2011; Tim Cera <tim@cerazone.net> -harmonics-dwf-free-20110410.ebuild, - +harmonics-dwf-free-20110410-r1.ebuild: - Changed location of the tide constituent database (tcd) file to - /usr/share/harmonics - -*harmonics-dwf-free-20110410 (23 Nov 2011) - - 23 Nov 2011; Tim Cera <tim@cerazone.net> -harmonics-dwf-free-20100529.ebuild, - +harmonics-dwf-free-20110410.ebuild: - Version bump and now creates a /etc/env.d/50xtide_harm file that contains the - HFILE_PATH environment variable pointing to all installed tidal constituent - databases. - -*harmonics-dwf-free-20100529 (19 Nov 2010) - - 19 Nov 2010; Tim Cera <tim@cerazone.net> - -harmonics-dwf-free-20071228.ebuild, -harmonics-dwf-free-20081228.ebuild, - +harmonics-dwf-free-20100529.ebuild: - Version bump. - -*harmonics-dwf-free-20081228 (12 Jun 2009) - - 12 Jun 2009; Tim Cera <tim@cerazone.net> - +harmonics-dwf-free-20081228.ebuild: - sci-geosciences/harmonics-dwf-free: Version bump to 20081228. - - 16 May 2008; Tim Cera <tim@cerazone.net> - +harmonics-dwf-free-20071228.ebuild, +metadata.xml: - Initial import. - diff --git a/sci-geosciences/harmonics-dwf-free/Manifest b/sci-geosciences/harmonics-dwf-free/Manifest deleted file mode 100644 index b774a906b..000000000 --- a/sci-geosciences/harmonics-dwf-free/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST harmonics-dwf-20120302-free.tar.bz2 503459 SHA256 3d562d71dfb2b7f9a025ca5444607e1433d14ada112a375631ab8a823c870cb7 SHA512 47040110aa34bb4e10969e86a7f6f8e1e7ba6d2b5f319c759b929cac1f51c66353641443856588691e587a16e236bdd1263043d4dd9873b23f6d993b66f2b31f WHIRLPOOL 07112c59a7c3d57823e250c28d3cb2a8d014f23a4a163822ad5fa1d7cc0ee06e46792a05e40a80d5e093da8899b48fc753c362ddf8800c59af566fc0135dd158 diff --git a/sci-geosciences/harmonics-dwf-free/harmonics-dwf-free-20120302.ebuild b/sci-geosciences/harmonics-dwf-free/harmonics-dwf-free-20120302.ebuild deleted file mode 100644 index 1e9d80fce..000000000 --- a/sci-geosciences/harmonics-dwf-free/harmonics-dwf-free-20120302.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -MY_P="${P/-free-/-}" - -DESCRIPTION="Tidal harmonics database for libtcd" -HOMEPAGE="http://www.flaterco.com/xtide/" -SRC_URI="ftp://ftp.flaterco.com/xtide/${MY_P}-free.tar.bz2" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -S="${WORKDIR}"/"${MY_P}" - -src_install() { - insinto /usr/share/harmonics - doins "${MY_P}"-free.tcd -} diff --git a/sci-geosciences/harmonics-dwf-free/metadata.xml b/sci-geosciences/harmonics-dwf-free/metadata.xml deleted file mode 100644 index cc03704e7..000000000 --- a/sci-geosciences/harmonics-dwf-free/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -Tidal harmonics database for libtcd. Free to use for any purpose. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/libtcd/ChangeLog b/sci-geosciences/libtcd/ChangeLog deleted file mode 100644 index 85eae5a91..000000000 --- a/sci-geosciences/libtcd/ChangeLog +++ /dev/null @@ -1,45 +0,0 @@ -# ChangeLog for sci-geosciences/libtcd -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> metadata.xml: - Drop local USE description - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> -libtcd-2.2.5-r1.ebuild, - libtcd-2.2.5_p2.ebuild, metadata.xml: - Bump to EAPI=5 - -*libtcd-2.2.5_p2 (16 Jun 2012) - - 16 Jun 2012; Tim Cera <tim@cerazone.net> +libtcd-2.2.5_p2.ebuild: - Version bump. Removed "non-commercial" use since upstream received a - take-down notice for that dataset and it is no longer available. Changed - naming convention since upstream was using -r# at the end of the download - files. Went with _p# replacing -r# so that -r# could be used by gentoo. - -*libtcd-2.2.5-r1 (13 Dec 2011) - - 13 Dec 2011; Tim Cera <tim@cerazone.net> -libtcd-2.2.5.ebuild, - +libtcd-2.2.5-r1.ebuild: - Version bump to force an update of DEPEND tidal constituent database (tcd) - files. - -*libtcd-2.2.5 (19 Nov 2010) - - 19 Nov 2010; Tim Cera <tim@cerazone.net> -libtcd-2.2.4.ebuild, - +libtcd-2.2.5.ebuild: - Version bump. - -*libtcd-2.2.4 (12 Jun 2009) - - 12 Jun 2009; Tim Cera <tim@cerazone.net> libtcd-2.2.3.ebuild, - +libtcd-2.2.4.ebuild: - sci-geosciences/libtcd: Version bump to 2.2.4, removed ~x86 - - 06 Jul 2008; Tim Cera <tim@cerazone.net> libtcd-2.2.3.ebuild: - Added ~x64 per http://bugs.gentoo.org/show_bug.cgi?id=214867#c4 - - 16 May 2008; Tim Cera <tim@cerazone.net> +libtcd-2.2.3.ebuild, - +metadata.xml: - Initial import - diff --git a/sci-geosciences/libtcd/Manifest b/sci-geosciences/libtcd/Manifest deleted file mode 100644 index 21b756fac..000000000 --- a/sci-geosciences/libtcd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libtcd-2.2.5-r2.tar.bz2 294449 SHA256 021d9f87986d41aa52c5318c04c49a36e6e122f6b1d16f1d91b82438ff8e767c SHA512 125b8f4258c576d82f86f75c9dec4e6e0dba8d46e897835ff8ee57cb58495c3f2ae42040719aa8a6f0fa70be40dbc3eb082250cfa197f15f0b23d2ee37a47fbd WHIRLPOOL 136c829b564382d0cbc07cdcf6fec885f7da67d2a1fade9405d5fe105d4c9274796d8efde22dc4e1f2697f5690775a17f2b6c7275ec809edb643a3669856ebfe diff --git a/sci-geosciences/libtcd/libtcd-2.2.5_p2.ebuild b/sci-geosciences/libtcd/libtcd-2.2.5_p2.ebuild deleted file mode 100644 index 5c8c8335f..000000000 --- a/sci-geosciences/libtcd/libtcd-2.2.5_p2.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -# Upstream used -r# at the end of their files which would mess up gentoo's use -# of -r#. Name ebuild _p# instead and replace as needed... -MY_P=${PN}-${PV/_p/-r} - -DESCRIPTION="Library for reading and writing Tide Constituent Database (TCD) files." -HOMEPAGE="http://www.flaterco.com/xtide/libtcd.html" -SRC_URI="ftp://ftp.flaterco.com/xtide/${MY_P}.tar.bz2" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc" - -DEPEND=">=sci-geosciences/harmonics-dwf-free-20120302" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${P%_*} - -src_install() { - default - - use doc && docinto html && dodoc libtcd.html -} diff --git a/sci-geosciences/libtcd/metadata.xml b/sci-geosciences/libtcd/metadata.xml deleted file mode 100644 index cfb6f5182..000000000 --- a/sci-geosciences/libtcd/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -Library for reading and writing Tide Constituent Database (TCD) files. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/pydap/metadata.xml b/sci-geosciences/pydap/metadata.xml index c1ce68b21..e86bec391 100644 --- a/sci-geosciences/pydap/metadata.xml +++ b/sci-geosciences/pydap/metadata.xml @@ -9,4 +9,7 @@ <longdescription lang="en"> Pydap is a pure Python library implementing the Data Access Protocol. </longdescription> + <upstream> + <remote-id type="pypi">Pydap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap/pydap-3.1.1.ebuild b/sci-geosciences/pydap/pydap-3.1.1.ebuild index 8f5f9d5af..86e0a773d 100644 --- a/sci-geosciences/pydap/pydap-3.1.1.ebuild +++ b/sci-geosciences/pydap/pydap-3.1.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap/pydap-3.1.ebuild b/sci-geosciences/pydap/pydap-3.1.ebuild index 8f5f9d5af..86e0a773d 100644 --- a/sci-geosciences/pydap/pydap-3.1.ebuild +++ b/sci-geosciences/pydap/pydap-3.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_cdms/metadata.xml b/sci-geosciences/pydap_handlers_cdms/metadata.xml index 329458eb3..8bf200966 100644 --- a/sci-geosciences/pydap_handlers_cdms/metadata.xml +++ b/sci-geosciences/pydap_handlers_cdms/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_cdms allows Pydap server to serve GRADS formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.cdms</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild b/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild index 2817889d5..a71911411 100644 --- a/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild +++ b/sci-geosciences/pydap_handlers_cdms/pydap_handlers_cdms-0.2.0.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_csv/metadata.xml b/sci-geosciences/pydap_handlers_csv/metadata.xml index 41d8db5a9..16bc3644d 100644 --- a/sci-geosciences/pydap_handlers_csv/metadata.xml +++ b/sci-geosciences/pydap_handlers_csv/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_csv allows Pydap server to serve CSV formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.csv</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild b/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild index deaee5827..5baaa7bb1 100644 --- a/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild +++ b/sci-geosciences/pydap_handlers_csv/pydap_handlers_csv-0.1.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_hdf5/metadata.xml b/sci-geosciences/pydap_handlers_hdf5/metadata.xml index 439a3377c..d4e710a9a 100644 --- a/sci-geosciences/pydap_handlers_hdf5/metadata.xml +++ b/sci-geosciences/pydap_handlers_hdf5/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_hdf5 allows Pydap server to serve hdf5 formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.hdf5</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild b/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild index fe55f1d32..2b6c51272 100644 --- a/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild +++ b/sci-geosciences/pydap_handlers_hdf5/pydap_handlers_hdf5-0.1.7.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_nca/metadata.xml b/sci-geosciences/pydap_handlers_nca/metadata.xml index 71fadebd8..2ed0280b3 100644 --- a/sci-geosciences/pydap_handlers_nca/metadata.xml +++ b/sci-geosciences/pydap_handlers_nca/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_nca allows Pydap server to serve aggregated NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.nca</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild b/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild index 3de229465..836e61d83 100644 --- a/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild +++ b/sci-geosciences/pydap_handlers_nca/pydap_handlers_nca-0.1.3.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_netcdf/metadata.xml b/sci-geosciences/pydap_handlers_netcdf/metadata.xml index a77356106..4e08c2427 100644 --- a/sci-geosciences/pydap_handlers_netcdf/metadata.xml +++ b/sci-geosciences/pydap_handlers_netcdf/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_netcdf allows Pydap server to serve NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.netcdf</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild b/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild index 49022722b..62271aca9 100644 --- a/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild +++ b/sci-geosciences/pydap_handlers_netcdf/pydap_handlers_netcdf-0.6.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_proxy/metadata.xml b/sci-geosciences/pydap_handlers_proxy/metadata.xml index 48f54b60b..52831c518 100644 --- a/sci-geosciences/pydap_handlers_proxy/metadata.xml +++ b/sci-geosciences/pydap_handlers_proxy/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_proxy allows Pydap server to serve data from other web sites. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.proxy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild b/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild index d8563556a..41ba2d74d 100644 --- a/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild +++ b/sci-geosciences/pydap_handlers_proxy/pydap_handlers_proxy-0.1.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_sql/metadata.xml b/sci-geosciences/pydap_handlers_sql/metadata.xml index 0a32c7494..a91b2e0e2 100644 --- a/sci-geosciences/pydap_handlers_sql/metadata.xml +++ b/sci-geosciences/pydap_handlers_sql/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_sql allows Pydap server to serve data from SQL databases. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.sql</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.3.0.ebuild b/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.3.0.ebuild index 379f9ddfe..03364f530 100644 --- a/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.3.0.ebuild +++ b/sci-geosciences/pydap_handlers_sql/pydap_handlers_sql-0.3.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_handlers_sqlite/metadata.xml b/sci-geosciences/pydap_handlers_sqlite/metadata.xml index 2709f644d..9c67dc99b 100644 --- a/sci-geosciences/pydap_handlers_sqlite/metadata.xml +++ b/sci-geosciences/pydap_handlers_sqlite/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_handlers_sqlite allows Pydap server to serve data from SQLite files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.handlers.sqlite</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild b/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild index e4f33db58..05086ce0b 100644 --- a/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild +++ b/sci-geosciences/pydap_handlers_sqlite/pydap_handlers_sqlite-0.1.0.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_responses_kml/metadata.xml b/sci-geosciences/pydap_responses_kml/metadata.xml index a558e81e7..e329976f7 100644 --- a/sci-geosciences/pydap_responses_kml/metadata.xml +++ b/sci-geosciences/pydap_responses_kml/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_kml allows Pydap server to use Google Earth to visualize data. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.kml</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild b/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild index 3f0c6c5d6..553bd5ac1 100644 --- a/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild +++ b/sci-geosciences/pydap_responses_kml/pydap_responses_kml-0.4.6.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_responses_matlab/metadata.xml b/sci-geosciences/pydap_responses_matlab/metadata.xml index 42f4380fb..b08b16747 100644 --- a/sci-geosciences/pydap_responses_matlab/metadata.xml +++ b/sci-geosciences/pydap_responses_matlab/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_responses_matlab allows Pydap server to deliver data to Matlab. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.matlab</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild b/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild index 9222f3f76..a9cd76c7a 100644 --- a/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild +++ b/sci-geosciences/pydap_responses_matlab/pydap_responses_matlab-0.2.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_responses_netcdf/metadata.xml b/sci-geosciences/pydap_responses_netcdf/metadata.xml index 974f6cb20..491527de1 100644 --- a/sci-geosciences/pydap_responses_netcdf/metadata.xml +++ b/sci-geosciences/pydap_responses_netcdf/metadata.xml @@ -10,4 +10,7 @@ Pydap is a pure Python library implementing the Data Access Protocol. pydap_responses_netcdf allows Pydap server to serve NetCDF formatted files. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.netcdf</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild b/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild index 4371c416c..ae50c2926 100644 --- a/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild +++ b/sci-geosciences/pydap_responses_netcdf/pydap_responses_netcdf-0.1.4.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_responses_wms/metadata.xml b/sci-geosciences/pydap_responses_wms/metadata.xml index d7bbe41b5..da0b5304a 100644 --- a/sci-geosciences/pydap_responses_wms/metadata.xml +++ b/sci-geosciences/pydap_responses_wms/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_wms allows Pydap server to deliver maps via Web Mapping Service protocol. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.wms</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild b/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild index f5e7755dd..9eb98971e 100644 --- a/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild +++ b/sci-geosciences/pydap_responses_wms/pydap_responses_wms-0.5.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/pydap_responses_xls/metadata.xml b/sci-geosciences/pydap_responses_xls/metadata.xml index 523b428a6..097b4dafd 100644 --- a/sci-geosciences/pydap_responses_xls/metadata.xml +++ b/sci-geosciences/pydap_responses_xls/metadata.xml @@ -11,4 +11,7 @@ pydap_responses_xls allows Pydap server to deliver an Excel file of the data. </longdescription> + <upstream> + <remote-id type="pypi">pydap.responses.xls</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild b/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild index 0bd4c3654..d1da8daab 100644 --- a/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild +++ b/sci-geosciences/pydap_responses_xls/pydap_responses_xls-0.1.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-geosciences/qgis/qgis-9999.ebuild b/sci-geosciences/qgis/qgis-9999.ebuild index bc44b6d99..dccc820ce 100644 --- a/sci-geosciences/qgis/qgis-9999.ebuild +++ b/sci-geosciences/qgis/qgis-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="sqlite" inherit cmake-utils gnome2-utils multilib python-single-r1 subversion eutils diff --git a/sci-geosciences/swmm/ChangeLog b/sci-geosciences/swmm/ChangeLog deleted file mode 100644 index f017aebd1..000000000 --- a/sci-geosciences/swmm/ChangeLog +++ /dev/null @@ -1,36 +0,0 @@ -# ChangeLog for sci-geosciences/swmm -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> swmm-5.0.022.ebuild, - metadata.xml: - Bump to EAPI=5 - -*swmm-5.0.022 (15 Jul 2011) - - 15 Jul 2011; Tim Cera <tim@cerazone.net> -swmm-5.0.020.ebuild, - +swmm-5.0.022.ebuild: - Version bump. - -*swmm-5.0.020 (04 Sep 2010) - - 04 Sep 2010; Tim Cera <tim@cerazone.net> -swmm-5.0.018.ebuild, - +swmm-5.0.020.ebuild: - Version bump. - -*swmm-5.0.018 (13 Dec 2009) - - 13 Dec 2009; Tim Cera <tim@cerazone.net> -swmm-5.0.015.ebuild, - +swmm-5.0.018.ebuild: - Changed to match upstream's new version numbering. Version bump. - -*swmm-5.0.015 (10 Jun 2009) - - 10 Jun 2009; Tim Cera <tim@cerazone.net> -swmm-5.0.013.ebuild, - +swmm-5.0.015.ebuild: - sci-geosciences/swmm: Version bump. - - 09 Oct 2008; Tim Cera <tim@cerazone.net> +swmm-5.0.013.ebuild, - +metadata.xml: - Initial ebuild. - diff --git a/sci-geosciences/swmm/Manifest b/sci-geosciences/swmm/Manifest deleted file mode 100644 index 6d5605973..000000000 --- a/sci-geosciences/swmm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST swmm50022_engine.zip 338011 SHA256 4dba36cbe5e39524c06b826e265ae8fdd2afb82b1c63bb5d9fd72214ed2d7409 diff --git a/sci-geosciences/swmm/metadata.xml b/sci-geosciences/swmm/metadata.xml deleted file mode 100644 index 9e77f8233..000000000 --- a/sci-geosciences/swmm/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -Storm Water Management Model - SWMM, hydrology, hydraulics, and water quality model. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/swmm/swmm-5.0.022.ebuild b/sci-geosciences/swmm/swmm-5.0.022.ebuild deleted file mode 100644 index 235a28ae0..000000000 --- a/sci-geosciences/swmm/swmm-5.0.022.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils versionator - -MY_PV=$(delete_all_version_separators) - -MY_SRC="swmm${MY_PV}_engine.zip" - -DESCRIPTION="Storm Water Management Model - SWMM, hydrology, hydraulics, and water quality model." -HOMEPAGE="http://www.epa.gov/ednnrmrl/models/swmm/index.htm" -SRC_URI="http://www.epa.gov/nrmrl/wswrd/wq/models/swmm/${MY_SRC}" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc" - -DEPEND="app-arch/unzip" -RDEPEND="" - -S="${WORKDIR}/${PN}" - -src_unpack() { - mkdir "${S}" && cd "${S}" || die - unpack "${MY_SRC}" - # Need to delete Readme.txt, because it is in makefiles.zip - rm Readme.txt || die - unpack ./makefiles.zip ./GNU_CON.zip ./source*.ZIP -} - -src_prepare(){ - # 'sed' command has to accomodate DOS formatted file. - sed -i \ - -e 's;^#define DLL;//#define DLL;' \ - -e 's;^//#define CLE;#define CLE;' \ - swmm5.c || die -} - -src_install(){ - # Don't like the version number in the name. - newbin swmm5 swmm - use doc && dodoc Roadmap.txt -} diff --git a/sci-geosciences/tappy/ChangeLog b/sci-geosciences/tappy/ChangeLog deleted file mode 100644 index 193e544b8..000000000 --- a/sci-geosciences/tappy/ChangeLog +++ /dev/null @@ -1,44 +0,0 @@ -# ChangeLog for sci-geosciences/tappy -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 04 Dec 2013; Justin Lecher <jlec@gentoo.org> tappy-0.9.0.ebuild, - metadata.xml: - Bump to distutils-r1 eclass - -*tappy-0.9.0 (19 Oct 2011) - - 19 Oct 2011; Tim Cera <tim@cerazone.net> -tappy-0.8.3.ebuild, - +tappy-0.9.0.ebuild: - Version bump. - - 29 Jun 2010; Justin Lecher <jlec@gentoo.org> tappy-0.8.3.ebuild: - Python ABI fixes - - 25 Jan 2010; Tim Cera <tim@cerazone.net> -tappy-0.8.2.ebuild: - Removed version 0.8.2. - -*tappy-0.8.3 (18 Jul 2009) - - 18 Jul 2009; Tim Cera <tim@cerazone.net> +tappy-0.8.3.ebuild: - Version bump. - -*tappy-0.8.2 (01 Jul 2009) - - 01 Jul 2009; Tim Cera <tim@cerazone.net> +tappy-0.8.2.ebuild: - sci-geosciences/tappy: Version bump. Fixed DEPEND and RDEPEND. - - 16 Nov 2008; Tim Cera <tim@cerazone.net> -tappy-0.8.0.ebuild, - +tappy-0.8.1.ebuild: - Version bump. - - 08 Jul 2008; Tim Cera <tim@cerazone.net> tappy-0.8.0.ebuild: - Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=138005#c8 - - 07 Jul 2008; Tim Cera <tim@cerazone.net> tappy-0.8.0.ebuild: - Added correct header. - - 07 Jul 2008; Tim Cera <tim@cerazone.net> +tappy-0.8.0.ebuild, - +metadata.xml: - Initial entry. - diff --git a/sci-geosciences/tappy/Manifest b/sci-geosciences/tappy/Manifest deleted file mode 100644 index 7eb7ed063..000000000 --- a/sci-geosciences/tappy/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tappy-0.9.0.tar.gz 1250867 SHA256 273dce2595a0c2161752d9cb26e4e2569d6f42028cdf0b418c90775ff2443bf0 SHA512 2f3c7676c166dbfe88436cac9a0c4e3d3d4c027e17c39617c45eb02c1c2eda9276afb1ceaa16afd54bb6de130248f83c8c66aeb3509483cce642d2eb631fb9df WHIRLPOOL 83c24a29c2818c0ed6767b8e18c6b899befd26935de31ac933d83c5dd5d0e74bd908f52a174fe6dff8fcdd47e4cad8658be5a9f3c2bf12d70978cb1c2edc7ed0 diff --git a/sci-geosciences/tappy/metadata.xml b/sci-geosciences/tappy/metadata.xml deleted file mode 100644 index bdb0263e7..000000000 --- a/sci-geosciences/tappy/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -TAPPY is a tidal analysis package. It breaks down a record of water levels into -the component sine waves. It is written in Python and uses the least squares -optimization and other functions in SciPy. The focus is to make the most -accurate analysis possible. TAPPY only determines the constituents that are -calculatable according to the length of the time series. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/tappy/tappy-0.9.0.ebuild b/sci-geosciences/tappy/tappy-0.9.0.ebuild deleted file mode 100644 index b4c852d45..000000000 --- a/sci-geosciences/tappy/tappy-0.9.0.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 - -DESCRIPTION="Tidal Analysis in Python" -HOMEPAGE="http://tappy.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]" -RDEPEND=">=sci-libs/scipy-0.3.2[${PYTHON_USEDEP}]" diff --git a/sci-geosciences/tcd-utils/ChangeLog b/sci-geosciences/tcd-utils/ChangeLog deleted file mode 100644 index 5f98df540..000000000 --- a/sci-geosciences/tcd-utils/ChangeLog +++ /dev/null @@ -1,22 +0,0 @@ -# ChangeLog for sci-geosciences/tcd-utils -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> -tcd-utils-20061127.ebuild, - tcd-utils-20080820.ebuild, metadata.xml: - Bump to EAPI=5 - -*tcd-utils-20080820 (12 Jun 2009) - - 12 Jun 2009; Tim Cera <tim@cerazone.net> tcd-utils-20061127.ebuild, - +tcd-utils-20080820.ebuild: - sci-geosciences/tcd-utils: Version bump to 20080820. Updated copyright - year. - - 06 Jul 2008; Tim Cera <tim@cerazone.net> tcd-utils-20061127.ebuild: - Added ~x86 per http://bugs.gentoo.org/show_bug.cgi?id=214875#c4 - - 16 May 2008; Tim Cera <tim@cerazone.net> +tcd-utils-20061127.ebuild, - +metadata.xml: - Initial import. - diff --git a/sci-geosciences/tcd-utils/Manifest b/sci-geosciences/tcd-utils/Manifest deleted file mode 100644 index f1946120a..000000000 --- a/sci-geosciences/tcd-utils/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tcd-utils-20080820.tar.bz2 111300 SHA256 61912e793ab58cd396c77721743f648f40b3806a05dbb1229b015fada0643260 diff --git a/sci-geosciences/tcd-utils/metadata.xml b/sci-geosciences/tcd-utils/metadata.xml deleted file mode 100644 index e1226bffc..000000000 --- a/sci-geosciences/tcd-utils/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -Utiliies for working with Tidal Constituent Databases. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/tcd-utils/tcd-utils-20080820.ebuild b/sci-geosciences/tcd-utils/tcd-utils-20080820.ebuild deleted file mode 100644 index fb49b6667..000000000 --- a/sci-geosciences/tcd-utils/tcd-utils-20080820.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -DESCRIPTION="Utiliies for working with Tidal Constituent Databases." -HOMEPAGE="http://www.flaterco.com/xtide/" -SRC_URI="ftp://ftp.flaterco.com/xtide/${P}.tar.bz2" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=">=sci-geosciences/libtcd-2.2.4" -RDEPEND="${DEPEND}" diff --git a/sci-geosciences/xtide/ChangeLog b/sci-geosciences/xtide/ChangeLog deleted file mode 100644 index b47ffbf77..000000000 --- a/sci-geosciences/xtide/ChangeLog +++ /dev/null @@ -1,51 +0,0 @@ -# ChangeLog for sci-geosciences/xtide -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 13 Nov 2014; Justin Lecher <jlec@gentoo.org> -xtide-2.12-r1.ebuild, - xtide-2.13.ebuild, metadata.xml: - Bump to EAPI=5; drop old - -*xtide-2.13 (16 Jun 2012) - - 16 Jun 2012; Tim Cera <tim@cerazone.net> +xtide-2.13.ebuild: - Version bump. Removed 'non-commercial' keyword since upstream was sent a - take-down notice for that data set and it is no longer available. - -*xtide-2.12-r1 (13 Dec 2011) - - 13 Dec 2011; Tim Cera <tim@cerazone.net> -xtide-2.12.ebuild, - +xtide-2.12-r1.ebuild: - Putting all tide constituent database (tcd) files in one directory: - /usr/share/harmonics - -*xtide-2.12 (23 Nov 2011) - - 23 Nov 2011; Tim Cera <tim@cerazone.net> -xtide-2.11.ebuild, - +xtide-2.12.ebuild: - Version bump and shifted configuration to the harmonics-dwf ebuilds. - -*xtide-2.11 (19 Nov 2010) - - 19 Nov 2010; Tim Cera <tim@cerazone.net> -xtide-2.10.ebuild, - -xtide-2.10-r1.ebuild, +xtide-2.11.ebuild: - Version bump. - - 25 Jan 2010; Tim Cera <tim@cerazone.net> xtide-2.10-r1.ebuild, - metadata.xml: - Fixed dependencies. - - 17 Jun 2009; Tim Cera <tim@cerazone.net> xtide-2.10-r1.ebuild: - sci-geosciences/xtide: Updated copyright years. Repoman complained about - '~x86' so removed since I haven't tested latest ebuilds on '~x86'. - - 07 Jul 2008; Tim Cera <tim@cerazone.net> xtide-2.10-r1.ebuild: - Added ~x86 per https://bugs.gentoo.org/show_bug.cgi?id=214868#c9 - - 06 Jul 2008; Tim Cera <tim@cerazone.net> +xtide-2.10-r1.ebuild: - Added dependencies to xtide-2.10-r1.ebuild. - - 16 May 2008; Tim Cera <tim@cerazone.net> +xtide-2.10.ebuild, - +metadata.xml: - Initial import. - diff --git a/sci-geosciences/xtide/Manifest b/sci-geosciences/xtide/Manifest deleted file mode 100644 index 9dcfd2228..000000000 --- a/sci-geosciences/xtide/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xtide-2.13.tar.bz2 465679 SHA256 a73c530c83a9346bf85fe9545551eef3fbedfb24adf18f63c9e7dba0388e0d0a SHA512 2324d3f5150a46ea1fd6c2af3379c8ea4f147034f153ac4b0393ef3aaa2178bfdafc01499f27db643b5ec78b4825c99b20957f5e47f6174fe1612480dc79dcd1 WHIRLPOOL af9fe8377fec84a449e06cfac542b2d792ebe1df904e036775b3e5b659e874d5193e0416b061dddcffc2419610d48864207bba27d557fe05fdcd7560c20afb53 diff --git a/sci-geosciences/xtide/metadata.xml b/sci-geosciences/xtide/metadata.xml deleted file mode 100644 index dc8684aef..000000000 --- a/sci-geosciences/xtide/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-geosciences</herd> - <maintainer> - <email>tim@cerazone.net</email> - <name>Tim Cera</name> - </maintainer> - <longdescription lang="en"> -XTide provides tide and current predictions in a wide variety of formats. -</longdescription> -</pkgmetadata> diff --git a/sci-geosciences/xtide/xtide-2.13.ebuild b/sci-geosciences/xtide/xtide-2.13.ebuild deleted file mode 100644 index 65f9a94d3..000000000 --- a/sci-geosciences/xtide/xtide-2.13.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="Tide and current predictions in a wide variety of formats" -HOMEPAGE="http://www.flaterco.com/xtide/" -SRC_URI="ftp://ftp.flaterco.com/xtide/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="" - -DEPEND=" - >=x11-libs/libXaw-1.0.3 - >=x11-libs/libXpm-3.5.6 - >=media-libs/libpng-1.2.25 - >=sci-geosciences/libtcd-2.2.5_p2" -RDEPEND="${DEPEND}" - -src_install() { - dobin xtide tide xttpd - doman *.[18] - - echo "HFILE_PATH=\"${EPREFIX}/usr/share/harmonics/\"" > 50xtide_harm - doenvd 50xtide_harm - - make_desktop_entry ${PN} 'Tide prediction' ${PN} 'Science' -} diff --git a/sci-libs/acml/ChangeLog b/sci-libs/acml/ChangeLog index 97bf101aa..f5909739e 100644 --- a/sci-libs/acml/ChangeLog +++ b/sci-libs/acml/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> acml-6.1.0.31.ebuild: + Fix #543740 (drop fma4) + *acml-6.1.0.31 (02 Feb 2015) 02 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> diff --git a/sci-libs/acml/acml-6.1.0.31.ebuild b/sci-libs/acml/acml-6.1.0.31.ebuild index 02dd4faf4..a64b8d003 100644 --- a/sci-libs/acml/acml-6.1.0.31.ebuild +++ b/sci-libs/acml/acml-6.1.0.31.ebuild @@ -19,7 +19,7 @@ SRC_URI="gfortran? ( ${P}-gfortran64.tgz )" LICENSE="ACML-EULA" SLOT="0" KEYWORDS="-* ~amd64 ~amd64-linux" -IUSE="doc examples cpu_flags_x86_fma4 +gfortran openmp test" +IUSE="doc examples +gfortran openmp test" RESTRICT="strip mirror" DEPEND="" @@ -87,7 +87,6 @@ src_install() { # default profile: first one matching use flags local opts=gfortran64 - use cpu_flags_x86_fma4 && opts+="_fma4" use openmp && opts+="_mp" dosym $(ls -1d */lib | grep ${opts}) /${ACML_INST_DIR}/${libdir} diff --git a/sci-libs/amdlibm/amdlibm-3.1.ebuild b/sci-libs/amdlibm/amdlibm-3.1.ebuild index 4b8d041c4..5d62ae37b 100644 --- a/sci-libs/amdlibm/amdlibm-3.1.ebuild +++ b/sci-libs/amdlibm/amdlibm-3.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -48,7 +48,7 @@ src_prepare() { } src_test() { - cd examples + cd examples || die sh build_and_run.sh || die } diff --git a/sci-libs/armadillo/ChangeLog b/sci-libs/armadillo/ChangeLog index 51b024fd4..908a93a3b 100644 --- a/sci-libs/armadillo/ChangeLog +++ b/sci-libs/armadillo/ChangeLog @@ -2,6 +2,60 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/armadillo: Updating remote-id in metadata.xml + + 26 May 2015; Marius Brehler <marbre@linux.sungazer.de> + -armadillo-5.000.1.ebuild, -armadillo-5.100.1.ebuild: + Drop old + +*armadillo-5.200.1 (26 May 2015) + + 26 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-5.200.1.ebuild: + Version bump + +*armadillo-5.100.2 (12 May 2015) + + 12 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-5.100.2.ebuild: + Version bump + +*armadillo-5.100.1 (04 May 2015) + + 04 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-5.100.1.ebuild: + Version bump + +*armadillo-5.000.1 (26 Apr 2015) + + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-5.000.1.ebuild: + Version bump + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + -armadillo-4.600.2.ebuild, -armadillo-4.600.4.ebuild, + -armadillo-4.650.2.ebuild: + Moved to tree; Drop old + +*armadillo-4.650.4 (24 Mar 2015) + + 24 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-4.650.4.ebuild: + Version bump + +*armadillo-4.650.2 (08 Mar 2015) + + 08 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +armadillo-4.650.2.ebuild: + Version bump + + 27 Feb 2015; Andreas K. Huettel <dilfridge@gentoo.org> + -armadillo-4.200.0.ebuild, -armadillo-4.300.8.ebuild, + -armadillo-4.300.9.ebuild, -files/armadillo-3.820.1-example-makefile.patch, + -files/armadillo-4.000.3-hdf5.patch: + Remove old + *armadillo-4.600.4 (27 Jan 2015) 27 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest index 853205a35..e8c1fa6b7 100644 --- a/sci-libs/armadillo/Manifest +++ b/sci-libs/armadillo/Manifest @@ -1,5 +1,3 @@ -DIST armadillo-4.200.0.tar.gz 5479492 SHA256 77d4c64346da9fb90d1150c290919e49530cef45713e830375e04566218335ff SHA512 83afccbf0ed4b8a7873b5fc5d47975600a71d7130e59716d9f044a2cd58343e4d0f5c0037abd1e6d110413d0192c5f0f87a2f3af8183189bd82032414237244d WHIRLPOOL c785cc5b89a542c276ec3cddd56ee40a766960353d7174356c0e891dd8744d08bff350405c3b629a7a4b66a4a8b7564697faa7e9600e57065a3f1cd5e1180bd9 -DIST armadillo-4.300.8.tar.gz 5484286 SHA256 1d1a77ad7a74e8b4a74d7b71c5e3fe488e26283907b316618de0a8558c60173a SHA512 3b5d6c9bcefb427e1dc15c259bd24154b6d2138a75be49275e2be5a456f4e2357852c7520b171109ee2b6a716c8ef2a19dea8c2a9b908b13fc2a1624500d54f3 WHIRLPOOL 90789113a10ca0e0264af3212f2c59f6f0b68cf726c22935433bc5d396c763143e6bd1b9d961ee6e5fd78adad3ee58bf1b532931761d9fbe51e99179beebf789 -DIST armadillo-4.300.9.tar.gz 5484297 SHA256 1cc96e7eb1cd3872c193f3954561e6d8539d2a4120235213c42c6db44b650d27 SHA512 5129c9ac8e76b6d367691380315d3f4e80e643349a9013238c0672b4d93aabc395d20b9fd95678dcc9172baa793eba5b54011bbf35f69913a7381ca2f62638d0 WHIRLPOOL a3c6c24cbbf85a585bb20c0773800f24065cf57976759543653bddbee0e09559cfad7de30829bc1b5db5583fe1d8c17112b5a463924deaaad5bebf41ec525f7f -DIST armadillo-4.600.2.tar.gz 5347346 SHA256 d5f85cac54db16d3cf25af54460eb5fde190c81ddbb8690a6c453012934891bf SHA512 b077ad19b7a3e996e9edeceaf980bea53ecaccb012dd2438a70bfc863bd8113e8308325ca91ce033c152bc757a0ac847d81ba99d87b5e4af28ae44dc71ed595b WHIRLPOOL 1d41ab103a7b89e2c11fc4b5b0a9649a690d704dcdd073bcc2de4ddb996a560e6e397309987c848443f294e83af2ae3e269c323ff68c1c8d512ad698861fa35a -DIST armadillo-4.600.4.tar.gz 5347594 SHA256 308835440ce3b17d7652156bad6c9fbc6f6881859e07467623676d4a35229ca8 SHA512 a7378e2fe5a4485f5df755cd3af9e54034f1a701bd185161a9945422598dd7e20327cf945075bca71d31a18eaf9f932ff39f204e96a48855ef013a962dd07fd8 WHIRLPOOL 2c0544a243f5632445a740148dfd4266a20815c017aa0f52dd20ac5c6ab9531da7ad388605c136fdacf254b724648ab0f7a0354554b85af1ed82be21f5e0ea6b +DIST armadillo-4.650.4.tar.gz 5408567 SHA256 ccc56580ec932ec9beade5679b07ecbed889e9b602866f673d1a05a7692b4bf8 SHA512 a548150ba5484fce35b0bc6023982939946f2f00b733dff2cd5b46101b1c344342061389cb4363cdaa04c5e3cca3278a40febe2ed705316552dd71f841c46037 WHIRLPOOL 331493d8b9c92b9e1908880c6f6510edb12e93193a9ceb77d0b8ce9d0bfb493dc48e590ea949d39c3c19f6fc3b05446b7e00525512e3055be0f907427c28f7d4 +DIST armadillo-5.100.2.tar.gz 5429961 SHA256 63150f12bf7c7c598ea55b7271d99fce349ff386a3dc2cae3904b244f6e35320 SHA512 2777b525bc62daddfb16eae7b74c29b6b695a7985c56d9dca727ae1e13aa4ea20ee85ea82233a5310b37c738838af07bb0fa7eea782e68e72cbe1cf46a0cc896 WHIRLPOOL df85a508875587651b187520b78900634402f2ca0fc2e64f43bd4a793e382e8cc6abd5b988267645bb02b3133d9aa99ab6d6ff5e200d1277093d4f7ce6e9d240 +DIST armadillo-5.200.1.tar.gz 5430678 SHA256 3673fc7cbeefca826108efe7c36e21322f259809f874c161ca284a114fb7f693 SHA512 750e18a7c464bfe17ed113014312cce54793780d2c5d1f6510faaedac44bc6c055955b0ffba6884ab1111be5c22740a0b3ddcd9533caf51afe1bda33074177f4 WHIRLPOOL ec7bffdb57943350fe31fce8926657c98de5e0a847d3ba04872c3644e8feed1cdcf467dc8359f302241f8b520f46465e5cd7843b55641bceb1d039e314f32474 diff --git a/sci-libs/armadillo/armadillo-4.200.0.ebuild b/sci-libs/armadillo/armadillo-4.200.0.ebuild deleted file mode 100644 index 6dab24828..000000000 --- a/sci-libs/armadillo/armadillo-4.200.0.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -CMAKE_IN_SOURCE_BUILD=1 - -inherit cmake-utils toolchain-funcs multilib eutils - -DESCRIPTION="Streamlined C++ linear algebra library" -HOMEPAGE="http://arma.sourceforge.net/" -SRC_URI="mirror://sourceforge/arma/${P}.tar.gz" - -LICENSE="MPL-2.0" -SLOT="0/4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl tbb test" -REQUIRED_USE="test? ( lapack )" - -RDEPEND=" - dev-libs/boost - arpack? ( sci-libs/arpack ) - atlas? ( sci-libs/atlas[lapack] ) - blas? ( virtual/blas ) - lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - arpack? ( virtual/pkgconfig ) - atlas? ( virtual/pkgconfig ) - blas? ( virtual/pkgconfig ) - hdf5? ( sci-libs/hdf5 ) - lapack? ( virtual/pkgconfig ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" -PDEPEND="${RDEPEND} - hdf5? ( sci-libs/hdf5 ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-4.000.3-hdf5.patch \ - "${FILESDIR}"/${PN}-3.820.1-example-makefile.patch - # avoid the automagic cmake macros - sed -i -e '/ARMA_Find/d' CMakeLists.txt || die -} - -src_configure() { - local mycmakeargs=( - -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" - $(cmake-utils_use debug ARMA_EXTRA_DEBUG) - $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC) - $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC) - ) - if use arpack; then - mycmakeargs+=( - -DARPACK_FOUND=ON - -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" - ) - fi - if use atlas; then - local c=atlas-cblas l=atlas-clapack - $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads - $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads - mycmakeargs+=( - -DCBLAS_FOUND=ON - -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" - -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" - -DCLAPACK_FOUND=ON - -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" - -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" - ) - fi - if use blas; then - mycmakeargs+=( - -DBLAS_FOUND=ON - -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" - ) - fi - if use hdf5; then - mycmakeargs+=( - -DHDF5_FOUND=ON - -DHDF5_LIBRARIES="-lhdf5" - ) - fi - if use lapack; then - mycmakeargs+=( - -DLAPACK_FOUND=ON - -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" - ) - fi - cmake-utils_src_configure -} - -src_test() { - pushd examples > /dev/null - emake \ - CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ - EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die - emake clean - popd > /dev/null -} - -src_install() { - cmake-utils_src_install - dodoc README.txt - use doc && dodoc *pdf && dohtml *html - if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples - fi -} diff --git a/sci-libs/armadillo/armadillo-4.300.9.ebuild b/sci-libs/armadillo/armadillo-4.300.9.ebuild deleted file mode 100644 index 96ac5823d..000000000 --- a/sci-libs/armadillo/armadillo-4.300.9.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -CMAKE_IN_SOURCE_BUILD=1 - -inherit cmake-utils toolchain-funcs multilib eutils - -DESCRIPTION="Streamlined C++ linear algebra library" -HOMEPAGE="http://arma.sourceforge.net/" -SRC_URI="mirror://sourceforge/arma/${P}.tar.gz" - -LICENSE="MPL-2.0" -SLOT="0/4" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl tbb test" -REQUIRED_USE="test? ( lapack )" - -RDEPEND=" - dev-libs/boost - arpack? ( sci-libs/arpack ) - atlas? ( sci-libs/atlas[lapack] ) - blas? ( virtual/blas ) - lapack? ( virtual/lapack )" -DEPEND="${RDEPEND} - arpack? ( virtual/pkgconfig ) - atlas? ( virtual/pkgconfig ) - blas? ( virtual/pkgconfig ) - hdf5? ( sci-libs/hdf5 ) - lapack? ( virtual/pkgconfig ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" -PDEPEND="${RDEPEND} - hdf5? ( sci-libs/hdf5 ) - mkl? ( sci-libs/mkl ) - tbb? ( dev-cpp/tbb )" - -PATCHES=( "${FILESDIR}"/${PN}-3.820.1-example-makefile.patch ) - -src_prepare() { - # avoid the automagic cmake macros - sed -i -e '/ARMA_Find/d' CMakeLists.txt || die - cmake-utils_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)" - $(cmake-utils_use debug ARMA_EXTRA_DEBUG) - $(cmake-utils_use mkl ARMA_USE_MKL_ALLOC) - $(cmake-utils_use tbb ARMA_USE_TBB_ALLOC) - ) - if use arpack; then - mycmakeargs+=( - -DARPACK_FOUND=ON - -DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)" - ) - fi - if use atlas; then - local c=atlas-cblas l=atlas-clapack - $(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads - $(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads - mycmakeargs+=( - -DCBLAS_FOUND=ON - -DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')" - -DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})" - -DCLAPACK_FOUND=ON - -DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')" - -DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})" - ) - fi - if use blas; then - mycmakeargs+=( - -DBLAS_FOUND=ON - -DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)" - ) - fi - if use hdf5; then - mycmakeargs+=( - -DHDF5_FOUND=ON - -DHDF5_LIBRARIES="-lhdf5" - ) - fi - if use lapack; then - mycmakeargs+=( - -DLAPACK_FOUND=ON - -DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)" - ) - fi - cmake-utils_src_configure -} - -src_test() { - pushd examples > /dev/null - emake \ - CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \ - EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)" - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die - LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die - emake clean - popd > /dev/null -} - -src_install() { - cmake-utils_src_install - dodoc README.txt - use doc && dodoc *pdf && dohtml *html - if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples - fi -} diff --git a/sci-libs/armadillo/armadillo-4.600.2.ebuild b/sci-libs/armadillo/armadillo-4.650.4.ebuild index 35856d707..35856d707 100644 --- a/sci-libs/armadillo/armadillo-4.600.2.ebuild +++ b/sci-libs/armadillo/armadillo-4.650.4.ebuild diff --git a/sci-libs/armadillo/armadillo-4.600.4.ebuild b/sci-libs/armadillo/armadillo-5.100.2.ebuild index 35856d707..8d63e069b 100644 --- a/sci-libs/armadillo/armadillo-4.600.4.ebuild +++ b/sci-libs/armadillo/armadillo-5.100.2.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-4.650.4.ebuild,v 1.1 2015/04/03 12:32:07 jlec Exp $ EAPI=5 diff --git a/sci-libs/armadillo/armadillo-4.300.8.ebuild b/sci-libs/armadillo/armadillo-5.200.1.ebuild index 96ac5823d..8d63e069b 100644 --- a/sci-libs/armadillo/armadillo-4.300.8.ebuild +++ b/sci-libs/armadillo/armadillo-5.200.1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-4.650.4.ebuild,v 1.1 2015/04/03 12:32:07 jlec Exp $ EAPI=5 @@ -37,8 +37,6 @@ PDEPEND="${RDEPEND} mkl? ( sci-libs/mkl ) tbb? ( dev-cpp/tbb )" -PATCHES=( "${FILESDIR}"/${PN}-3.820.1-example-makefile.patch ) - src_prepare() { # avoid the automagic cmake macros sed -i -e '/ARMA_Find/d' CMakeLists.txt || die @@ -108,7 +106,7 @@ src_install() { dodoc README.txt use doc && dodoc *pdf && dohtml *html if use examples; then - insinto /usr/share/doc/${PF} - doins -r examples + insinto /usr/share/examples/${PF} + doins -r examples/* fi } diff --git a/sci-libs/armadillo/files/armadillo-3.820.1-example-makefile.patch b/sci-libs/armadillo/files/armadillo-3.820.1-example-makefile.patch deleted file mode 100644 index 90169ed12..000000000 --- a/sci-libs/armadillo/files/armadillo-3.820.1-example-makefile.patch +++ /dev/null @@ -1,33 +0,0 @@ ---- examples/Makefile.cmake.orig 2013-04-29 09:13:58.164963641 -0700 -+++ examples/Makefile.cmake 2013-04-29 09:18:42.371460644 -0700 -@@ -1,7 +1,7 @@ - # The generated "Makefile" from "Makefile.cmake" is only usable after - # the Armadillo library has been configured and installed by CMake. - --CXX=g++ -+CXX:=g++ - #CXX=g++-4.2 - ## Under MacOS you may have an old compiler as default (e.g. GCC 4.0). - ## However, GCC 4.2 or later is available and preferable due to better -@@ -26,7 +26,7 @@ - - - --LIB_FLAGS = -larmadillo $(EXTRA_LIB_FLAGS) -+LIB_FLAGS = $(EXTRA_LIB_FLAGS) -larmadillo - ## NOTE: on Ubuntu and Debian based systems you may need to add - ## -lgfortran to LIB_FLAGS - -@@ -73,10 +73,10 @@ - all: example1 example2 - - example1: example1.cpp -- $(CXX) $(CXXFLAGS) -o $@ $< $(LIB_FLAGS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $< $(LIB_FLAGS) -o $@ - - example2: example2.cpp -- $(CXX) $(CXXFLAGS) -o $@ $< $(LIB_FLAGS) -+ $(CXX) $(CXXFLAGS) $(LDFLAGS) $< $(LIB_FLAGS) -o $@ - - - .PHONY: clean diff --git a/sci-libs/armadillo/files/armadillo-4.000.3-hdf5.patch b/sci-libs/armadillo/files/armadillo-4.000.3-hdf5.patch deleted file mode 100644 index 4510cd895..000000000 --- a/sci-libs/armadillo/files/armadillo-4.000.3-hdf5.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- armadillo-4.000.2/CMakeLists.txt.orig 2014-02-03 14:47:35.023255183 -0800 -+++ armadillo-4.000.2/CMakeLists.txt 2014-02-03 21:19:47.567376544 -0800 -@@ -227,11 +227,11 @@ - # find_package(HDF5) - # message(STATUS "HDF5_FOUND = ${HDF5_FOUND}") - # --# if(HDF5_FOUND) --# set(ARMA_USE_HDF5 true) --# set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${HDF5_INCLUDE_DIRS}) --# set(ARMA_LIBS ${ARMA_LIBS} ${HDF5_LIBRARIES}) --# endif() -+if(HDF5_FOUND) -+ set(ARMA_USE_HDF5 true) -+ set(CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES} ${HDF5_INCLUDE_DIRS}) -+ set(ARMA_LIBS ${ARMA_LIBS} ${HDF5_LIBRARIES}) -+ endif() - - - include(ARMA_FindARPACK) diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml index 385357d8a..dfc8f3007 100644 --- a/sci-libs/armadillo/metadata.xml +++ b/sci-libs/armadillo/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> Armadillo is a C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a @@ -14,20 +14,23 @@ need for temporaries. This is accomplished through recursive templates and template meta-programming. </longdescription> -<use> - <flag name="atlas"> + <use> + <flag name="atlas"> Link with <pkg>sci-libs/atlas</pkg> libraries for cblas and clapack </flag> - <flag name="arpack"> + <flag name="arpack"> Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition </flag> - <flag name='mkl'> + <flag name="mkl"> Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg> - </flag> - <flag name='tbb'> + </flag> + <flag name="tbb"> Use matrix allocation from the Threads Building Blocks <pkg>dev-cpp/tbb</pkg> - </flag> -</use> + </flag> + </use> + <upstream> + <remote-id type="sourceforge">arma</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/arrayfire/ChangeLog b/sci-libs/arrayfire/ChangeLog index 37799ee6d..61231847c 100644 --- a/sci-libs/arrayfire/ChangeLog +++ b/sci-libs/arrayfire/ChangeLog @@ -1,6 +1,46 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/FindBoostCompute.cmake, + +files/arrayfire-3.0_beta-FindBoostCompute.patch, + +files/arrayfire-3.0_beta-FindCBLAS.patch, + +files/arrayfire-3.0_beta-opencl_CMakeLists.patch, + +files/arrayfire-9999-FindCBLAS.patch, -files/FindBoostCompute.patch, + -files/FindCBLAS.patch, -files/opencl_CMakeLists.patch, arrayfire-9999.ebuild: + Split up ebuilds to fix 9999 + + 24 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + -files/arrayfire-0.9999-build_gtest.patch: + Drop patch, fixed upstream + + 24 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/FindBoostCompute.patch, +files/opencl_CMakeLists.patch, + arrayfire-9999.ebuild, metadata.xml: + Enable OpenCL backend + +*arrayfire-3.0_beta (23 Mar 2015) + + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +arrayfire-3.0_beta.ebuild, arrayfire-9999.ebuild: + Add 3.0_beta + + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + -files/arrayfire-0.9999-CMakeLists_examples.patch, + -files/arrayfire-9999-CMakeLists_examples.patch, arrayfire-9999.ebuild: + Drop patches, fix ebuild + + 08 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/arrayfire-0.9999-CMakeLists_examples.patch, + +files/arrayfire-0.9999-build_gtest.patch, + +files/arrayfire-9999-CMakeLists_examples.patch, + -files/CMakeLists_examples.patch, -files/build_gtest.patch, + arrayfire-9999.ebuild: + Update patches + + 19 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> arrayfire-9999.ebuild: + Fix SLOT operators + *arrayfire-0.9999 (12 Jan 2015) 12 jan 2015; Marius Brehler <marbre@linux.sungazer.de> diff --git a/sci-libs/arrayfire/arrayfire-0.9999.ebuild b/sci-libs/arrayfire/arrayfire-0.9999.ebuild index 71d00d46a..f8b1e5e75 120000..100644 --- a/sci-libs/arrayfire/arrayfire-0.9999.ebuild +++ b/sci-libs/arrayfire/arrayfire-0.9999.ebuild @@ -1 +1,95 @@ -arrayfire-9999.ebuild
\ No newline at end of file +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils git-r3 + +GTEST_PV="1.7.0" + +DESCRIPTION="A general purpose GPU library." +HOMEPAGE="http://www.arrayfire.com/" +EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git" +SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )" +KEYWORDS="" +# the remote HEAD points to devel, but we want to pull the master instead +EGIT_BRANCH="master" + +LICENSE="BSD" +SLOT="0" +IUSE="+examples +cpu cuda opencl test" + +RDEPEND=" + >=sys-devel/gcc-4.7:* + cuda? ( + >=dev-util/nvidia-cuda-toolkit-6.0 + dev-libs/boost + ) + cpu? ( + virtual/blas + virtual/cblas + sci-libs/fftw:3.0 + ) + opencl? ( + dev-libs/boost + dev-libs/boost-compute + sci-libs/clblas + sci-libs/clfft + )" +DEPEND="${RDEPEND}" + +BUILD_DIR="${S}/build" +CMAKE_BUILD_TYPE=Release + +PATCHES=( + "${FILESDIR}"/${PN}-3.0_beta-FindCBLAS.patch + "${FILESDIR}"/${PN}-3.0_beta-FindBoostCompute.patch + "${FILESDIR}"/${PN}-3.0_beta-opencl_CMakeLists.patch +) + +# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage +# user is (usually) not in the video group +RESTRICT="userpriv" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then + die "Compilation with gcc older than 4.7 is not supported." + fi + fi +} + +src_unpack() { + git-r3_src_unpack + + if use test; then + mkdir -p "${BUILD_DIR}"/third_party/src/ || die + cd "${BUILD_DIR}"/third_party/src/ || die + unpack ${A} + mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die + fi +} + +src_configure() { + if use cuda; then + addwrite /dev/nvidiactl + addwrite /dev/nvidia0 + addwrite /dev/nvidia-uvm + fi + + local mycmakeargs=( + $(cmake-utils_use_build cpu CPU) + $(cmake-utils_use_build cuda CUDA) + $(cmake-utils_use_build opencl OPENCL) + $(cmake-utils_use_build examples EXAMPLES) + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + + dobin "${BUILD_DIR}/bin2cpp" +} diff --git a/sci-libs/arrayfire/arrayfire-3.0_beta.ebuild b/sci-libs/arrayfire/arrayfire-3.0_beta.ebuild new file mode 100644 index 000000000..8a08c8c77 --- /dev/null +++ b/sci-libs/arrayfire/arrayfire-3.0_beta.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils git-r3 + +GTEST_PV="1.7.0" + +DESCRIPTION="A general purpose GPU library." +HOMEPAGE="http://www.arrayfire.com/" +EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git" +SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )" +KEYWORDS="~amd64" +EGIT_COMMIT="v3.0beta" + +LICENSE="BSD" +SLOT="0" +IUSE="+examples +cpu cuda opencl test" + +RDEPEND=" + >=sys-devel/gcc-4.7:* + cuda? ( + >=dev-util/nvidia-cuda-toolkit-6.0 + dev-libs/boost + ) + cpu? ( + virtual/blas + virtual/cblas + sci-libs/fftw:3.0 + ) + opencl? ( + dev-libs/boost + dev-libs/boost-compute + sci-libs/clblas + sci-libs/clfft + )" +DEPEND="${RDEPEND}" + +BUILD_DIR="${S}/build" +CMAKE_BUILD_TYPE=Release + +PATCHES=( + "${FILESDIR}"/${P}-FindCBLAS.patch + "${FILESDIR}"/${P}-FindBoostCompute.patch + "${FILESDIR}"/${P}-opencl_CMakeLists.patch +) + +# We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage +# user is (usually) not in the video group +RESTRICT="userpriv" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 7 ]] ) ; then + die "Compilation with gcc older than 4.7 is not supported." + fi + fi +} + +src_unpack() { + git-r3_src_unpack + + if use test; then + mkdir -p "${BUILD_DIR}"/third_party/src/ || die + cd "${BUILD_DIR}"/third_party/src/ || die + unpack ${A} + mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die + fi +} + +src_configure() { + if use cuda; then + addwrite /dev/nvidiactl + addwrite /dev/nvidia0 + addwrite /dev/nvidia-uvm + fi + + local mycmakeargs=( + $(cmake-utils_use_build cpu CPU) + $(cmake-utils_use_build cuda CUDA) + $(cmake-utils_use_build opencl OPENCL) + $(cmake-utils_use_build examples EXAMPLES) + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} + +src_install() { + cmake-utils_src_install + + dobin "${BUILD_DIR}/bin2cpp" +} diff --git a/sci-libs/arrayfire/arrayfire-9999.ebuild b/sci-libs/arrayfire/arrayfire-9999.ebuild index 69eb0e0f7..b976a150b 100644 --- a/sci-libs/arrayfire/arrayfire-9999.ebuild +++ b/sci-libs/arrayfire/arrayfire-9999.ebuild @@ -13,17 +13,13 @@ HOMEPAGE="http://www.arrayfire.com/" EGIT_REPO_URI="https://github.com/${PN}/${PN}.git git://github.com/${PN}/${PN}.git" SRC_URI="test? ( https://googletest.googlecode.com/files/gtest-${GTEST_PV}.zip )" KEYWORDS="" -if [[ ${PV} == "0.9999" ]] ; then - # the remote HEAD points to devel, but we want to pull the master instead - EGIT_BRANCH="master" -fi LICENSE="BSD" SLOT="0" -IUSE="+examples +cpu cuda test" +IUSE="+examples +cpu cuda opencl test" RDEPEND=" - >=sys-devel/gcc-4.7.3-r1 + >=sys-devel/gcc-4.7:* cuda? ( >=dev-util/nvidia-cuda-toolkit-6.0 dev-libs/boost @@ -31,7 +27,14 @@ RDEPEND=" cpu? ( virtual/blas virtual/cblas + virtual/lapacke sci-libs/fftw:3.0 + ) + opencl? ( + dev-libs/boost + dev-libs/boost-compute + sci-libs/clblas + sci-libs/clfft )" DEPEND="${RDEPEND}" @@ -39,9 +42,7 @@ BUILD_DIR="${S}/build" CMAKE_BUILD_TYPE=Release PATCHES=( - "${FILESDIR}"/FindCBLAS.patch - "${FILESDIR}"/CMakeLists_examples.patch - "${FILESDIR}"/build_gtest.patch + "${FILESDIR}"/${P}-FindCBLAS.patch ) # We need write acccess /dev/nvidiactl, /dev/nvidia0 and /dev/nvidia-uvm and the portage @@ -65,6 +66,9 @@ src_unpack() { unpack ${A} mv "${BUILD_DIR}"/third_party/src/gtest-"${GTEST_PV}" "${BUILD_DIR}"/third_party/src/googletest || die fi + + rm "${S}"/CMakeModules/build_boost_compute.cmake || die + cp "${FILESDIR}"/FindBoostCompute.cmake "${S}"/CMakeModules/ || die } src_configure() { @@ -77,7 +81,7 @@ src_configure() { local mycmakeargs=( $(cmake-utils_use_build cpu CPU) $(cmake-utils_use_build cuda CUDA) - -DBUILD_OPENCL=OFF + $(cmake-utils_use_build opencl OPENCL) $(cmake-utils_use_build examples EXAMPLES) $(cmake-utils_use_build test TEST) ) diff --git a/sci-libs/arrayfire/files/CMakeLists_examples.patch b/sci-libs/arrayfire/files/CMakeLists_examples.patch deleted file mode 100644 index 89020f675..000000000 --- a/sci-libs/arrayfire/files/CMakeLists_examples.patch +++ /dev/null @@ -1,15 +0,0 @@ -Adjust installation path of examples. - -Patch by Marius Brehler. - ---- b/examples/CMakeLists.txt -+++ a/examples/CMakeLists.txt -@@ -13,7 +13,7 @@ MACRO(CREATE_EXAMPLES BACKEND) - TARGET_LINK_LIBRARIES(${EXAMPLE_NAME} af${BACKEND} ${THREAD_LIB_FLAG}) - SET_TARGET_PROPERTIES(${EXAMPLE_NAME} PROPERTIES COMPILE_FLAGS -DAF_${DEF_NAME} OUTPUT_NAME ${FNAME}_${BACKEND}) - --# INSTALL(TARGETS ${EXAMPLE_NAME} DESTINATION arrayfire/examples) -+ INSTALL(TARGETS ${EXAMPLE_NAME} DESTINATION share/arrayfire/examples) - ENDFOREACH() - ENDMACRO(CREATE_EXAMPLES) - diff --git a/sci-libs/arrayfire/files/FindBoostCompute.cmake b/sci-libs/arrayfire/files/FindBoostCompute.cmake new file mode 100644 index 000000000..d98ea4b67 --- /dev/null +++ b/sci-libs/arrayfire/files/FindBoostCompute.cmake @@ -0,0 +1,18 @@ +# Downloads and builds the Boost Compute library from github.com +# Defines the following variables +# * BoostCompute_FOUND Flag for Boost Compute +# * BoostCompute_INCLUDE_DIR Location of the Boost Compute headers + + +set(BoostCompute_INCLUDE_DIR "/usr/include/compute") +SET( BoostCompute_FOUND ON CACHE BOOL "BoostCompute Found" ) + + +IF(NOT BoostCompute_FOUND) + MESSAGE(FATAL_ERROR, "Boost.Compute not found! Clone Boost.Compute from https://github.com/kylelutz/compute.git") +ENDIF(NOT BoostCompute_FOUND) + +MARK_AS_ADVANCED( + BoostCompute_FOUND + BoostCompute_INCLUDE_DIR + ) diff --git a/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch new file mode 100644 index 000000000..3052df20d --- /dev/null +++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindBoostCompute.patch @@ -0,0 +1,34 @@ +Set BoostCompute inlcude dir. + +Patch by Marius Brehler. + +--- CMakeModules/FindBoostCompute.cmake ++++ CMakeModules/FindBoostCompute.cmake +@@ -3,25 +3,10 @@ + # * BoostCompute_FOUND Flag for Boost Compute + # * BoostCompute_INCLUDE_DIR Location of the Boost Compute headers + +-# Look a directory above for the Boost Compute folder +-FIND_PATH( BoostCompute_SOURCE_DIR +- NAMES include/boost/compute.hpp +- PATH_SUFFIXES compute BoostCompute +- DOC "Location of the Boost Compute source directory" +- PATHS ${CMAKE_SOURCE_DIR}/.. +- ${CMAKE_SOURCE_DIR}/../.. +- /usr/local) + +-FIND_PATH( BoostCompute_INCLUDE_DIR +- NAMES boost/compute.hpp +- DOC "Location of the Boost Compute include directory." +- PATHS ${BoostCompute_SOURCE_DIR}/include) ++set(BoostCompute_INCLUDE_DIR "/usr/include/compute") ++SET( BoostCompute_FOUND ON CACHE BOOL "BoostCompute Found" ) + +-IF(BoostCompute_INCLUDE_DIR AND BoostCompute_SOURCE_DIR) +- SET( BoostCompute_FOUND ON CACHE BOOL "BoostCompute Found" ) +-ELSE() +- SET( BoostCompute_FOUND OFF CACHE BOOL "BoostCompute Found" ) +-ENDIF() + + IF(NOT BoostCompute_FOUND) + MESSAGE(FATAL_ERROR, "Boost.Compute not found! Clone Boost.Compute from https://github.com/kylelutz/compute.git") diff --git a/sci-libs/arrayfire/files/FindCBLAS.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindCBLAS.patch index 263c62aaf..263c62aaf 100644 --- a/sci-libs/arrayfire/files/FindCBLAS.patch +++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-FindCBLAS.patch diff --git a/sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch b/sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch new file mode 100644 index 000000000..7279afaa6 --- /dev/null +++ b/sci-libs/arrayfire/files/arrayfire-3.0_beta-opencl_CMakeLists.patch @@ -0,0 +1,26 @@ +Do not install clFFT/clBLAS headers. + +Patch by Marius Brehler. + +--- src/backend/opencl/CMakeLists.txt ++++ src/backend/opencl/CMakeLists.txt +@@ -18,9 +18,6 @@ ADD_DEFINITIONS(-DAF_OPENCL + FIND_PACKAGE(CLBLAS REQUIRED) + INCLUDE_DIRECTORIES(${CLBLAS_INCLUDE_DIRS}) + LINK_DIRECTORIES(${CLBLAS_LIBRARY_DIR}) +-# Custom install command +-INSTALL(DIRECTORY "${CLBLAS_PACKAGE_DIR}/include/" DESTINATION include +- COMPONENT headers) + IF(UNIX) + FILE(GLOB CLBLAS_LIBS "${CLBLAS_PACKAGE_DIR}/lib64/*${CMAKE_SHARED_LIBRARY_SUFFIX}*") + ELSEIF(WIN32) +@@ -33,9 +30,6 @@ INSTALL(FILES ${CLBLAS_LIBS} DESTINATION + FIND_PACKAGE(clFFT REQUIRED) + INCLUDE_DIRECTORIES(${CLFFT_INCLUDE_DIRS}) + LINK_DIRECTORIES(${CLFFT_LIBRARY_DIR}) +-# Custom install command +-INSTALL(DIRECTORY "${CLFFT_BUILD_DIR}/package/include/" DESTINATION include +- COMPONENT headers) + IF(UNIX) + FILE(GLOB CLFFT_LIBS "${CLFFT_BUILD_DIR}/package/lib64/*${CMAKE_SHARED_LIBRARY_SUFFIX}*") + ELSE(UNIX) diff --git a/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch b/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch new file mode 100644 index 000000000..7f757e8a2 --- /dev/null +++ b/sci-libs/arrayfire/files/arrayfire-9999-FindCBLAS.patch @@ -0,0 +1,52 @@ +Use pkg-config to find cblas. + +Patch by Marius Brehler. + +--- CMakeModules/FindCBLAS.cmake 2015-05-23 17:12:41.000000000 +0200 ++++ CMakeModules/FindCBLAS.cmake.new 2015-05-23 17:13:51.000000000 +0200 +@@ -1,3 +1,9 @@ ++# ++# Version modified for Gentoo Linux ++# If a valid PkgConfig configuration for cblas is found, this overrides and cancels ++# all further checks. ++# ++ + # Using FindCBLAS.cmake from the following repo + # https://github.com/clementfarabet/THC/blob/master/COPYRIGHT.txt + +@@ -21,6 +27,29 @@ SET(CBLAS_INCLUDE_DIR CACHE STRING + SET(CBLAS_INCLUDE_FILE CACHE STRING + "CBLAS header name") + ++ ++# ++# first, try PkgConfig ++# ++find_package(PkgConfig REQUIRED) ++pkg_check_modules(PC_CBLAS cblas) ++if(PC_CBLAS_FOUND) ++ foreach(PC_LIB ${PC_CBLAS_LIBRARIES}) ++ find_library(${PC_LIB}_LIBRARY NAMES ${PC_LIB} HINTS ${PC_CBLAS_LIBRARY_DIRS} ) ++ if (NOT ${PC_LIB}_LIBRARY) ++ message(FATAL_ERROR "Something is wrong in your pkg-config file - lib ${PC_LIB} not found in ${PC_CBLAS_LIBRARY_DIRS}") ++ endif (NOT ${PC_LIB}_LIBRARY) ++ list(APPEND CBLAS_LIBRARIES ${${PC_LIB}_LIBRARY}) ++ endforeach(PC_LIB) ++ find_package_handle_standard_args(CBLAS DEFAULT_MSG CBLAS_LIBRARIES) ++ mark_as_advanced(CBLAS_LIBRARIES) ++else(PC_CBLAS_FOUND) ++message(STATUS "No PkgConfig configuration for CBLAS found; starting more extensive search.") ++ ++ ++ ++ ++ + SET(INTEL_MKL_ROOT_DIR CACHE STRING + "Root directory of the Intel MKL") + +@@ -277,3 +306,5 @@ IF(NOT CBLAS_FIND_QUIETLY) + MESSAGE(STATUS "CBLAS library not found.") + ENDIF() + ENDIF(NOT CBLAS_FIND_QUIETLY) ++ ++endif(PC_CBLAS_FOUND) diff --git a/sci-libs/arrayfire/files/build_gtest.patch b/sci-libs/arrayfire/files/build_gtest.patch deleted file mode 100644 index 4b777c4fa..000000000 --- a/sci-libs/arrayfire/files/build_gtest.patch +++ /dev/null @@ -1,55 +0,0 @@ -Don't fetch googletest from SVN. - -Patch by Marius Brehler. - ---- CMakeModules/build_gtest.cmake -+++ CMakeModules/build_gtest.cmake -@@ -1,27 +1,4 @@ --#Downloads and installs GTest into the third_party directory -- --# We apply a patch to subversion, thus we need to find it. --FIND_PACKAGE(Subversion REQUIRED) -- --# Create patch file for gtest with MSVC 2012 --if(MSVC_VERSION EQUAL 1700) -- file(WRITE "${CMAKE_BINARY_DIR}/gtest.patch" "Index: cmake/internal_utils.cmake\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "===================================================================\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "--- cmake/internal_utils.cmake (revision 660)\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "+++ cmake/internal_utils.cmake (working copy)\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "@@ -66,6 +66,9 @@\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " # Resolved overload was found by argument-dependent lookup.\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " set(cxx_base_flags \"\${cxx_base_flags} -wd4675\")\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " endif()\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "+ if (MSVC_VERSION EQUAL 1700)\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "+ set(cxx_base_flags \"\${cxx_base_flags} -D_VARIADIC_MAX=10\")\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" "+ endif ()\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " set(cxx_base_flags \"\${cxx_base_flags} -D_UNICODE -DUNICODE -DWIN32 -D_WIN32\")\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " set(cxx_base_flags \"\${cxx_base_flags} -DSTRICT -DWIN32_LEAN_AND_MEAN\")\n") -- file(APPEND "${CMAKE_BINARY_DIR}/gtest.patch" " set(cxx_exception_flags \"-EHsc -D_HAS_EXCEPTIONS=1\")\n") --else() -- file(WRITE "${CMAKE_BINARY_DIR}/gtest.patch" "") --endif() -+#Installs GTest into the third_party directory - - # Enable ExternalProject CMake module - include(ExternalProject) -@@ -37,10 +14,6 @@ set_directory_properties(PROPERTIES EP_P - # Add gtest - ExternalProject_Add( - googletest -- SVN_REPOSITORY http://googletest.googlecode.com/svn/trunk/ -- SVN_REVISION -r 660 -- TIMEOUT 10 -- PATCH_COMMAND "${Subversion_SVN_EXECUTABLE}" patch "${CMAKE_BINARY_DIR}/gtest.patch" "${CMAKE_BINARY_DIR}/third_party/src/googletest" - # Force separate output paths for debug and release builds to allow easy - # identification of correct lib in subsequent TARGET_LINK_LIBRARIES commands - CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -@@ -54,8 +27,6 @@ ExternalProject_Add( - # Disable install step - INSTALL_COMMAND "" - # Wrap download, configure and build steps in a script to log output -- LOG_DOWNLOAD 0 -- LOG_UPDATE 0 - LOG_CONFIGURE 0 - LOG_BUILD 0) - diff --git a/sci-libs/arrayfire/metadata.xml b/sci-libs/arrayfire/metadata.xml index 0ef39acf5..d7715cbba 100644 --- a/sci-libs/arrayfire/metadata.xml +++ b/sci-libs/arrayfire/metadata.xml @@ -20,5 +20,8 @@ <flag name="cuda"> Enable CUDA Build. </flag> + <flag name="opencl"> + Enable OpenCL Build. + </flag> </use> </pkgmetadata> diff --git a/sci-libs/atlas/ChangeLog b/sci-libs/atlas/ChangeLog index d0a2ccaf8..cf7b7732c 100644 --- a/sci-libs/atlas/ChangeLog +++ b/sci-libs/atlas/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/atlas -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/atlas: Updating remote-id in metadata.xml + 02 Feb 2014; Reinis Danne <rei4dan@gmail.com> atlas-3.10.1-r1.ebuild, atlas-3.10.1-r2.ebuild: Fix cpu governor check. diff --git a/sci-libs/atlas/metadata.xml b/sci-libs/atlas/metadata.xml index fde6aff3c..31d8b7462 100644 --- a/sci-libs/atlas/metadata.xml +++ b/sci-libs/atlas/metadata.xml @@ -13,4 +13,7 @@ <use> <flag name="generic">Build atlas assuming a fairly generic architecture (sse2 for x86, core2 for amd64)</flag> </use> + <upstream> + <remote-id type="sourceforge">math-atlas</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/bliss/ChangeLog b/sci-libs/bliss/ChangeLog deleted file mode 100644 index 7041e0587..000000000 --- a/sci-libs/bliss/ChangeLog +++ /dev/null @@ -1,14 +0,0 @@ - - 11 Jul 2013; Christoph Junghans <ottxor@gentoo.org> - files/bliss-0.72-autotools.patch: - install heads into a bliss subdir - - 28 Apr 2013; Christoph Junghans <ottxor@gentoo.org> bliss-0.72.ebuild: - remove la files, added static-libs use flag - -*bliss-0.72 (28 Apr 2013) - - 28 Apr 2013; Christoph Junghans <ottxor@gentoo.org> +bliss-0.72.ebuild, - +files/bliss-0.72-autotools.patch, +files/bliss-0.72-fedora.patch, - +metadata.xml: - initial commit diff --git a/sci-libs/bliss/Manifest b/sci-libs/bliss/Manifest deleted file mode 100644 index be3eecb6e..000000000 --- a/sci-libs/bliss/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bliss-0.72.zip 90970 SHA256 528d192b1e30722fc60f5f12c9d6c12b374d838198ae7f18fb41bedabf735ed3 SHA512 a09b3cea26e3ff5f5733f10bfaadaf6fb5a3f443e1cc306fad16af2f7b4cd97c90652315f911a324d6d71426a3d098cd5c7e5721f69c599fe2e0d6d34caa0ef5 WHIRLPOOL afbc41c04e843d383a2da8d5e26ec2882c847e8e5f1e71c05f884396fcc79eab764df628523336b88e0c6ef4fbf073a52870e2c68ded428002d9391894cb53d6 diff --git a/sci-libs/bliss/bliss-0.72.ebuild b/sci-libs/bliss/bliss-0.72.ebuild deleted file mode 100644 index 8967db7a0..000000000 --- a/sci-libs/bliss/bliss-0.72.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit autotools-utils - -SRC_URI="http://www.tcs.hut.fi/Software/${PN}/${P}.zip" -DESCRIPTION="A Tool for Computing Automorphism Groups and Canonical Labelings of Graphs" -HOMEPAGE="http://www.tcs.hut.fi/Software/bliss/index.shtml" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc gmp static-libs" - -RDEPEND="gmp? ( dev-libs/gmp )" - -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -AUTOTOOLS_AUTORECONF=1 -AUTOTOOLS_PRUNE_LIBTOOL_FILES="all" #comes with pkg-config file - -PATCHES=( - "${FILESDIR}/${P}-fedora.patch" - "${FILESDIR}/${P}-autotools.patch" -) - -src_configure() { - local myeconfargs=( $(use_with gmp) ) - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - if use doc; then - cd "${BUILD_DIR}" - emake html - dohtml -r html - fi -} diff --git a/sci-libs/bliss/files/bliss-0.72-autotools.patch b/sci-libs/bliss/files/bliss-0.72-autotools.patch deleted file mode 100644 index d30c51622..000000000 --- a/sci-libs/bliss/files/bliss-0.72-autotools.patch +++ /dev/null @@ -1,159 +0,0 @@ -Replace simple Makefile by autotools -- allow shared library -- parallel build -- added pkg-config support - -Author: Christoph Junghans <ottxor@gentoo.org> - -diff -Naur bliss-0.72-fedora/config/.dummy bliss-0.72/config/.dummy ---- bliss-0.72-fedora/config/.dummy 1969-12-31 17:00:00.000000000 -0700 -+++ bliss-0.72/config/.dummy 2013-04-28 14:43:06.143760368 -0600 -@@ -0,0 +1 @@ -+Dummy file to make patch create config dir, which is needed for autotools -diff -Naur bliss-0.72-fedora/configure.ac bliss-0.72/configure.ac ---- bliss-0.72-fedora/configure.ac 1969-12-31 17:00:00.000000000 -0700 -+++ bliss-0.72/configure.ac 2013-04-28 14:40:42.283242722 -0600 -@@ -0,0 +1,31 @@ -+AC_PREREQ([2.65]) -+AC_INIT([bliss], [0.72], [Tommi.Junttil@kk.fi]) -+ -+AC_CONFIG_AUX_DIR(config) -+AC_CONFIG_MACRO_DIR(config) -+ -+AM_INIT_AUTOMAKE([1.8 foreign]) -+ -+SHARED_VERSION_INFO="1:0:0" -+AC_SUBST(SHARED_VERSION_INFO) -+ -+# Checks for programs. -+AC_PROG_CXX -+ -+LT_INIT -+# Checks for libraries. -+AC_ARG_WITH([gmp], -+ [AS_HELP_STRING([--with-gmp], [enable support for GNU Multiple Precision Arithmetic Library @<:@default=check@:>@])], -+ [], [with_readline=no]) -+AS_IF([test "x$with_readline" != xno], -+ [AC_CHECK_HEADERS([gmp.h],,AC_MSG_ERROR([Cannot find gmp.h header])) -+ AC_CHECK_LIB([gmp],_init,,AC_MSG_ERROR([Cannot find gmp library])) -+ AC_SUBST([GMP],[-lgmp]) -+ [CPPFLAGS="$CPPFLAGS -DBLISS_USE_GMP"]]) -+ -+AC_CHECK_PROG(DOXYGEN,doxygen,doxygen,no) -+AM_CONDITIONAL(HAVE_DOXYGEN,[test .$DOXYGEN != .no]) -+ -+AC_CONFIG_FILES([Makefile]) -+AC_CONFIG_FILES([bliss.pc]) -+AC_OUTPUT -diff -Naur bliss-0.72-fedora/bliss.pc.in bliss-0.72/bliss.pc.in ---- bliss-0.72-fedora/bliss.pc.in 1969-12-31 17:00:00.000000000 -0700 -+++ bliss-0.72/bliss.pc.in 2013-04-28 14:40:54.223285686 -0600 -@@ -0,0 +1,13 @@ -+prefix=@prefix@ -+exec_prefix=@exec_prefix@ -+libdir=@libdir@ -+includedir=@includedir@ -+ -+Name: bliss -+Description: Library for Computing Automorphism Groups and Canonical Labelings of Graphs -+URL: http://www.tcs.hut.fi/Software/bliss/index.shtml -+Version: @VERSION@ -+Requires: -+Libs: -L${libdir} -lbliss @GMP@ -+Libs.private: -lm -+Cflags: -I${includedir} -diff -Naur bliss-0.72-fedora/Makefile bliss-0.72/Makefile ---- bliss-0.72-fedora/Makefile 2013-04-28 14:40:10.543128514 -0600 -+++ bliss-0.72/Makefile 1969-12-31 17:00:00.000000000 -0700 -@@ -1,57 +0,0 @@ --CFLAGS = -I. --CFLAGS += -g --#CFLAGS += -pg --CFLAGS += -Wall --CFLAGS += --pedantic --CFLAGS += -O9 --#CFLAGS += -DBLISS_DEBUG --CFLAGS += -fPIC -- --SRCS = defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc --SRCS += timer.cc utils.cc bliss_C.cc -- --OBJS = $(addsuffix .o, $(basename $(SRCS))) -- --GMPOBJS = $(addsuffix g, $(OBJS)) -- --LIB = --#LIB += /usr/lib/ccmalloc.o -ldl -- --CC = g++ --RANLIB = ranlib --AR = ar --BLISSLIB = libbliss.a -- --gmp: LIB += -lgmp --gmp: CFLAGS += -DBLISS_USE_GMP -- --normal: bliss --gmp: bliss_gmp -- -- --all:: lib bliss -- --%.o %.og: %.cc -- $(CC) $(CFLAGS) -c -o $@ $< -- --lib: $(OBJS) -- rm -f $(BLISSLIB) -- $(AR) cr $(BLISSLIB) $(OBJS) -- $(RANLIB) $(BLISSLIB) -- --lib_gmp: $(GMPOBJS) -- rm -f $(BLISSLIB) -- $(AR) cr $(BLISSLIB) $(GMPOBJS) -- $(RANLIB) $(BLISSLIB) -- --bliss: bliss.o lib $(OBJS) -- $(CC) $(CFLAGS) -o bliss bliss.o $(OBJS) $(LIB) -- --bliss_gmp: bliss.og lib_gmp $(GMPOBJS) -- $(CC) $(CFLAGS) -o bliss bliss.og $(GMPOBJS) $(LIB) -- -- --clean: -- rm -f bliss $(BLISSLIB) $(OBJS) bliss.o $(GMPOBJS) bliss.og -- --# DO NOT DELETE -diff -Naur bliss-0.72-fedora/Makefile.am bliss-0.72/Makefile.am ---- bliss-0.72-fedora/Makefile.am 1969-12-31 17:00:00.000000000 -0700 -+++ bliss-0.72/Makefile.am 2013-04-28 14:47:26.944698789 -0600 -@@ -0,0 +1,30 @@ -+ACLOCAL_AMFLAGS = -I config -+ -+lib_LTLIBRARIES = libbliss.la -+ -+libbliss_la_LDFLAGS = -no-undefined -version-info @SHARED_VERSION_INFO@ -+libbliss_la_SOURCES = \ -+ defs.cc graph.cc partition.cc orbit.cc uintseqhash.cc heap.cc \ -+ timer.cc utils.cc bliss_C.cc -+ -+pkginclude_HEADERS = \ -+ bignum.hh bliss_C.h defs.hh graph.hh heap.hh kqueue.hh kstack.hh \ -+ orbit.hh partition.hh timer.hh uintseqhash.hh utils.hh -+ -+bin_PROGRAMS = bliss -+bliss_SOURCES = bliss.cc -+bliss_LDADD = libbliss.la -+dist_man1_MANS = bliss.1 -+ -+pkgconfigdir = $(libdir)/pkgconfig -+pkgconfig_DATA = bliss.pc -+ -+html-local: Doxyfile -+if HAVE_DOXYGEN -+ $(DOXYGEN) $(srcdir)/Doxyfile -+else -+ @echo "doxygen was not found, please re-run configure" -+endif -+ -+clean-local: -+ -rm -rf html diff --git a/sci-libs/bliss/files/bliss-0.72-fedora.patch b/sci-libs/bliss/files/bliss-0.72-fedora.patch deleted file mode 100644 index e1f8b6685..000000000 --- a/sci-libs/bliss/files/bliss-0.72-fedora.patch +++ /dev/null @@ -1,648 +0,0 @@ -Pulled on 28-04-13 from -http://pkgs.fedoraproject.org/cgit/bliss.git/tree/ - -- Man page written by Jerry James using text borrowed from the sources. - The man page therefore has the same copyright and license as the sources. -- Don't call exit() in library code. -- Patch from Thomas Rehn, also sent upstream. Fix one bug and add one - performance enhancement. - -diff -Naur bliss-0.72.orig/bliss.1 bliss-0.72/bliss.1 ---- bliss-0.72.orig/bliss.1 1969-12-31 17:00:00.000000000 -0700 -+++ bliss-0.72/bliss.1 2013-04-28 14:35:37.000000000 -0600 -@@ -0,0 +1,55 @@ -+.TH "BLISS" "1" "@VERSION@" "Tommi Junttila & Petteri Kaski" "User Commands" -+.SH "NAME" -+bliss \- Compute automorphism groups and canonical labelings of graphs -+.SH "SYNOPSIS" -+.B bliss -+[\fIOPTIONS\fR] [<\fIGRAPH FILE\fR>] -+.SH "DESCRIPTION" -+.PP -+Bliss is an open source tool for computing automorphism groups and -+canonical forms of graphs. The graphs are specified in DIMACS format. -+.TP -+\fB\-directed\fR -+the input graph is directed -+.TP -+\fB\-can\fR -+compute canonical form -+.TP -+\fB\-ocan\fR=\fIf\fR -+compute canonical form and output it in file \fIf\fR -+.TP -+\fB\-v\fR=\fIN\fR -+set verbosity level to N [N >= 0, default: 1] -+.TP -+\fB\-sh\fR=\fIX\fR -+select splitting heuristics, where X is: -+.TS -+tab(;); -+R L. -+f;first non-singleton cell -+fl;first largest non-singleton cell -+fs;first smallest non-singleton cell -+fm;first maximally non-trivially connected non-singleton cell -+flm;first largest maximally non-trivially connected -+;non-singleton cell -+fsm;first smallest maximally non-trivially connected -+;non-singleton cell (default) -+.TE -+.TP -+\fB\-fr\fR=\fIX\fR -+use failure recording? [X=y/n, default: y] -+.TP -+\fB\-cr\fR=\fIX\fR -+use component recursion? [X=y/n, default: y] -+.TP -+\fB\-version\fR -+print the version number and exit -+.TP -+\fB\-help\fR -+print this help and exit -+.SH "AUTHORS" -+Bliss was written by Tommi Junttila <Tommi.Junttila@tkk.fi> and -+Petteri Kaski <petteri.kaski@aalto.fi>. -+.PP -+This man page was written by Jerry James <loganjerry@gmail.com>. -+It is distributed under the same terms as bliss. -diff -Naur bliss-0.72.orig/bliss.cc bliss-0.72/bliss.cc ---- bliss-0.72.orig/bliss.cc 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/bliss.cc 2013-04-28 14:36:28.792330603 -0600 -@@ -276,13 +276,16 @@ - if(opt_canonize == false) - { - /* No canonical labeling, only automorphism group */ -- g->find_automorphisms(stats, &report_aut, stdout); -+ if (!g->find_automorphisms(stats, &report_aut, stdout)) -+ exit(1); - } - else - { - /* Canonical labeling and automorphism group */ - const unsigned int* cl = g->canonical_form(stats, &report_aut, stdout); - -+ if (!cl) -+ exit(1); - fprintf(stdout, "Canonical labeling: "); - bliss::print_permutation(stdout, g->get_nof_vertices(), cl, 1); - fprintf(stdout, "\n"); -@@ -290,6 +293,8 @@ - if(opt_output_can_file) - { - bliss::AbstractGraph* cf = g->permute(cl); -+ if (!cf) -+ exit(1); - FILE* const fp = fopen(opt_output_can_file, "w"); - if(!fp) - _fatal("Cannot open '%s' for outputting the canonical form, aborting", opt_output_can_file); -diff -Naur bliss-0.72.orig/bliss_C.cc bliss-0.72/bliss_C.cc ---- bliss-0.72.orig/bliss_C.cc 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/bliss_C.cc 2013-04-28 14:36:28.792330603 -0600 -@@ -131,7 +131,7 @@ - } - - extern "C" --void -+int - bliss_find_automorphisms(BlissGraph *graph, - void (*hook)(void *user_param, - unsigned int n, -@@ -142,7 +142,8 @@ - bliss::Stats s; - assert(graph); - assert(graph->g); -- graph->g->find_automorphisms(s, hook, hook_user_param); -+ if (!graph->g->find_automorphisms(s, hook, hook_user_param)) -+ return 0; - - if(stats) - { -@@ -154,6 +155,7 @@ - stats->nof_generators = s.get_nof_generators(); - stats->max_level = s.get_max_level(); - } -+ return 1; - } - - -@@ -173,7 +175,7 @@ - - canonical_labeling = graph->g->canonical_form(s, hook, hook_user_param); - -- if(stats) -+ if(canonical_labeling && stats) - { - stats->group_size_approx = s.get_group_size_approx(); - stats->nof_nodes = s.get_nof_nodes(); -diff -Naur bliss-0.72.orig/bliss_C.h bliss-0.72/bliss_C.h ---- bliss-0.72.orig/bliss_C.h 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/bliss_C.h 2013-04-28 14:36:28.792330603 -0600 -@@ -156,6 +156,7 @@ - * The argument \a perm should be an array of - * N=bliss::bliss_get_nof_vertices(\a graph) elements describing - * a bijection on {0,...,N-1}. -+ * Returns NULL if insufficient memory or internal error. - */ - BlissGraph *bliss_permute(BlissGraph *graph, const unsigned int *perm); - -@@ -174,8 +175,9 @@ - * if you want to use the automorphism later, you have to take a copy of it. - * Do not call bliss_* functions in the hook. - * If \a stats is non-null, then some search statistics are copied there. -+ * \return nonzero if successful, zero if insufficient memory or internal error - */ --void -+int - bliss_find_automorphisms(BlissGraph *graph, - void (*hook)(void *user_param, - unsigned int N, -@@ -194,6 +196,7 @@ - * then bliss_permute() with the returned canonical labeling. - * Note that the computed canonical version may depend on the applied version - * of bliss. -+ * Returns NULL if insufficient memory or internal error. - */ - const unsigned int * - bliss_find_canonical_labeling(BlissGraph *graph, -diff -Naur bliss-0.72.orig/defs.cc bliss-0.72/defs.cc ---- bliss-0.72.orig/defs.cc 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/defs.cc 2013-04-28 14:36:28.792330603 -0600 -@@ -33,7 +33,6 @@ - vfprintf(stderr, fmt, ap); - fprintf(stderr, "\nAborting!\n"); - va_end(ap); -- exit(1); - } - - } -diff -Naur bliss-0.72.orig/graph.cc bliss-0.72/graph.cc ---- bliss-0.72.orig/graph.cc 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/graph.cc 2013-04-28 14:37:16.162501050 -0600 -@@ -34,7 +34,10 @@ - namespace bliss { - - #define _INTERNAL_ERROR() fatal_error("%s:%d: internal error",__FILE__,__LINE__) --#define _OUT_OF_MEMORY() fatal_error("%s:%d: out of memory",__FILE__,__LINE__) -+#define _OUT_OF_MEMORY(label) do { \ -+ fatal_error("%s:%d: out of memory",__FILE__,__LINE__); \ -+ goto label; \ -+ } while (0) - - /*------------------------------------------------------------------------- - * -@@ -279,20 +282,6 @@ - *perm = i; - } - --bool --AbstractGraph::is_automorphism(unsigned int* const perm) --{ -- _INTERNAL_ERROR(); -- return false; --} -- --bool --AbstractGraph::is_automorphism(const std::vector<unsigned int>& perm) const --{ -- _INTERNAL_ERROR(); -- return false; --} -- - - - -@@ -608,17 +597,7 @@ - }; - - -- -- --typedef struct { -- unsigned int splitting_element; -- unsigned int certificate_index; -- unsigned int subcertificate_length; -- UintSeqHash eqref_hash; --} PathInfo; -- -- --void -+bool - AbstractGraph::search(const bool canonical, Stats& stats) - { - const unsigned int N = get_nof_vertices(); -@@ -658,7 +637,7 @@ - if(N == 0) - { - /* Nothing to do, return... */ -- return; -+ return true; - } - - /* Initialize the partition ... */ -@@ -696,10 +675,10 @@ - */ - if(first_path_labeling) free(first_path_labeling); - first_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int)); -- if(!first_path_labeling) _OUT_OF_MEMORY(); -+ if(!first_path_labeling) _OUT_OF_MEMORY(oom1); - if(best_path_labeling) free(best_path_labeling); - best_path_labeling = (unsigned int*)calloc(N, sizeof(unsigned int)); -- if(!best_path_labeling) _OUT_OF_MEMORY(); -+ if(!best_path_labeling) _OUT_OF_MEMORY(oom2); - - /* - * Is the initial partition discrete? -@@ -710,7 +689,7 @@ - update_labeling(best_path_labeling); - /* Update statistics */ - stats.nof_leaf_nodes = 1; -- return; -+ return true; - } - - /* -@@ -718,20 +697,39 @@ - */ - if(first_path_labeling_inv) free(first_path_labeling_inv); - first_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int)); -- if(!first_path_labeling_inv) _OUT_OF_MEMORY(); -+ if(!first_path_labeling_inv) _OUT_OF_MEMORY(oom3); - if(best_path_labeling_inv) free(best_path_labeling_inv); - best_path_labeling_inv = (unsigned int*)calloc(N, sizeof(unsigned int)); -- if(!best_path_labeling_inv) _OUT_OF_MEMORY(); -+ if(!best_path_labeling_inv) _OUT_OF_MEMORY(oom4); - - /* - * Allocate space for the automorphisms - */ - if(first_path_automorphism) free(first_path_automorphism); - first_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int)); -- if(!first_path_automorphism) _OUT_OF_MEMORY(); -+ if(!first_path_automorphism) _OUT_OF_MEMORY(oom5); - if(best_path_automorphism) free(best_path_automorphism); - best_path_automorphism = (unsigned int*)malloc(N * sizeof(unsigned int)); -- if(!best_path_automorphism) _OUT_OF_MEMORY(); -+ if(!best_path_automorphism) { -+ _OUT_OF_MEMORY(oom6); -+ oom6: -+ free(first_path_automorphism); -+ first_path_automorphism = NULL; -+ oom5: -+ free(best_path_labeling_inv); -+ best_path_labeling_inv = NULL; -+ oom4: -+ free(first_path_labeling_inv); -+ first_path_labeling_inv = NULL; -+ oom3: -+ free(best_path_labeling); -+ best_path_labeling = NULL; -+ oom2: -+ free(first_path_labeling); -+ first_path_labeling = NULL; -+ oom1: -+ return false; -+ } - - /* - * Initialize orbit information so that all vertices are in their own orbits -@@ -745,7 +743,6 @@ - initialize_certificate(); - - std::vector<TreeNode> search_stack; -- std::vector<PathInfo> first_path_info; - std::vector<PathInfo> best_path_info; - - search_stack.clear(); -@@ -974,7 +971,6 @@ - */ - { - unsigned int next_split_element = UINT_MAX; -- unsigned int* next_split_element_pos = 0; - unsigned int* ep = p.elements + cell->first; - if(current_node.fp_on) - { -@@ -985,7 +981,6 @@ - *ep < next_split_element and - first_path_orbits.is_minimal_representative(*ep)) { - next_split_element = *ep; -- next_split_element_pos = ep; - } - } - } -@@ -1001,7 +996,6 @@ - current_node.long_prune_redundant.find(*ep) == - current_node.long_prune_redundant.end())) { - next_split_element = *ep; -- next_split_element_pos = ep; - } - } - } -@@ -1015,7 +1009,6 @@ - current_node.long_prune_redundant.find(*ep) == - current_node.long_prune_redundant.end())) { - next_split_element = *ep; -- next_split_element_pos = ep; - } - } - } -@@ -1203,8 +1196,10 @@ - - #if defined(BLISS_VERIFY_EQUITABLEDNESS) - /* The new partition should be equitable */ -- if(!is_equitable()) -+ if(!is_equitable()) { - fatal_error("consistency check failed - partition after refinement is not equitable"); -+ return false; -+ } - #endif - - /* -@@ -1366,6 +1361,7 @@ - goto handle_first_path_automorphism; - /* Should never get here because of CR:FP */ - _INTERNAL_ERROR(); -+ return false; - } - } - -@@ -1598,8 +1594,10 @@ - - #if defined(BLISS_VERIFY_AUTOMORPHISMS) - /* Verify that it really is an automorphism */ -- if(!is_automorphism(best_path_automorphism)) -+ if(!is_automorphism(best_path_automorphism)) { - fatal_error("Best path automorhism validation check failed"); -+ return false; -+ } - #endif - - unsigned int gca_level_with_first = 0; -@@ -1666,6 +1664,7 @@ - - - _INTERNAL_ERROR(); -+ return false; - - - handle_first_path_automorphism: -@@ -1701,8 +1700,10 @@ - - #if defined(BLISS_VERIFY_AUTOMORPHISMS) - /* Verify that it really is an automorphism */ -- if(!is_automorphism(first_path_automorphism)) -+ if(!is_automorphism(first_path_automorphism)) { - fatal_error("First path automorphism validation check failed"); -+ return false; -+ } - #endif - - if(opt_use_long_prune) -@@ -1749,12 +1750,13 @@ - /* Release component recursion data in partition */ - if(opt_use_comprec) - p.cr_free(); -+ return true; - } - - - - --void -+bool - AbstractGraph::find_automorphisms(Stats& stats, - void (*hook)(void *user_param, - unsigned int n, -@@ -1764,7 +1766,8 @@ - report_hook = hook; - report_user_param = user_param; - -- search(false, stats); -+ if (!search(false, stats)) -+ return false; - - if(first_path_labeling) - { -@@ -1776,6 +1779,7 @@ - free(best_path_labeling); - best_path_labeling = 0; - } -+ return true; - } - - -@@ -1790,7 +1794,8 @@ - report_hook = hook; - report_user_param = user_param; - -- search(true, stats); -+ if (!search(true, stats)) -+ return NULL; - - return best_path_labeling; - } -@@ -3480,15 +3485,17 @@ - * Check whether perm is an automorphism. - * Slow, mainly for debugging and validation purposes. - */ --bool -+int - Digraph::is_automorphism(unsigned int* const perm) - { - std::set<unsigned int, std::less<unsigned int> > edges1; - std::set<unsigned int, std::less<unsigned int> > edges2; - - #if defined(BLISS_CONSISTENCY_CHECKS) -- if(!is_permutation(get_nof_vertices(), perm)) -+ if(!is_permutation(get_nof_vertices(), perm)) { - _INTERNAL_ERROR(); -+ return -1; -+ } - #endif - - for(unsigned int i = 0; i < get_nof_vertices(); i++) -@@ -3507,7 +3514,7 @@ - ei++) - edges2.insert(*ei); - if(!(edges1 == edges2)) -- return false; -+ return 0; - - edges1.clear(); - for(std::vector<unsigned int>::iterator ei = v1.edges_out.begin(); -@@ -3520,10 +3527,10 @@ - ei++) - edges2.insert(*ei); - if(!(edges1 == edges2)) -- return false; -+ return 0; - } - -- return true; -+ return 1; - } - - bool -@@ -4330,8 +4337,10 @@ - Graph::permute(const unsigned int* perm) const - { - #if defined(BLISS_CONSISTENCY_CHECKS) -- if(!is_permutation(get_nof_vertices(), perm)) -+ if(!is_permutation(get_nof_vertices(), perm)) { - _INTERNAL_ERROR(); -+ return NULL; -+ } - #endif - - Graph* const g = new Graph(get_nof_vertices()); -@@ -5270,15 +5279,17 @@ - * - *-------------------------------------------------------------------------*/ - --bool -+int - Graph::is_automorphism(unsigned int* const perm) - { - std::set<unsigned int, std::less<unsigned int> > edges1; - std::set<unsigned int, std::less<unsigned int> > edges2; - - #if defined(BLISS_CONSISTENCY_CHECKS) -- if(!is_permutation(get_nof_vertices(), perm)) -+ if(!is_permutation(get_nof_vertices(), perm)) { - _INTERNAL_ERROR(); -+ return -1; -+ } - #endif - - for(unsigned int i = 0; i < get_nof_vertices(); i++) -@@ -5298,10 +5309,10 @@ - edges2.insert(*ei); - - if(!(edges1 == edges2)) -- return false; -+ return 0; - } - -- return true; -+ return 1; - } - - -@@ -5444,7 +5455,7 @@ - component.clear(); - component_elements = 0; - sh_return = 0; -- unsigned int sh_first = 0; -+ unsigned int sh_first = 1 << 31; - unsigned int sh_size = 0; - unsigned int sh_nuconn = 0; - -diff -Naur bliss-0.72.orig/graph.hh bliss-0.72/graph.hh ---- bliss-0.72.orig/graph.hh 2013-04-28 14:35:20.582085167 -0600 -+++ bliss-0.72/graph.hh 2013-04-28 14:37:16.162501050 -0600 -@@ -109,9 +109,12 @@ - unsigned long int get_max_level() const {return max_level;} - }; - -- -- -- -+typedef struct { -+ unsigned int splitting_element; -+ unsigned int certificate_index; -+ unsigned int subcertificate_length; -+ UintSeqHash eqref_hash; -+} PathInfo; - - - /** -@@ -270,7 +273,7 @@ - void reset_permutation(unsigned int *perm); - - /* Mainly for debugging purposes */ -- virtual bool is_automorphism(unsigned int* const perm); -+ virtual int is_automorphism(unsigned int* const perm) = 0; - - std::vector<unsigned int> certificate_current_path; - std::vector<unsigned int> certificate_first_path; -@@ -284,7 +287,11 @@ - virtual Partition::Cell* find_next_cell_to_be_splitted(Partition::Cell *cell) = 0; - - -- void search(const bool canonical, Stats &stats); -+ /** -+ * \return true if successful, false if insufficient memory to complete or -+ * other internal error -+ */ -+ bool search(const bool canonical, Stats &stats); - - - void (*report_hook)(void *user_param, -@@ -351,7 +358,7 @@ - */ - unsigned int cr_component_elements; - -- -+ std::vector<PathInfo> first_path_info; - - - public: -@@ -362,7 +369,7 @@ - * Check whether \a perm is an automorphism of this graph. - * Unoptimized, mainly for debugging purposes. - */ -- virtual bool is_automorphism(const std::vector<unsigned int>& perm) const; -+ virtual bool is_automorphism(const std::vector<unsigned int>& perm) const = 0; - - - -@@ -427,8 +434,10 @@ - * if you want to use the automorphism later, you have to take a copy of it. - * Do not call any member functions in the hook. - * The search statistics are copied in \a stats. -+ * \return true if successful, false if insufficient memory to search or -+ * other internal error. - */ -- void find_automorphisms(Stats& stats, -+ bool find_automorphisms(Stats& stats, - void (*hook)(void* user_param, - unsigned int n, - const unsigned int* aut), -@@ -448,6 +457,8 @@ - * Note that the computed canonical version may depend on the applied version - * of bliss as well as on some other options (for instance, the splitting - * heuristic selected with bliss::Graph::set_splitting_heuristic()). -+ * This function returns NULL if there is insufficient memory, or another -+ * internal error occurs. - */ - const unsigned int* canonical_form(Stats& stats, - void (*hook)(void* user_param, -@@ -500,6 +511,10 @@ - opt_use_long_prune = active; - } - -+ /** -+ * Get an information vector about the first path. -+ */ -+ std::vector<PathInfo> get_first_path_info() { return first_path_info; } - }; - - -@@ -615,7 +630,7 @@ - - void initialize_certificate(); - -- bool is_automorphism(unsigned int* const perm); -+ int is_automorphism(unsigned int* const perm); - - - bool nucr_find_first_component(const unsigned int level); -@@ -856,7 +871,7 @@ - - void initialize_certificate(); - -- bool is_automorphism(unsigned int* const perm); -+ int is_automorphism(unsigned int* const perm); - - void sort_edges(); - diff --git a/sci-libs/bliss/metadata.xml b/sci-libs/bliss/metadata.xml deleted file mode 100644 index 119d0fde1..000000000 --- a/sci-libs/bliss/metadata.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/bloom/ChangeLog b/sci-libs/bloom/ChangeLog new file mode 100644 index 000000000..915cec270 --- /dev/null +++ b/sci-libs/bloom/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-libs/bloom +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*bloom-9999 (01 May 2015) + + 01 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +bloom-9999.ebuild, + +metadata.xml: + sci-libs/bloom: new package diff --git a/sci-libs/bloom/bloom-9999.ebuild b/sci-libs/bloom/bloom-9999.ebuild new file mode 100644 index 000000000..a60b7ba70 --- /dev/null +++ b/sci-libs/bloom/bloom-9999.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +[ "$PV" == "9999" ] && inherit subversion + +DESCRIPTION="C++ Bloom Filter Library" +HOMEPAGE="https://code.google.com/p/bloom" +if [ "$PV" == "9999" ]; then + ESVN_REPO_URI="http://bloom.googlecode.com/svn/trunk" +else + SRC_URI="" +fi + +LICENSE="MPL-1.1" +SLOT="0" +KEYWORDS="" +IUSE="" + +DEPEND="" +RDEPEND="${DEPEND}" + +src_prepare(){ + sed -e "s#-c++#$(tc-getCC)#;s#-O3#${CXXFLAGS}#" -i Makefile || die + sed -e "s#-pedantic-errors -ansi -Wall -Wextra -Werror -Wno-long-long##" -i Makefile || die +} diff --git a/sci-libs/bloom/metadata.xml b/sci-libs/bloom/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-libs/bloom/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/calculix-ccx/Manifest b/sci-libs/calculix-ccx/Manifest index 62639c473..9f4a5bdaa 100644 --- a/sci-libs/calculix-ccx/Manifest +++ b/sci-libs/calculix-ccx/Manifest @@ -1,3 +1,6 @@ DIST ccx_2.7.ps.tar.bz2 2395486 SHA256 e757b93d6279d49aa33c623a4d598382c55f1b35a4f0ffa43b2651c1f2baccc5 SHA512 987b5fb33ebbf8ebc989e276d7fe7c33edae8b72c52c3ad06c4a5c31476082b1a225387636ecc312b1cac5f6cbc4873bd94c74eb6cdb8f36b506db316c5089aa WHIRLPOOL 8a49560523f4045263e0ddc8dfb47ce32dc7fada099abe1998a95835f880eeefdf06097dc70fb3beed26a326a33781514089145d088205a45b02ac1cfc3db908 DIST ccx_2.7.src.tar.bz2 825264 SHA256 85fa68ec855e4e445f01be011f4cada238043ba4c5b7eaa38e19777bce2382d7 SHA512 e66c7df2d5c195112bf117aaf11ed9d1e9fc73b530a828f0f45a5574accc4093683307a637bba38cb9af1063a5b3f507e53570c970e38c48893758612de52cc8 WHIRLPOOL 5df3cada0ba41a5c2015907884c14f0e2d1c272e55a8b9c044f303c073624e7b5083a5605a83965505246ded428a0a291cf932520f2d404dd147f1711829282c DIST ccx_2.7.test.tar.bz2 8450942 SHA256 e339c9093b876c43b4a9b4a8ee80af60eb4146a1a89ff01f1dcf2f13aaaeb0d5 SHA512 01830b50524da5116c1dea8867ed8178577e665e29fffc33394490023111cebc3739293e2de5ec89b73c62ed913aa6a80bec58dcb989d9f24aa781f61e679afc WHIRLPOOL 320517c68da32ccca0fcc1bb8ee12357a1978f1d32e9ec989a63fbd82d5aab0b84d2978b46a555b1b0d3e3ea83b65ac6b5adaa1b8721b53bd19b1f70a041cbfd +DIST ccx_2.8p2.ps.tar.bz2 2404566 SHA256 8dda526c5b7911446ecadb3ded32e3d2b3daa7f232bfc88a2ad69d807acacc61 SHA512 abfe8d76e2c4fa55dea43c9a819e84dd4f8511bdb1f97c2862eb8faaa5bf314f88efabf1d8507db45d10e698cf0da0e546e108919bf4e82099f817237c1f08de WHIRLPOOL 635d5def9ae884bd2407c062afb727ab0235b64e844f6d5c302bea2fcd8e6798b930bba68c855b77ea4b4276c151bb0588e4132cd583d097908ceffa49ade4c4 +DIST ccx_2.8p2.src.tar.bz2 919489 SHA256 a21feb1a498b5925ddc9f7f58cb486d930435db4a47d5c583dd73f5160431eb2 SHA512 0ec53027ec7b072da33432b903048c5932cc51d43f5156a1ae64daf08924ed68f6bc70ea4b7fa4db9ad750bccd64c347fc7aec24418c67acaaf75c05a5988ab3 WHIRLPOOL 80587ca75690e7252303950e68b4071f14ce224d32297870589841ea1cbc7a3ad1ca257e87d84ef5ad47d688623b8cf950f2f508f4b8b9b235c9493657ada5a7 +DIST ccx_2.8p2.test.tar.bz2 9014544 SHA256 a859389cb1405a6130e06215715d4aac93b7877825d7d30a78ef3ab1f3df3662 SHA512 3d96041307b36fe342bf8ca63b041357ba818c0f72ff6217d07e0e72613aec1322a797ff2c03ecdf9cbd853f0bb79fb2e32868dc4a8ed2f20dc936a9142f9c2f WHIRLPOOL 7c859d25b3f8a9595b65bc6bb5a5f5fd8c7cd4fd0857a29b114cc0bcafc17aaf3c0c487a81ff4521ec70b2e076c4119e4913649507ea6db7900cfcf6fc79f052 diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild index a511dc9a0..5dc1f0073 100644 --- a/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild +++ b/sci-libs/calculix-ccx/calculix-ccx-2.7-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -59,7 +59,7 @@ src_install () { dosym ${MY_P} /usr/bin/ccx if use doc; then - cd "${S}/../doc" + cd "${S}/../doc" || die ps2pdf ${MY_P}.ps ${MY_P}.pdf dodoc ${MY_P}.pdf fi diff --git a/sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild b/sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild new file mode 100644 index 000000000..07020226d --- /dev/null +++ b/sci-libs/calculix-ccx/calculix-ccx-2.8_p2.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils toolchain-funcs flag-o-matic fortran-2 + +MY_P=ccx_${PV/_/} + +DESCRIPTION="A Free Software Three-Dimensional Structural Finite Element Program" +HOMEPAGE="http://www.calculix.de/" +SRC_URI=" + http://www.dhondt.de/${MY_P}.src.tar.bz2 + doc? ( http://www.dhondt.de/${MY_P}.ps.tar.bz2 ) + examples? ( http://www.dhondt.de/${MY_P}.test.tar.bz2 )" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="arpack doc examples threads" + +RDEPEND=" + arpack? ( >=sci-libs/arpack-3.1.3 ) + >=sci-libs/spooles-2.2[threads=] + virtual/lapack + virtual/blas" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( app-text/ghostscript-gpl )" + +S=${WORKDIR}/CalculiX/${MY_P}/src + +src_prepare (){ + epatch "${FILESDIR}/01_${MY_P}_Makefile_custom_cc_flags_spooles_arpack.patch" +} + +src_configure() { + # Technically we currently only need this when arpack is not used. + # Keeping things this way in case we change pkgconfig for arpack + export LAPACK=$($(tc-getPKG_CONFIG) --libs lapack) + + append-cflags "-I/usr/include/spooles -DSPOOLES" + if use threads; then + append-cflags "-DUSE_MT" + fi + + if use arpack; then + export ARPACKLIB=$($(tc-getPKG_CONFIG) --libs arpack) + append-cflags "-DARPACK" + fi + export CC="$(tc-getCC)" + export FC="$(tc-getFC)" +} + +src_install () { + dobin ${MY_P} + dosym ${MY_P} /usr/bin/ccx + + if use doc; then + cd "${S}/../doc" || die + ps2pdf ${MY_P}.ps ${MY_P}.pdf || die "ps2pdf failed" + dodoc ${MY_P}.pdf + fi + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins -r "${S}"/../test/* + fi +} diff --git a/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch b/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch new file mode 100644 index 000000000..a47fdc6f1 --- /dev/null +++ b/sci-libs/calculix-ccx/files/01_ccx_2.8p2_Makefile_custom_cc_flags_spooles_arpack.patch @@ -0,0 +1,32 @@ +Fix Makefile to make it use custom CFLAGS and system libraries. + +--- CalculiX.orig/ccx_2.8p2/src/Makefile 2015-05-21 11:04:58.125111330 +0300 ++++ CalculiX/ccx_2.8p2/src/Makefile 2015-05-21 11:08:26.848130631 +0300 +@@ -1,9 +1,9 @@ + +-CFLAGS = -Wall -O3 -I ../../../SPOOLES.2.2 -DARCH="Linux" -DSPOOLES -DARPACK -DMATRIXSTORAGE +-FFLAGS = -Wall -O3 -fopenmp ++CFLAGS := -Wall -O3 -DARCH="Linux" -DMATRIXSTORAGE $(CFLAGS) ++FFLAGS := -Wall -O3 $(FFLAGS) + +-CC=cc +-FC=gfortran ++#CC=cc ++#FC=gfortran + + .c.o : + $(CC) $(CFLAGS) -c $< +@@ -18,12 +18,7 @@ + OCCXC = $(SCCXC:.c=.o) + OCCXMAIN = $(SCCXMAIN:.c=.o) + +-DIR=../../../SPOOLES.2.2 +- +-LIBS = \ +- $(DIR)/spooles.a \ +- ../../../ARPACK/libarpack_INTEL.a \ +- -lpthread -lm -lc ++LIBS = $(ARPACKLIB) $(LAPACK) -lm -lc -lspooles -lpthread + + ccx_2.8p2: $(OCCXMAIN) ccx_2.8p2.a $(LIBS) + ./date.pl; $(CC) $(CFLAGS) -c ccx_2.8p2.c; $(FC) -fopenmp -Wall -O3 -o $@ $(OCCXMAIN) ccx_2.8p2.a $(LIBS) diff --git a/sci-libs/ccif/ChangeLog b/sci-libs/ccif/ChangeLog index 09ecdb00d..15efc4d8f 100644 --- a/sci-libs/ccif/ChangeLog +++ b/sci-libs/ccif/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-libs/ccif -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 23 May 2015; Marius Brehler <marbre@linux.sungazer.de> + ccif-0.3.20111209.ebuild: + Bump to EAPI=5 + 24 Jan 2012; Justin Lecher <jlec@gentoo.org> ccif-0.3.20111209.ebuild: Dropped DOCS as it is handled by default @@ -13,4 +17,3 @@ 04 Jan 2012; Justin Lecher <jlec@gentoo.org> +ccif-0.3.20111209.ebuild, +metadata.xml: Initial commit - diff --git a/sci-libs/ccif/ccif-0.3.20111209.ebuild b/sci-libs/ccif/ccif-0.3.20111209.ebuild index 792067ee8..b4e066a34 100644 --- a/sci-libs/ccif/ccif-0.3.20111209.ebuild +++ b/sci-libs/ccif/ccif-0.3.20111209.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit autotools-utils fortran-2 diff --git a/sci-libs/cgnslib/ChangeLog b/sci-libs/cgnslib/ChangeLog deleted file mode 100644 index 6925f152e..000000000 --- a/sci-libs/cgnslib/ChangeLog +++ /dev/null @@ -1,71 +0,0 @@ -# ChangeLog for sci-libs/cgnslib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*cgnslib-3.2.1 (29 Dec 2013) - - 29 Dec 2013; Justin Lecher <jlec@gentoo.org> +cgnslib-3.2.1.ebuild, - +files/cgnslib-3.2.1-cmake.patch, metadata.xml: - Version Bump - - 22 May 2012; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.4.ebuild, - metadata.xml: - Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits - - 24 Jun 2011; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.4.ebuild: - Streamlined fortran-2 eclass usage - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.4.ebuild: - Added fortran-2.eclass support - - 10 Jan 2011; Oliver Borm (boroli) <oli.borm@web.de> -cgnslib-2.5.3.ebuild, - -files/cgnslib-2.5.3_hdf5.patch, -files/cgnslib-2.5.3.patch, - cgnslib-2.5.4.ebuild, files/cgnslib-2.5.4_hdf5.patch: - delete old version, made hdf5 really apply again - - 16 Dec 2010; Justin Lecher <jlec@gentoo.org> cgnslib-2.5.3.ebuild, - cgnslib-2.5.4.ebuild: - Removal of fortran.eclass, #348851 - - 11 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - files/cgnslib-2.5.3_hdf5.patch, files/cgnslib-2.5.4_hdf5.patch: - Made the hdf5 patches apply again. - - 11 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - cgnslib-2.5.3.ebuild: - Removed hdf5 functionality since the required libraries are not available - anymore. - - 26 Jun 2010; Justin Lecher <jlec@gentoo.org> files/cgnslib-2.5.3.patch, - cgnslib-2.5.4.ebuild, files/cgnslib-2.5.4.patch: - Respecting LDFLAGS - - 15 Oct 2009; Etienne Lorriaux <etienne.lorriaux@gmail.com> - cgnslib-2.5.3.ebuild, cgnslib-2.5.4.ebuild: - Fixed DEPEND and RDEPEND confusion - - 03 Sep 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - Reintroduced cgnslib-2.5.3, as it needs <sci-libs/hdf5-1.8 - - 03 Sep 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - Needs now >=sci-libs/hdf5-1.8 - - 03 Sep 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - Corrected checksums, as upstream changed tarball. - - 27 Aug 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - sci-libs/cgnslib: Version bump, restricted to <sci-libs/hdf5-1.8 - - 22 Jul 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - executable rights for adf2hdf/hdf2adf - - 21 Jul 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - Installs ADF.h even without hdf5 USE-flag - - 21 Jul 2009; Oliver Borm (boroli) <oli.borm@web.de> ChangeLog: - Added patches from debian, changed to EAPI=2 - - 26 Aug 2008; Oliver Borm (boroli) <oli.borm@web.de> +cgnslib-2.5.3.ebuild, - +metadata.xml: - Ebuild for cgnslib from bug 176455 - diff --git a/sci-libs/cgnslib/Manifest b/sci-libs/cgnslib/Manifest deleted file mode 100644 index bed2c2af5..000000000 --- a/sci-libs/cgnslib/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cgnslib_2.5-4.tar.gz 398419 SHA256 0485b32649f1e15de2e85a17f0cb2b5fe4d2522415eafe1f6c8cfa4820719964 SHA512 12b73c5435d5bd3e1bc593efbf9c3479dbe436db721d0e0a95f5ab000cd707c11707d331dd2594a71338bc818f10c6019f491ce80554fe63c424c96819e57de7 WHIRLPOOL 27136cc88fe576563a39f10d57395ab0883829e3e4ba4d8a55a5ec47899fdc57ef5fc63c1a412fccca404e45f4e5ebbf267b4864f59e95bdc252a45c88b3b7ae -DIST cgnslib_3.2.1.tar.gz 865223 SHA256 34306316f04dbf6484343a4bc611b3bf912ac7dbc3c13b581defdaebbf6c1fc3 SHA512 318fda24e7f5f20407c6026ad4b10a84a0ea02a04d3dab3e0e2277d21cbc1b43f04eb65c4b912a7964e1219cf83afdabb357d25b40e76add9bed8bd2564a674e WHIRLPOOL 5f49f3e19712da5b178f7e40deb024a3287835613d61a46e2b7cb24fa4c9253dd87499b0e34a024945ced686b3a0d5c62ffbde88070f4d204d19f0651f8545f1 diff --git a/sci-libs/cgnslib/cgnslib-2.5.4.ebuild b/sci-libs/cgnslib/cgnslib-2.5.4.ebuild deleted file mode 100644 index f31ca4d86..000000000 --- a/sci-libs/cgnslib/cgnslib-2.5.4.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit eutils fortran-2 toolchain-funcs versionator - -MY_P="${PN}_$(replace_version_separator 2 '-')" -MY_S="${PN}_$(get_version_component_range 1-2)" - -DESCRIPTION="The CFD General Notation System (CGNS) is a standard for CFD data" -HOMEPAGE="http://www.cgns.org/" -SRC_URI="mirror://sourceforge/cgns/${MY_P}.tar.gz" - -LICENSE="ZLIB" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="fortran hdf5 szip zlib" - -DEPEND=" - fortran? ( virtual/fortran ) - hdf5? ( >=sci-libs/hdf5-1.8 ) - szip? ( sci-libs/szip ) - zlib? ( sys-libs/zlib )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${MY_S} - -pkg_setup() { - use fortran && fortran-2_pkg_setup -} - -src_prepare() { - epatch "${FILESDIR}"/${P}.patch - use hdf5 && epatch "${FILESDIR}"/${P}_hdf5.patch -} - -src_configure() { - local myconf="--enable-gcc --enable-lfs --enable-shared=all --enable-64bit" - - tc-export CC FC - - econf \ - ${myconf} \ - $(use_with fortran) \ - $(use_with hdf5) \ - $(use_with zlib) \ - $(use_with szip) -} - -src_install() { - emake DESTDIR="${D}" install - use hdf5 && \ - fperms 755 /usr/bin/{hdf2adf,adf2hdf} || \ - rm -f "${D}"/usr/bin/{hdf2adf,adf2hdf} -} diff --git a/sci-libs/cgnslib/cgnslib-3.2.1.ebuild b/sci-libs/cgnslib/cgnslib-3.2.1.ebuild deleted file mode 100644 index 509426624..000000000 --- a/sci-libs/cgnslib/cgnslib-3.2.1.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -FORTRAN_NEEDED="fortran" - -inherit cmake-utils fortran-2 versionator - -MY_P="${PN}_$(replace_version_separator 3 '-')" -MY_S="${PN}_$(get_version_component_range 1-2)" - -DESCRIPTION="The CFD General Notation System (CGNS) is a standard for CFD data" -HOMEPAGE="http://www.cgns.org/" -SRC_URI="mirror://sourceforge/project/cgns/${MY_S}/${MY_P}.tar.gz" - -LICENSE="ZLIB" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="fortran hdf5 legacy mpi szip zlib" - -DEPEND=" - hdf5? ( >=sci-libs/hdf5-1.8[mpi=] ) - szip? ( sci-libs/szip ) - zlib? ( sys-libs/zlib )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/${PN}_${PV} - -PATCHES=( - "${FILESDIR}"/${P}-cmake.patch -) - -pkg_setup() { - use fortran && fortran-2_pkg_setup -} - -src_configure() { - local mycmakeargs=( - -DCGNS_ENABLE_64BIT=ON - $(usex x86 -DCGNS_ENABLE_LFS=ON) - $(cmake-utils_use fortran CGNS_ENABLE_FORTRAN) - $(cmake-utils_use hdf5 CGNS_ENABLE_HDF5) - $(cmake-utils_use legacy CGNS_ENABLE_LEGACY) - $(cmake-utils_use mpi HDF5_NEED_MPI) - ) - cmake-utils_src_configure -} diff --git a/sci-libs/cgnslib/files/cgnslib-2.5.4.patch b/sci-libs/cgnslib/files/cgnslib-2.5.4.patch deleted file mode 100644 index a78f9a723..000000000 --- a/sci-libs/cgnslib/files/cgnslib-2.5.4.patch +++ /dev/null @@ -1,71 +0,0 @@ ---- cgnslib_2.5.orig/Makefile.in 2008-01-19 04:45:16.000000000 +0100 -+++ cgnslib_2.5/Makefile.in 2008-10-16 00:31:07.000000000 +0200 -@@ -75,15 +75,18 @@ - -$(RM) config.log config.status Makefile - - install : $(CGNSLIB) -- $(INSTALL_DATA) cgnslib.h $(INCLUDEDIR)/cgnslib.h -- $(INSTALL_DATA) cgnslib_f.h $(INCLUDEDIR)/cgnslib_f.h -- $(INSTALL_DATA) cgnswin_f.h $(INCLUDEDIR)/cgnswin_f.h -- $(INSTALL_DATA) $(CGNSLIB) $(LIBDIR)/$(INSTLIB) -+ $(INSTALL_DATA) -D cgnslib.h $(DESTDIR)/$(INCLUDEDIR)/cgnslib.h -+ $(INSTALL_DATA) -D cgnslib_f.h $(DESTDIR)/$(INCLUDEDIR)/cgnslib_f.h -+ $(INSTALL_DATA) -D cgnswin_f.h $(DESTDIR)/$(INCLUDEDIR)/cgnswin_f.h -+ $(INSTALL_DATA) -D cgns_header.h $(DESTDIR)/$(INCLUDEDIR)/cgns_header.h -+ $(INSTALL_DATA) -D adf/ADF.h $(DESTDIR)/$(INCLUDEDIR)/adf/ADF.h -+ $(INSTALL_DATA) -D $(CGNSLIB) $(DESTDIR)/$(LIBDIR)/$(INSTLIB).2.0.0 -+ (cd $(DESTDIR)/$(LIBDIR)/; ln -s $(INSTLIB).2.0.0 $(INSTLIB); ln -s $(INSTLIB).2.0.0 $(INSTLIB).2) - - uninstall : -- -$(RM) $(INCLUDEDIR)/cgnslib.h -- -$(RM) $(INCLUDEDIR)/cgnslib_f.h -- -$(RM) $(INCLUDEDIR)/cgnswin_f.h -+ -$(RM) $(DESTDIR)/$(INCLUDEDIR)/cgnslib.h -+ -$(RM) $(DESTDIR)/$(INCLUDEDIR)/cgnslib_f.h -+ -$(RM) $(DESTDIR)/$(INCLUDEDIR)/cgnswin_f.h - -$(RM) $(LIBDIR)/$(INSTLIB) - - #---------- mid-level library ---- cgnslib_2.5.orig/configure.in 2008-01-19 04:45:16.000000000 +0100 -+++ cgnslib_2.5/configure.in 2008-10-15 22:58:22.000000000 +0200 -@@ -423,7 +423,7 @@ - shared=no - else - CFGFLAGS="-fPIC $CFGFLAGS" -- AR="\$(CC) -shared $SYSCFLAGS -Wl,-rpath,$cgnsdir/\$(SYSTEM)" -+ AR="\$(CC) -shared $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" - LIBEXT=so - fi - fi ---- cgnslib_2.5.orig/configure 2008-01-19 04:45:16.000000000 +0100 -+++ cgnslib_2.5/configure 2008-10-15 23:11:41.000000000 +0200 -@@ -2048,7 +2048,7 @@ - shared=no - else - CFGFLAGS="-fPIC $CFGFLAGS" -- AR="\$(CC) -shared $SYSCFLAGS -Wl,-rpath,$cgnsdir/\$(SYSTEM)" -+ AR="\$(CC) -shared $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" - LIBEXT=so - fi - fi ---- cgnslib_2.5.orig/make.defs.in 2006-10-03 01:06:41.000000000 +0200 -+++ cgnslib_2.5/make.defs.in 2008-10-15 23:49:36.000000000 +0200 -@@ -34,7 +34,7 @@ - O = @OBJEXT@ - A = @LIBEXT@ - EXE = @EXEEXT@ --LIBCGNS = @SYSTEM@/libcgns.@LIBEXT@ -+LIBCGNS = @SYSTEM@/libcgns.@LIBEXT@.2 - - #------------------------------------------------------------------------ - # CC - C compiler -@@ -75,7 +75,7 @@ - # strip command for executables - set to true if not used - #------------------------------------------------------------------------ - --STRIP = @STRIP@ -+STRIP = true - - #------------------------------------------------------------------------ - # library archiver and ranlib - diff --git a/sci-libs/cgnslib/files/cgnslib-2.5.4_hdf5.patch b/sci-libs/cgnslib/files/cgnslib-2.5.4_hdf5.patch deleted file mode 100644 index 2ff7c2ce8..000000000 --- a/sci-libs/cgnslib/files/cgnslib-2.5.4_hdf5.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -r -u cgnslib_2.5.orig/Makefile.in cgnslib_2.5/Makefile.in ---- cgnslib_2.5.orig/Makefile.in 2010-07-11 20:22:55.044206152 +0200 -+++ cgnslib_2.5/Makefile.in 2010-07-11 20:23:14.304264503 +0200 -@@ -79,7 +79,10 @@ - $(INSTALL_DATA) -D cgnslib_f.h $(DESTDIR)/$(INCLUDEDIR)/cgnslib_f.h - $(INSTALL_DATA) -D cgnswin_f.h $(DESTDIR)/$(INCLUDEDIR)/cgnswin_f.h - $(INSTALL_DATA) -D cgns_header.h $(DESTDIR)/$(INCLUDEDIR)/cgns_header.h -- $(INSTALL_DATA) -D adf/ADF.h $(DESTDIR)/$(INCLUDEDIR)/adf/ADF.h -+ $(INSTALL_DATA) -D adfh/ADF.h $(DESTDIR)/$(INCLUDEDIR)/adfh/ADF.h -+ $(INSTALL_DATA) -D adfh/ADFH.h $(DESTDIR)/$(INCLUDEDIR)/adfh/ADFH.h -+ $(INSTALL_DATA) -D $(OBJDIR)/adf2hdf$(EXE) $(DESTDIR)/usr/bin/adf2hdf$(EXE) -+ $(INSTALL_DATA) -D $(OBJDIR)/hdf2adf$(EXE) $(DESTDIR)/usr/bin/hdf2adf$(EXE) - $(INSTALL_DATA) -D $(CGNSLIB) $(DESTDIR)/$(LIBDIR)/$(INSTLIB).2.0.0 - (cd $(DESTDIR)/$(LIBDIR)/; ln -s $(INSTLIB).2.0.0 $(INSTLIB); ln -s $(INSTLIB).2.0.0 $(INSTLIB).2) - -diff -r -u cgnslib_2.5.orig/configure cgnslib_2.5/configure ---- cgnslib_2.5.orig/configure 2010-07-11 20:22:55.047417614 +0200 -+++ cgnslib_2.5/configure 2010-07-11 20:24:38.922295750 +0200 -@@ -2048,7 +2048,7 @@ - shared=no - else - CFGFLAGS="-fPIC $CFGFLAGS" -- AR="\$(CC) -shared $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" -+ AR="\$(CC) -shared -lhdf5 $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" - LIBEXT=so - fi - fi -diff -r -u cgnslib_2.5.orig/configure.in cgnslib_2.5/configure.in ---- cgnslib_2.5.orig/configure.in 2010-07-11 20:22:55.045204905 +0200 -+++ cgnslib_2.5/configure.in 2010-07-11 20:24:05.021200131 +0200 -@@ -423,7 +423,7 @@ - shared=no - else - CFGFLAGS="-fPIC $CFGFLAGS" -- AR="\$(CC) -shared $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" -+ AR="\$(CC) -shared -lhdf5 $SYSCFLAGS ${LDFLAGS} -Wl,-soname,libcgns.so.2" - LIBEXT=so - fi - fi diff --git a/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch b/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch deleted file mode 100644 index bf8ea5f2b..000000000 --- a/sci-libs/cgnslib/files/cgnslib-3.2.1-cmake.patch +++ /dev/null @@ -1,149 +0,0 @@ - CMakeLists.txt | 20 +-------------- - src/CMakeLists.txt | 72 +++++++++++++++++++++++++++--------------------------- - 2 files changed, 37 insertions(+), 55 deletions(-) - -diff --git a/CMakeLists.txt b/CMakeLists.txt -index d9c1b3c..d4c2bf7 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -81,7 +81,7 @@ if (CGNS_ENABLE_LFS) - if (HAVE_OPEN64) - add_definitions(-DHAVE_LSEEK64) - endif (HAVE_OPEN64) -- if (HAVE_OPEN64) -+ if (HAVE_LSEEK64) - add_definitions(-DHAVE_LSEEK64) - endif (HAVE_LSEEK64) - endif (WIN32) -@@ -254,24 +254,6 @@ else (CGNS_ENABLE_HDF5 AND HDF5_NEED_MPI) - mark_as_advanced(FORCE CGNS_ENABLE_PARALLEL) - endif (CGNS_ENABLE_HDF5 AND HDF5_NEED_MPI) - --#################### --# RPATH Management # --#################### -- --# use, i.e. don't skip the full RPATH for the build tree --set(CMAKE_SKIP_BUILD_RPATH FALSE) -- --# when building, don't use the install RPATH already --# (but later on when installing) --set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) -- --# the RPATH to be used when installing --set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") -- --# add the automatically determined parts of the RPATH --# which point to directories outside the build tree to the install RPATH --set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) -- - ######## - # CGNS # - ######## -diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt -index 3c12c6d..694da42 100644 ---- a/src/CMakeLists.txt -+++ b/src/CMakeLists.txt -@@ -69,7 +69,7 @@ set(SYSCFLAGS "") - set(CFGFLAGS "") - set(LIBS "") - --file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/lib LIBDIR) -+file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX} LIBDIR) - file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/include INCLUDEDIR) - file(TO_NATIVE_PATH ${CMAKE_C_COMPILER} CC) - if (WIN32) -@@ -102,42 +102,42 @@ set(ZLIBLIB "") - set(MPIINC "") - set(MPILIBS "") - --macro(native_paths INPUT_PATH_VARIABLE RESULT_VARIABLE)
-- set(${RESULT_VARIABLE} "")
-- foreach(PATH ${${INPUT_PATH_VARIABLE}})
-- file(TO_NATIVE_PATH ${PATH} NATIVE_PATH)
-- list(APPEND ${RESULT_VARIABLE} ${NATIVE_PATH})
-- endforeach(PATH ${${INPUT_PATH_VARIABLE}})
--endmacro(native_paths)
-+macro(native_paths INPUT_PATH_VARIABLE RESULT_VARIABLE) -+ set(${RESULT_VARIABLE} "") -+ foreach(PATH ${${INPUT_PATH_VARIABLE}}) -+ file(TO_NATIVE_PATH ${PATH} NATIVE_PATH) -+ list(APPEND ${RESULT_VARIABLE} ${NATIVE_PATH}) -+ endforeach(PATH ${${INPUT_PATH_VARIABLE}}) -+endmacro(native_paths) - - if (CGNS_ENABLE_HDF5) - set(BUILDHDF5 1) -- if (HDF5_INCLUDE_PATH)
-- native_paths(HDF5_INCLUDE_PATH HDF5INC)
-- endif (HDF5_INCLUDE_PATH)
-- if (HDF5_LIBRARY)
-- native_paths(HDF5_LIBRARY HDF5LIB)
-- endif (HDF5_LIBRARY)
-- if (HDF5_NEED_SZIP)
-- set(H5NEEDSZIP 1)
-- if (SZIP_LIBRARY)
-- native_paths(SZIP_LIBRARY SZIPLIB)
-- endif (SZIP_LIBRARY)
-- endif (HDF5_NEED_SZIP)
-- if (HDF5_NEED_ZLIB)
-- set(H5NEEDZLIB 1)
-- if (ZLIB_LIBRARY)
-- native_paths(${ZLIB_LIBRARY} ZLIBLIB)
-- endif (ZLIB_LIBRARY)
-- endif (HDF5_NEED_ZLIB)
-- if (HDF5_NEED_MPI)
-- set(H5NEEDMPI 1)
-- if (MPI_INC)
-- native_paths(MPI_INC MPIINC)
-- endif (MPI_INC)
-- if (MPI_LIBS)
-- native_paths(MPI_LIBS MPILIBS)
-- endif (MPI_LIBS)
-+ if (HDF5_INCLUDE_PATH) -+ native_paths(HDF5_INCLUDE_PATH HDF5INC) -+ endif (HDF5_INCLUDE_PATH) -+ if (HDF5_LIBRARY) -+ native_paths(HDF5_LIBRARY HDF5LIB) -+ endif (HDF5_LIBRARY) -+ if (HDF5_NEED_SZIP) -+ set(H5NEEDSZIP 1) -+ if (SZIP_LIBRARY) -+ native_paths(SZIP_LIBRARY SZIPLIB) -+ endif (SZIP_LIBRARY) -+ endif (HDF5_NEED_SZIP) -+ if (HDF5_NEED_ZLIB) -+ set(H5NEEDZLIB 1) -+ if (ZLIB_LIBRARY) -+ native_paths(${ZLIB_LIBRARY} ZLIBLIB) -+ endif (ZLIB_LIBRARY) -+ endif (HDF5_NEED_ZLIB) -+ if (HDF5_NEED_MPI) -+ set(H5NEEDMPI 1) -+ if (MPI_INC) -+ native_paths(MPI_INC MPIINC) -+ endif (MPI_INC) -+ if (MPI_LIBS) -+ native_paths(MPI_LIBS MPILIBS) -+ endif (MPI_LIBS) - if (CGNS_ENABLE_PARALLEL) - set(BUILDPARALLEL 1) - endif (CGNS_ENABLE_PARALLEL) -@@ -251,7 +251,7 @@ if(CGNS_BUILD_SHARED) - endif(CGNS_BUILD_SHARED) - - # Set the install path of the static library --install(TARGETS cgns_static ARCHIVE DESTINATION lib) -+install(TARGETS cgns_static ARCHIVE DESTINATION lib${LIB_SUFFIX}) - # Set the install path of the shared library - if(CGNS_BUILD_SHARED) - # for windows, need to install both cgnsdll.dll and cgnsdll.lib -@@ -259,7 +259,7 @@ if(CGNS_BUILD_SHARED) - install(TARGETS cgns_shared ARCHIVE DESTINATION lib) - install(TARGETS cgns_shared RUNTIME DESTINATION lib) - else (WIN32 OR CYGWIN) -- install(TARGETS cgns_shared LIBRARY DESTINATION lib) -+ install(TARGETS cgns_shared LIBRARY DESTINATION lib${LIB_SUFFIX}) - endif (WIN32 OR CYGWIN) - endif(CGNS_BUILD_SHARED) - diff --git a/sci-libs/cgnslib/metadata.xml b/sci-libs/cgnslib/metadata.xml deleted file mode 100644 index 70658221b..000000000 --- a/sci-libs/cgnslib/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <use> - <flag name="legacy">Enable or disable building legacy code (3.0 compatible)</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/cgnstools/ChangeLog b/sci-libs/cgnstools/ChangeLog index 5c8516431..504626e52 100644 --- a/sci-libs/cgnstools/ChangeLog +++ b/sci-libs/cgnstools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/cgnstools: Updating remote-id in metadata.xml + 07 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> cgnstools-2.5.4-r1.ebuild: Move to EAPI=5 @@ -29,4 +32,3 @@ 26 Aug 2008; Oliver Borm (boroli) <oli.borm@web.de> +cgnstools-2.5.2.ebuild, +metadata.xml: Ebuild for cgnstools from bug 176455 - diff --git a/sci-libs/cgnstools/metadata.xml b/sci-libs/cgnstools/metadata.xml index b229aec85..f9c8ebc15 100644 --- a/sci-libs/cgnstools/metadata.xml +++ b/sci-libs/cgnstools/metadata.xml @@ -1,5 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> + <upstream> + <remote-id type="sourceforge">cgns</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clblas/ChangeLog b/sci-libs/clblas/ChangeLog new file mode 100644 index 000000000..e6656f8f5 --- /dev/null +++ b/sci-libs/clblas/ChangeLog @@ -0,0 +1,51 @@ +# ChangeLog for sci-libs/clblas +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*clblas-2.4-r1 (06 Jun 2015) + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.4-r1.ebuild, + +files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch, + -clblas-2.4.ebuild, clblas-9999.ebuild: + sci-libs/clblas: Fix installation of cmake configuration + + 06 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> -clblas-2.2.ebuild, + -files/clblas-2.2-client_CMakeLists.patch, + -files/clblas-2.2-library_tools_tune_CMakeLists.patch: + sci-libs/clblas: Drop old + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> clblas-2.2.ebuild, + clblas-2.4.ebuild, clblas-9999.ebuild: + sci-libs/clblas: Cleanup ebuilds + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> clblas-2.2.ebuild, + clblas-9999.ebuild: + sci-libs/clblas: Move to python-single-r1.eclass + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clblas: Add github to remote-id in metadata.xml + +*clblas-2.4 (09 May 2015) + + 09 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.4.ebuild: + Version bump + + 09 May 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/clblas-2.2-client_CMakeLists.patch, + +files/clblas-2.2-library_tools_tune_CMakeLists.patch, + -files/clblas-client_CMakeLists.patch, + -files/clblas-library_tools_tune_CMakeLists.patch, clblas-9999.ebuild: + Adjust patchset + + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/clblas-client_CMakeLists.patch, clblas-9999.ebuild: + Fix client installation + +*clblas-2.2 (23 Mar 2015) +*clblas-9999 (23 Mar 2015) + + 23 Mar 2015; Marius Brehler <marbre@linux.sungazer.de> +clblas-2.2.ebuild, + +clblas-9999.ebuild, +files/clblas-library_tools_tune_CMakeLists.patch, + +files/clblas-samples_CMakeLists.patch, + +files/clblas-scripts_perf_CMakeLists.patch, +metadata.xml: + New package diff --git a/sci-libs/clblas/Manifest b/sci-libs/clblas/Manifest new file mode 100644 index 000000000..47dd24365 --- /dev/null +++ b/sci-libs/clblas/Manifest @@ -0,0 +1 @@ +DIST clblas-2.4.tar.gz 800848 SHA256 3e9b8e138c465df1daff0235d9c93b0005986a7257a3739aea2d4c8b60b7ed37 SHA512 ae8c1fc1bef7573b12279977fc32f9e97c9b81b9167994ca6f352587a670dcee0f486ab2b7d5191092324f5e8fc00f9a2ea29303a026a0c1201be31d384cafe7 WHIRLPOOL a97537d7390055ad608eeac66679362956db7acfa96cf1165581ff8f9adfe309b8ff8231225bd8ca6247c8f588bff24d6f648e131cec52f8e3093168a3f26f82 diff --git a/sci-libs/clblas/clblas-2.4-r1.ebuild b/sci-libs/clblas/clblas-2.4-r1.ebuild new file mode 100644 index 000000000..00133c2e3 --- /dev/null +++ b/sci-libs/clblas/clblas-2.4-r1.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils python-single-r1 + +MY_PN="clBLAS" + +DESCRIPTION="A software library containing BLAS routines for OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clBLAS" +SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" +S="${WORKDIR}/${MY_PN}-${PV}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="+client examples +ktest performance test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) + dev-libs/boost + performance? ( ${PYTHON_DEPS} ) + " +DEPEND="${RDEPEND}" +# test? ( +# >=dev-cpp/gtest-1.6.0 +# >=sci-libs/acml-6.1.0.3 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clblas-samples_CMakeLists.patch + "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build client CLIENT) + $(cmake-utils_use_build examples SAMPLE) + $(cmake-utils_use_build ktest KTEST) + $(cmake-utils_use_build performance PERFORMANCE) + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clblas/clblas-9999.ebuild b/sci-libs/clblas/clblas-9999.ebuild new file mode 100644 index 000000000..bb47c0d37 --- /dev/null +++ b/sci-libs/clblas/clblas-9999.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit cmake-utils git-r3 python-single-r1 + +MY_PN="clBLAS" + +DESCRIPTION="A software library containing BLAS routines for OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clBLAS" +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +S="${WORKDIR}/${P}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="+client examples +ktest performance test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) + dev-libs/boost + performance? ( ${PYTHON_DEPS} ) + " +DEPEND="${RDEPEND}" +# test? ( +# >=dev-cpp/gtest-1.6.0 +# >=sci-libs/acml-6.1.0.3 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clblas-samples_CMakeLists.patch + "${FILESDIR}"/clblas-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build client CLIENT) + $(cmake-utils_use_build examples SAMPLE) + $(cmake-utils_use_build ktest KTEST) + $(cmake-utils_use_build performance PERFORMANCE) + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch new file mode 100644 index 000000000..32cb7b553 --- /dev/null +++ b/sci-libs/clblas/files/clblas-2.4-Install-cmake-configuration-to-lib-cmake-clBLAS.patch @@ -0,0 +1,25 @@ +From b83750ab917b12500f9755dc4c81f99eb55bb67e Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marius.brehler@tu-dortmund.de> +Date: Sat, 6 Jun 2015 10:35:32 +0200 +Subject: [PATCH] Install cmake configuration to lib/cmake/clBLAS + +--- + src/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index a23cd37..5c378dc 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -300,7 +300,7 @@ endif( ) + if(WIN32) + set(destdir CMake) + else() +- set(destdir share/clBLAS) ++ set(destdir lib${SUFFIX_LIB}/cmake/clBLAS) + endif() + string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") + configure_file( +-- +2.3.6 + diff --git a/sci-libs/clblas/files/clblas-samples_CMakeLists.patch b/sci-libs/clblas/files/clblas-samples_CMakeLists.patch new file mode 100644 index 000000000..8b5a762b1 --- /dev/null +++ b/sci-libs/clblas/files/clblas-samples_CMakeLists.patch @@ -0,0 +1,20 @@ +Install samples to /usr/share/clBLAS/samples. + +Patch by Marius Brehler. +--- samples/CMakeLists.txt ++++ samples/CMakeLists.txt +@@ -274,7 +274,7 @@ install( TARGETS example_sgemm example_s + example_snrm2 example_sasum example_isamax + + version +- RUNTIME DESTINATION bin${SUFFIX_BIN} ++ RUNTIME DESTINATION share/clBLAS/samples + LIBRARY DESTINATION lib${SUFFIX_LIB} + ARCHIVE DESTINATION lib${SUFFIX_LIB}/import + ) +@@ -333,4 +333,4 @@ install(FILES + ${PROJECT_BINARY_DIR}/samples/CMakeLists.txt + + DESTINATION +- samples ) ++ share/clBLAS/samples/src ) diff --git a/sci-libs/clblas/files/clblas-scripts_perf_CMakeLists.patch b/sci-libs/clblas/files/clblas-scripts_perf_CMakeLists.patch new file mode 100644 index 000000000..7b9b58d97 --- /dev/null +++ b/sci-libs/clblas/files/clblas-scripts_perf_CMakeLists.patch @@ -0,0 +1,11 @@ +Install Python scripts to /usr/share/clBLAS and not to /usr/bin. + +Patch by Marius Brehler. +--- scripts/perf/CMakeLists.txt ++++ scripts/perf/CMakeLists.txt +@@ -21,4 +21,4 @@ set(GRAPHING_SCRIPTS measurePerformance + performanceUtility.py + ) + +-install( FILES ${GRAPHING_SCRIPTS} DESTINATION bin${SUFFIX_BIN} ) ++install( FILES ${GRAPHING_SCRIPTS} DESTINATION share/clBLAS ) diff --git a/sci-libs/clblas/metadata.xml b/sci-libs/clblas/metadata.xml new file mode 100644 index 000000000..1541b5a57 --- /dev/null +++ b/sci-libs/clblas/metadata.xml @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <longdescription> + clBLAS is the code for the OpenCL BLAS portion of clMath. The + complete set of BLAS level 1, 2 and 3 routines is implemented. See + Netlib BLAS for the list of supported routines. In addition to GPU + devices, the library also supports running on CPU devices to + facilitate debugging and multicore programming. + </longdescription> + <use> + <flag name="client"> + Build a command line clBLAS client program. + </flag> + <flag name="ktest"> + A command line tool for testing single clBLAS kernel. + </flag> + <flag name="performance"> + Copy performance scripts that can measure and graph performance. + </flag> + </use> + <upstream> + <remote-id type="github">clMathLibraries/clBLAS</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/clfft/ChangeLog b/sci-libs/clfft/ChangeLog index 0cdca0349..eb0991326 100644 --- a/sci-libs/clfft/ChangeLog +++ b/sci-libs/clfft/ChangeLog @@ -2,6 +2,35 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*clfft-2.4-r1 (05 Jun 2015) + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> +clfft-2.4-r1.ebuild, + +files/clfft-2.4-fix-cmake-config-install.patch, + +files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch, + -clfft-2.2.ebuild, -clfft-2.4.ebuild, clfft-0.9999.ebuild, clfft-9999.ebuild: + sci-libs/clfft: Drop old; Install cmake configuration + + 05 Jun 2015; Marius Brehler <marbre@linux.sungazer.de> clfft-0.9999.ebuild, + clfft-2.4.ebuild, clfft-9999.ebuild: + sci-libs/clfft: Cleanup ebuilds + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clfft: Add github to remote-id in metadata.xml + +*clfft-0.9999 (11 May 2015) + + 11 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clfft-0.9999.ebuild, + clfft-9999.ebuild: + clfft-9999 points to develop branch + + 04 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + files/clfft-client_CMakeLists.patch, + files/clfft-scripts_perf_CMakeLists.patch: + Replace patches by upstream patches + + 19 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> clfft-9999.ebuild: + Fix SLOT operators + *clfft-2.4 (18 Feb 2015) 18 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> +clfft-2.4.ebuild: diff --git a/sci-libs/clfft/Manifest b/sci-libs/clfft/Manifest index 6d6894071..65c5acaf2 100644 --- a/sci-libs/clfft/Manifest +++ b/sci-libs/clfft/Manifest @@ -1,2 +1 @@ -DIST clfft-2.2.tar.gz 678144 SHA256 eed3cc196c1b18785291261294655daa4c7d4d9e8b4a3aad26004db55f544e0d SHA512 b7a2e7e3c0c1f7126c37e4a39f09c72c2ac0d3a29e12a3f86deaae7090114dae8e925a03fcc8d39f8530c200de7ec6e3cfc4c8ad76ed5a39f555e76082c86850 WHIRLPOOL 8f7a1919aff1e5cd1044ba4c17cd2b98b652e65b74b7dc8400020071d9a949f0981ed1c578d0916397ca5c171bd8a378788f3cedaf70a9d255de96de67ce4718 DIST clfft-2.4.tar.gz 678262 SHA256 d77506af774bbe8ccf4226a58e623c8a29587edcf02984e72851099be0efe04b SHA512 3450f3ee962e1722c765e962178c57df0bf298508603ac5b4ec12bd6396dc10279136d5b91383b9da56d95cebd0e552bf78e2c01ccaeb8cd43ed947b7d536209 WHIRLPOOL 6ec21e182deac2a8c0a102a96c974289e56cf3f9908fbf067d7105f50646270bee2e17cf98fdf6cecf8ce28c8714c710ce46f514f7cfc1de205d5ef48bb5a0ed diff --git a/sci-libs/clfft/clfft-0.9999.ebuild b/sci-libs/clfft/clfft-0.9999.ebuild new file mode 100644 index 000000000..0aebebb39 --- /dev/null +++ b/sci-libs/clfft/clfft-0.9999.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils git-r3 + +MY_PN="clFFT" + +DESCRIPTION="A software library containing FFT functions written in OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clFFT" +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +S="${WORKDIR}/${P}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + dev-libs/boost" +DEPEND="${RDEPEND}" +# test? ( +# dev-cpp/gtest +# sci-libs/fftw:3.0 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clfft-client_CMakeLists.patch + "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clfft-2.4-fix-cmake-config-install.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clfft/clfft-2.2.ebuild b/sci-libs/clfft/clfft-2.2.ebuild deleted file mode 120000 index b6c165da9..000000000 --- a/sci-libs/clfft/clfft-2.2.ebuild +++ /dev/null @@ -1 +0,0 @@ -clfft-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/clfft/clfft-2.4-r1.ebuild b/sci-libs/clfft/clfft-2.4-r1.ebuild new file mode 100644 index 000000000..6b9893890 --- /dev/null +++ b/sci-libs/clfft/clfft-2.4-r1.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +MY_PN="clFFT" + +DESCRIPTION="A software library containing FFT functions written in OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clFFT" +SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" +S="${WORKDIR}/${MY_PN}-${PV}/src" + +LICENSE="Apache-2.0" +SLOT="0" +IUSE="test" + +RDEPEND=" + >=sys-devel/gcc-4.6:* + virtual/opencl + dev-libs/boost" +DEPEND="${RDEPEND}" +# test? ( +# dev-cpp/gtest +# sci-libs/fftw:3.0 +# )" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +PATCHES=( + "${FILESDIR}"/clfft-client_CMakeLists.patch + "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clfft-2.4-fix-cmake-config-install.patch +) + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 6 ]] ) ; then + die "Compilation with gcc older than 4.6 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clfft/clfft-2.4.ebuild b/sci-libs/clfft/clfft-2.4.ebuild deleted file mode 120000 index b6c165da9..000000000 --- a/sci-libs/clfft/clfft-2.4.ebuild +++ /dev/null @@ -1 +0,0 @@ -clfft-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/clfft/clfft-9999.ebuild b/sci-libs/clfft/clfft-9999.ebuild index 36e38a301..96b7dcdf3 100644 --- a/sci-libs/clfft/clfft-9999.ebuild +++ b/sci-libs/clfft/clfft-9999.ebuild @@ -4,29 +4,22 @@ EAPI=5 -inherit cmake-utils +inherit cmake-utils git-r3 MY_PN="clFFT" DESCRIPTION="A software library containing FFT functions written in OpenCL" HOMEPAGE="https://github.com/clMathLibraries/clFFT" - -if [ ${PV} == "9999" ] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" - S="${WORKDIR}/${P}/src" -else - SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" - S="${WORKDIR}/${MY_PN}-${PV}/src" -fi +EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" +EGIT_BRANCH="develop" +S="${WORKDIR}/${P}/src" LICENSE="Apache-2.0" SLOT="0" IUSE="test" RDEPEND=" - >=sys-devel/gcc-4.6 + >=sys-devel/gcc-4.6:* virtual/opencl dev-libs/boost" DEPEND="${RDEPEND}" @@ -40,8 +33,7 @@ DEPEND="${RDEPEND}" RESTRICT="test" PATCHES=( - "${FILESDIR}"/clfft-client_CMakeLists.patch - "${FILESDIR}"/clfft-scripts_perf_CMakeLists.patch + "${FILESDIR}"/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch ) pkg_pretend() { diff --git a/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch b/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch new file mode 100644 index 000000000..6dd1e15db --- /dev/null +++ b/sci-libs/clfft/files/clfft-2.4-fix-cmake-config-install.patch @@ -0,0 +1,128 @@ +Upstream patch, with modified destdir +https://github.com/clMathLibraries/clFFT/pull/88 + + +Description: install missing cmake config module +Author: <kent.knox@amd> +Origin: upstream +Forwarded: not-needed +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -283,6 +283,29 @@ else( ) + message( "GoogleTest unit tests will NOT be built" ) + endif( ) + ++if( BUILD_EXAMPLES ) ++ add_subdirectory( examples ) ++endif() ++ ++if(WIN32) ++ set(destdir CMake) ++else() ++ set(destdir lib${SUFFIX_LIB}/cmake/clFFT) ++endif() ++string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") ++configure_file( ++ ${CMAKE_CURRENT_SOURCE_DIR}/clFFTConfigVersion.cmake.in ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfigVersion.cmake ++ @ONLY) ++configure_file( ++ ${CMAKE_CURRENT_SOURCE_DIR}/clFFTConfig.cmake.in ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfig.cmake ++ @ONLY) ++install(EXPORT Library DESTINATION ${destdir} FILE clFFTTargets.cmake) ++install(FILES ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfigVersion.cmake ++ ${CMAKE_CURRENT_BINARY_DIR}/clFFTConfig.cmake ++ DESTINATION ${destdir}) ++ + # The following code is setting variables to control the behavior of CPack to generate our + if( WIN32 ) + set( CPACK_SOURCE_GENERATOR "ZIP" ) +diff --git a/src/clFFTConfig.cmake.in b/src/clFFTConfig.cmake.in +new file mode 100644 +index 0000000..5b58c35 +--- /dev/null ++++ b/src/clFFTConfig.cmake.in +@@ -0,0 +1,3 @@ ++include(${CMAKE_CURRENT_LIST_DIR}/clFFTTargets.cmake) ++get_filename_component(CLFFT_INCLUDE_DIRS ${CMAKE_CURRENT_LIST_DIR}/@reldir@/include ABSOLUTE) ++set(CLFFT_LIBRARIES clFFT) +diff --git a/src/clFFTConfigVersion.cmake.in b/src/clFFTConfigVersion.cmake.in +new file mode 100644 +index 0000000..e358473 +--- /dev/null ++++ b/src/clFFTConfigVersion.cmake.in +@@ -0,0 +1,46 @@ ++# This is a basic version file for the Config-mode of find_package(). ++# It is used by write_basic_package_version_file() as input file for configure_file() ++# to create a version-file which can be installed along a config.cmake file. ++# ++# The created file sets PACKAGE_VERSION_EXACT if the current version string and ++# the requested version string are exactly the same and it sets ++# PACKAGE_VERSION_COMPATIBLE if the current version is >= requested version, ++# but only if the requested major version is the same as the current one. ++# The variable CLFFT_VERSION must be set before calling configure_file(). ++ ++ ++set(PACKAGE_VERSION "@CLFFT_VERSION@") ++ ++if("${PACKAGE_VERSION}" VERSION_LESS "${PACKAGE_FIND_VERSION}" ) ++ set(PACKAGE_VERSION_COMPATIBLE FALSE) ++else() ++ ++ if("@CLFFT_VERSION@" MATCHES "^([0-9]+)\\.") ++ set(CLFFT_VERSION_MAJOR "${CMAKE_MATCH_1}") ++ else() ++ set(CLFFT_VERSION_MAJOR "@CLFFT_VERSION@") ++ endif() ++ ++ if("${PACKAGE_FIND_VERSION_MAJOR}" STREQUAL "${CLFFT_VERSION_MAJOR}") ++ set(PACKAGE_VERSION_COMPATIBLE TRUE) ++ else() ++ set(PACKAGE_VERSION_COMPATIBLE FALSE) ++ endif() ++ ++ if( "${PACKAGE_FIND_VERSION}" STREQUAL "${PACKAGE_VERSION}") ++ set(PACKAGE_VERSION_EXACT TRUE) ++ endif() ++endif() ++ ++ ++# if the installed or the using project don't have CMAKE_SIZEOF_VOID_P set, ignore it: ++if("${CMAKE_SIZEOF_VOID_P}" STREQUAL "" OR "@CMAKE_SIZEOF_VOID_P@" STREQUAL "") ++ return() ++endif() ++ ++# check that the installed version has the same 32/64bit-ness as the one which is currently searching: ++if(NOT "${CMAKE_SIZEOF_VOID_P}" STREQUAL "@CMAKE_SIZEOF_VOID_P@") ++ math(EXPR installedBits "@CMAKE_SIZEOF_VOID_P@ * 8") ++ set(PACKAGE_VERSION "${PACKAGE_VERSION} (${installedBits}bit)") ++ set(PACKAGE_VERSION_UNSUITABLE TRUE) ++endif() +diff --git a/src/library/CMakeLists.txt b/src/library/CMakeLists.txt +index 63ac0f9..0d400d8 100644 +--- a/src/library/CMakeLists.txt ++++ b/src/library/CMakeLists.txt +@@ -95,6 +95,7 @@ endif( ) + + # CPack configuration; include the executable into the package + install( TARGETS clFFT ++ EXPORT Library + RUNTIME DESTINATION bin${SUFFIX_BIN} + LIBRARY DESTINATION lib${SUFFIX_LIB} + ARCHIVE DESTINATION lib${SUFFIX_LIB}/import +diff --git a/src/statTimer/CMakeLists.txt b/src/statTimer/CMakeLists.txt +index a635bf1..3dc026f 100644 +--- a/src/statTimer/CMakeLists.txt ++++ b/src/statTimer/CMakeLists.txt +@@ -80,6 +80,7 @@ endif( ) + + # CPack configuration; include the executable into the package + install( TARGETS StatTimer ++ EXPORT Library + RUNTIME DESTINATION bin${SUFFIX_BIN} + LIBRARY DESTINATION lib${SUFFIX_LIB} + ARCHIVE DESTINATION lib${SUFFIX_LIB}/import +-- +2.1.4 + diff --git a/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch b/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch new file mode 100644 index 000000000..dc317d40d --- /dev/null +++ b/sci-libs/clfft/files/clfft-9999-Install-cmake-configuration-to-lib-cmake-clFFT.patch @@ -0,0 +1,25 @@ +From 6a3ba77529987d5906ba6f734bc2fa66a9155a1c Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marbre@linux.sungazer.de> +Date: Fri, 5 Jun 2015 14:59:29 +0200 +Subject: [PATCH] Install cmake configuration to lib/cmake/clFFT + +--- + src/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index ad15e4a..73200fa 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -290,7 +290,7 @@ endif() + if(WIN32) + set(destdir CMake) + else() +- set(destdir share/clFFT) ++ set(destdir lib${SUFFIX_LIB}/cmake/clFFT) + endif() + string(REGEX REPLACE "[^/]+" ".." reldir "${destdir}") + configure_file( +-- +2.0.5 + diff --git a/sci-libs/clfft/files/clfft-client_CMakeLists.patch b/sci-libs/clfft/files/clfft-client_CMakeLists.patch index d779b45d9..b6cc53095 100644 --- a/sci-libs/clfft/files/clfft-client_CMakeLists.patch +++ b/sci-libs/clfft/files/clfft-client_CMakeLists.patch @@ -1,26 +1,41 @@ -Change the client binary's name to clfft-client. +Upstream patch to change the client binary's name to clFFT-client. +Remove for clfft-9999 as soon as develop branch is merged into master. -Patch by Marius Brehler. ---- client/CMakeLists.txt -+++ client/CMakeLists.txt + +From f3cbd72953094217dfeb41c4e2a328d4b4a494e0 Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marius.brehler@tu-dortmund.de> +Date: Wed, 18 Feb 2015 09:15:13 +0100 +Subject: [PATCH] Rename Client to clFFT-client + +--- + src/client/CMakeLists.txt | 10 +++++----- + 1 file changed, 5 insertions(+), 5 deletions(-) + +diff --git a/src/client/CMakeLists.txt b/src/client/CMakeLists.txt +index fdf209f..3b38b95 100644 +--- a/src/client/CMakeLists.txt ++++ b/src/client/CMakeLists.txt @@ -43,15 +43,15 @@ endif( ) # Include standard OpenCL headers include_directories( ${Boost_INCLUDE_DIRS} ${OPENCL_INCLUDE_DIRS} ../../../common ${PROJECT_BINARY_DIR}/include ../include ) -add_executable( Client ${Client.Files} ) -+add_executable( clfft-client ${Client.Files} ) ++add_executable( clFFT-client ${Client.Files} ) -target_link_libraries( Client clFFT ${Boost_LIBRARIES} ${OPENCL_LIBRARIES} ${DL_LIB} ) -+target_link_libraries( clfft-client clFFT ${Boost_LIBRARIES} ${OPENCL_LIBRARIES} ${DL_LIB} ) ++target_link_libraries( clFFT-client clFFT ${Boost_LIBRARIES} ${OPENCL_LIBRARIES} ${DL_LIB} ) -set_target_properties( Client PROPERTIES VERSION ${CLFFT_VERSION} ) -set_target_properties( Client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) -+set_target_properties( clfft-client PROPERTIES VERSION ${CLFFT_VERSION} ) -+set_target_properties( clfft-client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) ++set_target_properties( clFFT-client PROPERTIES VERSION ${CLFFT_VERSION} ) ++set_target_properties( clFFT-client PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/staging" ) # CPack configuration; include the executable into the package -install( TARGETS Client -+install( TARGETS clfft-client ++install( TARGETS clFFT-client RUNTIME DESTINATION bin${SUFFIX_BIN} LIBRARY DESTINATION lib${SUFFIX_LIB} ARCHIVE DESTINATION lib${SUFFIX_LIB}/import +-- +2.0.4 + diff --git a/sci-libs/clfft/files/clfft-scripts_perf_CMakeLists.patch b/sci-libs/clfft/files/clfft-scripts_perf_CMakeLists.patch index 2976a5e63..eec9169c1 100644 --- a/sci-libs/clfft/files/clfft-scripts_perf_CMakeLists.patch +++ b/sci-libs/clfft/files/clfft-scripts_perf_CMakeLists.patch @@ -1,13 +1,33 @@ -Install Python scripts to /usr/share/clfft and not to /usr/bin. +Upstream patch to install Python scripts to /usr/share/clfft and not to /usr/bin. +Remove for clfft-9999 as soon as develop branch is merged into master. -Patch by Marius Brehler. ---- scripts/perf/CMakeLists.txt -+++ scripts/perf/CMakeLists.txt -@@ -21,4 +21,4 @@ set(GRAPHING_SCRIPTS measurePerformance +From 37b1f443e516f0a87c4a728cac8291148bb31b72 Mon Sep 17 00:00:00 2001 +From: Marius Brehler <marius.brehler@tu-dortmund.de> +Date: Wed, 18 Feb 2015 08:59:06 +0100 +Subject: [PATCH] Install scripts/perf to share/clFFT on non WIN32 + systems + +--- + src/scripts/perf/CMakeLists.txt | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/src/scripts/perf/CMakeLists.txt b/src/scripts/perf/CMakeLists.txt +index 3733789..ca45b92 100644 +--- a/src/scripts/perf/CMakeLists.txt ++++ b/src/scripts/perf/CMakeLists.txt +@@ -20,5 +20,8 @@ set(GRAPHING_SCRIPTS measurePerformance.py + errorHandler.py performanceUtility.py ) - +- -install( FILES ${GRAPHING_SCRIPTS} DESTINATION bin${SUFFIX_BIN} ) \ No newline at end of file -+install( FILES ${GRAPHING_SCRIPTS} DESTINATION share/clfft/${SUFFIX_BIN} ) ++if( WIN32 ) ++ install( FILES ${GRAPHING_SCRIPTS} DESTINATION bin${SUFFIX_BIN} ) ++else ( ) ++ install( FILES ${GRAPHING_SCRIPTS} DESTINATION share/clFFT ) ++endif( ) \ No newline at end of file +-- +2.0.4 + diff --git a/sci-libs/clfft/metadata.xml b/sci-libs/clfft/metadata.xml index 14184f9aa..910e9921c 100644 --- a/sci-libs/clfft/metadata.xml +++ b/sci-libs/clfft/metadata.xml @@ -14,4 +14,7 @@ clFFT is part of the clMath sofware library, which is the successor of APPML. </longdescription> + <upstream> + <remote-id type="github">clMathLibraries/clFFT</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/clrng/ChangeLog b/sci-libs/clrng/ChangeLog new file mode 100644 index 000000000..1e0a15e1f --- /dev/null +++ b/sci-libs/clrng/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-libs/clrng +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/clrng: Add github to remote-id in metadata.xml + +*clrng-9999 (11 May 2015) + + 11 May 2015; Marius Brehler <marbre@linux.sungazer.de> +clrng-9999.ebuild, + +metadata.xml: + Initial ebuild diff --git a/sci-libs/clrng/clrng-9999.ebuild b/sci-libs/clrng/clrng-9999.ebuild new file mode 100644 index 000000000..fa1a8301c --- /dev/null +++ b/sci-libs/clrng/clrng-9999.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils + +MY_PN="clRNG" + +DESCRIPTION="A library for uniform random number generation in OpenCL" +HOMEPAGE="https://github.com/clMathLibraries/clRNG" + +if [ ${PV} == "9999" ] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/clMathLibraries/${MY_PN}.git git://github.com/clMathLibraries/${MY_PN}.git" + S="${WORKDIR}/${P}/src" +else + SRC_URI="https://github.com/clMathLibraries/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/${MY_PN}-${PV}/src" +fi + +LICENSE="BSD-2 BSD" +SLOT="0" +IUSE="+client test" + +RDEPEND=" + >=sys-devel/gcc-4.8:* + virtual/opencl + || ( >=dev-util/amdapp-2.9 dev-util/intel-ocl-sdk ) + dev-libs/boost + " +DEPEND="${RDEPEND}" + +# The tests only get compiled to an executable named Test, which is not recogniozed by cmake. +# Therefore src_test() won't execute any test. +RESTRICT="test" + +pkg_pretend() { + if [[ ${MERGE_TYPE} != binary ]]; then + if [[ $(gcc-major-version) -lt 4 ]] || ( [[ $(gcc-major-version) -eq 4 && $(gcc-minor-version) -lt 8 ]] ) ; then + die "Compilation with gcc older than 4.8 is not supported." + fi + fi +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_build client CLIENT) + $(cmake-utils_use_build test TEST) + ) + cmake-utils_src_configure +} diff --git a/sci-libs/clrng/metadata.xml b/sci-libs/clrng/metadata.xml new file mode 100644 index 000000000..25fe2a5cf --- /dev/null +++ b/sci-libs/clrng/metadata.xml @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> + <use> + <flag name="client"> + Build a command line clRNG client program. + </flag> + </use> + <upstream> + <remote-id type="github">clMathLibraries/clRNG</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/dcmtk/ChangeLog b/sci-libs/dcmtk/ChangeLog index 3177dd50c..869f1ff5c 100644 --- a/sci-libs/dcmtk/ChangeLog +++ b/sci-libs/dcmtk/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-libs/dcmtk -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 10 Mar 2015; Justin Lecher <jlec@gentoo.org> dcmtk-3.6.0.ebuild: + sci-libs/dcmtk: Fix compilation with USE=-doc, fixes https://github.com + /gentoo-science/sci/issues/385 + 13 Nov 2014; Justin Lecher <jlec@gentoo.org> dcmtk-3.6.0.ebuild, metadata.xml: Move large patch into patch dir diff --git a/sci-libs/dcmtk/dcmtk-3.6.0.ebuild b/sci-libs/dcmtk/dcmtk-3.6.0.ebuild index 67d2bb86f..b78553d32 100644 --- a/sci-libs/dcmtk/dcmtk-3.6.0.ebuild +++ b/sci-libs/dcmtk/dcmtk-3.6.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -19,7 +19,7 @@ SLOT="0" IUSE="doc png ssl tcpd +threads tiff xml zlib" RDEPEND=" - virtual/jpeg + virtual/jpeg:0= png? ( media-libs/libpng:0= ) ssl? ( dev-libs/openssl:= ) tcpd? ( sys-apps/tcp-wrappers ) @@ -71,5 +71,5 @@ src_configure() { } src_compile() { - cmake-utils_src_compile all $(usex doc "html") + cmake-utils_src_compile all $(usex doc "html" "") } diff --git a/sci-libs/dealii/ChangeLog b/sci-libs/dealii/ChangeLog index 1b5b46aa4..c900cbe52 100644 --- a/sci-libs/dealii/ChangeLog +++ b/sci-libs/dealii/ChangeLog @@ -2,6 +2,20 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> dealii-8.1.0-r2.ebuild, + dealii-8.2.1-r1.ebuild, dealii-9999.ebuild: + sci-libs/dealii: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/dealii: Add github to remote-id in metadata.xml + +*dealii-8.2.1-r1 (28 Mar 2015) + + 28 Mar 2015; Matthias Maier <tamiko@gentoo.org> +dealii-8.2.1-r1.ebuild, + -dealii-8.2.1.ebuild, dealii-8.1.0-r2.ebuild, dealii-8.2.0.ebuild, + dealii-9999.ebuild: + sci-libs/dealii: Ebuild maintenance, remove wrong avx2 use flag + 29 Jan 2015; Matthias Maier <tamiko@gentoo.org> dealii-8.1.0-r2.ebuild, dealii-8.2.1.ebuild, dealii-9999.ebuild, metadata.xml: Convert to CPU_FLAGS_X86 diff --git a/sci-libs/dealii/dealii-8.1.0-r2.ebuild b/sci-libs/dealii/dealii-8.1.0-r2.ebuild index 7e174ffa8..0703aa8af 100644 --- a/sci-libs/dealii/dealii-8.1.0-r2.ebuild +++ b/sci-libs/dealii/dealii-8.1.0-r2.ebuild @@ -44,9 +44,9 @@ RDEPEND="dev-libs/boost metis? ( >=sci-libs/parmetis-4 ) mpi? ( virtual/mpi ) mumps? ( sci-libs/mumps[mpi] ) - netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) ) + netcdf? ( sci-libs/netcdf-cxx:0 ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) diff --git a/sci-libs/dealii/dealii-8.2.0.ebuild b/sci-libs/dealii/dealii-8.2.0.ebuild index e7cf68128..c0e321cf2 120000 --- a/sci-libs/dealii/dealii-8.2.0.ebuild +++ b/sci-libs/dealii/dealii-8.2.0.ebuild @@ -1 +1 @@ -dealii-8.2.1.ebuild
\ No newline at end of file +dealii-8.2.1-r1.ebuild
\ No newline at end of file diff --git a/sci-libs/dealii/dealii-8.2.1.ebuild b/sci-libs/dealii/dealii-8.2.1-r1.ebuild index 07c31a30f..331dd0dce 100644 --- a/sci-libs/dealii/dealii-8.2.1.ebuild +++ b/sci-libs/dealii/dealii-8.2.1-r1.ebuild @@ -31,10 +31,9 @@ fi LICENSE="LGPL-2.1+" SLOT="0" IUSE=" - arpack cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 c++11 - +debug doc +examples hdf5 +lapack mesh_converter metis mpi mumps - muparser opencascade netcdf p4est parameter_gui petsc +sparse - static-libs +tbb trilinos + arpack cpu_flags_x86_avx cpu_flags_x86_sse2 c++11 +debug doc +examples + hdf5 +lapack mesh_converter metis mpi mumps muparser opencascade netcdf + p4est parameter_gui petsc +sparse static-libs +tbb trilinos " # TODO: add slepc use flag once slepc is packaged for gentoo-science @@ -53,10 +52,10 @@ RDEPEND="dev-libs/boost mpi? ( virtual/mpi ) mumps? ( sci-libs/mumps[mpi] ) muparser? ( dev-cpp/muParser ) - netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) ) - opencascade? ( sci-libs/opencascade ) + netcdf? ( sci-libs/netcdf-cxx:0 ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) @@ -86,7 +85,6 @@ src_configure() { $(cmake-utils_use arpack DEAL_II_WITH_ARPACK) $(cmake-utils_use c++11 DEAL_II_WITH_CXX11) $(cmake-utils_use cpu_flags_x86_avx DEAL_II_HAVE_AVX) - $(cmake-utils_use cpu_flags_x86_avx2 DEAL_II_HAVE_AVX512) $(cmake-utils_use cpu_flags_x86_sse2 DEAL_II_HAVE_SSE2) $(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION) $(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES) diff --git a/sci-libs/dealii/dealii-9999.ebuild b/sci-libs/dealii/dealii-9999.ebuild index 2774e75cb..c00c3835f 100644 --- a/sci-libs/dealii/dealii-9999.ebuild +++ b/sci-libs/dealii/dealii-9999.ebuild @@ -31,10 +31,9 @@ fi LICENSE="LGPL-2.1+" SLOT="0" IUSE=" - arpack cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_sse2 c++11 - +debug doc +examples hdf5 +lapack mesh_converter metis mpi muparser - opencascade netcdf p4est parameter_gui petsc +sparse static-libs +tbb - trilinos + arpack cpu_flags_x86_avx cpu_flags_x86_sse2 c++11 +debug doc +examples + hdf5 +lapack mesh_converter metis mpi muparser opencascade + netcdf p4est parameter_gui petsc +sparse static-libs +tbb trilinos " # TODO: add slepc use flag once slepc is packaged for gentoo-science @@ -51,10 +50,10 @@ RDEPEND="dev-libs/boost metis? ( >=sci-libs/parmetis-4 ) mpi? ( virtual/mpi ) muparser? ( dev-cpp/muParser ) - netcdf? ( || ( <sci-libs/netcdf-4.2[cxx] sci-libs/netcdf-cxx ) ) - opencascade? ( sci-libs/opencascade ) + netcdf? ( sci-libs/netcdf-cxx:0 ) + opencascade? ( sci-libs/opencascade:* ) p4est? ( sci-libs/p4est[mpi] ) - parameter_gui? ( dev-qt/qtgui ) + parameter_gui? ( dev-qt/qtgui:4 ) petsc? ( sci-mathematics/petsc[mpi=] ) sparse? ( sci-libs/umfpack ) tbb? ( dev-cpp/tbb ) @@ -82,7 +81,6 @@ src_configure() { $(cmake-utils_use arpack DEAL_II_WITH_ARPACK) $(cmake-utils_use c++11 DEAL_II_WITH_CXX11) $(cmake-utils_use cpu_flags_x86_avx DEAL_II_HAVE_AVX) - $(cmake-utils_use cpu_flags_x86_avx2 DEAL_II_HAVE_AVX512) $(cmake-utils_use cpu_flags_x86_sse2 DEAL_II_HAVE_SSE2) $(cmake-utils_use doc DEAL_II_COMPONENT_DOCUMENTATION) $(cmake-utils_use examples DEAL_II_COMPONENT_EXAMPLES) diff --git a/sci-libs/dealii/metadata.xml b/sci-libs/dealii/metadata.xml index e838dc172..bce7b01bc 100644 --- a/sci-libs/dealii/metadata.xml +++ b/sci-libs/dealii/metadata.xml @@ -31,4 +31,7 @@ and extra output. If you want to get meaningful backtraces see <flag name="tbb">Add threading support with the help of the tbb library (<pkg>dev-cpp/tbb</pkg>)</flag> <flag name="trilinos">Add support for trilinos (<pkg>sci-libs/trilinos</pkg>)</flag> </use> + <upstream> + <remote-id type="github">dealii/dealii</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/elmer-eio/Manifest b/sci-libs/elmer-eio/Manifest index 4b4383312..2fe59554f 100644 --- a/sci-libs/elmer-eio/Manifest +++ b/sci-libs/elmer-eio/Manifest @@ -1 +1 @@ -DIST elmer-eio-6.0_p4651.tar.gz 147064 SHA256 98979ce8f3d3ee9f0f06a1c07a9021d5ffdc7e16a739ba90724257cc21fc0c88 SHA512 744615444f131fe4a1dd789ff4197cc86d24991a21a9c04b1ea3815ca7c6346b7d211ae47bc77bf49ca2e763a5daf6b0fef3b2b1d71697ed93fbc557ca5825a7 WHIRLPOOL 207abde5b60b5527cb5ea538746a4cf7d30f76a1979f84ddad697b741dd9abb391e1ef5ceee0f461c207aec709743723fcd8846b6b76f1c09ae22ecf07eada4b +DIST elmer-eio-6.0_p4651.tar.gz 147064 SHA256 80748e1386f03ef4b3a4c68271b1c724563a8960ffffcc36ba23e70e8519426e SHA512 52ce490810787e5100524858d41f3ad3d17ebfe5b747ea042acd8b8106028bb3aa7dd87ef80d3ce4ae2ffbf9439ad86c5f1a5f2e2c3cfb1cca5800c0fa166924 WHIRLPOOL 28837ee89756d81db5be96909f9682b1c627f31955179b668097c4d9c3efd55936a8e4c7334eda76051664dbb7043b246ad5d77a6b8950bb20f11a88ae53aa89 diff --git a/sci-libs/etsf_io/ChangeLog b/sci-libs/etsf_io/ChangeLog index 918ee5ffe..de46375fb 100644 --- a/sci-libs/etsf_io/ChangeLog +++ b/sci-libs/etsf_io/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/etsf_io -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*etsf_io-1.0.4-r1 (22 Apr 2015) + + 22 Apr 2015; Honza Macháček <Hloupy.Honza@centrum.cz> + -etsf_io-1.0.4.ebuild, +etsf_io-1.0.4-r1.ebuild, metadata.xml: + Added pic USE flag, needed by sci-physics/bigdft + 15 Apr 2014; Honza Macháček <Hloupy.Honza@centrum.cz> etsf_io-1.0.4.ebuild: From sci-libs/etsf_io-1.0.4 removed -fPIC, probably not needed, just introduced by mistake. diff --git a/sci-libs/etsf_io/etsf_io-1.0.4.ebuild b/sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild index 7fe4fceb9..60ab08895 100644 --- a/sci-libs/etsf_io/etsf_io-1.0.4.ebuild +++ b/sci-libs/etsf_io/etsf_io-1.0.4-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -12,7 +12,7 @@ SRC_URI="http://www.etsf.eu/system/files/${P}.tar.gz" LICENSE="LGPL-2" SLOT="0" -IUSE="examples" +IUSE="examples pic" KEYWORDS="~amd64 ~x86" RDEPEND=" @@ -28,6 +28,7 @@ FORTRAN_STANDARD="90" src_configure() { # fortran 90 uses FCFLAGS export FCFLAGS="${FFLAGS:--O2}" + use pic && export FCFLAGS="-fPIC ${FCFLAGS}" econf \ $(use_enable examples build-tutorials) \ --prefix="${EPREFIX}/usr" \ diff --git a/sci-libs/etsf_io/metadata.xml b/sci-libs/etsf_io/metadata.xml index b229aec85..d6ac3f95d 100644 --- a/sci-libs/etsf_io/metadata.xml +++ b/sci-libs/etsf_io/metadata.xml @@ -1,5 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> + <maintainer> + <email>sci@gentoo.org</email> + </maintainer> + <use> + <flag name="pic">Compile Position Independent Code</flag> + </use> </pkgmetadata> diff --git a/sci-libs/fftw/ChangeLog b/sci-libs/fftw/ChangeLog index 971318cde..918dd73c4 100644 --- a/sci-libs/fftw/ChangeLog +++ b/sci-libs/fftw/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 13 Apr 2015; Justin Lecher <jlec@gentoo.org> fftw-3.3.4-r1.ebuild: + sci-libs/fftw: Drop emul package support + + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> fftw-3.3.4-r1.ebuild: + dropped sparc + *fftw-3.3.4-r1 (17 Feb 2015) 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +fftw-3.3.4-r1.ebuild: diff --git a/sci-libs/fftw/fftw-3.3.4-r1.ebuild b/sci-libs/fftw/fftw-3.3.4-r1.ebuild index cd36caa98..7a8442187 100644 --- a/sci-libs/fftw/fftw-3.3.4-r1.ebuild +++ b/sci-libs/fftw/fftw-3.3.4-r1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-libs/fftw/fftw-3.3.4.ebuild,v 1.7 2015/02/08 06:33:37 jer Exp $ +# $Header: $ EAPI=5 @@ -18,7 +18,7 @@ if [[ ${PV} = *9999 ]]; then AUTOTOOLS_AUTORECONF=1 else SRC_URI="http://www.fftw.org/${P}.tar.gz" - KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos" fi LICENSE="GPL-2" @@ -26,9 +26,7 @@ SLOT="3.0/3" IUSE="altivec cpu_flags_x86_avx doc cpu_flags_x86_fma3 cpu_flags_x86_fma4 fortran mpi neon openmp quad cpu_flags_x86_sse cpu_flags_x86_sse2 static-libs test threads zbus" RDEPEND=" - mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP}] ) - abi_x86_32? ( !<=app-emulation/emul-linux-x86-soundlibs-20130224-r2 - !app-emulation/emul-linux-x86-soundlibs[-abi_x86_32(-)] )" + mpi? ( >=virtual/mpi-2.0-r4[${MULTILIB_USEDEP}] )" DEPEND="${RDEPEND} test? ( dev-lang/perl )" diff --git a/sci-libs/framewave/ChangeLog b/sci-libs/framewave/ChangeLog new file mode 100644 index 000000000..9cb20eeb1 --- /dev/null +++ b/sci-libs/framewave/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-libs/framewave +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/framewave: Updating remote-id in metadata.xml + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> framewave-1.3.1.ebuild: + Bump to EAPI=5; Cleanup diff --git a/sci-libs/framewave/framewave-1.3.1.ebuild b/sci-libs/framewave/framewave-1.3.1.ebuild index 22fbc7426..8e858cb24 100644 --- a/sci-libs/framewave/framewave-1.3.1.ebuild +++ b/sci-libs/framewave/framewave-1.3.1.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 MY_P="FRAMEWAVE_${PV}_SRC" @@ -26,7 +26,7 @@ src_prepare() { } src_compile() { - cd Framewave + cd Framewave || die local bits="32" use amd64 && bits="64" @@ -40,8 +40,8 @@ src_install() { local bits="32" use amd64 && bits="64" - dolib.so Framewave/build/bin/release_shared_${bits}/*.so* || die "doins failed" + dolib.so Framewave/build/bin/release_shared_${bits}/*.so* insinto /usr/include - doins Framewave/build/include/* || die "doins failed" + doins Framewave/build/include/* } diff --git a/sci-libs/framewave/metadata.xml b/sci-libs/framewave/metadata.xml index 14ebbb547..cef6a6f41 100644 --- a/sci-libs/framewave/metadata.xml +++ b/sci-libs/framewave/metadata.xml @@ -7,4 +7,7 @@ routines designed to accelerate application development, debugging, multi-threading and optimization on x86-class processor platforms. </longdescription> + <upstream> + <remote-id type="sourceforge">framewave</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/geom/ChangeLog b/sci-libs/geom/ChangeLog index bef4c80d9..8e017978d 100644 --- a/sci-libs/geom/ChangeLog +++ b/sci-libs/geom/ChangeLog @@ -1,10 +1,15 @@ # ChangeLog for sci-libs/geom -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/geom: Updating remote-id in metadata.xml + + 23 May 2015; Marius Brehler <marbre@linux.sungazer.de> geom-5.1.2.7.ebuild: + Bump to EAPI=5 + *geom-5.1.2.7 (09 Mar 2011) 09 Mar 2011; Oliver Borm (boroli) <oli.borm@web.de> +geom-5.1.2.7.ebuild, +metadata.xml: sci-libs/geom: New ebuild from bug 358061 - diff --git a/sci-libs/geom/Manifest b/sci-libs/geom/Manifest index ed41324cf..557594be2 100644 --- a/sci-libs/geom/Manifest +++ b/sci-libs/geom/Manifest @@ -1 +1 @@ -DIST geom-5.1.2.7.tar.gz 612914 SHA256 c0685d82535db3899d9321d72237b5d1be2dbafd1c85f990f767d5cd88571055 +DIST geom-5.1.2.7.tar.gz 612914 SHA256 c0685d82535db3899d9321d72237b5d1be2dbafd1c85f990f767d5cd88571055 SHA512 06454a4a92959fa08f2e81d8e5fcfdb957a49cdf51bd5e7efd6895ab2d1aedbd99dfb30ddc4b278b10d125f9d2d66260eff584e670716c96e2d0ec10b169fb08 WHIRLPOOL 0d9d11efe518c98788e921336552435639eb3bd8f53e39381babc1baaa3c609c37c9aa21e320a3342fbe03472f557e32f94e8fd8658e8b1017d99672ee618fc3 diff --git a/sci-libs/geom/geom-5.1.2.7.ebuild b/sci-libs/geom/geom-5.1.2.7.ebuild index 5ad13c7a9..98331d566 100644 --- a/sci-libs/geom/geom-5.1.2.7.ebuild +++ b/sci-libs/geom/geom-5.1.2.7.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit autotools eutils @@ -27,14 +27,14 @@ src_prepare() { } src_compile() { - emake || die 'emake failed' + default if use doc ; then - cd ../../doc/src + cd ../../doc/src || die doxygen || die 'doxygen failed' fi } src_install() { - emake DESTDIR="${D}" install || die "emake install failed!" + default use doc && dohtml -r ../../doc/html/* } diff --git a/sci-libs/geom/metadata.xml b/sci-libs/geom/metadata.xml index 2974a0288..f97ec5f49 100644 --- a/sci-libs/geom/metadata.xml +++ b/sci-libs/geom/metadata.xml @@ -1,7 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> + <herd>sci</herd> <use> </use> + <upstream> + <remote-id type="sourceforge">salomegeometry</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild index 54b46f29c..9f8a4138a 100644 --- a/sci-libs/ghmm/ghmm-9999.ebuild +++ b/sci-libs/ghmm/ghmm-9999.ebuild @@ -6,7 +6,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=true -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit autotools-utils distutils-r1 subversion diff --git a/sci-libs/gotoblas2/ChangeLog b/sci-libs/gotoblas2/ChangeLog index 77c5817c8..77caeaac5 100644 --- a/sci-libs/gotoblas2/ChangeLog +++ b/sci-libs/gotoblas2/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-libs/gotoblas2 -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 Jun 2015; Justin Lecher <jlec@gentoo.org> gotoblas2-1.13.ebuild, + metadata.xml: + sci-libs/gotoblas2: Bump EAPI + 15 Mar 2012; François Bissey <francois.bissey@canterbury.ac.nz> gotoblas2-1.13.ebuild, files/gotoblas2-1.13-sharedlibs.patch: More OS X fixes @@ -40,4 +44,3 @@ +gotoblas2-1.13.ebuild, +files/gotoblas2-1.13-dynamic.patch, +files/gotoblas2-1.13-sharedlibs.patch, +metadata.xml: Initial import - diff --git a/sci-libs/gotoblas2/gotoblas2-1.13.ebuild b/sci-libs/gotoblas2/gotoblas2-1.13.ebuild index 49022f82f..b96298bd7 100644 --- a/sci-libs/gotoblas2/gotoblas2-1.13.ebuild +++ b/sci-libs/gotoblas2/gotoblas2-1.13.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit eutils toolchain-funcs alternatives-2 multilib diff --git a/sci-libs/gotoblas2/metadata.xml b/sci-libs/gotoblas2/metadata.xml index 7ec44c058..300266bab 100644 --- a/sci-libs/gotoblas2/metadata.xml +++ b/sci-libs/gotoblas2/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The GotoBLAS codes are one of the fastest implementations of the Basic Linear Algebra Subroutines(BLAS). To achieve performance it starts by observing that for current @@ -11,9 +11,9 @@ is also taken into consideration, it is the minimization of such TLB misses that drives the approach. </longdescription> -<use> - <flag name='int64'>Build the 64 bits integer library</flag> - <flag name='incblas'>Build the CBLAS interface</flag> - <flag name='dynamic'>Build dynamic architecture detection at run time (for multi targets)</flag> -</use> + <use> + <flag name="int64">Build the 64 bits integer library</flag> + <flag name="incblas">Build the CBLAS interface</flag> + <flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag> + </use> </pkgmetadata> diff --git a/sci-libs/gsl/ChangeLog b/sci-libs/gsl/ChangeLog index 0ffe3bda8..936c4dff6 100644 --- a/sci-libs/gsl/ChangeLog +++ b/sci-libs/gsl/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-libs/gsl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-libs/gsl/ChangeLog,v 1.77 2010/08/09 09:32:55 xarthisius Exp $ + 16 Jun 2015; Justin Lecher <jlec@gentoo.org> -gsl-1.16-r1.ebuild, + gsl-1.16-r2.ebuild, metadata.xml: + sci-libs/gsl: Fix problems during installation with multilib and alternatives, + https://github.com/gentoo-science/sci/issues/438 + *gsl-1.16-r2 (10 Nov 2014) 10 Nov 2014; Christoph Junghans <ottxor@gentoo.org> +gsl-1.16-r2.ebuild: diff --git a/sci-libs/gsl/gsl-1.16-r1.ebuild b/sci-libs/gsl/gsl-1.16-r1.ebuild deleted file mode 100644 index f19bba153..000000000 --- a/sci-libs/gsl/gsl-1.16-r1.ebuild +++ /dev/null @@ -1,60 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=1 - -inherit alternatives-2 autotools-utils eutils toolchain-funcs - -DESCRIPTION="GNU Scientific Library" -HOMEPAGE="http://www.gnu.org/software/gsl/" -SRC_URI="mirror://gnu/${PN}/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~mips ~ppc ~ppc64 ~s390 ~sh ~sparc ~x86 ~x86-fbsd ~x86-interix ~amd64-linux ~x86-linux ~x86-macos ~x64-macos ~sparc-solaris ~x86-solaris" -IUSE="cblas-external static-libs" - -RDEPEND="cblas-external? ( virtual/cblas )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${P}-cblas-external.patch ) - -src_configure() { - if use cblas-external; then - export CBLAS_LIBS="$($(tc-getPKG_CONFIG) --libs cblas)" - export CBLAS_CFLAGS="$($(tc-getPKG_CONFIG) --cflags cblas)" - fi - local myeconfargs=( - $(use_with cblas-external) - ) - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - local libname=gslcblas - - cat <<-EOF > ${libname}.pc - prefix=${EPREFIX}/usr - libdir=\${prefix}/$(get_libdir) - includedir=\${prefix}/include - Name: ${libname} - Description: ${DESCRIPTION} CBLAS implementation - Version: ${PV} - URL: ${HOMEPAGE} - Libs: -L\${libdir} -l${libname} - Libs.private: -lm - Cflags: -I\${includedir} - EOF - insinto /usr/$(get_libdir)/pkgconfig - doins ${libname}.pc - - # Don't add gsl as a cblas alternative if using cblas-external - use cblas-external || alternatives_for cblas gsl 0 \ - /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc \ - /usr/include/cblas.h gsl/gsl_cblas.h -} diff --git a/sci-libs/gsl/gsl-1.16-r2.ebuild b/sci-libs/gsl/gsl-1.16-r2.ebuild index 7cf440230..fada1472a 100644 --- a/sci-libs/gsl/gsl-1.16-r2.ebuild +++ b/sci-libs/gsl/gsl-1.16-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -53,8 +53,12 @@ multilib_src_install() { insinto /usr/$(get_libdir)/pkgconfig doins ${libname}.pc + GSL_ALTERNATIVES+=( /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc ) +} + +multilib_src_install_all() { # Don't add gsl as a cblas alternative if using cblas-external use cblas-external || alternatives_for cblas gsl 0 \ - /usr/$(get_libdir)/pkgconfig/cblas.pc ${libname}.pc \ + ${GSL_ALTERNATIVES[@]} \ /usr/include/cblas.h gsl/gsl_cblas.h } diff --git a/sci-libs/gsl/metadata.xml b/sci-libs/gsl/metadata.xml index 9be87cabc..2d7f4e76e 100644 --- a/sci-libs/gsl/metadata.xml +++ b/sci-libs/gsl/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> The GNU Scientific Library (GSL) is a collection of routines for numerical analysis. The routines are written from scratch by the GSL team in C, and present a modern API for C programmers, while allowing @@ -15,8 +15,8 @@ differential equations, quadrature, Monte Carlo integration, special functions, physical constants, and much more. </longdescription> -<use> - <flag name="cblas-external">Link gsl with external cblas provided by + <use> + <flag name="cblas-external">Link gsl with external cblas provided by (<pkg>virtual/cblas</pkg>) instead of shipped internal version</flag> -</use> + </use> </pkgmetadata> diff --git a/sci-libs/iml/ChangeLog b/sci-libs/iml/ChangeLog index 8bee9988f..c2e50b6f3 100644 --- a/sci-libs/iml/ChangeLog +++ b/sci-libs/iml/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-libs/iml -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*iml-1.0.4 (03 Apr 2015) + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> + +files/iml-1.0.4-use-any-cblas-implementation.patch, +iml-1.0.4.ebuild: + Version bump + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> iml-1.0.3-r2.ebuild: + Bump to EAPI=5 + *iml-1.0.3-r2 (13 Sep 2012) 13 Sep 2012; François Bissey <francois.bissey@canterbury.ac.nz> @@ -18,4 +27,3 @@ +files/iml-1.0.3-cblas.patch, +files/fix-undefined-symbol.patch, +metadata.xml: Initial import - diff --git a/sci-libs/iml/Manifest b/sci-libs/iml/Manifest index 2f658aa1e..3d9e920c6 100644 --- a/sci-libs/iml/Manifest +++ b/sci-libs/iml/Manifest @@ -1 +1,2 @@ DIST iml-1.0.3.tar.gz 395160 SHA256 fc626debbf8f84689398f4b941a6c1ded0910eea4388e169bf63c48e257b0395 SHA512 92e76a7c08ca6e425153d8c614783064a80077ad9859e1c1460595b5e29e614c6eaf8b330a5f3c1b564209ca8265f93d8485cd5cb376e96f01dc81bf9751a67a WHIRLPOOL c0b65d570513ee74d1659863005f2922f9e91e423ef5c701b665912a3d1fa9c5c389a9d97a0eabbed3334ac0111e815b37a69748a50326a6100903c5ac521722 +DIST iml-1.0.4.tar.bz2 407347 SHA256 88a310d527d98be0219c98a669336a14e7cebf596b439a4494fdfc1492902fd3 SHA512 21cb4f124b7e06526238aff053eb9249eece9342122ec00e7ab2aec68b1c6298a30bee3dd183e322ad4cce636faa679d11422d7cc72b524d8a9b5936017fd209 WHIRLPOOL 2499d0a0a86dc62cccfc342a10398dd0ee3778a3e601d6ecbf4490493d0de09c409d457ee0b5ea0fe908c507aeb7cf67e78645bcae45eb226b7fa1e8b44f8bf3 diff --git a/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch b/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch new file mode 100644 index 000000000..3d88a3906 --- /dev/null +++ b/sci-libs/iml/files/iml-1.0.4-use-any-cblas-implementation.patch @@ -0,0 +1,22 @@ +Patch to detect ATLAS or cblas. Ported from 1.0.3 to 1.0.4. + +Patch by Marius Brehler. +--- configure.ac ++++ configure.ac +@@ -76,15 +76,7 @@ location with the options --with-gmp-inc + respectively when running configure. + )]) + +-IML_CHECK_CBLAS(,,[AC_MSG_WARN( +-CBLAS not found! +-Please make sure that --with-cblas=<linker flags> and optional --with-cblas-include=<path> and --with-cblas-lib=<path> are correctly set. +-Trying legacy ATLAS configuration.) +-IML_CHECK_ATLAS(,,[AC_MSG_ERROR( +-ATLAS not found! +-ATLAS version 3.0 or greater is required for this library to compile. Please make sure ATLAS is installed and specify the header and libraries location with the options --with-atlas-include=<path> and --with-atlas-lib=<path> respectively when running configure.) +-]) +-]) ++PKG_CHECK_MODULES([ATLAS], [cblas]) + + AC_SUBST(LIBIML_LDFLAGS) + AC_SUBST(LDFLAGS) diff --git a/sci-libs/iml/iml-1.0.3-r2.ebuild b/sci-libs/iml/iml-1.0.3-r2.ebuild index 739b90c45..319ba9f51 100644 --- a/sci-libs/iml/iml-1.0.3-r2.ebuild +++ b/sci-libs/iml/iml-1.0.3-r2.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="4" +EAPI=5 inherit autotools-utils diff --git a/sci-libs/iml/iml-1.0.4.ebuild b/sci-libs/iml/iml-1.0.4.ebuild new file mode 100644 index 000000000..8be9c4731 --- /dev/null +++ b/sci-libs/iml/iml-1.0.4.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit autotools-utils + +DESCRIPTION="Integer Matrix Library" +HOMEPAGE="http://www.cs.uwaterloo.ca/~astorjoh/iml.html" +SRC_URI="http://www.cs.uwaterloo.ca/~astorjoh/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="static-libs" + +RESTRICT="mirror" + +DEPEND="virtual/cblas" +RDEPEND="${DEPEND}" + +AUTOTOOLS_AUTORECONF=yes +AT_M4DIR="config" +DOCS=( AUTHORS ChangeLog README ) +PATCHES=( + "${FILESDIR}"/${P}-use-any-cblas-implementation.patch +) + +src_configure() { + myeconfargs=( + --with-default="${EPREFIX}"/usr + ) + autotools-utils_src_configure +} diff --git a/sci-libs/itk/ChangeLog b/sci-libs/itk/ChangeLog index f623cac73..e20aac9e9 100644 --- a/sci-libs/itk/ChangeLog +++ b/sci-libs/itk/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/itk: Updating remote-id in metadata.xml + 01 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> itk-4.4.2.ebuild, itk-4.4.2-r1.ebuild, itk-4.5.1.ebuild: Convert sse2 to cpu_flags_x86_sse2 diff --git a/sci-libs/itk/itk-4.4.2-r1.ebuild b/sci-libs/itk/itk-4.4.2-r1.ebuild index 5aa31c845..ba6e9a8c3 100644 --- a/sci-libs/itk/itk-4.4.2-r1.ebuild +++ b/sci-libs/itk/itk-4.4.2-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils toolchain-funcs cmake-utils python-single-r1 diff --git a/sci-libs/itk/itk-4.4.2.ebuild b/sci-libs/itk/itk-4.4.2.ebuild index 07c0a91f0..5febd1967 100644 --- a/sci-libs/itk/itk-4.4.2.ebuild +++ b/sci-libs/itk/itk-4.4.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils toolchain-funcs cmake-utils python-single-r1 diff --git a/sci-libs/itk/itk-4.5.1.ebuild b/sci-libs/itk/itk-4.5.1.ebuild index ed7f18368..3b308abc0 100644 --- a/sci-libs/itk/itk-4.5.1.ebuild +++ b/sci-libs/itk/itk-4.5.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils toolchain-funcs cmake-utils python-single-r1 diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml index 7789e7619..ca42e5f1f 100644 --- a/sci-libs/itk/metadata.xml +++ b/sci-libs/itk/metadata.xml @@ -15,4 +15,7 @@ <flag name="review">Enable compilation of methods under review</flag> <flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> </use> + <upstream> + <remote-id type="sourceforge">itk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/jhdf5/ChangeLog b/sci-libs/jhdf5/ChangeLog new file mode 100644 index 000000000..48f71af49 --- /dev/null +++ b/sci-libs/jhdf5/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-libs/jhdf5 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*jhdf5-14.12.1 (10 Jun 2015) + + 10 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> + +jhdf5-14.12.1.ebuild, +metadata.xml: + a skeleton for a java package diff --git a/sci-libs/jhdf5/Manifest b/sci-libs/jhdf5/Manifest new file mode 100644 index 000000000..f3fa49b3f --- /dev/null +++ b/sci-libs/jhdf5/Manifest @@ -0,0 +1 @@ +DIST sis-jhdf5-14.12.1-r33502.zip 30916751 SHA256 6ec8979ca84f13201b0fad8fe5b678827e7c79511f4eb08a06d9ac447a656bb9 SHA512 bc6104a829f50639cf913b3497c6ca815aff70782de0c509d9091087d7bcbd01649d5955e2df91d23ed4e058cdf90f7acfa40f1170059ca4039ba376ca11f800 WHIRLPOOL 83cb95d95f33fb73617bdc7cc604f6ab55bef51e2103f414e4a8b8cabb02b6c6628cf6dd84f73742203007e948a050fc59934cbcb88df433bb204e9cf203c2c8 diff --git a/sci-libs/jhdf5/jhdf5-14.12.1.ebuild b/sci-libs/jhdf5/jhdf5-14.12.1.ebuild new file mode 100644 index 000000000..da6b58456 --- /dev/null +++ b/sci-libs/jhdf5/jhdf5-14.12.1.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java binding for HDF5 compatible with HDF5 1.6/1.8" +HOMEPAGE="https://wiki-bsse.ethz.ch/display/JHDF5 + https://wiki-bsse.ethz.ch/pages/viewpage.action?pageId=26609113" +SRC_URI="https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.1-r33502.zip" +# first SIS release: https://wiki-bsse.ethz.ch/download/attachments/26609237/sis-jhdf5-14.12.0-r33145.zip +# last CISD release: https://wiki-bsse.ethz.ch/download/attachments/26609237/cisd-jhdf5-13.06.2-r29633.zip + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="" +IUSE="" + +# versions <=12.02 required >=java-1.5 +DEPEND=">=virtual/jdk-1.6:*" +RDEPEND="${DEPEND} + >=virtual/jre-1.6:*" + +S="${WORKDIR}"/sis-jhdf5 diff --git a/sci-libs/jhdf5/metadata.xml b/sci-libs/jhdf5/metadata.xml new file mode 100644 index 000000000..2bc893037 --- /dev/null +++ b/sci-libs/jhdf5/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/k3match/k3match-1.1.ebuild b/sci-libs/k3match/k3match-1.1.ebuild index 010be9585..aac8fb573 100644 --- a/sci-libs/k3match/k3match-1.1.ebuild +++ b/sci-libs/k3match/k3match-1.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="threads" inherit distutils-r1 diff --git a/sci-libs/lapackpp/ChangeLog b/sci-libs/lapackpp/ChangeLog index 53d273f9c..f467421ce 100644 --- a/sci-libs/lapackpp/ChangeLog +++ b/sci-libs/lapackpp/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/lapackpp -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/lapackpp: Updating remote-id in metadata.xml + 12 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> lapackpp-2.5.4.ebuild: sci-libs/lapackpp: Use latest pkg-config diff --git a/sci-libs/lapackpp/metadata.xml b/sci-libs/lapackpp/metadata.xml index 717c30874..5789093f2 100644 --- a/sci-libs/lapackpp/metadata.xml +++ b/sci-libs/lapackpp/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> LAPACK++ (Linear Algebra PACKage in C++) is a software library for numerical linear algebra that solves systems of linear equations and eigenvalue problems on high performance computer architectures. @@ -14,4 +14,7 @@ matrices, symmetric positive definite systems, and solving linear least-square systems. </longdescription> + <upstream> + <remote-id type="sourceforge">lapackpp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/levmar/ChangeLog b/sci-libs/levmar/ChangeLog deleted file mode 100644 index 3089ff150..000000000 --- a/sci-libs/levmar/ChangeLog +++ /dev/null @@ -1,12 +0,0 @@ -# ChangeLog for sci-libs/levmar -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 12 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> levmar-2.6.ebuild: - sci-libs/levmar: Use virtual/pkgconfig and prefix keywords - -*levmar-2.6 (13 Apr 2012) - - 13 Apr 2012; Sébastien Fabbro <bicatali@gentoo.org> - +files/levmar-2.6-shared.patch, +levmar-2.6.ebuild, +metadata.xml: - sci-libs/levmar: Initial import diff --git a/sci-libs/levmar/Manifest b/sci-libs/levmar/Manifest deleted file mode 100644 index eed2a8fea..000000000 --- a/sci-libs/levmar/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST levmar-2.6.tgz 81143 SHA256 3bf4ef1ea4475ded5315e8d8fc992a725f2e7940a74ca3b0f9029d9e6e94bad7 SHA512 5b4c64b63be9b29d6ad2df435af86cd2c2e3216313378561a670ac6a392a51bbf1951e96c6b1afb77c570f23dd8e194017808e46929fec2d8d9a7fe6cf37022b WHIRLPOOL fd9f45474a2fbc57f3a542480271d90a15163edebc6e9b70444f2d9d4c9ad1a3c1301d77cee5c5d41944224c888547c069ee7443a09ff478ea996c3358f81023 diff --git a/sci-libs/levmar/files/levmar-2.6-shared.patch b/sci-libs/levmar/files/levmar-2.6-shared.patch deleted file mode 100644 index e89750cc0..000000000 --- a/sci-libs/levmar/files/levmar-2.6-shared.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Nur levmar-2.6.orig/CMakeLists.txt levmar-2.6/CMakeLists.txt ---- levmar-2.6.orig/CMakeLists.txt 2012-04-13 04:53:53.000000000 +0100 -+++ levmar-2.6/CMakeLists.txt 2012-04-13 04:54:20.000000000 +0100 -@@ -60,7 +60,7 @@ - ENDIF(HAVE_PLASMA)
-
- # levmar library source files
--ADD_LIBRARY(levmar STATIC
-+ADD_LIBRARY(levmar SHARED
- lm.c Axb.c misc.c lmlec.c lmbc.c lmblec.c lmbleic.c
- levmar.h misc.h compiler.h
- )
diff --git a/sci-libs/levmar/levmar-2.6.ebuild b/sci-libs/levmar/levmar-2.6.ebuild deleted file mode 100644 index 22e0b29bb..000000000 --- a/sci-libs/levmar/levmar-2.6.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit cmake-utils eutils toolchain-funcs - -DESCRIPTION="Levenberg-Marquardt nonlinear least squares C library" -HOMEPAGE="http://www.ics.forth.gr/~lourakis/levmar/" -SRC_URI="${HOMEPAGE}/${P}.tgz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="plasma" - -RDEPEND=" - virtual/blas - virtual/lapack - plasma? ( sci-libs/plasma )" -DEPEND="${RDEPEND} - virtual/pkgconfig" - -PATCHES=( "${FILESDIR}"/${P}-shared.patch ) - -src_configure() { - local mycmakeargs+=( - -DNEED_F2C=OFF - -DHAVE_LAPACK=ON - -DLAPACKBLAS_LIB_NAMES="$($(tc-getPKG_CONFIG) --libs blas lapack)" - $(cmake-utils_use plasma PLASMA) - $(cmake-utils_use test BUILD_DEMO) - ) - cmake-utils_src_configure -} - -src_test() { - cd ${CMAKE_BUILD_DIR} - ./lmdemo || die -} - -src_install() { - dolib.so ${CMAKE_BUILD_DIR}/liblevmar.so - insinto /usr/include - doins levmar.h -} diff --git a/sci-libs/levmar/metadata.xml b/sci-libs/levmar/metadata.xml deleted file mode 100644 index 3260b94c8..000000000 --- a/sci-libs/levmar/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> - levmar is a native ANSI C implementation of the Levenberg-Marquardt - optimization algorithm. Both unconstrained and constrained (under - linear equations, inequality and box constraints) - Levenberg-Marquardt variants are included. The LM algorithm is an - iterative technique that finds a local minimum of a function that is - expressed as the sum of squares of nonlinear functions. -</longdescription> -<use> - <flag name="plasma">Use the multi-threaded <pkg>sci-libs/plasma</pkg> library for linear algebra</flag> -</use> -</pkgmetadata> diff --git a/sci-libs/libgeodecomp/ChangeLog b/sci-libs/libgeodecomp/ChangeLog index 6f5ecda1b..c734a2bc5 100644 --- a/sci-libs/libgeodecomp/ChangeLog +++ b/sci-libs/libgeodecomp/ChangeLog @@ -1,8 +1,12 @@ # ChangeLog for sci-libs/libgeodecomp -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Apr 2015; Justin Lecher <jlec@gentoo.org> -Manifest, + -libgeodecomp-0.1.0.ebuild, -libgeodecomp-0.2.0.ebuild, + -libgeodecomp-0.3.1.ebuild: + sci-libs/libgeodecomp: In CVS + 22 Mar 2014; Justin Lecher <jlec@gentoo.org> libgeodecomp-9999.ebuild, metadata.xml: Add missing die - diff --git a/sci-libs/libgeodecomp/Manifest b/sci-libs/libgeodecomp/Manifest deleted file mode 100644 index f9f5d7631..000000000 --- a/sci-libs/libgeodecomp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST libgeodecomp-0.1.0.tar.bz2 581136 SHA256 71442a60e7cc5c3f38e462d5d52010a948bd089759487687f217e4dec4dffae5 SHA512 56de4e6bfc92f8dda4d4931559a553a7a2c847205637394ea87f73dfb5a34776cb043beba2857bbe07c52a61ed457f22b7d76e4e23c183c8bd25868d36df4704 WHIRLPOOL df2b5c6830dbc92befd873bdced1712687046a43e814f7676271a2041a58c9e2562a86c6b4034343499f813136f38e298b33fa9a67911b726f42f323f666b03e -DIST libgeodecomp-0.2.0.tar.bz2 672860 SHA256 6137061ae9f6589759a86fb1bad1a5e56b345f6c48cd753927ff4dc7ed541ad1 SHA512 e8aea7d86605837a76a3af23a28c2093f86a531239b3796c084a27b3e0d5bd32df44c2f7bc8a6530307aa40b0cbadb587ad8285e55534816548405bc8e2e6d75 WHIRLPOOL dd62161ffd76bbec0367383c57aab2af9661bccb92cdc1a91f5e3dfd4208913d517f2bfb3c27d513d58fc48718bd3f0abf983e92deacd535c5d0928bf6f44db4 -DIST libgeodecomp-0.3.1.tar.bz2 740341 SHA256 3c49a238472a82be3a6e2411a20bda85672aac01d4a87bb0e63ccbff1385ea64 SHA512 28f0ea04e45cb0a5b81b18efd3e3a011d58c077562f8039ff42e701cc362f86dff90bd505690ec22c8a42e9de1236d5b6c61d288ad4c154289e92700a2a7fcc0 WHIRLPOOL 3827974861556ab84a16e81b8cece2cff4d9e88a1559d99192fa47efd571639b252423038b3b579811c7d57452e94ae96b99f7209e87af46b752b5a193dc9994 diff --git a/sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild b/sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild deleted file mode 100644 index 6cee3bec3..000000000 --- a/sci-libs/libgeodecomp/libgeodecomp-0.1.0.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit cmake-utils - -DESCRIPTION="An auto-parallelizing library to speed up computer simulations" -HOMEPAGE="http://www.libgeodecomp.org" -SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2" - -SLOT="0" -LICENSE="LGPL-3" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="" - -RDEPEND=">=dev-libs/boost-1.48" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${P}/src" -PATCHES=( "${FILESDIR}/cmake.patch" ) - -src_test() { - cmake-utils_src_make test -}
\ No newline at end of file diff --git a/sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild b/sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild deleted file mode 100644 index 798adad55..000000000 --- a/sci-libs/libgeodecomp/libgeodecomp-0.2.0.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit cmake-utils - -DESCRIPTION="An auto-parallelizing library to speed up computer simulations" -HOMEPAGE="http://www.libgeodecomp.org" -SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2" - -SLOT="0" -LICENSE="LGPL-3" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="doc" - -RDEPEND=">=dev-libs/boost-1.48" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${P}/src" - -src_compile() { - cmake-utils_src_compile - use doc && cmake-utils_src_make doc -} - -src_install() { - DOCS=( ../README ) - use doc && HTML_DOCS=( ../doc/html/* ) - cmake-utils_src_install -} - -src_test() { - cmake-utils_src_make test -} diff --git a/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild b/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild deleted file mode 100644 index 31d1e6bb3..000000000 --- a/sci-libs/libgeodecomp/libgeodecomp-0.3.1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit cmake-utils - -DESCRIPTION="An auto-parallelizing library to speed up computer simulations" -HOMEPAGE="http://www.libgeodecomp.org" -SRC_URI="http://www.libgeodecomp.org/archive/${P}.tar.bz2" - -SLOT="0" -LICENSE="Boost-1.0" -KEYWORDS="~amd64 ~ppc ~x86" -IUSE="doc" - -RDEPEND=">=dev-libs/boost-1.48" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${P}/src" - -src_compile() { - cmake-utils_src_compile - use doc && cmake-utils_src_make doc -} - -src_install() { - DOCS=( ../README ) - use doc && HTML_DOCS=( ../doc/html/* ) - cmake-utils_src_install -} - -src_test() { - cmake-utils_src_make test -} diff --git a/sci-libs/libmaus/ChangeLog b/sci-libs/libmaus/ChangeLog new file mode 100644 index 000000000..57677bce1 --- /dev/null +++ b/sci-libs/libmaus/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-libs/libmaus +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libmaus: Add github to remote-id in metadata.xml diff --git a/sci-libs/libmaus/metadata.xml b/sci-libs/libmaus/metadata.xml index 72461eb47..c0feca39e 100644 --- a/sci-libs/libmaus/metadata.xml +++ b/sci-libs/libmaus/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<longdescription lang="en"> + <herd>sci-biology</herd> + <longdescription lang="en"> libmaus is a collection of data structures and algorithms. It contains I/O classes (single byte and UTF-8) @@ -11,4 +11,7 @@ I/O classes (single byte and UTF-8) BAM sequence alignment files input/output (simple and collating) and many lower level support classes. </longdescription> + <upstream> + <remote-id type="github">gt1/libmaus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libsc/ChangeLog b/sci-libs/libsc/ChangeLog index db89785ac..6925e4156 100644 --- a/sci-libs/libsc/ChangeLog +++ b/sci-libs/libsc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/libsc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> libsc-1.0.ebuild: + sci-libs/libsc: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libsc: Add github to remote-id in metadata.xml + *libsc-1.1 (13 Oct 2014) 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> +libsc-1.1.ebuild, diff --git a/sci-libs/libsc/libsc-1.0.ebuild b/sci-libs/libsc/libsc-1.0.ebuild index c0cb21288..64b597f49 100644 --- a/sci-libs/libsc/libsc-1.0.ebuild +++ b/sci-libs/libsc/libsc-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,19 +8,19 @@ WANT_AUTOMAKE=1.11 inherit autotools-utils toolchain-funcs eutils multilib -DESCRIPTION="The SC Library provides support for parallel scientific applications." +DESCRIPTION="Support for parallel scientific applications" HOMEPAGE="http://www.p4est.org/" SRC_URI="https://github.com/cburstedde/libsc/archive/v${PV}.tar.gz -> ${P}.tar.gz" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" LICENSE="LGPL-2.1+" SLOT="0" - +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="debug examples mpi romio static-libs" + REQUIRED_USE="romio? ( mpi )" RDEPEND=" - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack @@ -55,8 +55,7 @@ src_configure() { src_install() { autotools-utils_src_install - if use examples - then + if use examples; then docinto examples dodoc -r example/* docompress -x /usr/share/doc/${PF}/examples diff --git a/sci-libs/libsc/metadata.xml b/sci-libs/libsc/metadata.xml index 6d4eba7c1..b145b03cb 100644 --- a/sci-libs/libsc/metadata.xml +++ b/sci-libs/libsc/metadata.xml @@ -13,4 +13,7 @@ This support library is primarily used by the p4est library. <use> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libsufr/ChangeLog b/sci-libs/libsufr/ChangeLog index bf9407adb..d45f80c94 100644 --- a/sci-libs/libsufr/ChangeLog +++ b/sci-libs/libsufr/ChangeLog @@ -1,7 +1,27 @@ # ChangeLog for sci-libs/libsufr -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/libsufr: Updating remote-id in metadata.xml + +*libsufr-0.6.4 (09 May 2015) + + 09 May 2015; AstroFloyd <AstroFloyd@gmail.com> -libsufr-0.6.2.ebuild, + +libsufr-0.6.4.ebuild: + Version bump + + 05 May 2015; AstroFloyd <AstroFloyd@gmail.com> + -files/libsufr-0.3.0-multilib.patch: + Removed obsolete files/ directory + +*libsufr-0.6.3 (05 May 2015) +*libsufr-0.6.2 (05 May 2015) + + 05 May 2015; AstroFloyd <AstroFloyd@gmail.com> -libsufr-0.4.1.ebuild, + -libsufr-0.5.2.ebuild, +libsufr-0.6.2.ebuild, +libsufr-0.6.3.ebuild: + Version bump + *libsufr-0.5.4 (27 Oct 2013) 27 Oct 2013; AstroFloyd <AstroFloyd@gmail.com> -libsufr-0.3.3.ebuild, @@ -34,6 +54,5 @@ 09 Nov 2011; Kacper Kowalik <xarthisius@gentoo.org> +libsufr-0.3.0.ebuild, +files/libsufr-0.3.0-multilib.patch, +metadata.xml: - Initial import, ebuild written by Marc van der Sluys <sluys@astro.ru.nl>, + Initial import, ebuild written by AstroFloyd <AstroFloyd@gmail.com>, edited by me - diff --git a/sci-libs/libsufr/Manifest b/sci-libs/libsufr/Manifest index 01910bbba..8d02301fc 100644 --- a/sci-libs/libsufr/Manifest +++ b/sci-libs/libsufr/Manifest @@ -1,3 +1,3 @@ -DIST libsufr-0.4.1.tar.gz 52219 SHA256 8826f7bc2f3db8c6fea37896211bbbf933ba8cc3f06465ce42266a9193891ec1 SHA512 d51bcc26957bb8c11845d16d1ace3753eb9a8e42367ddc5c4d35dc3208f03c016e7a46700d462a8705a9ba4ef821bc240852b2fad95605f2abd3dd59d06f08cc WHIRLPOOL 8886b3983516a431cd1d14dbe884a67d1592b1f5f3c2d8255cac5ad716ba42d0b0d8cc144353ffd8b6c180c0c40fddf60f9218b7da65c1ebdedd368f1f3ee9bb -DIST libsufr-0.5.2.tar.gz 56965 SHA256 b4ff25038b7ec0378c2db83150547603a06be23ef3173f66e76fbff5a62f1f6c SHA512 ddb559243c56dbe165a65a26d2278f3b70ebd740eb3516e712d64ce59bde42f7cabc7daacd4caa742bcdfd402c51f8e07f41daf3dba352787887b0698f71f138 WHIRLPOOL 17298acdc964708537f57188d9fc7bc887ec12a2857a1b4f4b2ca47f232b87f6a1f50603dbc86bd6a7d938eb8e8ef02f26d1750eb18fd444062161eadc22630f DIST libsufr-0.5.4.tar.gz 59469 SHA256 d7c98a0cf2ce184751fba9cde4583811a3593f5ae34a8d32715ed8e32971f14b SHA512 3711af7db10398e8dcb92982d4fedcc866fa5257f8a3b108ad1a5caef174fa4c0c9ed0b4e3e3b620d0e0d5f4cdaa56691c9657e57980c27a7aef00e45fcdd773 WHIRLPOOL 9f93a84653855fe7b52807bc0c482bfb6e9aeb82f4c8e4343a5f313b93ea279e6e3f23227a59821e37f140fc37cd581d7472b79389fa096f020bf334ca23210f +DIST libsufr-0.6.3.tar.gz 65861 SHA256 d1ec6564469cce4ea0f66e2468419d3e360805440a5f6fc43a439b486ff33bd6 SHA512 e7ba094a5891d7f08dd9bfe4670d45378973bbabae289465c54436886fa1e2e66da8106a3abad86b33f494970bf2afe3727ef6f56f7177f7c5ca536ff3e55ecf WHIRLPOOL 646aabd62a2f628486e477d16093a6c87de134a87d17f13bdf417628e90f7cd706a9b8b631aad24cbad3ae7c3e2e8026ff6bb729b85c718605ae2b2dd90ab6fb +DIST libsufr-0.6.4.tar.gz 66073 SHA256 e16b8579eb11d5cbf32bf82942a7915febc02117e36c9ce79f150df60a827783 SHA512 cf3f610d418664265e854a8a2def0fce11918748231eec025a43c72a172481a8d1336b30c204ef43ea1e0cf44353f2e0083992d6417a94ccd9445dd184b24fc7 WHIRLPOOL 4e638f3b0a1bff88389439d85600d751766f26acc14afe942cc9b39842cce4a3b503f73c237baea1a5563fbd1a1cdff6f15138d844ee64fb34800674a5b81ffb diff --git a/sci-libs/libsufr/files/libsufr-0.3.0-multilib.patch b/sci-libs/libsufr/files/libsufr-0.3.0-multilib.patch deleted file mode 100644 index 142766258..000000000 --- a/sci-libs/libsufr/files/libsufr-0.3.0-multilib.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -46,7 +46,7 @@ - set( MODULE_DIRECTORY "${CMAKE_SOURCE_DIR}/usr/include/libSUFR" ) - endif( COMPILER_SPECIFIC_LIBS ) - --set( LIBRARY_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/usr/lib" ) -+set( LIBRARY_OUTPUT_PATH "${CMAKE_SOURCE_DIR}/usr/lib${LIB_SUFFIX}" ) - - - # Set source files: diff --git a/sci-libs/libsufr/libsufr-0.4.1.ebuild b/sci-libs/libsufr/libsufr-0.6.3.ebuild index 7e4456fe1..ac4e76a61 100644 --- a/sci-libs/libsufr/libsufr-0.4.1.ebuild +++ b/sci-libs/libsufr/libsufr-0.6.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-libs/libsufr/libsufr-0.5.2.ebuild b/sci-libs/libsufr/libsufr-0.6.4.ebuild index 7e4456fe1..ac4e76a61 100644 --- a/sci-libs/libsufr/libsufr-0.5.2.ebuild +++ b/sci-libs/libsufr/libsufr-0.6.4.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-libs/libsufr/metadata.xml b/sci-libs/libsufr/metadata.xml index ec7105731..009574ec1 100644 --- a/sci-libs/libsufr/metadata.xml +++ b/sci-libs/libsufr/metadata.xml @@ -1,13 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>AstroFloyd@gmail.com</email> - <name>AstroFloyd</name> - </maintainer> - <maintainer> - <email>xarthisius@gentoo.org</email> - <name>Kacper Kowalik</name> - </maintainer> + <herd>sci</herd> + <maintainer> + <email>AstroFloyd@gmail.com</email> + <name>AstroFloyd</name> + </maintainer> + <maintainer> + <email>xarthisius@gentoo.org</email> + <name>Kacper Kowalik</name> + </maintainer> + <upstream> + <remote-id type="sourceforge">libsufr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/libxc/ChangeLog b/sci-libs/libxc/ChangeLog index 3a0421dc7..5246c8b84 100644 --- a/sci-libs/libxc/ChangeLog +++ b/sci-libs/libxc/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-libs/libxc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*libxc-2.2.2 (22 Apr 2015) +*libxc-2.1.2 (22 Apr 2015) + + 22 Apr 2015; Honza Macháček <Hloupy.Honza@centrum.cz> -libxc-2.1.1.ebuild, + +libxc-2.1.2.ebuild, -libxc-2.2.1.ebuild, +libxc-2.2.2.ebuild: + Version bump to sci-libs/libxc-2.1.2 and 2.2.2 pair + *libxc-2.2.1 (10 Dec 2014) *libxc-2.1.1 (10 Dec 2014) diff --git a/sci-libs/libxc/Manifest b/sci-libs/libxc/Manifest index 899e4f577..ae4b317bb 100644 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@ -1,2 +1,2 @@ -DIST libxc-2.1.1.tar.gz 723464 SHA256 99c5435f6cabfa5ad2de55d631451532235b7e32d9505ad4c179b840afd584bf SHA512 2c4f327f1ed08344546bdf8ed4d32fb6462d11acf85f167783a859cae43554f776f98bd682fc58e54ba6f3c66d82eeb1ec78649c5503b2c683f7b0ca9f461e4b WHIRLPOOL bc1247231289408c894fab379648f8e8e0032722716095cf0891af62a22d21b9f1abc091bd086d15a7bb7b249b82f41225e05bf9a9ccd6dbc19e9a2c0c6ab66b -DIST libxc-2.2.1.tar.gz 707236 SHA256 ade61c1fa4ed238edd56408fd8ee6c2e305a3d5753e160017e2a71817c98fd00 SHA512 3457013786d35ae7dc837126a273714fbf08ed8b2386b7e26312d2c795332dbd598e4aa0cdb4ceb80acf26e38a86ab3caa7b3198d6ac8a878523d90f02843d05 WHIRLPOOL 4916a0491460a1c34dea99e2034ff3721d7102a1107480a8f12b569dcd57dcae8a0b8553a37a307cea7d5b556a6214ca3c140bf400ef655c6d0e6be0852dc151 +DIST libxc-2.1.2.tar.gz 724139 SHA256 6c866168fa6245e6777cec8a1da257975e2e4cf410681416e248fbff2b03e55d SHA512 9f5f02686d2d9c320a27c013ca95705a71b7c59a8d8974c0492f8fe09d87c9261600c891fc56b2b1bdfc30079769f488f5924b8b742a61275822b35a858f85ac WHIRLPOOL 05300948f389846934f20d9a51c3697305326584606f1ac1cc0415f26e5d9a92d387dfb892f8313c6b689b24f58476b95fa717bb7fd3db759444ab4e993862e4 +DIST libxc-2.2.2.tar.gz 707711 SHA256 6ca1d0bb5fdc341d59960707bc67f23ad54de8a6018e19e02eee2b16ea7cc642 SHA512 8ba8cce5d2c1ad16c176faf2afaea511955dbd88fab0e87975429b6e2bf787d389977cda3481d7ea8df89676de40ecdced7b0e465cdb065351008b8701cab8ad WHIRLPOOL be0061560372fba7dcce6b47c367c6c221b00bc3347412d2b8e7564cb8f4ec98b7f8a182ae954625087687a7adb1152ce7d817c885a0ba2401e17dfa27781e93 diff --git a/sci-libs/libxc/libxc-2.1.1.ebuild b/sci-libs/libxc/libxc-2.1.2.ebuild index 60a65494d..e6a7572ec 100644 --- a/sci-libs/libxc/libxc-2.1.1.ebuild +++ b/sci-libs/libxc/libxc-2.1.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-libs/libxc/libxc-2.2.1.ebuild b/sci-libs/libxc/libxc-2.2.2.ebuild index 60a65494d..e6a7572ec 100644 --- a/sci-libs/libxc/libxc-2.2.1.ebuild +++ b/sci-libs/libxc/libxc-2.2.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-libs/lwpr/ChangeLog b/sci-libs/lwpr/ChangeLog index bc8987cf1..48ee04760 100644 --- a/sci-libs/lwpr/ChangeLog +++ b/sci-libs/lwpr/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/lwpr -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/lwpr: Updating remote-id in metadata.xml + *lwpr-1.2.5 (25 Jun 2013) 25 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +lwpr-1.2.5.ebuild, diff --git a/sci-libs/lwpr/metadata.xml b/sci-libs/lwpr/metadata.xml index b9d1fd6a7..a8ec3ab22 100644 --- a/sci-libs/lwpr/metadata.xml +++ b/sci-libs/lwpr/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription> + <herd>sci-mathematics</herd> + <longdescription> Locally Weighted Projection Regression (LWPR) is a recent algorithm that achieves nonlinear function approximation in high dimensional spaces with redundant and irrelevant input dimensions. At its core, it uses @@ -11,7 +11,10 @@ weighted variant of Partial Least Squares (PLS) is employed for doing the dimensionality reduction. </longdescription> -<use> - <flag name='octave'>Add <pkg>sci-mathematics/octave</pkg> support</flag> -</use> + <use> + <flag name="octave">Add <pkg>sci-mathematics/octave</pkg> support</flag> + </use> + <upstream> + <remote-id type="sourceforge">lwpr</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/matc/ChangeLog b/sci-libs/matc/ChangeLog index 37a972540..ea7705062 100644 --- a/sci-libs/matc/ChangeLog +++ b/sci-libs/matc/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-libs/matc -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*matc-8.0 (31 May 2015) + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> +matc-8.0.ebuild: + Version bump + + 31 May 2015; Marius Brehler <marbre@linux.sungazer.de> matc-9999.ebuild: + Source moved from sf.net to github; Fix LICENSE + 03 Dec 2013; Justin Lecher <jlec@gentoo.org> -matc-5.4.1.ebuild, +matc-6.0_p4651.ebuild, matc-9999.ebuild, -files/matc-5.4.1-shared.patch, +files/matc-6.0_p4651-shared.patch: @@ -14,4 +22,3 @@ +metadata.xml: Bump EAPI; fix license; fix DESCRIPTION; drop keywords from live ebuild; use correct phase functions; simplify configure; build shared libraries - diff --git a/sci-libs/matc/Manifest b/sci-libs/matc/Manifest index f4abaedf9..90b95448c 100644 --- a/sci-libs/matc/Manifest +++ b/sci-libs/matc/Manifest @@ -1,2 +1,3 @@ -DIST MATCManual.pdf 82222 SHA256 a32d6201021d988242e7ab193c865c1aef3e51b7c7a509978edd9360dcef7c52 SHA512 7703f05a9d23b683e9a7030fbbad0b5438de5dbfb22479a2c070e02830ef233697ea2d1f67efbdd958ada537388f1b3449dd2e73a2bd86c66338636cef0c4ea1 WHIRLPOOL 72aca6508a12cc4370e996caf60b61740ecd4aa7eab460d601cfcf5d6a0ee11a3556ef7637c85a6a747cc3d6529c5ac514f95510813720dd093054af48346893 -DIST matc-6.0_p4651.tar.gz 203543 SHA256 e49d5599231ee68f4b0e46a75d4cb2c476eab5608b881b7741aed9b125f92f8d SHA512 1675c880929031caaceb67091903ae306db30810847886fb1f56cb4c0f5e05ee4a9a11eaed8f29d3fbca4bf222268fe62ffddabc62a3b08322c362dd9ce566e0 WHIRLPOOL 73de50b2ee9cd9183b503eedc51a3cfa06eeb9e99fa3929ee610a5fc0be9a3ebb9c963553986f00e9ef9ce1f4d3ce5a17c6be9205d0eff080c4ab7240cfc0816 +DIST MATCManual.pdf 103341 SHA256 a49945c6965cdb28dfaa98f36d46813a56c7f792c4b5634d02e6afc0ae361e9c SHA512 0f9efea84ed2f6848c431b0a9647c8d300b3bcf06a83c4f6bc7cd3640ec5fc003516b442f90b022a246b3cac54f2cdac1118283e929d2c9547f5469f2b9912cb WHIRLPOOL 27eedcf4b62cedacaaa8821d87e2d2ee8a0623cf7e48f99c3310e292d0ee5a3f412546e8cbfcce34a274cf318be2b86c96af6053ff2add24c7c8569a75f670fd +DIST matc-6.0_p4651.tar.gz 203543 SHA256 b174036ebafa2d0bff51db283831e4f9a165e6fa9798224dc3658dc2dc5e99b1 SHA512 ada3e4a1d02a0125ee5ccb7a791975d3f728d89ff21fac6461060e4458b086edb34adef058f3aa84f924f28b7d652a539d63f61d9bfce208d0b8540b812ef7be WHIRLPOOL b47b025bff1fbb88ccbabb0c42a8656c905f09ce4345c12cd83e8effb6b9c12f5cfece69741c2655fc3c60dd4e652a9867c14989d9043ae23b338815f800927a +DIST matc-8.0.tar.gz 45051199 SHA256 ac7cb29e1dba205113ed9705a5852ee11117252495fa2b125adecd2b057c8a8f SHA512 bc34c6dbbdb2c24f2110d377e02c4515cb4886de36b30bc3caf79c9b954e5b7ba81cabedaa35fad1802287c396ab88ef074505efc904411061f7c98c9bea3497 WHIRLPOOL 99004464347f58fd388e52eb7457f2739efc3ba19fd69c328c49c2998a6131c46682417c176a39239fdb92574a4df5244b8d657e584d644fdb7c550279b8e631 diff --git a/sci-libs/matc/matc-8.0.ebuild b/sci-libs/matc/matc-8.0.ebuild new file mode 100644 index 000000000..565962490 --- /dev/null +++ b/sci-libs/matc/matc-8.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true + +inherit autotools-utils + +DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library" +HOMEPAGE="http://www.csc.fi/english/pages/elmer" +SRC_URI=" + https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz + doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )" + +LICENSE="GPL-2 LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc debug static-libs" + +RDEPEND=" + sys-libs/ncurses + sys-libs/readline:0" +DEPEND="${RDEPEND}" + +S="${WORKDIR}/elmerfem-release-${PV}/${PN}" + +#PATCHES=( "${FILESDIR}"/${P}-shared.patch ) + +src_configure() { + local myeconfargs=( + --enable-shared + $(use_with debug) + ) + autotools-utils_src_configure +} + +src_install() { + use doc && DOCS=( "${DISTDIR}"/MATCManual.pdf ) + autotools-utils_src_install +} diff --git a/sci-libs/matc/matc-9999.ebuild b/sci-libs/matc/matc-9999.ebuild index b787716a9..2b8aa00c6 100644 --- a/sci-libs/matc/matc-9999.ebuild +++ b/sci-libs/matc/matc-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=true -inherit autotools-utils subversion +inherit autotools-utils git-r3 ELMER_ROOT="elmerfem" MY_PN=${PN/elmer-/} @@ -14,27 +14,21 @@ MY_PN=${PN/elmer-/} DESCRIPTION="Finite element programs, libraries, and visualization tools - math C library" HOMEPAGE="http://www.csc.fi/english/pages/elmer" SRC_URI="doc? ( http://www.nic.funet.fi/pub/sci/physics/elmer/doc/MATCManual.pdf )" -ESVN_REPO_URI="https://elmerfem.svn.sourceforge.net/svnroot/elmerfem/trunk/${MY_PN}" -ESVN_PROJECT="${MY_PN}" +EGIT_REPO_URI="https://github.com/ElmerCSC/elmerfem.git git://github.com/ElmerCSC/elmerfem.git" -LICENSE="GPL-2" +LICENSE="GPL-2 LGPL-2.1" SLOT="0" KEYWORDS="" IUSE="doc debug static-libs" RDEPEND=" sys-libs/ncurses - sys-libs/readline" + sys-libs/readline:0" DEPEND="${RDEPEND}" -S="${WORKDIR}"/${PN} +S="${WORKDIR}/${P}/${PN}" -PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch ) - -src_prepare() { - subversion_src_prepare - autotools-utils_src_prepare -} +#PATCHES=( "${FILESDIR}"/${PN}-6.0_p4651-shared.patch ) src_configure() { local myeconfargs=( diff --git a/sci-libs/matio/ChangeLog b/sci-libs/matio/ChangeLog deleted file mode 100644 index bed9be26c..000000000 --- a/sci-libs/matio/ChangeLog +++ /dev/null @@ -1,43 +0,0 @@ -# ChangeLog for sci-libs/matio -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> matio-1.3.4.ebuild: - Move to EAPI=5, cleanup the ebuild - - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> matio-1.3.4.ebuild: - Added fortran-2.eclass support - -*matio-1.3.4 (10 Aug 2010) - - 10 Aug 2010; Sébastien Fabbro <bicatali@gentoo.org> -matio-1.3.3.ebuild, - -files/matio-1.3.3-makefile.patch, +matio-1.3.4.ebuild, - +files/matio-1.3.4-autotools.patch: - Version bump. Ebuild modernisation. Disabling doc generation (bug #330237) - -*matio-1.3.3 (22 Jan 2009) - - 22 Jan 2009; Sébastien Fabbro <bicatali@gentoo.org> - +sci-libs/matio/files/matio-1.3.3-makefile.patch, - sci-astronomy/scamp/metadata.xml, sci-libs/matio/metadata.xml, - sci-mathematics/gap/metadata.xml: - Version bump - -*matio-1.3.1 (20 Sep 2006) - - 20 Sep 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +matio-1.3.1.ebuild, -matio-1.3.0.ebuild, -files/matio-1.1.4.patch: - version bump, now at sourceforge - -*matio-1.3.0 (28 August 2006) - - 28 August 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +matio-1.3.0.ebuild, -matio-1.1.4.ebuild: - version bump - -*matio-1.1.4 (16 June 2006) - - 16 June 2006; Andrey Grozin <A.G.Grozin@inp.nsk.su> - +metadata.xml, +matio-1.1.4.ebuild, +files/matio-1.1.4.patch: - Initial import. diff --git a/sci-libs/matio/Manifest b/sci-libs/matio/Manifest deleted file mode 100644 index 7e3a6e6dd..000000000 --- a/sci-libs/matio/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST matio-1.3.4.tar.gz 450343 SHA256 7261880b18a661e5d206b4e479d4334b47549f093130df42f7204fd05dfe0bc5 diff --git a/sci-libs/matio/files/matio-1.3.4-autotools.patch b/sci-libs/matio/files/matio-1.3.4-autotools.patch deleted file mode 100644 index c9e6a0412..000000000 --- a/sci-libs/matio/files/matio-1.3.4-autotools.patch +++ /dev/null @@ -1,29 +0,0 @@ ---- configure.ac.orig 2010-08-10 20:36:52.000000000 +0100 -+++ configure.ac 2010-08-10 20:39:03.000000000 +0100 -@@ -5,7 +5,7 @@ - AC_INIT([MATIO],[1.3.4],[cch@isl-inc.com],[]) - AC_CONFIG_SRCDIR([src/matio.h]) - AC_CONFIG_AUX_DIR(config) --AC_CONFIG_MACRO_DIR([m4]) -+ - dnl AM_INIT_AUTOMAKE([-no-undefined]) - AM_INIT_AUTOMAKE - AM_MAINTAINER_MODE ---- src/Makefile.am.orig 2010-08-10 20:31:41.000000000 +0100 -+++ src/Makefile.am 2010-08-10 20:34:44.000000000 +0100 -@@ -17,6 +17,7 @@ - lib_LTLIBRARIES = libmatio.la - libmatio_la_SOURCES = snprintf.c endian.c io.c $(ZLIB_SRC) read_data.c \ - mat5.c mat4.c mat.c -+libmatio_la_LIBADD = $(ZLIB_LIBS) - - if ENABLE_FORTRAN - AM_FCFLAGS = -I. -I$(top_builddir)/src/fortran -@@ -25,6 +26,7 @@ - noinst_HEADERS += fortran/create.f90 fortran/read_data.f90 \ - fortran/write_data.f90 fortran/write.f90 - libmatio_la_SOURCES += fortran/matio_internal.c fortran/matio.f90 -+$(top_builddir)/src/matio.mod: libmatio.la - endif - - dosubst = sed -e 's,[@]PACKAGE[@],$(PACKAGE),g' \ diff --git a/sci-libs/matio/matio-1.3.4.ebuild b/sci-libs/matio/matio-1.3.4.ebuild deleted file mode 100644 index 8d2b050d5..000000000 --- a/sci-libs/matio/matio-1.3.4.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -AUTOTOOLS_AUTORECONF=1 -inherit autotools-utils eutils fortran-2 - -DESCRIPTION="Library for reading and writing matlab files" -HOMEPAGE="http://sourceforge.net/projects/matio/" -SLOT="0" -LICENSE="LGPL-2.1" -KEYWORDS="~amd64 ~x86" -# disabling (until fix) doxygen doc generation -IUSE="examples fortran static-libs" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" -#DEPEND="doc? ( app-doc/doxygen virtual/latex-base )" -RDEPEND="" - -PATCHES=( "${FILESDIR}/${P}"-autotools.patch ) - -src_configure() { - local myeconfargs=( - --disable-test - #$(use_enable doc docs) - ) - autotools-utils_src_configure -} - -src_install() { - autotools-utils_src_install - #if use doc; then - # insinto /usr/share/doc/${PF} - # doins -r doxygen/html || die - #fi - if use examples; then - insinto /usr/share/doc/${PF}/examples - doins test/test* - insinto /usr/share/${PN} - doins share/test* - fi -} diff --git a/sci-libs/mkl/ChangeLog b/sci-libs/mkl/ChangeLog index 6d2a9a914..15a1473e2 100644 --- a/sci-libs/mkl/ChangeLog +++ b/sci-libs/mkl/ChangeLog @@ -10,7 +10,7 @@ *mkl-11.2.1.133 (02 Dec 2014) 02 Dec 2014; Justin Lecher <jlec@gentoo.org> +mkl-11.2.1.133.ebuild: - Version BUmp + Version Bump *mkl-11.2.0.090 (15 Sep 2014) diff --git a/sci-libs/msms/msms-1.5.6.ebuild b/sci-libs/msms/msms-1.5.6.ebuild index b9b7618fa..3a57f7d19 100644 --- a/sci-libs/msms/msms-1.5.6.ebuild +++ b/sci-libs/msms/msms-1.5.6.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-libs/nibabel/ChangeLog b/sci-libs/nibabel/ChangeLog index c31cec79e..237f97ecf 100644 --- a/sci-libs/nibabel/ChangeLog +++ b/sci-libs/nibabel/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-libs/nibabel -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 11 Jun 2015; Chymera <chymera@gentoo.org> nibabel-1.3.0.ebuild: + now downloading as tarball + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> nibabel-1.3.0.ebuild, nibabel-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 - diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest index e3f8516ac..0c4e51b19 100644 --- a/sci-libs/nibabel/Manifest +++ b/sci-libs/nibabel/Manifest @@ -1 +1 @@ -DIST 1.3.0.zip 2266889 SHA256 70f7bb33f7c49c94cd264001a89c2df8c455f21d8530e5fb0780e432259edc40 SHA512 31c524385ef68cd6a4693d739d8bcda6c73e48a66417d59fe3825bfacf512117346f610d3aeef1adc62bb95564f52e6a29a64f72de57c86e8e6205fff2c24522 WHIRLPOOL 65ec60d7726eb323522d2efbad4b12747a084fb6b8dd720338a42bc47c7a814217b9ed6fd0c09dfb5fb02188bf2827cd9287f4dea24db920c53c42173513127f +DIST nibabel-1.3.0.tar.gz 2184060 SHA256 21488202a655eae76bb0c1170271c894bbf08bfae8246e79c71706233d4964b1 SHA512 6970a1345ce9c4ead484a15696bdcd918a292c354d0d5799359f1260a26e0b49a32507511ad5a9446a50c1d374113863e4d717c9b7bd16feecbe49d4f3da6119 WHIRLPOOL d117160713d9e2557cc957ffecc29a339f6ef14c0e60d962768cd4c8b2bbd4ef6a498b3f96f084256a4638a8264b6c8cd0189979329168d2d47c1ea119581541 diff --git a/sci-libs/nibabel/nibabel-1.3.0.ebuild b/sci-libs/nibabel/nibabel-1.3.0.ebuild index c3d5d279e..886434fba 100644 --- a/sci-libs/nibabel/nibabel-1.3.0.ebuild +++ b/sci-libs/nibabel/nibabel-1.3.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,7 +10,7 @@ inherit distutils-r1 DESCRIPTION="Access a cacophony of neuro-imaging file formats" HOMEPAGE="http://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.zip" +SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64 ~x86" diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml index 05f4d5beb..2468f9eb6 100644 --- a/sci-libs/nipy/metadata.xml +++ b/sci-libs/nipy/metadata.xml @@ -9,4 +9,7 @@ <longdescription lang="en"> NIPY is a python project for analysis of structural and functional neuroimaging data. </longdescription> + <upstream> + <remote-id type="pypi">nipy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/nipype/ChangeLog b/sci-libs/nipype/ChangeLog index e4f160f49..09e140793 100644 --- a/sci-libs/nipype/ChangeLog +++ b/sci-libs/nipype/ChangeLog @@ -1,8 +1,10 @@ # ChangeLog for sci-libs/nipype -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Horea Christian <h.chr@mail.ru> nipype-9999.ebuild: + no longer depending on outdated version + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> nipype-9999.ebuild, metadata.xml: Switch from git-2 to git-r3 - diff --git a/sci-libs/nipype/nipype-9999.ebuild b/sci-libs/nipype/nipype-9999.ebuild index 75495c857..018340f60 100644 --- a/sci-libs/nipype/nipype-9999.ebuild +++ b/sci-libs/nipype/nipype-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -6,7 +6,7 @@ EAPI=5 # pyamg missing py3 support # PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 @@ -23,7 +23,7 @@ IUSE="" DEPEND=" dev-python/setuptools[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}]" + sci-libs/nibabel[${PYTHON_USEDEP}]" RDEPEND=" sci-libs/scipy[${PYTHON_USEDEP}] dev-python/traits[${PYTHON_USEDEP}] diff --git a/sci-libs/o2scl/ChangeLog b/sci-libs/o2scl/ChangeLog index 37af49301..e0817cd7a 100644 --- a/sci-libs/o2scl/ChangeLog +++ b/sci-libs/o2scl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/o2scl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/o2scl: Updating remote-id in metadata.xml + *o2scl-0.915 (02 Jun 2014) 02 Jun 2014; Sébastien Fabbro <bicatali@gentoo.org> +o2scl-0.915.ebuild, diff --git a/sci-libs/o2scl/metadata.xml b/sci-libs/o2scl/metadata.xml index 6f32b1540..dd14258df 100644 --- a/sci-libs/o2scl/metadata.xml +++ b/sci-libs/o2scl/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<longdescription lang="en"> + <herd>sci</herd> + <longdescription lang="en"> O2scl is a C++ class library for object-oriented numerical programming. It includes classes based on numerical routines from GSL and CERNLIB and two sub-libraries: thermodynamics of ideal and nearly-ideal particles with quantum statistics and e quations of state for finite density relevant for neutron stars. </longdescription> + <upstream> + <remote-id type="sourceforge">o2scl</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/oasa/oasa-0.13.1.ebuild b/sci-libs/oasa/oasa-0.13.1.ebuild index 56795d388..e4b0ea44f 100644 --- a/sci-libs/oasa/oasa-0.13.1.ebuild +++ b/sci-libs/oasa/oasa-0.13.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-libs/omalloc/ChangeLog b/sci-libs/omalloc/ChangeLog index 66d538e57..1c6f721a9 100644 --- a/sci-libs/omalloc/ChangeLog +++ b/sci-libs/omalloc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/omalloc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> omalloc-0.9.6.ebuild: + Bump to EAPI=5 + 13 Jul 2010; Kacper Kowalik <xarthisius@gentoo.org> omalloc-0.9.6.ebuild, +files/omalloc-0.9.6-gentoo.diff, files/parallel-build.patch, metadata.xml: @@ -13,4 +16,3 @@ +files/parallel-build.patch, +metadata.xml: new package: sci-libs/omalloc new dependency of sci-mathematics/singular - diff --git a/sci-libs/omalloc/omalloc-0.9.6.ebuild b/sci-libs/omalloc/omalloc-0.9.6.ebuild index 70770e2a1..53c4e2f1c 100644 --- a/sci-libs/omalloc/omalloc-0.9.6.ebuild +++ b/sci-libs/omalloc/omalloc-0.9.6.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 inherit eutils toolchain-funcs versionator @@ -40,10 +40,10 @@ src_configure() { src_test () { if use debug; then - emake check || die + emake check fi } src_install () { - emake DESTDIR="${D}" install || die + emake DESTDIR="${D}" install } diff --git a/sci-libs/openblas/ChangeLog b/sci-libs/openblas/ChangeLog index fee083536..e783b9d38 100644 --- a/sci-libs/openblas/ChangeLog +++ b/sci-libs/openblas/ChangeLog @@ -1,7 +1,22 @@ # ChangeLog for sci-libs/openblas -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> openblas-0.2.11.ebuild, + openblas-0.2.8.ebuild, openblas-9999.ebuild: + sci-libs/openblas: Add missing eclass + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/openblas: Add github to remote-id in metadata.xml + + 02 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> openblas-9999.ebuild: + Fix Bug 528974 + +*openblas-0.2.14 (27 Mar 2015) + + 27 Mar 2015; Denis Dupeyron <calchan@gentoo.org> +openblas-0.2.14.ebuild: + Version bump. + 20 Oct 2014; Mark Wright <gienah@gentoo.org> openblas-9999.ebuild: Thanks to kiwifb for reporting https://github.com/gentoo-science/sci/issues/280 - Fix openblas: discrepancy diff --git a/sci-libs/openblas/Manifest b/sci-libs/openblas/Manifest index 9d1272898..c32e9aeaf 100644 --- a/sci-libs/openblas/Manifest +++ b/sci-libs/openblas/Manifest @@ -1,4 +1,5 @@ DIST openblas-0.2.11-gentoo.patch 246353 SHA256 68c13526f37bf510f02961eb3a7918feb98f6bb10a0d888b8575b9146fd56c09 SHA512 4d8fcec9e44f873c31214d48492a171dd00dc18524a7ab51e51fa27c038b62bfd07be281b5af899943e10fb45c6d0b5b704ba3fa93c6bec74aca0a3a6c0f48ab WHIRLPOOL a4b1078f6ba06a6530a9267d950df8824abccd41aa432ce6568641329f828cc1abea7324f588b0b3d1d3339c36b79ea7147d64f0c8b27d12f87bf8be2a97e92a DIST openblas-0.2.11.tar.gz 9765198 SHA256 babe5898c05da8a95249c1b038f7fbe14a95e35fee75358d649009f93ef444ed SHA512 4b7928613356848628c0230dc5990d269a3899beb700617cd385529aa5c26f0d0063081a25cbd8ab924d41b5f8a079385e12da3e156d784406290c5c0c40a0e2 WHIRLPOOL 66d0895c76b02625354db157319ee12be62928d2f9ea4241e898e227f466fcbed496e934f413a570c3a105e7d75973b2af9cbabc8a9c78922f240f6bddf36160 DIST openblas-0.2.12.tar.gz 9852709 SHA256 0f1727700e3991aea6d4dab11daa1254603b19a73df0a2eb474f6db7bc6d090d SHA512 ab00eecef89fc40d7b298958b261d76fcb1d8f26970d24d663bf27f1c6b258d952da6bc2565d905e9267cd97e5450025f2a80a8bffabd202e99f35d40c1e412d WHIRLPOOL 253617f204564b480ac96e53e3edfee4044537c26e98bafee47226dc619852910dbc548a44cdf9c78aa044e05930c295b127accd816778d65987bc9d11a7f2f4 +DIST openblas-0.2.14.tar.gz 9862952 SHA256 aba5088534719cefd77e4155c281c56a3accd3eea218574c2c3d236952bb632b SHA512 5028c0cae1eea168593d951c053d2c3692ea4bf34257b2d6cd533d43dd98d1e4ab982f56c57232e53dcc358a2f8e1e51e15a746235ff6eb64d427a97b1449b60 WHIRLPOOL 2fe8a6afee19327deb962dd9f270b2c3dbf0ee8c92d59050fec4f0d4bacdf1d97801f28a1127804e8464c3c19d7e40b293c3b4d5b5b7e43f0061346c03909e64 DIST openblas-0.2.8.tar.gz 9471072 SHA256 048986f4e0a8d480c5e6d439915738f3298f2629d6a399a1ddb16e1629b07901 SHA512 590ffc77377e3d40f91bd91156554140da0f3eee334098cfdbd53d427173cd4374eca0f8f9a167054ea88bdcc1b3a685a6ecdc5fd70f3df0ad267d569049db79 WHIRLPOOL 550fab60c2dc8e6e94b7d5d6c5e05b19c297b63495521667e5abde087713fcc678f4be31641eaf5354a6dae1f8229cade361c35f70309f947c02fb8c5fe49f59 diff --git a/sci-libs/openblas/metadata.xml b/sci-libs/openblas/metadata.xml index 32441d18a..6ef9b5417 100644 --- a/sci-libs/openblas/metadata.xml +++ b/sci-libs/openblas/metadata.xml @@ -10,4 +10,7 @@ <flag name="int64">Build the 64 bits integer library</flag> <flag name="dynamic">Build dynamic architecture detection at run time (for multi targets)</flag> </use> + <upstream> + <remote-id type="github">xianyi/OpenBLAS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/openblas/openblas-0.2.11.ebuild b/sci-libs/openblas/openblas-0.2.11.ebuild index 2381753b7..c69932e42 120000..100644 --- a/sci-libs/openblas/openblas-0.2.11.ebuild +++ b/sci-libs/openblas/openblas-0.2.11.ebuild @@ -1 +1,227 @@ -openblas-9999.ebuild
\ No newline at end of file +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +EBASE_PROFNAME="openblas" +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 + +SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" +if [[ ${PV} == "9999" ]] ; then + EGIT_REPO_URI="https://github.com/xianyi/OpenBLAS.git" + EGIT_BRANCH="develop" + inherit git-r3 + KEYWORDS="" +else + SRC_URI+=" http://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos ~ppc-macos ~x64-macos" +fi + +DESCRIPTION="Optimized BLAS library based on GotoBLAS2" +HOMEPAGE="http://xianyi.github.com/OpenBLAS/" +LICENSE="BSD" +SLOT="0" +IUSE="dynamic int64 openmp static-libs threads" + +RDEPEND="" +DEPEND="${RDEPEND} + virtual/pkgconfig" +PDEPEND=" + >=virtual/blas-2.1-r2[int64?] + >=virtual/cblas-2.0-r1[int64?]" + +MULTILIB_WRAPPED_HEADERS=( + /usr/include/openblas/cblas.h + /usr/include/openblas/f77blas.h + /usr/include/openblas/openblas_config.h +) + +get_openblas_flags() { + local openblas_flags="" + use dynamic && \ + openblas_flags+=" DYNAMIC_ARCH=1 TARGET=GENERIC NUM_THREADS=64 NO_AFFINITY=1" + $(fortran-int64_is_int64_build) && \ + openblas_flags+=" INTERFACE64=1" + # choose posix threads over openmp when the two are set + # yet to see the need of having the two profiles simultaneously + if use threads; then + openblas_flags+=" USE_THREAD=1 USE_OPENMP=0" + elif use openmp; then + openblas_flags+=" USE_THREAD=0 USE_OPENMP=1" + fi + local profname=$(fortran-int64_get_profname) + local libname="${profname//-/_}" + local underscoresuffix="${libname#${PN}}" + if [[ "${underscoresuffix}" != "_" ]]; then + local libnamesuffix="${underscoresuffix#_}" + openblas_flags+=" LIBNAMESUFFIX=${libnamesuffix}" + fi + echo "${openblas_flags}" +} + +get_openblas_abi_cflags() { + local openblas_abi_cflags="" + if [[ "${ABI}" == "x86" ]]; then + openblas_abi_cflags="-DOPENBLAS_ARCH_X86=1 -DOPENBLAS___32BIT__=1" + else + openblas_abi_cflags="-DOPENBLAS_ARCH_X86_64=1 -DOPENBLAS___64BIT__=1" + fi + $(fortran-int64_is_int64_build) && \ + openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT" + echo "${openblas_abi_cflags}" +} + +src_unpack() { + if [[ ${PV} == "9999" ]] ; then + git-r3_src_unpack + else + default + if [[ ${PV} != "9999" ]] ; then + find "${WORKDIR}" -maxdepth 1 -type d -name \*OpenBLAS\* && \ + mv "${WORKDIR}"/*OpenBLAS* "${S}" + fi + fi +} + +src_prepare() { + local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) ) + epatch "${DISTDIR}/${PN}-0.2.11-gentoo.patch" + if [[ ${PV} == "0.2.11" ]] ; then + epatch "${FILESDIR}/${PN}-0.2.11-cpuid_x86.patch" + fi + # lapack and lapacke are not modified from upstream lapack + sed \ + -e "s:^#\s*\(NO_LAPACK\)\s*=.*:\1=1:" \ + -e "s:^#\s*\(NO_LAPACKE\)\s*=.*:\1=1:" \ + -i Makefile.rule || die + multibuild_copy_sources +} + +src_configure() { + local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) ) + my_configure() { + local openblas_abi_cflags="$(get_openblas_abi_cflags)" + local internal_openblas_abi_cflags="${openblas_abi_cflags//OPENBLAS_}" + sed \ + -e "s:^#\s*\(CC\)\s*=.*:\1=$(tc-getCC) $(get_abi_CFLAGS):" \ + -e "s:^#\s*\(FC\)\s*=.*:\1=$(tc-getFC) $(get_abi_CFLAGS):" \ + -e "s:^#\s*\(COMMON_OPT\)\s*=.*:\1=${CFLAGS} ${internal_openblas_abi_cflags}:" \ + -i Makefile.rule || die + } + multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_configure +} + +src_compile() { + local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) ) + # openblas already does multi-jobs + MAKEOPTS+=" -j1" + my_src_compile () { + local openblas_flags=$(get_openblas_flags) + local profname=$(fortran-int64_get_profname) + local libname="${profname//-/_}" + einfo "Compiling profile ${profname}" + # cflags already defined twice + unset CFLAGS + emake clean + emake libs shared ${openblas_flags} + mkdir -p libs && mv libopenblas* libs/ + # avoid pic when compiling static libraries, so re-compiling + if use static-libs; then + emake clean + emake libs ${openblas_flags} NO_SHARED=1 NEED_PIC= + mv libopenblas* libs/ + fi + # Fix Bug 524612 - [science overlay] sci-libs/openblas-0.2.11 - Assembler messages: + # ../kernel/x86_64/gemm_kernel_8x4_barcelona.S:451: Error: missing ')' + # The problem is applying this patch in src_prepare() causes build failures on + # assembler code as the assembler does not understand sizeof(float). So + # delay applying the patch until after building the libraries. + epatch "${FILESDIR}/${PN}-0.2.11-openblas_config_header_same_between_ABIs.patch" + rm -f config.h config_last.h + # Note: prints this spurious warning: make: Nothing to be done for 'config.h'. + emake config.h + cp config.h config_last.h || die + cat <<-EOF > ${profname}.pc + prefix=${EPREFIX}/usr + libdir=\${prefix}/$(get_libdir) + includedir=\${prefix}/include + Name: ${profname} + Description: ${DESCRIPTION} + Version: ${PV} + URL: ${HOMEPAGE} + Libs: -L\${libdir} -l${libname} + Libs.private: -lm + EOF + local openblas_abi_cflags=$(get_openblas_abi_cflags) + local openblas_abi_fflags=$(fortran-int64_get_fortran_int64_abi_fflags) + cat <<-EOF >> ${profname}.pc + Cflags: -I\${includedir}/${PN} ${openblas_abi_cflags} + Fflags=${openblas_abi_fflags} + EOF + mv libs/libopenblas* . || die + } + multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_src_compile +} + +src_test() { + local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) ) + my_src_test () { + local openblas_flags=$(get_openblas_flags) + emake tests ${openblas_flags} + } + multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_src_test +} + +src_install() { + local MULTIBUILD_VARIANTS=( $(fortran-int64_multilib_get_enabled_abis) ) + my_src_install() { + local openblas_flags=$(get_openblas_flags) + local profname=$(fortran-int64_get_profname) + local pcfile + for pcfile in *.pc; do + local profname=${pcfile%.pc} + # The file /usr/include/openblas/openblas_config.h is generated during the install. + # The sed on config_last.h removes the #define's OPENBLAS_USE64BITINT + # OPENBLASS__32BIT__ OPENBLASS__64BIT__ OPENBLAS__ARCH_X86 OPENBLAS__ARCH_X86_64 + # from /usr/include/openblas/openblas_config.h. We then specify it in Cflags in + # the /usr/lib64/pkg-config/openblas-int64-{threads,openmp}.pc file. + sed -e '/#define USE64BITINT/d' \ + -e '/#define ARCH_X86/d' \ + -e '/#define __\(32\|64\)BIT__/d' \ + -i config_last.h \ + || die "Could not ensure there is no definition of USE64BITINT in config_last.h" + emake install \ + PREFIX="${ED}"usr ${openblas_flags} \ + OPENBLAS_INCLUDE_DIR="${ED}"usr/include/${PN} \ + OPENBLAS_LIBRARY_DIR="${ED}"usr/$(get_libdir) + use static-libs || rm "${ED}"usr/$(get_libdir)/lib*.a + alternatives_for $(fortran-int64_get_blas_provider) ${profname} 0 \ + /usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_blas_provider).pc ${pcfile} + alternatives_for $(fortran-int64_get_cblas_provider) ${profname} 0 \ + /usr/$(get_libdir)/pkgconfig/$(fortran-int64_get_cblas_provider).pc ${pcfile} \ + /usr/include/cblas.h ${PN}/cblas.h + insinto /usr/$(get_libdir)/pkgconfig + doins ${pcfile} + done + + if [[ ${CHOST} == *-darwin* ]] ; then + cd "${ED}"/usr/$(get_libdir) + local d + for d in *.dylib ; do + ebegin "Correcting install_name of ${d}" + install_name_tool -id "${EPREFIX}/usr/$(get_libdir)/${d}" "${d}" + eend $? + done + fi + if [[ ${#MULTIBUILD_VARIANTS[@]} -gt 1 ]]; then + multilib_prepare_wrappers + multilib_check_headers + fi + } + multibuild_foreach_variant run_in_build_dir fortran-int64_multilib_multibuild_wrapper my_src_install + multilib_install_wrappers + + dodoc GotoBLAS_{01Readme,03FAQ,04FAQ,05LargePage,06WeirdPerformance}.txt + dodoc *md Changelog.txt +} diff --git a/sci-libs/openblas/openblas-0.2.14.ebuild b/sci-libs/openblas/openblas-0.2.14.ebuild new file mode 120000 index 000000000..2381753b7 --- /dev/null +++ b/sci-libs/openblas/openblas-0.2.14.ebuild @@ -0,0 +1 @@ +openblas-9999.ebuild
\ No newline at end of file diff --git a/sci-libs/openblas/openblas-0.2.8.ebuild b/sci-libs/openblas/openblas-0.2.8.ebuild index 96ca05b80..565215bb9 100644 --- a/sci-libs/openblas/openblas-0.2.8.ebuild +++ b/sci-libs/openblas/openblas-0.2.8.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 -inherit eutils toolchain-funcs alternatives-2 multilib fortran-2 +inherit eutils multilib toolchain-funcs alternatives-2 multilib fortran-2 DESCRIPTION="Optimized BLAS library based on GotoBLAS2" HOMEPAGE="http://xianyi.github.com/OpenBLAS/" diff --git a/sci-libs/openblas/openblas-9999.ebuild b/sci-libs/openblas/openblas-9999.ebuild index a532fe81f..c5166a35f 100644 --- a/sci-libs/openblas/openblas-9999.ebuild +++ b/sci-libs/openblas/openblas-9999.ebuild @@ -1,11 +1,11 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ EAPI=5 EBASE_PROFNAME="openblas" -inherit alternatives-2 eutils fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 +inherit alternatives-2 eutils multilib fortran-2 multibuild multilib-build toolchain-funcs fortran-int64 SRC_URI+="http://dev.gentoo.org/~gienah/distfiles/${PN}-0.2.11-gentoo.patch" if [[ ${PV} == "9999" ]] ; then @@ -48,7 +48,7 @@ get_openblas_flags() { if use threads; then openblas_flags+=" USE_THREAD=1 USE_OPENMP=0" elif use openmp; then - openblas_flags+=" USE_THREAD=0 USE_OPENMP=1" + openblas_flags+=" USE_OPENMP=1" fi local profname=$(fortran-int64_get_profname) local libname="${profname//-/_}" diff --git a/sci-libs/p4est/ChangeLog b/sci-libs/p4est/ChangeLog index 61500661e..42e91d06a 100644 --- a/sci-libs/p4est/ChangeLog +++ b/sci-libs/p4est/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/p4est -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> p4est-1.0.ebuild: + sci-libs/p4est: Add SLOT operators + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/p4est: Add github to remote-id in metadata.xml + 13 Oct 2014; Matthias Maier <tamiko@gentoo.org> p4est-1.0.ebuild: sci-libs/p4est: Fix build dependencies diff --git a/sci-libs/p4est/metadata.xml b/sci-libs/p4est/metadata.xml index c8a9acb72..85fc0a1a7 100644 --- a/sci-libs/p4est/metadata.xml +++ b/sci-libs/p4est/metadata.xml @@ -16,4 +16,7 @@ processor cores. <flag name="vtk-binary">Enable binary vtk output. If disabled vtk files will be written in ASCII text format.</flag> <flag name="romio">Build with support for the ROMIO MPI-IO component</flag> </use> + <upstream> + <remote-id type="github">cburstedde/libsc</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/p4est/p4est-1.0.ebuild b/sci-libs/p4est/p4est-1.0.ebuild index 4c6946d94..e753ed7e1 100644 --- a/sci-libs/p4est/p4est-1.0.ebuild +++ b/sci-libs/p4est/p4est-1.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -24,7 +24,7 @@ REQUIRED_USE="romio? ( mpi )" RDEPEND=" >=sci-libs/libsc-1.0[mpi,romio] - dev-lang/lua + dev-lang/lua:* sys-apps/util-linux virtual/blas virtual/lapack diff --git a/sci-libs/pagmo/pagmo-9999.ebuild b/sci-libs/pagmo/pagmo-9999.ebuild index d6e77d3c5..de9181d21 100644 --- a/sci-libs/pagmo/pagmo-9999.ebuild +++ b/sci-libs/pagmo/pagmo-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils git-r3 python-single-r1 diff --git a/sci-libs/pg2plplot/ChangeLog b/sci-libs/pg2plplot/ChangeLog index 45e2bb9f5..64756b86b 100644 --- a/sci-libs/pg2plplot/ChangeLog +++ b/sci-libs/pg2plplot/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/pg2plplot -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/pg2plplot: Updating remote-id in metadata.xml + *pg2plplot-0.3.1 (28 Apr 2014) 28 Apr 2014; Sébastien Fabbro <bicatali@gentoo.org> +pg2plplot-0.3.1.ebuild, diff --git a/sci-libs/pg2plplot/metadata.xml b/sci-libs/pg2plplot/metadata.xml index d843d11b1..e39c33fca 100644 --- a/sci-libs/pg2plplot/metadata.xml +++ b/sci-libs/pg2plplot/metadata.xml @@ -1,13 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>AstroFloyd@gmail.com</email> - <name>AstroFloyd</name> -</maintainer> -<longdescription> + <herd>sci</herd> + <maintainer> + <email>AstroFloyd@gmail.com</email> + <name>AstroFloyd</name> + </maintainer> + <longdescription> PG2PLplot is code intended to help the transition from Fortran code linked against PGPlot to linking it against PLplot. </longdescription> + <upstream> + <remote-id type="sourceforge">pg2plplot</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/pmx/pmx-9999.ebuild b/sci-libs/pmx/pmx-9999.ebuild index fe50df549..d1d965c81 100644 --- a/sci-libs/pmx/pmx-9999.ebuild +++ b/sci-libs/pmx/pmx-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils distutils-r1 git-r3 diff --git a/sci-libs/pydicom/ChangeLog b/sci-libs/pydicom/ChangeLog index dd3589ee2..9f5b12ac9 100644 --- a/sci-libs/pydicom/ChangeLog +++ b/sci-libs/pydicom/ChangeLog @@ -1,8 +1,34 @@ # ChangeLog for sci-libs/pydicom -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 04 May 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild, + pydicom-9999.ebuild: + updated homepage + + 06 Apr 2015; Horea Christian <h.chr@mail.ru> pydicom-9999.ebuild: + no keywords in live ebuilds + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild, + pydicom-9999.ebuild: + gentoo does not support python 2.6 and 3.2 + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-9999.ebuild: + new live ebuild supporting various python versions + +*pydicom-9999 (31 Mar 2015) + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> +pydicom-9999.ebuild: + new live ebuild + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild: + removed python 3 support (only inofficial: + https://dcmstack.readthedocs.org/en/latest/Introduction.html#dependencies ) + added python 2.6 support + + 31 Mar 2015; Horea Christian <h.chr@mail.ru> pydicom-0.9.8.ebuild: + added python 3.3 compatibility + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> pydicom-0.9.8.ebuild, +metadata.xml: Add missing metadata.xml - diff --git a/sci-libs/pydicom/pydicom-0.9.8.ebuild b/sci-libs/pydicom/pydicom-0.9.8.ebuild index 923ef5a19..ad575a675 100644 --- a/sci-libs/pydicom/pydicom-0.9.8.ebuild +++ b/sci-libs/pydicom/pydicom-0.9.8.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="https://code.google.com/p/pydicom/" +HOMEPAGE="http://www.pydicom.org/" SRC_URI="https://pydicom.googlecode.com/files/${P}.zip" LICENSE="MIT" diff --git a/sci-libs/pydicom/pydicom-9999.ebuild b/sci-libs/pydicom/pydicom-9999.ebuild new file mode 100644 index 000000000..bc09e8ca9 --- /dev/null +++ b/sci-libs/pydicom/pydicom-9999.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 python3_3 python3_4 ) + +inherit distutils-r1 git-r3 + +DESCRIPTION="A pure python package for parsing DICOM files" +HOMEPAGE="http://www.pydicom.org/" +SRC_URI="" +EGIT_REPO_URI="https://github.com/darcymason/pydicom" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="" +IUSE="" + +S="${S}/source" diff --git a/sci-libs/scikits_image/scikits_image-9999.ebuild b/sci-libs/scikits_image/scikits_image-9999.ebuild index c8945312f..9d6def5d4 100644 --- a/sci-libs/scikits_image/scikits_image-9999.ebuild +++ b/sci-libs/scikits_image/scikits_image-9999.ebuild @@ -6,7 +6,7 @@ EAPI=5 # pyamg missing py3 support #PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 git-r3 diff --git a/sci-libs/silo/Manifest b/sci-libs/silo/Manifest deleted file mode 100644 index dcd0e04f5..000000000 --- a/sci-libs/silo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST silo-4.9.1.tar.gz 12038537 SHA256 4908eb77577e26948aedee5976deedc3d2c1fd01b6fc5bd9cb61772cbbe2a56e SHA512 512e16ec6bd62deb3596d918895a0c82606a9f519345e4c4abd1a19eb40172576b70313472b75ae4183ee9d86a0f19443504f232ca6e633b1652f9d547927b83 WHIRLPOOL 7cd875ce28bac86cbe68e931d95cf5543671aa7142ab672f5bdc23da9467eb6b755b2e8f06bb2871686aa01e835a5495697a454bcb36153adf86be09735219d9 diff --git a/sci-libs/silo/files/silo-4.9.1-qtlibs.patch b/sci-libs/silo/files/silo-4.9.1-qtlibs.patch deleted file mode 100644 index e8fc4284c..000000000 --- a/sci-libs/silo/files/silo-4.9.1-qtlibs.patch +++ /dev/null @@ -1,66 +0,0 @@ -diff -ru silo-4.9.1-old/configure silo-4.9.1-new/configure ---- silo-4.9.1-old/configure 2014-01-18 23:19:15.755030306 +0100 -+++ silo-4.9.1-new/configure 2014-01-18 23:20:52.595031159 +0100 -@@ -27503,7 +27503,7 @@ - ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | - sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" - fi -- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - else - # Use cached value or do search, starting with suggestions from - # the command line -@@ -27577,7 +27577,7 @@ - ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | - sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" - fi -- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - else - # There is no valid definition for $QTDIR as Trolltech likes to see it - ax_qt_dir= -@@ -27589,7 +27589,7 @@ - ax_qt_lib="`ls $ax_qt_lib_dir/libQt* | sed -n 1p | - sed s@$ax_qt_lib_dir/lib@@ | sed s@[.].*@@`" - fi -- ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ ax_qt_LIBS="-L$ax_qt_lib_dir -l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - else - # Normally, when there is no traditional Trolltech installation, - # the library is installed in a place where the linker finds it -@@ -27607,7 +27607,7 @@ - # See if we find the library without any special options. - # Don't add top $LIBS permanently yet - ax_save_LIBS="$LIBS" -- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - ax_qt_LIBS="$LIBS" - ax_save_CXXFLAGS="$CXXFLAGS" - CXXFLAGS="-I$ax_qt_include_dir -I$ax_qt_include_dir/Qt -I$ax_qt_include_dir/QtCore -I$ax_qt_include_dir/QtGui" -@@ -27668,7 +27668,7 @@ - # That did not work. Try the multi-threaded version - echo "Non-critical error, please neglect the above." >&5 - ax_qt_lib=qt-mt -- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ - _ACEOF -@@ -27726,7 +27726,7 @@ - # That did not work. Try the OpenGL version - echo "Non-critical error, please neglect the above." >&5 - ax_qt_lib=qt-gl -- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ - _ACEOF -@@ -27809,7 +27809,7 @@ - fi - done - # Try with that one -- LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" -+ LIBS="-l$ax_qt_lib $X_PRE_LIBS $X_LIBS -lQtCore -lQtGui -lX11 -lXext -lXmu -lXt -lXi $X_EXTRA_LIBS" - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ - _ACEOF diff --git a/sci-libs/silo/metadata.xml b/sci-libs/silo/metadata.xml deleted file mode 100644 index 2ee5908ca..000000000 --- a/sci-libs/silo/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>cluster</herd> - <longdescription> - Silo is a library for reading and writing a wide variety of - scientific data to binary, disk files. The files Silo produces and - the data within them can be easily shared and exchanged between - wholly independently developed applications running on disparate - computing platforms. - </longdescription> - <use> - <flag name="silex">Build silex data browser</flag> - </use> - <maintainer> - <email>gentryx@gmx.de</email> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/silo/silo-4.9.1.ebuild b/sci-libs/silo/silo-4.9.1.ebuild deleted file mode 100644 index 9cfc91415..000000000 --- a/sci-libs/silo/silo-4.9.1.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="A mesh and field I/O library and scientific database" -HOMEPAGE="https://wci.llnl.gov/codes/silo" -SRC_URI="https://wci.llnl.gov/codes/silo/${P}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="hdf5 qt4 +silex static-libs" - -REQUIRED_USE="silex? ( qt4 )" - -RDEPEND=" - hdf5? ( sci-libs/hdf5 ) - qt4? ( dev-qt/qtgui:4 )" -DEPEND="${RDEPEND}" - -src_prepare() { - epatch "${FILESDIR}/${P}-qtlibs.patch" -} - -src_configure() { - econf \ - --enable-install-lite-headers \ - --enable-shared \ - $(use_enable silex silex ) \ - $(use_enable static-libs static ) \ - $(use_with qt4 Qt-lib-dir "${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX}/qt4 ) \ - $(use_with qt4 Qt-include-dir "${EPREFIX}"/usr/include/qt4 ) \ - $(use_with hdf5 hdf5 ${EPREFIX}"/usr/include,${EPREFIX}"/usr/lib${LIB_LOCATION_SUFFIX} ) -} diff --git a/sci-libs/symmetrica/ChangeLog b/sci-libs/symmetrica/ChangeLog index 60e980dfd..279686487 100644 --- a/sci-libs/symmetrica/ChangeLog +++ b/sci-libs/symmetrica/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/symmetrica -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*symmetrica-2.0-r1 (20 Feb 2015) + + 20 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> + +symmetrica-2.0-r1.ebuild: + sci-libs/symmetrica: Apply patches; Raise revision + 11 Jan 2015; Marius Brehler <marbre@linux.sungazer.de> symmetrica-2.0.ebuild: Move to EAPI=5 and clean the ebuild @@ -19,4 +25,3 @@ 18 Jul 2008; Francois Bissey <f.r.bissey@massey.ac.nz> ChangeLog: Initial import, see bug #232014 - diff --git a/sci-libs/symmetrica/Manifest b/sci-libs/symmetrica/Manifest index 8237f5653..eee856864 100644 --- a/sci-libs/symmetrica/Manifest +++ b/sci-libs/symmetrica/Manifest @@ -1 +1 @@ -DIST SYM2_0.tar.gz 720154 SHA256 bf52788dedc14c482e89f5e7efe8c60864a633314ddd446dd4602d5fdaca0ee2 +DIST symmetrica-2.0.tar.gz 720154 SHA256 bf52788dedc14c482e89f5e7efe8c60864a633314ddd446dd4602d5fdaca0ee2 SHA512 48be02bc17311003741c5d87df53e8168635d45cbe2e0890b465e41e27a934f882e876d03f8b0910305daefb05c298386c3641bb59302397ede34f45f8e41e36 WHIRLPOOL 3a05a73fe493cbd976ccf8a18c7088409164497c4bb366297ec6d96f5c740401f0a39501329bae7cf98f64d6e5202ba1c20b6fd80cccc3cdc435d7e61adb67ac diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch b/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch new file mode 100644 index 000000000..ec4aa2000 --- /dev/null +++ b/sci-libs/symmetrica/files/symmetrica-2.0-banner.patch @@ -0,0 +1,11 @@ +--- src/de.c ++++ b/de.c +@@ -24,7 +24,7 @@ + OP cons_negeins;/* global INTEGER variable -1 */ + OP cons_null; /* global INTEGER variable 0 */ + FILE *texout; /* global variable for texoutput */ +-INT no_banner = FALSE; /* AK 281293 */ ++INT no_banner = TRUE; /* AK 281293 */ + INT no_mem_check=TRUE; /* AK 100893 */ + INT english_tableau=FALSE; /* AK 290995 */ + diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch b/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch new file mode 100644 index 000000000..935cc6ab5 --- /dev/null +++ b/sci-libs/symmetrica/files/symmetrica-2.0-freeing_errors.patch @@ -0,0 +1,39 @@ +Patch imported from sage-on-gentoo. +--- src/bruch.c ++++ b/bruch.c +@@ -975,14 +975,16 @@ + ggterg = ggt_i(S_B_UI(bruch),S_B_OI(bruch)); + + if (ggterg == S_B_UI(bruch)) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(S_B_OI(bruch) / ggterg,bruch); ++ M_I_I(tmp / ggterg,bruch); + goto ende; + } + + if (-ggterg == S_B_UI(bruch)) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(- S_B_OI(bruch) / ggterg,bruch); ++ M_I_I(- tmp / ggterg,bruch); + goto ende; + } + +@@ -1032,12 +1034,14 @@ + + if (S_O_K(S_B_U(bruch)) == INTEGER) + if (S_B_UI(bruch) == 1) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I(S_B_OI(bruch),bruch); ++ M_I_I(tmp,bruch); + goto ende; } + else if (S_B_UI(bruch) == -1) { ++ INT tmp = S_B_OI(bruch); + freeself_bruch(bruch); +- M_I_I( - S_B_OI(bruch),bruch); ++ M_I_I( - tmp,bruch); + goto ende; } + if (NEGP(S_B_O(bruch)) && NEGP(S_B_U(bruch))) + { diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch b/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch new file mode 100644 index 000000000..66a156cc1 --- /dev/null +++ b/sci-libs/symmetrica/files/symmetrica-2.0-function_names.patch @@ -0,0 +1,329 @@ +Patch imported from sage-on-gentoo. +--- a/bar.c ++++ b/bar.c +@@ -237,7 +237,7 @@ + g = callocobject(); + e = S_V_I(a,0L); + f = S_V_I(a,1L); +- erg += sum(f,g); ++ erg += sym_sum(f,g); + j=0L; + for (i=0L;i<S_V_LI(e);i++) + j += S_V_II(e,i)*(i+1L); +@@ -427,7 +427,7 @@ + for (i=0L;i<S_V_LI(b);i++) + erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(b,i)); + erg += freeall(c); +- erg += sort(b); /* AK 130592 */ ++ erg += sym_sort(b); /* AK 130592 */ + ENDR("makevectorof_class_bar"); + } + +@@ -615,7 +615,7 @@ + c = callocobject(); + d = callocobject(); + erg += lehmercode_bar(a,c); +- erg += sum(S_V_I(c,1L),b); ++ erg += sym_sum(S_V_I(c,1L),b); + for(i=0L;i<S_P_LI(a);i++) + { + if (S_V_II(S_V_I(c,0L),i) == 1L) +--- a/def.h ++++ b/def.h +@@ -3105,7 +3105,7 @@ + extern INT so_character (); + extern INT so_dimension (); + extern OBJECTKIND s_o_k(); +-extern INT sort(); ++extern INT sym_sort(); + extern INT sort_rows_tableaux_apply(); + extern INT sort_vector(); + extern OBJECTSELF s_o_s(); +@@ -3271,7 +3271,7 @@ + extern INT sub_part_part(); + extern INT substitute_one_matrix (); + extern INT substitute_one_monopoly (); +-extern INT sum(); ++extern INT sym_sum(); + extern INT sum_integervector(); + extern INT sum_matrix(); + extern INT sum_vector(); +--- a/di.c ++++ b/di.c +@@ -1355,7 +1355,7 @@ + m_il_nv(0L,weight_watcher); + m_il_nv(0L,perm_vec); + copy(S_V_I(FP,0L),fix); +- sort(fix); ++ sym_sort(fix); + + get_perm(hweight,p,b,S_I_I(n),S_I_I(m),0L, + perm_vec,weight_watcher,fix); +@@ -1502,7 +1502,7 @@ + if(ind == m) + { + mult_perm_fix(p,fix,hfix); +- sort(hfix); ++ sym_sort(hfix); + if(!hfix_in_ww(hfix,ww)) + { + inc(ww); +--- a/ga.c ++++ b/ga.c +@@ -632,7 +632,7 @@ + else if (what == 0L) + erg += vertikal_sum(S_V_L(a),c); + erg += copy(a,d); +- erg += sort(d); ++ erg += sym_sort(d); + erg += m_il_p(S_V_II(d,S_V_LI(d)-1L),e); /* identitaet */ + for (i=0L,k=0L,j=S_V_LI(d);i<S_P_LI(e);i++) + if (i+1L == S_V_II(d,k) ) +@@ -722,7 +722,7 @@ + + j=0L; + erg += append(h,g,h2); +- erg += sort(h2); ++ erg += sym_sort(h2); + for (i=0L;i<S_V_LI(g);i++) + { + erg += m_i_i(S_V_II(g,i),S_P_I(a,j)); +--- a/galois.c ++++ b/galois.c +@@ -758,7 +758,7 @@ + } + } + FREEALL2(v,nv); +- sort(res); ++ sym_sort(res); + } + S3R(k,phg_c,phg_d,"all_points_phg_store",res); + ENDR("all_points"); +--- a/macro.h ++++ b/macro.h +@@ -1,6 +1,8 @@ + /* file: macro.h symmetrica source code */ + #ifndef MACRO_H + ++#include "string.h" ++ + #ifdef SYMMAGMA + #define SYM_MALLOC(a) mem_malloc(a) + #else + #define C_O_K(a,b) ((a)->ob_kind = (OBJECTKIND)(b)) +--- a/nc.c ++++ b/nc.c +@@ -204,7 +204,7 @@ + erg += mult(S_NC_C(a),S_NC_C(b),d); + erg += m_gl_co(S_NC_GL(a),e); + erg += mult_apply(e,d); +- erg += sum(d,e); ++ erg += sym_sum(d,e); + erg += m_gl_go(S_NC_GL(a),d); + erg += div(e,d,c); + erg += freeall(e); +@@ -617,7 +617,7 @@ + erg += mult_nc_kranz(c,a,e); + erg += mult(S_V_I(e,1L),f,c); + erg += div(c,g,c); +- erg += sum(c,S_V_I(S_NC_C(b),S_I_I(d))); ++ erg += sym_sum(c,S_V_I(S_NC_C(b),S_I_I(d))); + } + erg += freeall(c); + erg += freeall(d); +@@ -712,7 +712,7 @@ + for(j = 0L; j<S_V_LI(c);j++) { + kranztypus_to_matrix(S_V_I(c,j),S_V_I(a,j)); + } +- sort(a); ++ sym_sort(a); + freeall(f); freeall(h); freeall(c); + return OK; + } +@@ -739,7 +739,7 @@ + kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); + } + +- sort(h); ++ sym_sort(h); + m_l_v(S_V_L(h),a); + for(j = 0L; j<S_V_LI(c);j++) { + typusorder(S_V_I(h,j), zb, za, S_V_I(a,j), f); +@@ -789,7 +789,7 @@ + erg += kranztypus_to_matrix(S_V_I(c,j),S_V_I(h,j)); + } + +- erg += sort(h); ++ erg += sym_sort(h); + erg += typusorder(S_V_I(h,S_I_I(i)), zb, za, a, f); + erg += freeall(f); + erg += freeall(c); +--- a/nu.c ++++ b/nu.c +@@ -531,13 +531,13 @@ + ENDR("add"); + } + +-INT sort(a) OP a; ++INT sym_sort(a) OP a; + /* sortiert das object in aufsteigender reihenfolge AK 270787 */ + /* AK 160986 */ /* AK 280689 V1.0 */ /* AK 050390 V1.1 */ + /* AK 070891 V1.3 */ + { + INT erg = OK; +- EOP("sort(1)",a); ++ EOP("sym_sort(1)",a); + + switch(S_O_K(a)) + { +@@ -547,9 +547,9 @@ + erg += sort_vector(a);break; + #endif /* VECTORTRUE */ + default: +- erg += WTO("sort",a); break; ++ erg += WTO("sym_sort",a); break; + }; +- ENDR("sort"); ++ ENDR("sym_sort"); + } + + INT length(a,d) OP a,d; +@@ -641,7 +641,7 @@ + ENDR("content"); + } + +-INT sum(a,res) OP a,res; ++INT sym_sum(a,res) OP a,res; + /* AK 280689 V1.0 */ /* AK 050390 V1.1 */ /* AK 120391 V1.2 */ + /* AK 140891 V1.3 */ + /* AK 170298 V2.0 */ +@@ -649,7 +649,7 @@ + INT erg = OK; + COP("sum(1)",a); + COP("sum(2)",res); +- CE2(a,res,sum); ++ CE2(a,res,sym_sum); + + switch(S_O_K(a)) + { +@@ -680,7 +680,7 @@ + erg += WTO("sum",a); break; + }; + +- ENDR("sum"); ++ ENDR("sym_sum"); + } + + +--- a/part.c ++++ b/part.c +@@ -347,7 +347,7 @@ + if (a == b) { /* a := a+a */ + if (S_PA_K(a) == VECTOR) { + erg += append_apply_vector(S_PA_S(a),S_PA_S(b)); +- erg += sort(S_PA_S(a)); ++ erg += sym_sort(S_PA_S(a)); + goto endr_ende; + } + else if (S_PA_K(a) == EXPONENT) { +@@ -406,7 +406,7 @@ + k=S_PA_LI(b)-1; + /* + erg += append_apply_vector(S_PA_S(a),S_PA_S(b)); +- erg += sort(S_PA_S(a)); ++ erg += sym_sort(S_PA_S(a)); + */ + inc_vector_co(S_PA_S(a),S_PA_LI(b)); + for (j=S_PA_LI(a)-1;j>=0;j--) +--- a/perm.c ++++ b/perm.c +@@ -833,9 +833,9 @@ + /* s = Anzahl der spalten */ + + s = S_V_LI(S_V_I(a,0L)); +- sum(S_V_I(a,0L),summe);/* composition ist vector */ ++ sym_sum(S_V_I(a,0L),summe);/* composition ist vector */ + z = S_I_I(summe); +- FREEALL(summe); ++ FREEALL(summe); + m_ilih_nm(s,z,b); + C_O_K(b,KRANZTYPUS); + for (i=0L;i<s;i++) +@@ -1114,7 +1114,7 @@ + erg += kranztypus_to_matrix(S_V_I(c,i),S_V_I(h,i)); + } + +- erg += sort(h); ++ erg += sym_sort(h); + + erg += chartafel(b,ct); + +@@ -1926,7 +1926,7 @@ + OP c; + c = CALLOCOBJECT(); + erg += lehmercode_permutation(a,c); /*result is a vector */ +- erg += sum(c,b); ++ erg += sym_sum(c,b); + FREEALL(c); + } + ENDR("numberof_inversionen"); +@@ -2364,7 +2364,7 @@ + COP("rz_lehmercode(2)",b); + + zw = callocobject(); +- erg += sum(lc,zw); ++ erg += sym_sum(lc,zw); + if (NULLP(zw)) + { + erg += m_il_integervector((INT)0,b); +--- a/rest.c ++++ b/rest.c +@@ -3998,7 +3998,7 @@ + oj = j; + } + } +- erg += sum(c,b); ++ erg += sym_sum(c,b); + eee: + erg += freeall(c); + ENDR("charge_word"); +--- a/ta.c ++++ b/ta.c +@@ -1596,7 +1596,7 @@ + { + OP d,e; + e = CALLOCOBJECT(); +- erg += sum(content,e); /* AK 271098 */ ++ erg += sym_sum(content,e); /* AK 271098 */ + d = CALLOCOBJECT(); + erg += weight(shape,d); + if (NEQ(d,e)) +@@ -1821,7 +1821,7 @@ + CE3(matrix, column_index, row_index,matrix_twoword); + c = callocobject(); + erg += zeilen_summe(matrix,c); +- erg += sum(c,c); ++ erg += sym_sum(c,c); + erg += m_l_v(c,column_index); + erg += m_l_v(c,row_index); + for(i=0,l=0;i<S_M_HI(matrix);i++) +--- a/zyk.c ++++ b/zyk.c +@@ -804,7 +804,7 @@ + zykeltypvec = CALLOCOBJECT(); + ak_order = CALLOCOBJECT(); + +- sum(numztvec,ak_order); /* AK 060295 */ ++ sym_sum(numztvec,ak_order); /* AK 060295 */ + + + +@@ -1176,7 +1176,7 @@ + erg += m_i_i(0,c); + while (z!=NULL) + { +- erg += sum(S_PO_S(z),e); ++ erg += sym_sum(S_PO_S(z),e); + erg += hoch(b,e,e); + erg += mult_apply(S_PO_K(z),e); + erg += add_apply(e,c); diff --git a/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch b/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch new file mode 100644 index 000000000..32e5751df --- /dev/null +++ b/sci-libs/symmetrica/files/symmetrica-2.0-integersize.patch @@ -0,0 +1,37 @@ +Patch imported from sage-on-gentoo. +--- src/def.h ++++ c/def.h +@@ -2,14 +2,9 @@ + /* INT should always be 4 byte */ + #ifndef DEF_H + +- +-#ifdef __alpha +-typedef int INT; +-typedef unsigned int UINT; +-#else /* __alpha */ +-typedef long INT; +-typedef unsigned long UINT; +-#endif /* __alpha */ ++#include <stdint.h> ++typedef int32_t INT; ++typedef uint32_t UINT; + + #include <stdio.h> + #include <memory.h> +@@ -65,10 +60,13 @@ + + + /* definitionen fuer object.c */ +-typedef INT OBJECTKIND; /* 4 byte */ ++/* NOTE: partition code assumes that there is no unused space in the ++ * object struct when an INT is stored. This requires both OBJECTKIND ++ * and OBJECTSELF to have a size equal to a machine word. */ ++typedef intptr_t OBJECTKIND; + + typedef union { +- INT ob_INT; ++ intptr_t ob_INT; + INT * ob_INTpointer; + char *ob_charpointer; + struct bruch *ob_bruch; diff --git a/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild b/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild new file mode 100644 index 000000000..ff79ec556 --- /dev/null +++ b/sci-libs/symmetrica/symmetrica-2.0-r1.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A collection of routine to handle a variety of topics" +HOMEPAGE="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/index.html" +MY_P=SYM${PV//./_} +SRC_URI="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/${MY_P}_tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~ppc64" +IUSE="doc" + +S="${WORKDIR}" + +PATCHES=( + "${FILESDIR}/${P}-banner.patch" + "${FILESDIR}/${P}-freeing_errors.patch" + "${FILESDIR}/${P}-function_names.patch" + "${FILESDIR}/${P}-integersize.patch" +) + +src_prepare() { + epatch ${PATCHES[@]} + # symmetrica by itself is just a bunch of files and a few headers + # plus documentation that you can use as you wish in your programs. + # For sage and ease of use we make it into a library with the following + # makefile (developped by F. Bissey and T. Abbott (sage on debian). + cp "${FILESDIR}/makefile" "${S}/makefile" || die +} + +src_install() { + default + use doc && dodoc *.doc +} diff --git a/sci-libs/symmetrica/symmetrica-2.0.ebuild b/sci-libs/symmetrica/symmetrica-2.0.ebuild index 5677cdaa2..cb10a0a94 100644 --- a/sci-libs/symmetrica/symmetrica-2.0.ebuild +++ b/sci-libs/symmetrica/symmetrica-2.0.ebuild @@ -7,7 +7,7 @@ EAPI=5 DESCRIPTION="A collection of routine to handle a variety of topics" HOMEPAGE="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/index.html" MY_P=SYM${PV//./_} -SRC_URI="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/${MY_P}_tar.gz -> ${MY_P}.tar.gz" +SRC_URI="http://www.neu.uni-bayreuth.de/de/Uni_Bayreuth/Fakultaeten/1_Mathematik_Physik_und_Informatik/Fachgruppe_Informatik/prof_diskrete_algorithmen/en/research/SYMMETRICA/${MY_P}_tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/sci-libs/trilinos/ChangeLog b/sci-libs/trilinos/ChangeLog index 82242b87f..b773567bf 100644 --- a/sci-libs/trilinos/ChangeLog +++ b/sci-libs/trilinos/ChangeLog @@ -1,7 +1,28 @@ # ChangeLog for sci-libs/trilinos -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*trilinos-11.12.1-r1 (13 Mar 2015) +*trilinos-11.14.1-r1 (13 Mar 2015) + + 13 Mar 2015; Matthias Maier <tamiko@gentoo.org> +trilinos-11.12.1-r1.ebuild, + +trilinos-11.14.1-r1.ebuild, -trilinos-11.12.1.ebuild, + -trilinos-11.14.1.ebuild, files/trilinos-11.12.1-fix-install-paths.patch, + files/trilinos-11.14.1-fix-install-paths.patch: + sci-libs/trilinos: fix location of target config files + +*trilinos-11.14.1 (13 Mar 2015) + + 13 Mar 2015; Matthias Maier <tamiko@gentoo.org> + +files/trilinos-11.14.1-fix-install-paths.patch, + +files/trilinos-11.14.1-fix_install_paths_for_destdir.patch, + +trilinos-11.14.1.ebuild, metadata.xml: + sci-libs/trilinos: version bump, some preliminary metadata + + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> trilinos-11.0.3.ebuild, + trilinos-11.10.2.ebuild, trilinos-11.12.1.ebuild, trilinos-11.4.2.ebuild: + BSD/LGPL-2.1 never implies a fetch restriction, updated Manifest + *trilinos-11.12.1 (06 Dec 2014) 06 Dec 2014; Matthias Maier <tamiko@gentoo.org> diff --git a/sci-libs/trilinos/Manifest b/sci-libs/trilinos/Manifest index e4ac6e9b1..7eb84e016 100644 --- a/sci-libs/trilinos/Manifest +++ b/sci-libs/trilinos/Manifest @@ -1,5 +1,6 @@ DIST trilinos-11.0.3-Source.tar.gz 107076534 SHA256 4e9d68d23eac1076200a3224fab14cd3a63a77574f1456d1bff931b2887b5c63 SHA512 9c449c6f9b2bc6346867bc68c29f83edc81790889d483129a98d149e1ff79d32b13310e8fcb3b4412b2f722b5d7efedd2a65f2e882b38629d4a1d50ecfc9783f WHIRLPOOL 7af72bd92cb4aa72ec8d98065570c9af2cc04187b7b2cce5d701e25d2c25efdc8826a4359b035008b8cf086026b88126bcfa6e807cac4f18d5fb745a48568f10 -DIST trilinos-11.10.2-Source.tar.bz2 110633685 SHA256 d3a39b7ad5c61d1e1413f9e550f0a81832a36e4a3072b8b99cebed6900d2d0ea SHA512 0147ed8d4483765ef03114eaed8098b0b41f81dde09147e584ce4e3f8fd2465ad11a6edd288f9ed857bfc163ed45d1a728989a185c22c819434cbb1ffdadd7cb WHIRLPOOL 7229a984a2c894f8edab01ec675fc5582553ca4ef652bda3006318b91d1d56f581ecc5eaed4a023e20cb25e9969a57e61735e415f6c734d41796b905fa9978ae -DIST trilinos-11.12.1-Source.tar.bz2 119524933 SHA256 a41539414529c65905260b3befe3aee4f1dd1015ff719f0f6b5a10902d576fda SHA512 84e76f21494da39b3742b15a7203c98d6ae761a628add384fa0494bed89a2eb37aacc9fd4731ed9e06a4c81b75fd73b05b5e627e10fb2a4a67fc937903c78fd8 WHIRLPOOL 90a4f5cbf1ac91583ca5ff8287fa1898859b7f243b497e3001dd173be504b5c566c31bc38a08e4d001c5672e7ecb9118ceabbe8c76851e2d623403c3a9038b0a -DIST trilinos-11.2.3-Source.tar.bz2 101522486 SHA256 e8c7a899b9cbb1a8b168b3da5621eb34c9e48c2d48dfbf651366a50a465772c2 SHA512 9a64fd092012a67e0c317fb242a5e6378e543f8aa11d0f9e0bb45569c5f7e146f97e85a462305fe3c92436cc2540b95597c2ffc9bbcfc4b7ee08d9a09dbcdb80 WHIRLPOOL ac27521c7c5ca2e4337ff1aa9f18e68bcde8c5130821dfc8cda5af10c91e2e79e20017c2b76773ca412234b43885df30d781a0cb67ae2c15c47c091f548bdb8e -DIST trilinos-11.4.2-Source.tar.bz2 104205684 SHA256 9bbf33936c5c1e83e0c5a5e336fbdac8e59d0bebf766a4369ad32bfdf15f4199 SHA512 06e8d6873409b8aae3660890a1d3f05467f137a9ec28780ec600531907627e3f123a97e2d3681510d18762beea8dca4fa859308797d75c1862c51c06890ae1da WHIRLPOOL 1b774b77d4efbc582012240290aa7d03df0ae12e87530da1b87be3ce591db60b793941c9f6b70df596fb1e29c33208d1a0c4353c278bc394711477e9a9e47d23 +DIST trilinos-11.10.2-Source.tar.gz 127593733 SHA256 03c435d40157857fecca5db79c1e307ab683857ff2aa60f1c15926c8c4a4e0e2 SHA512 2accdc5500b486312741f44ce7b3e166cd6a38a98e9accb4d59e20f2dd145f78904f1149fc40eb9b00d63fcafd99dcd8bca0f55e06d809a7224f387afc0dabcc WHIRLPOOL 9fc5a0419aa8d43b0bd9bd0d5049a0b441a1921bc317322986f081952c1308f3f96b36a5fdb0eecb5de0ab3faeb6773885a61c631e6ffd59e02e728cfc7c9648 +DIST trilinos-11.12.1-Source.tar.gz 138102285 SHA256 a86861a630a4d516d9f7e7512402b4696a3a8eec9c4b0c639af72b4cc2bcece9 SHA512 da538c42e56e82c530d10ff5e5c7edee8c1f54ccd9730bfd9b63c284d28ace932cc4aa591817c314d1a0df9bb469efbe03244feacf1f452d90b98419d041d000 WHIRLPOOL 2482a108123609f8f9e4c8fbade68d91814861b35202ede2f07c40b62802c6337a4dc1da80d95489744b5bfbf8098726bd36ee29d804afc358b9a33ba306a7b6 +DIST trilinos-11.14.1-Source.tar.gz 132562115 SHA256 bc538eb8cef4e38ac45efdd5ce4601908339483581d138f91d2354299c547867 SHA512 136ba9304897be1c5b13f31f5bb1c27dc64b5d8473316d6ca13bc79c6a116262420ac005d35ca984afb4776072916fafff826f8057aed80ea243e528b86e127f WHIRLPOOL a4c9447ee490450623b045d8c89280f6427a7692b5450462d87cb7b493791044efb1e460f6784b7a674aaf7a02c67b1a728fa0d837acdc04e26a9594a7b82ea6 +DIST trilinos-11.2.3-Source.tar.gz 116546590 SHA256 eb773a488bb0939bbbc4d25a668c491c2a120a8c17a930a429fc69e5f110293f SHA512 31695cd1f69443705d173d3fca95aafedaa0541d77304c87e482d353fd0c289a05c98e1240158dd518e40e45b5a616027c1084f214aee65bdf361fae36b49dce WHIRLPOOL 400742caf17e62c3a38646cdf08c7afea1a46a831570995548317ca62014160d18ac3a230074c5142feacd47e94b734ec39cd87239ac56d196203653914c3b84 +DIST trilinos-11.4.2-Source.tar.gz 119343356 SHA256 5f020b642feb3c1b3610d3832dda4701db7d25eaafa6e4636b47381b72136965 SHA512 61234ffb596cdc511b5a7eae25709b820c1a765b0f8e4042c345558e639d0a1de893631bda5bbddda9a14704ade731d41c9bd013c60f55015f00e0216641b943 WHIRLPOOL 9badc7e8185b2466f1257ecb3597f9f30c0e65466ebec07811873b86047d4aa32b260a6650d5d3a1c4ff39bbdff646077899f614f6083a71df88e8c9cd96a4ce diff --git a/sci-libs/trilinos/files/trilinos-11.12.1-fix-install-paths.patch b/sci-libs/trilinos/files/trilinos-11.12.1-fix-install-paths.patch index 130f3cee3..9a0229239 100644 --- a/sci-libs/trilinos/files/trilinos-11.12.1-fix-install-paths.patch +++ b/sci-libs/trilinos/files/trilinos-11.12.1-fix-install-paths.patch @@ -26,7 +26,7 @@ index e1c633f..864488f 100644 INSTALL( EXPORT ${PACKAGE_NAME} - DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PACKAGE_NAME}" -+ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PROJECT_NAME}" ++ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PACKAGE_NAME}" FILE ${PACKAGE_NAME}Targets.cmake ) ENDIF() diff --git a/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch b/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch new file mode 100644 index 000000000..32f25f326 --- /dev/null +++ b/sci-libs/trilinos/files/trilinos-11.14.1-fix-install-paths.patch @@ -0,0 +1,61 @@ +diff --git a/cmake/tribits/package_arch/TribitsWriteClientExportFiles.cmake b/cmake/tribits/package_arch/TribitsWriteClientExportFiles.cmake +index e1c633f..864488f 100644 +--- a/cmake/tribits/core/package_arch/TribitsWriteClientExportFiles.cmake ++++ b/cmake/tribits/core/package_arch/TribitsWriteClientExportFiles.cmake +@@ -494,8 +494,8 @@ INCLUDE(\"${PROJECT_BINARY_DIR}/${PACKAGE_NAME}Targets.cmake\")" + FOREACH(PATH ${PATH_LIST}) + SET(RELATIVE_PATH "${RELATIVE_PATH}/..") + ENDFOREACH() +- SET(FULL_LIBRARY_DIRS_SET "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_LIB_DIR}") +- SET(FULL_INCLUDE_DIRS_SET "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}") ++ SET(FULL_LIBRARY_DIRS_SET "${${PROJECT_NAME}_INSTALL_LIB_DIR}") ++ SET(FULL_INCLUDE_DIRS_SET "${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}") + + # Custom code in configuration file. + SET(PACKAGE_CONFIG_CODE "") +@@ -574,14 +574,14 @@ FUNCTION(TRIBITS_WRITE_PROJECT_CLIENT_EXPORT_FILES_INSTALL_TARGETS PACKAGE_NAME) + IF (${PROJECT_NAME}_ENABLE_INSTALL_CMAKE_CONFIG_FILES) + INSTALL( + FILES ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${PACKAGE_NAME}Config_install.cmake +- DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PACKAGE_NAME}" ++ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PACKAGE_NAME}" + RENAME ${PACKAGE_NAME}Config.cmake + ) + + IF(${PACKAGE_NAME}_HAS_NATIVE_LIBRARIES) + INSTALL( + EXPORT ${PACKAGE_NAME} +- DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PACKAGE_NAME}" ++ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PACKAGE_NAME}" + FILE ${PACKAGE_NAME}Targets.cmake + ) + ENDIF() +@@ -819,8 +819,8 @@ include(\"${${TRIBITS_PACKAGE}_BINARY_DIR}/${TRIBITS_PACKAGE}Config.cmake\")") + FOREACH(PATH ${PATH_LIST}) + SET(RELATIVE_PATH "${RELATIVE_PATH}/..") + ENDFOREACH() +- SET(${PROJECT_NAME}_CONFIG_INCLUDE_DIRS "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}") +- SET(${PROJECT_NAME}_CONFIG_LIBRARY_DIRS "\${CMAKE_CURRENT_LIST_DIR}/${RELATIVE_PATH}/${${PROJECT_NAME}_INSTALL_LIB_DIR}") ++ SET(${PROJECT_NAME}_CONFIG_INCLUDE_DIRS "${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}") ++ SET(${PROJECT_NAME}_CONFIG_LIBRARY_DIRS "${${PROJECT_NAME}_INSTALL_LIB_DIR}") + + # Write the specification of the rpath if necessary. This is only needed if we're building shared libraries. + IF(BUILD_SHARED_LIBS) +@@ -845,7 +845,7 @@ include(\"\${CMAKE_CURRENT_LIST_DIR}/../${TRIBITS_PACKAGE}/${TRIBITS_PACKAGE}Con + + INSTALL( + FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Config_install.cmake +- DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PROJECT_NAME}" ++ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PROJECT_NAME}" + RENAME ${PROJECT_NAME}Config.cmake + ) + ENDIF() +@@ -890,7 +890,7 @@ include(\"\${CMAKE_CURRENT_LIST_DIR}/../${TRIBITS_PACKAGE}/${TRIBITS_PACKAGE}Con + ) + INSTALL( + FILES ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake +- DESTINATION "${${PROJECT_NAME}_INSTALL_LIB_DIR}/cmake/${PROJECT_NAME}" ++ DESTINATION "${${PROJECT_NAME}_INSTALL_CONFIG_DIR}/${PROJECT_NAME}" + ) + + ENDFUNCTION() diff --git a/sci-libs/trilinos/files/trilinos-11.14.1-fix_install_paths_for_destdir.patch b/sci-libs/trilinos/files/trilinos-11.14.1-fix_install_paths_for_destdir.patch new file mode 100644 index 000000000..e24fc495b --- /dev/null +++ b/sci-libs/trilinos/files/trilinos-11.14.1-fix_install_paths_for_destdir.patch @@ -0,0 +1,617 @@ +diff --git a/commonTools/gtest/CMakeLists.txt b/commonTools/gtest/CMakeLists.txt +index 9367010..17f8892 100644 +--- a/commonTools/gtest/CMakeLists.txt ++++ b/commonTools/gtest/CMakeLists.txt +@@ -31,7 +31,7 @@ TRIBITS_ADD_LIBRARY( + ) + + #install gtest header into the correct subdir. +-INSTALL(FILES ${HEADERS} DESTINATION ${CMAKE_INSTALL_PREFIX}/${Trilinos_INSTALL_INCLUDE_DIR}/gtest/) ++INSTALL(FILES ${HEADERS} DESTINATION ${Trilinos_INSTALL_INCLUDE_DIR}/gtest/) + + + +diff --git a/packages/kokkos/TPL/CMakeLists.txt b/packages/kokkos/TPL/CMakeLists.txt +index 8119c31..2d74336 100644 +--- a/packages/kokkos/TPL/CMakeLists.txt ++++ b/packages/kokkos/TPL/CMakeLists.txt +@@ -1,7 +1,7 @@ +
+ TRIBITS_SUBPACKAGE(TPL)
+
+-SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
++SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
+
+ IF( Kokkos_ENABLE_Cuda )
+
+diff --git a/packages/kokkos/containers/src/CMakeLists.txt b/packages/kokkos/containers/src/CMakeLists.txt +index da5a791..65a7c76 100644 +--- a/packages/kokkos/containers/src/CMakeLists.txt ++++ b/packages/kokkos/containers/src/CMakeLists.txt +@@ -15,7 +15,7 @@ FILE(GLOB HEADERS *.hpp) + FILE(GLOB HEADERS_IMPL impl/*.hpp)
+ FILE(GLOB SOURCES impl/*.cpp)
+
+-SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
++SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
+
+ INSTALL(FILES ${HEADERS_IMPL} DESTINATION ${TRILINOS_INCDIR}/impl/)
+
+diff --git a/packages/kokkos/core/src/CMakeLists.txt b/packages/kokkos/core/src/CMakeLists.txt +index 7e0e150..d1ed33a 100644 +--- a/packages/kokkos/core/src/CMakeLists.txt ++++ b/packages/kokkos/core/src/CMakeLists.txt +@@ -13,7 +13,7 @@ INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}) +
+ #-----------------------------------------------------------------------------
+
+-SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
++SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
+
+ #-----------------------------------------------------------------------------
+
+diff --git a/packages/kokkos/core/src/impl/CMakeLists.txt b/packages/kokkos/core/src/impl/CMakeLists.txt +index c543194..1021f42 100644 +--- a/packages/kokkos/core/src/impl/CMakeLists.txt ++++ b/packages/kokkos/core/src/impl/CMakeLists.txt +@@ -12,7 +12,7 @@ TRIBITS_ADD_LIBRARY( + DEPLIBS
+ )
+
+-SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
++SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR})
+
+ INSTALL(FILES ${HEADERS} DESTINATION ${TRILINOS_INCDIR}/impl/)
+
+diff --git a/packages/seacas/libraries/ioss/src/init/CMakeLists.txt b/packages/seacas/libraries/ioss/src/init/CMakeLists.txt +index 573c972..8056913 100644 +--- a/packages/seacas/libraries/ioss/src/init/CMakeLists.txt ++++ b/packages/seacas/libraries/ioss/src/init/CMakeLists.txt +@@ -50,5 +50,5 @@ IF (BUILD_TESTING) + ENDIF (BUILD_TESTING) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${Trilinos_INSTALL_INCLUDE_DIR}/init/) ++ ${Trilinos_INSTALL_INCLUDE_DIR}/init/) + +diff --git a/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt b/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt +index 695b21d..8f2045c 100644 +--- a/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_adapt/stk_adapt/CMakeLists.txt +@@ -46,7 +46,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +-${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/) ++${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/) + + ADD_SUBDIRECTORY(main) + +diff --git a/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt b/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt +index db930be..c3cd3b4 100644 +--- a/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_adapt/stk_adapt/sierra_element/CMakeLists.txt +@@ -34,5 +34,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/sierra_element/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_adapt/sierra_element/) + +diff --git a/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt b/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt +index ec7f650..a98b073 100644 +--- a/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_algsup/stk_algsup/CMakeLists.txt +@@ -22,5 +22,5 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_algsup/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_algsup/) + +diff --git a/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt b/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt +index e738def..e8ad166 100644 +--- a/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_expreval/stk_expreval/CMakeLists.txt +@@ -47,4 +47,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval) +diff --git a/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt b/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt +index 38d9b5c..7b1d105 100644 +--- a/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_io/stk_io/CMakeLists.txt +@@ -50,7 +50,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +-${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/) ++${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/) + + # AGS: I moved this to the bottom so that the link order was correct + # with -lstk_io_uti before -lstk_io. I think the DEPLIBS added in +diff --git a/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt b/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt +index 0412574..b15f54a 100644 +--- a/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_io/stk_io/util/CMakeLists.txt +@@ -46,4 +46,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/) +diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt +index 71c6697..770eb52 100644 +--- a/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/base/CMakeLists.txt +@@ -55,7 +55,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/) + + INSTALL(FILES ${HEADERS_IMPL} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/) +diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt +index 844088a..398640d 100644 +--- a/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/fem/CMakeLists.txt +@@ -49,5 +49,5 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fem/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fem/) + +diff --git a/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt b/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt +index 7162134..4738933 100644 +--- a/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_mesh/stk_mesh/fixtures/CMakeLists.txt +@@ -55,4 +55,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/) +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt +index 854268d..68b3533 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/CMakeLists.txt +@@ -68,5 +68,5 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +-${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/) ++${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt +index 10868c3..fa854bc 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/fixtures/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/fixtures/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/fixtures/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt +index a60a1a8..6f2d965 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/function/CMakeLists.txt +@@ -37,5 +37,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt +index ebea648..e6f5344 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/function/internal/CMakeLists.txt +@@ -36,5 +36,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/internal/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/function/internal/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt +index 2b256f1..b27238f 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/math/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/math/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/math/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt +index 2acb307..411ab23 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/mesh/gen/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/mesh/gen/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/mesh/gen/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt +index e9c2a8c..2353f6c 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/norm/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/norm/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/norm/) + +diff --git a/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt b/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt +index 63ae85d..3978bf5 100644 +--- a/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_percept/stk_percept/util/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_percept/util/) + +diff --git a/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt b/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt +index 90ab292..930279b 100644 +--- a/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_rebalance/stk_rebalance/CMakeLists.txt +@@ -47,4 +47,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance/) +diff --git a/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt b/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt +index 2582b19..2f35d7a 100644 +--- a/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_rebalance/stk_rebalance_utils/CMakeLists.txt +@@ -19,4 +19,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance_utils) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_rebalance_utils) +diff --git a/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt b/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt +index a70b0b8..3f8d6ac 100644 +--- a/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_search/stk_search/CMakeLists.txt +@@ -63,4 +63,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) +diff --git a/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt b/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt +index 55a388e..9a5cbfb 100644 +--- a/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_search/stk_search/diag/CMakeLists.txt +@@ -35,5 +35,5 @@ ENDIF() + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search/diag/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search/diag/) + +diff --git a/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt b/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt +index 33de7e0..d904256 100644 +--- a/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_search_util/stk_search_util/stk_mesh/CMakeLists.txt +@@ -55,4 +55,4 @@ TRIBITS_ADD_LIBRARY( + ) + + #INSTALL(FILES ${HEADERS} DESTINATION +-# ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) ++# ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt +index 4a91d34..c00793d 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/CMakeLists.txt +@@ -16,6 +16,6 @@ ENDIF() + TRIBITS_CONFIGURE_FILE(${PACKAGE_NAME}_config.h) + + INSTALL(FILES stk_config.h DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) + INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/STKClassic_config.h DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt +index 354b70c..5b8ec85 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/diag/CMakeLists.txt +@@ -83,5 +83,5 @@ TRIBITS_ADD_LIBRARY( + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/) + +diff --git a/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt +index 3d295e3..aa5869c 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/environment/CMakeLists.txt +@@ -81,4 +81,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt +index f441b60..e64f34d 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/parallel/CMakeLists.txt +@@ -62,4 +62,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt +index 11fb404..b2225e3 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/unit_test_support/CMakeLists.txt +@@ -51,4 +51,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt +index ed25e41..9314e7a 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/use_cases/CMakeLists.txt +@@ -50,4 +50,4 @@ TRIBITS_ADD_LIBRARY( + ) + + #INSTALL(FILES ${HEADERS} DESTINATION +-# ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/use_cases/) ++# ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/use_cases/) +diff --git a/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt b/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt +index 56b7873..8d83357 100644 +--- a/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt ++++ b/packages/stk/stk_classic/stk_util/stk_util/util/CMakeLists.txt +@@ -47,4 +47,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/) +diff --git a/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt b/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt +index 467dfa1..605aefd 100644 +--- a/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt ++++ b/packages/stk/stk_expreval/stk_expreval/CMakeLists.txt +@@ -78,4 +78,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_expreval) +diff --git a/packages/stk/stk_io/stk_io/CMakeLists.txt b/packages/stk/stk_io/stk_io/CMakeLists.txt +index 1cc9609..16e1fe0 100644 +--- a/packages/stk/stk_io/stk_io/CMakeLists.txt ++++ b/packages/stk/stk_io/stk_io/CMakeLists.txt +@@ -80,7 +80,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +-${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/) ++${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/) + + # AGS: I moved this to the bottom so that the link order was correct + # with -lstk_io_uti before -lstk_io. I think the DEPLIBS added in +diff --git a/packages/stk/stk_io/stk_io/util/CMakeLists.txt b/packages/stk/stk_io/stk_io/util/CMakeLists.txt +index beee08b..1d78255 100644 +--- a/packages/stk/stk_io/stk_io/util/CMakeLists.txt ++++ b/packages/stk/stk_io/stk_io/util/CMakeLists.txt +@@ -77,4 +77,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_io/util/) +diff --git a/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt b/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt +index 5db69c1..9e60c2e 100644 +--- a/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt ++++ b/packages/stk/stk_mesh/stk_mesh/base/CMakeLists.txt +@@ -80,7 +80,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/base/) + + INSTALL(FILES ${HEADERS_IMPL} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/baseImpl/) +diff --git a/packages/stk/stk_mesh/stk_mesh/fixtures/CMakeLists.txt b/packages/stk/stk_mesh/stk_mesh/fixtures/CMakeLists.txt +index f28c06c..c5e817e 100644 +--- a/packages/stk/stk_mesh/stk_mesh/fixtures/CMakeLists.txt ++++ b/packages/stk/stk_mesh/stk_mesh/fixtures/CMakeLists.txt +@@ -72,4 +72,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_mesh/fixtures/) +diff --git a/packages/stk/stk_search/stk_search/CMakeLists.txt b/packages/stk/stk_search/stk_search/CMakeLists.txt +index ae6cc04..199c82f 100644 +--- a/packages/stk/stk_search/stk_search/CMakeLists.txt ++++ b/packages/stk/stk_search/stk_search/CMakeLists.txt +@@ -69,4 +69,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search) +diff --git a/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt b/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt +index ca6e439..dd460d4 100644 +--- a/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt ++++ b/packages/stk/stk_search_util/stk_search_util/CMakeLists.txt +@@ -68,5 +68,5 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search_util) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_search_util) + +diff --git a/packages/stk/stk_topology/stk_topology/CMakeLists.txt b/packages/stk/stk_topology/stk_topology/CMakeLists.txt +index 7364267..f1d03d3 100644 +--- a/packages/stk/stk_topology/stk_topology/CMakeLists.txt ++++ b/packages/stk/stk_topology/stk_topology/CMakeLists.txt +@@ -72,7 +72,7 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/) + + INSTALL(FILES ${DETAIL_HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/topology_detail) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_topology/topology_detail) +diff --git a/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt b/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt +index 667cb5d..ce11394 100644 +--- a/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt ++++ b/packages/stk/stk_transfer/stk_transfer/CMakeLists.txt +@@ -5,4 +5,4 @@ + FILE(GLOB HEADERS *.hpp) + + INSTALL(FILES ${HEADERS} DESTINATION +-${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_transfer/) ++${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_transfer/) +diff --git a/packages/stk/stk_util/stk_util/CMakeLists.txt b/packages/stk/stk_util/stk_util/CMakeLists.txt +index 02f4bf2..e95b05c 100644 +--- a/packages/stk/stk_util/stk_util/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/CMakeLists.txt +@@ -18,6 +18,6 @@ TRIBITS_CONFIGURE_FILE(STK_Trilinos_config.h) + INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR}) + + INSTALL(FILES stk_config.h DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) + INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/STK_Trilinos_config.h DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/) +diff --git a/packages/stk/stk_util/stk_util/diag/CMakeLists.txt b/packages/stk/stk_util/stk_util/diag/CMakeLists.txt +index 32115b6..184062a 100644 +--- a/packages/stk/stk_util/stk_util/diag/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/diag/CMakeLists.txt +@@ -76,5 +76,5 @@ TRIBITS_ADD_LIBRARY( + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/diag/) + +diff --git a/packages/stk/stk_util/stk_util/environment/CMakeLists.txt b/packages/stk/stk_util/stk_util/environment/CMakeLists.txt +index f3ecc5d..8268018 100644 +--- a/packages/stk/stk_util/stk_util/environment/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/environment/CMakeLists.txt +@@ -74,4 +74,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/environment/) +diff --git a/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt b/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt +index 51e11fd..dba3e15 100644 +--- a/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/parallel/CMakeLists.txt +@@ -93,4 +93,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/parallel/) +diff --git a/packages/stk/stk_util/stk_util/registry/CMakeLists.txt b/packages/stk/stk_util/stk_util/registry/CMakeLists.txt +index 2fa8a9b..dbc5000 100644 +--- a/packages/stk/stk_util/stk_util/registry/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/registry/CMakeLists.txt +@@ -71,5 +71,5 @@ TRIBITS_ADD_LIBRARY( + + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/registry/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/registry/) + +diff --git a/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt b/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt +index 4a39491..ed521a4 100644 +--- a/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/unit_test_support/CMakeLists.txt +@@ -79,4 +79,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/unit_test_support/) +diff --git a/packages/stk/stk_util/stk_util/util/CMakeLists.txt b/packages/stk/stk_util/stk_util/util/CMakeLists.txt +index b12d75e..054f60d 100644 +--- a/packages/stk/stk_util/stk_util/util/CMakeLists.txt ++++ b/packages/stk/stk_util/stk_util/util/CMakeLists.txt +@@ -76,4 +76,4 @@ TRIBITS_ADD_LIBRARY( + ) + + INSTALL(FILES ${HEADERS} DESTINATION +- ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/) ++ ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}/stk_util/util/) +diff --git a/packages/teuchos/kokkoscompat/src/CMakeLists.txt b/packages/teuchos/kokkoscompat/src/CMakeLists.txt +index 44e6593..7048850 100644 +--- a/packages/teuchos/kokkoscompat/src/CMakeLists.txt ++++ b/packages/teuchos/kokkoscompat/src/CMakeLists.txt +@@ -35,7 +35,7 @@ ENDIF() + # FIXME (mfh 19 Dec 2014) We should rely on TriBITS to handle + # installation. + +-SET(TRILINOS_INCDIR ${CMAKE_INSTALL_PREFIX}/${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}) ++SET(TRILINOS_INCDIR ${${PROJECT_NAME}_INSTALL_INCLUDE_DIR}) + + INSTALL(FILES ${HEADERS} DESTINATION ${TRILINOS_INCDIR}/) + +diff --git a/packages/trios/libraries/support/CMakeLists.txt b/packages/trios/libraries/support/CMakeLists.txt +index 3b8c4fd..175f736 100644 +--- a/packages/trios/libraries/support/CMakeLists.txt ++++ b/packages/trios/libraries/support/CMakeLists.txt +@@ -168,6 +168,6 @@ TRIBITS_ADD_LIBRARY( + + ########### install targets ############### + +-# INSTALL(FILES ${MODULES} DESTINATION ${CMAKE_INSTALL_PREFIX}/include) ++# INSTALL(FILES ${MODULES} DESTINATION include) + + TRIBITS_SUBPACKAGE_POSTPROCESS() +diff --git a/packages/zoltan/src/CMakeLists.txt b/packages/zoltan/src/CMakeLists.txt +index c312433..8a52ec4 100644 +--- a/packages/zoltan/src/CMakeLists.txt ++++ b/packages/zoltan/src/CMakeLists.txt +@@ -678,5 +678,5 @@ TRIBITS_ADD_LIBRARY( + IMPORTEDLIBS ${IMPORTEDLIBS} + ) + +-INSTALL(FILES ${MODULES} DESTINATION ${CMAKE_INSTALL_PREFIX}/include) ++INSTALL(FILES ${MODULES} DESTINATION include) + +diff --git a/packages/zoltan/src/fdriver/CMakeLists.txt b/packages/zoltan/src/fdriver/CMakeLists.txt +index 64345d3..e60c2e3 100644 +--- a/packages/zoltan/src/fdriver/CMakeLists.txt ++++ b/packages/zoltan/src/fdriver/CMakeLists.txt +@@ -35,6 +35,6 @@ TRIBITS_ADD_EXECUTABLE( + + # What is a good location for executables zdrive and zCPPdrive? + # When should they be moved there? During install? Or build? +-#INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/zfdrive.exe DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) ++#INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/zfdrive.exe DESTINATION bin) + + ENDIF() diff --git a/sci-libs/trilinos/metadata.xml b/sci-libs/trilinos/metadata.xml index 7d6e9e9c7..e1bfe00c5 100644 --- a/sci-libs/trilinos/metadata.xml +++ b/sci-libs/trilinos/metadata.xml @@ -1,40 +1,43 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>andyspiros@gmail.com</email> - </maintainer> - <longdescription lang="en"> - The Trilinos Project is an effort to develop algorithms and enabling - technologies within an object-oriented software framework for the solution - of large-scale, complex multi-physics engineering and scientific problems. + <herd>sci</herd> + <maintainer> + <email>andyspiros@gmail.com</email> + </maintainer> +<longdescription lang="en"> + The Trilinos Project is an effort to develop algorithms and enabling + technologies within an object-oriented software framework for the solution + of large-scale, complex multi-physics engineering and scientific problems. </longdescription> - <use> - <flag name="adolc">Undocumented USE</flag> - <flag name="arprec">Undocumented USE</flag> - <flag name="boost">Undocumented USE</flag> - <flag name="clp">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="cuda">Undocumented USE</flag> - <flag name="eigen">Undocumented USE</flag> - <flag name="glpk">Undocumented USE</flag> - <flag name="gtest">Undocumented USE</flag> - <flag name="hwloc">Undocumented USE</flag> - <flag name="hypre">Undocumented USE</flag> - <flag name="metis">Undocumented USE</flag> - <flag name="mkl">Undocumented USE</flag> - <flag name="mumps">Undocumented USE</flag> - <flag name="petsc">Undocumented USE</flag> - <flag name="qd">Undocumented USE</flag> - <flag name="scalapack">Undocumented USE</flag> - <flag name="scotch">Undocumented USE</flag> - <flag name="sparse">Undocumented USE</flag> - <flag name="superlu">Undocumented USE</flag> - <flag name="taucs">Undocumented USE</flag> - <flag name="tbb">Undocumented USE</flag> - <flag name="tvmet">Undocumented USE</flag> - <flag name="umfpack">Undocumented USE</flag> - <flag name="yaml">Undocumented USE</flag> - </use> +<use> + <flag name="adolc">Add support for adolc (<pkg>sci-libs/adolc</pkg>)</flag> + <flag name="arprec">Add support for arprec (<pkg>sci-libs/arprec</pkg>)</flag> + <flag name="boost">Add support for boost (<pkg>dev-libs/boost</pkg>)</flag> + <flag name="clp">Add support for clp (<pkg>sci-libs/coinor-clp</pkg>)</flag> + <flag name="cppunit">Add support for (<pkg></pkg>)</flag> + <flag name="cuda">Add support for cuda (<pkg>dev-util/nvidia-cuda-toolkit</pkg>)</flag> + <flag name="eigen">Add support for eigen (<pkg>dev-cpp/eigen</pkg>)</flag> + <flag name="glpk">Add support for (<pkg></pkg>)</flag> + <flag name="gtest">Add support for gtest (<pkg>dev-cpp/gtest</pkg>)</flag> + <flag name="hwloc">Add support for hwloc (<pkg>sys-apps/hwloc</pkg>)</flag> + <flag name="hdf5">Add support for hdf5 (<pkg>sci-libs/hdf5</pkg>)</flag> + <flag name="hypre">Add support for hypre (<pkg>sci-libs/hypre</pkg>)</flag> + <flag name="matio">Add support for matio (<pkg>sci-libs/matio</pkg>)</flag> + <flag name="metis">Add support for metis (<pkg>sci-libs/(par)metis</pkg>)</flag> + <flag name="mkl">Add support for mkl (<pkg>sci/libs/mkl</pkg>)</flag> + <flag name="mumps">Add support for mumps (<pkg>sci-libs/mumps</pkg>)</flag> + <flag name="netcdf">Add support for netcdf (<pkg>sci-libs/netcdf</pkg>)</flag> + <flag name="petsc">Add support for petsc (<pkg>sci-mathematics/petsc</pkg>)</flag> + <flag name="qd">Add support for qd (<pkg>sci-libs/qd</pkg>)</flag> + <flag name="scalapack">Add support for scalapack (<pkg>virtual/scalapack</pkg>)</flag> + <flag name="scotch">Add support for scotch (<pkg>sci-libs/scotch</pkg>)</flag> + <flag name="sparse">Add support for sparse matrix solvers (<pkg>sci-libs/umfpack</pkg>)</flag> + <flag name="superlu">Add support for superlu (<pkg>sci-libs/superlu</pkg>)</flag> + <flag name="taucs">Add support for taucs (<pkg>sci-libs/taucs</pkg>)</flag> + <flag name="tbb">Add support for threading building blocks library (<pkg>dev-cpp/tbb</pkg>)</flag> + <flag name="tvmet">Add support for tvmet (<pkg>dev-libs/tvmet</pkg>)</flag> + <flag name="umfpack">Add support for umfpack (<pkg>sci-libs/umfpack</pkg>)</flag> + <flag name="yaml">Add support for yaml (<pkg>dev-cpp-yaml</pkg>)</flag> +</use> </pkgmetadata> diff --git a/sci-libs/trilinos/trilinos-11.0.3.ebuild b/sci-libs/trilinos/trilinos-11.0.3.ebuild index e50a2e1af..7075a106b 100644 --- a/sci-libs/trilinos/trilinos-11.0.3.ebuild +++ b/sci-libs/trilinos/trilinos-11.0.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,7 @@ inherit cmake-utils toolchain-funcs DESCRIPTION="Scientific library collection for large scale problems" HOMEPAGE="http://trilinos.sandia.gov/" -SRC_URI="${P}-Source.tar.gz" +SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz" SRC_PAGE="11.0" SLOT="0" @@ -16,8 +16,6 @@ LICENSE="BSD LGPL-2.1" KEYWORDS="~amd64 ~x86" IUSE="arprec boost cuda hdf5 hwloc netcdf qd qt4 scotch taucs tbb test umfpack zlib" -RESTRICT="fetch" - RDEPEND=" virtual/blas virtual/lapack diff --git a/sci-libs/trilinos/trilinos-11.10.2.ebuild b/sci-libs/trilinos/trilinos-11.10.2.ebuild index 39f3a44ac..56696fa52 100644 --- a/sci-libs/trilinos/trilinos-11.10.2.ebuild +++ b/sci-libs/trilinos/trilinos-11.10.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,7 @@ inherit cmake-utils toolchain-funcs multilib toolchain-funcs DESCRIPTION="Scientific library collection for large scale problems" HOMEPAGE="http://trilinos.sandia.gov/" -SRC_URI="${P}-Source.tar.bz2" +SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -23,7 +23,7 @@ IUSE=" " # TODO: fix export cmake function for tests -RESTRICT="test fetch" +RESTRICT="test" RDEPEND=" virtual/blas diff --git a/sci-libs/trilinos/trilinos-11.12.1.ebuild b/sci-libs/trilinos/trilinos-11.12.1-r1.ebuild index 51734a4e3..237bcf447 100644 --- a/sci-libs/trilinos/trilinos-11.12.1.ebuild +++ b/sci-libs/trilinos/trilinos-11.12.1-r1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,7 @@ inherit cmake-utils toolchain-funcs multilib toolchain-funcs DESCRIPTION="Scientific library collection for large scale problems" HOMEPAGE="http://trilinos.sandia.gov/" -SRC_URI="${P}-Source.tar.bz2" +SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -23,7 +23,7 @@ IUSE=" " # TODO: fix export cmake function for tests -RESTRICT="test fetch" +RESTRICT="test" RDEPEND=" virtual/blas diff --git a/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild b/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild new file mode 100644 index 000000000..668ae4804 --- /dev/null +++ b/sci-libs/trilinos/trilinos-11.14.1-r1.ebuild @@ -0,0 +1,207 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils toolchain-funcs multilib toolchain-funcs + +DESCRIPTION="Scientific library collection for large scale problems" +HOMEPAGE="http://trilinos.sandia.gov/" +SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +LICENSE="BSD LGPL-2.1" +SLOT="0" + +IUSE=" + adolc arprec boost clp cppunit cuda eigen glpk gtest hdf5 hwloc hypre + matio metis mkl mumps netcdf petsc qd qt4 scalapack scotch sparse + superlu taucs tbb test threads tvmet yaml zlib +" + +# TODO: fix export cmake function for tests +RESTRICT="test" + +RDEPEND=" + virtual/blas + virtual/lapack + virtual/mpi + adolc? ( sci-libs/adolc ) + arprec? ( sci-libs/arprec ) + boost? ( dev-libs/boost ) + clp? ( sci-libs/coinor-clp ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 ) + eigen? ( dev-cpp/eigen:3 ) + gtest? ( dev-cpp/gtest ) + hdf5? ( sci-libs/hdf5[mpi] ) + hypre? ( sci-libs/hypre ) + hwloc? ( sys-apps/hwloc ) + matio? ( sci-libs/matio ) + mkl? ( sci-libs/mkl ) + metis? ( || ( sci-libs/parmetis sci-libs/metis ) ) + mumps? ( sci-libs/mumps ) + netcdf? ( sci-libs/netcdf ) + petsc? ( sci-mathematics/petsc ) + qd? ( sci-libs/qd ) + qt4? ( dev-qt/qtgui:4 ) + scalapack? ( virtual/scalapack ) + scotch? ( sci-libs/scotch ) + sparse? ( sci-libs/cxsparse sci-libs/umfpack ) + superlu? ( sci-libs/superlu ) + taucs? ( sci-libs/taucs ) + tbb? ( dev-cpp/tbb ) + tvmet? ( dev-libs/tvmet ) + yaml? ( dev-cpp/yaml-cpp ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${P}-Source" + +trilinos_conf() { + local dirs libs d + for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do + dirs="${dirs};${d:2}" + done + [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" ) + for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do + libs="${libs};${d:2}" + done + [[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" ) + dirs="" + for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do + dirs="${dirs};${d:2}" + done + [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" ) +} + +trilinos_enable() { + cmake-utils_use $1 TPL_ENABLE_${2:-${1^^}} +} + +src_prepare() { + epatch "${FILESDIR}"/${P}-fix-install-paths.patch + epatch "${FILESDIR}"/${P}-fix_install_paths_for_destdir.patch +} + +src_configure() { + + # temporarily disable SEACAS and pyTrilinos compilation + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DCMAKE_INSTALL_PREFIX="${EPREFIX}" + -DTrilinos_ENABLE_ALL_PACKAGES=ON + -DTrilinos_ENABLE_SEACAS=OFF + -DTrilinos_ENABLE_PyTrilinos=OFF + -DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos" + -DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos" + -DTrilinos_INSTALL_CONFIG_DIR="${EPREFIX}/usr/$(get_libdir)/cmake" + -DTPL_ENABLE_BinUtils=ON + -DTPL_ENABLE_MPI=ON + -DTPL_ENABLE_BLAS=ON + -DTPL_ENABLE_LAPACK=ON + $(cmake-utils_use test Trilinos_ENABLE_TESTS) + $(trilinos_enable adolc) + $(trilinos_enable arprec) + $(trilinos_enable boost Boost) + $(trilinos_enable boost BoostLib) + $(trilinos_enable cppunit Cppunit) + $(trilinos_enable clp Clp) + $(trilinos_enable cuda) + $(trilinos_enable cuda CUSPARSE) + $(trilinos_enable cuda Thrust) + $(trilinos_enable eigen Eigen) + $(trilinos_enable gtest gtest) + $(trilinos_enable glpk) + $(trilinos_enable hdf5) + $(trilinos_enable hwloc) + $(trilinos_enable hypre) + $(trilinos_enable matio) + $(trilinos_enable metis) + $(trilinos_enable mkl) + $(trilinos_enable mkl PARDISO_MKL) + $(trilinos_enable mumps) + $(trilinos_enable netcdf Netcdf) + $(trilinos_enable petsc) + $(trilinos_enable qd) + $(trilinos_enable qt4 QT) + $(trilinos_enable scalapack) + $(trilinos_enable scalapack BLACS) + $(trilinos_enable scotch Scotch) + $(trilinos_enable sparse AMD) + $(trilinos_enable sparse CSparse) + $(trilinos_enable sparse UMFPACK) + $(trilinos_enable superlu SuperLU) + $(trilinos_enable taucs) + $(trilinos_enable tbb) + $(trilinos_enable threads Pthread) + $(trilinos_enable tvmet) + $(trilinos_enable yaml yaml-cpp) + $(trilinos_enable zlib Zlib) + ) + + use eigen && \ + mycmakeargs+=( + -DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3" + ) + use hypre && \ + mycmakeargs+=( + -DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre" + ) + use scotch && \ + mycmakeargs+=( + -DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch" + ) + + # cxsparse is a rewrite of csparse + extras + use sparse && \ + mycmakeargs+=( + -DCSparse_LIBRARY_NAMES="cxsparse" + ) + + # mandatory blas and lapack + trilinos_conf blas BLAS + trilinos_conf lapack LAPACK + use superlu && trilinos_conf superlu SuperLU + use metis && trilinos_conf metis METIS + + # blacs library is included in scalapack these days + if use scalapack; then + trilinos_conf scalapack SCALAPACK + mycmakeargs+=( + -DBLACS_LIBRARY_NAMES="scalapack" + -DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs" + ) + fi + + # TODO: do we need that line? + export CC=mpicc CXX=mpicxx && tc-export CC CXX + + # cmake-utils eclass patches the base directory CMakeLists.txt + # which does not work for complex Trilinos CMake modules + CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure + + # TODO: + # python bindings with python-r1 + # fix hypre bindings + # fix hdf5 + # cuda/thrust is untested + # do we always need mpi? and for all packages: blah[mpi] ? + # install docs, examples + # see what packages are related, do we need REQUIRED_USE + # proper use flags description + # add more use flags/packages ? +} + +src_install() { + cmake-utils_src_install + + # register $(get_libdir)/trilinos in LDPATH so that the dynamic linker + # has a chance to pick up the libraries... + cat >> "${T}"/99trilinos <<- EOF + LDPATH="${EPREFIX}/usr/$(get_libdir)/trilinos" + EOF + doenvd "${T}"/99trilinos +} diff --git a/sci-libs/trilinos/trilinos-11.4.2.ebuild b/sci-libs/trilinos/trilinos-11.4.2.ebuild index 51734a4e3..237bcf447 100644 --- a/sci-libs/trilinos/trilinos-11.4.2.ebuild +++ b/sci-libs/trilinos/trilinos-11.4.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -8,7 +8,7 @@ inherit cmake-utils toolchain-funcs multilib toolchain-funcs DESCRIPTION="Scientific library collection for large scale problems" HOMEPAGE="http://trilinos.sandia.gov/" -SRC_URI="${P}-Source.tar.bz2" +SRC_URI="http://trilinos.org/oldsite/download/files/${P}-Source.tar.gz" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -23,7 +23,7 @@ IUSE=" " # TODO: fix export cmake function for tests -RESTRICT="test fetch" +RESTRICT="test" RDEPEND=" virtual/blas diff --git a/sci-libs/wannier90/ChangeLog b/sci-libs/wannier90/ChangeLog index c778e5eee..8d5bf129b 100644 --- a/sci-libs/wannier90/ChangeLog +++ b/sci-libs/wannier90/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-libs/wannier90 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*wannier90-2.0.1 (22 Apr 2015) + + 22 Apr 2015; Honza Macháček <Hloupy.Honza@centrum.cz> + +wannier90-2.0.1.ebuild: + Version bump to sci-libs/wannier90-2.0.1, new dependency on dev-tex/revtex + introduced if USE=doc + *wannier90-2.0.0 (10 Dec 2014) *wannier90-1.2-r3 (10 Dec 2014) diff --git a/sci-libs/wannier90/Manifest b/sci-libs/wannier90/Manifest index 8a8829898..6702b0b7c 100644 --- a/sci-libs/wannier90/Manifest +++ b/sci-libs/wannier90/Manifest @@ -1,2 +1,3 @@ DIST wannier90-1.2.tar.gz 5643731 SHA256 a76f88eef01c5a40aaa2c74ee393ede8a57bd9085f6b7f2ab656b50c1a30ece4 SHA512 323d078d0cdeeb361389600c39501410ca0da2879e8ba7d3262b49a76167e5385c09484eed47607d83feb68c9f16cfb6cdcebe89f7846157e0c71a8598238853 WHIRLPOOL 7e3288a85188d4661467d293d4a57973e926bf5a3b5736f83ed51e16a0fc4155ecc86e4e6dc6638b8a4d6373ca718ffd341cc11bde466d0166c1e591a9ac33c5 DIST wannier90-2.0.0.tar.gz 46152394 SHA256 e419a721541c16e89de66b8eefe2c41042dd7ff78a1fe8d61554a00efe79382a SHA512 87d9ae7f0f0343e188711bc2cea2124ef1e13482e87a0c2a7d250c36cabeb9d0a6da9eba92781763a0e65665c48f9bae4cd12f5f5390f87a7e8f15c508411efc WHIRLPOOL d9bafcab196735d182518dd71fc4ae7618a4cfdd9e21e450f4d5b17b288bb1ae43c93bdde5d3fca0b180377881f7443b00cc7dc989edf5609133271d01c00bab +DIST wannier90-2.0.1.tar.gz 48327121 SHA256 05ea7cd421a219ce19d379ad6ae3d9b1a84be4ffb367506ffdfab1e729309e94 SHA512 dd7deb43272a9f0697ae59e272816a74ae15f7adb95f4c5d7ea40d98f8293b678da97494df471077a096f207d7a194a27ed09d6f456a8db20fe91e4f596602c4 WHIRLPOOL ab153c1983fc092b4de0312fc93506f0cf8622655fedecdf852e0b9a4f861d8913387007fd3aac780556ea33930efb39377d6469f5e943410c8a5300cff271a4 diff --git a/sci-libs/wannier90/wannier90-2.0.1.ebuild b/sci-libs/wannier90/wannier90-2.0.1.ebuild new file mode 100644 index 000000000..b0125e65d --- /dev/null +++ b/sci-libs/wannier90/wannier90-2.0.1.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils fortran-2 multilib toolchain-funcs + +DESCRIPTION="Calculates maximally localized Wannier functions (MLWFs)" +HOMEPAGE="http://www.wannier.org/" +SRC_URI="http://wannier.org/code/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="doc examples perl test" + +RDEPEND=" + virtual/blas + virtual/lapack + perl? ( dev-lang/perl )" +DEPEND="${RDEPEND} + virtual/pkgconfig + doc? ( virtual/latex-base + dev-texlive/texlive-latexextra + dev-tex/revtex + )" + +src_configure() { + cat <<- EOF >> "${S}"/make.sys + F90 = $(tc-getFC) + FCOPTS = ${FCFLAGS:- ${FFLAGS:- -O2}} + LDOPTS = ${LDFLAGS} + LIBS = $($(tc-getPKG_CONFIG) --libs blas lapack) + EOF +} + +src_compile() { + emake -j1 wannier + emake -j1 lib + if use doc; then + VARTEXFONTS="${T}/fonts" + emake -j1 doc + fi +} + +src_test() { + einfo "Compare the 'Standard' and 'Current' outputs of this test." + pushd tests + emake test + cat wantest.log +} + +src_install() { + dobin wannier90.x + use perl && dobin utility/kmesh.pl + dolib.a libwannier.a + insinto /usr/include + doins src/obj/*.mod + if use examples; then + insinto /usr/share/${PN} + doins -r examples + fi + use doc && dodoc doc/*.pdf + dodoc README README.install CHANGE.log +} diff --git a/sci-libs/xraylib/ChangeLog b/sci-libs/xraylib/ChangeLog index 0698f696d..38be18a88 100644 --- a/sci-libs/xraylib/ChangeLog +++ b/sci-libs/xraylib/ChangeLog @@ -1,7 +1,18 @@ # ChangeLog for sci-libs/xraylib -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> xraylib-2.16.0.ebuild, + xraylib-3.1.0.ebuild: + sci-libs/xraylib: Add slot operators + + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/xraylib: Add github to remote-id in metadata.xml + +*xraylib-3.1.0 (03 Apr 2015) + + 03 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> +xraylib-3.1.0.ebuild: + Version bump, fixes Bug 538232 + 08 Dec 2013; Justin Lecher <jlec@gentoo.org> xraylib-2.16.0.ebuild: Make python stuff optional under USE=python - diff --git a/sci-libs/xraylib/Manifest b/sci-libs/xraylib/Manifest index eaaa7282f..40ddde60f 100644 --- a/sci-libs/xraylib/Manifest +++ b/sci-libs/xraylib/Manifest @@ -1 +1,2 @@ DIST xraylib-2.16.0.tar.gz 39669898 SHA256 84dcf6b3171d17ac8f78ac85d39c1a0e1f8567e69eac8552ece0cea5c85c2733 SHA512 0232bea0f934cb13fd30a9964aa52fc8eeae82fc40c263f7196041d58b272c99e177254268b43f091361b51c0046bedb9dfce88684a01c9da0ad33878b2b753c WHIRLPOOL 3e44e524380657a940a77ed210cf054a00c8b636cece794a6d2bdc32cce82f8bdd1c3eb77c5eae80d21a7e9c73ab4c104414e60c57147cfbf02d8b279db7aeeb +DIST xraylib-3.1.0.tar.gz 32882324 SHA256 32263a234801ab12641b4660cb5fecf531edf85be09ca936a14b18b053324015 SHA512 0b090e6096d047a32552477a4cfe46203b69f8d858bae2b053f877cf713219432b8a0779dfc6eaa48c82568407ba56bbf565c8491d6416001f9c8fb80b714f01 WHIRLPOOL 2d4c74a590d80bdd6d2325f49db61582eab86041af527f4bb44b1357f8b66cdf9daad68351077eeae830632bfaad9dcc1203644afa476e24b0dac73c1dbe223b diff --git a/sci-libs/xraylib/metadata.xml b/sci-libs/xraylib/metadata.xml index a592314d3..16a3a5861 100644 --- a/sci-libs/xraylib/metadata.xml +++ b/sci-libs/xraylib/metadata.xml @@ -35,4 +35,7 @@ </longdescription> <use> </use> + <upstream> + <remote-id type="github">tschoonj/xraylib</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/xraylib/xraylib-2.16.0.ebuild b/sci-libs/xraylib/xraylib-2.16.0.ebuild index bce10688a..5d9e764cf 100644 --- a/sci-libs/xraylib/xraylib-2.16.0.ebuild +++ b/sci-libs/xraylib/xraylib-2.16.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -7,7 +7,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=true FORTRAN_NEEDED=fortran FORTRAN_STANDARD=2003 -PYTHON_COMPAT=( python{2_6,2_7} ) # python 3 supported by github master +PYTHON_COMPAT=( python2_7 ) # python 3 supported by github master inherit eutils autotools-utils python-single-r1 java-pkg-opt-2 fortran-2 @@ -23,13 +23,13 @@ IUSE="examples fortran java lua perl python" REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" RDEPEND=" - java? ( >=virtual/jre-1.4 ) - lua? ( dev-lang/lua ) + java? ( >=virtual/jre-1.4:* ) + lua? ( dev-lang/lua:0 ) perl? ( dev-lang/perl ) python? ( ${PYTHON_DEPS} )" DEPEND="${RDEPEND} - java? ( >=virtual/jdk-1.4 )" + java? ( >=virtual/jdk-1.4:* )" S="${WORKDIR}/${PN}-${P}" diff --git a/sci-libs/xraylib/xraylib-3.1.0.ebuild b/sci-libs/xraylib/xraylib-3.1.0.ebuild new file mode 100644 index 000000000..5d9e764cf --- /dev/null +++ b/sci-libs/xraylib/xraylib-3.1.0.ebuild @@ -0,0 +1,84 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=true +FORTRAN_NEEDED=fortran +FORTRAN_STANDARD=2003 +PYTHON_COMPAT=( python2_7 ) # python 3 supported by github master + +inherit eutils autotools-utils python-single-r1 java-pkg-opt-2 fortran-2 + +DESCRIPTION="A library for X-ray matter interaction cross sections for X-ray fluorescence applications" +HOMEPAGE="https://github.com/tschoonj/xraylib" +SRC_URI="https://github.com/tschoonj/xraylib/archive/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="examples fortran java lua perl python" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RDEPEND=" + java? ( >=virtual/jre-1.4:* ) + lua? ( dev-lang/lua:0 ) + perl? ( dev-lang/perl ) + python? ( ${PYTHON_DEPS} )" + +DEPEND="${RDEPEND} + java? ( >=virtual/jdk-1.4:* )" + +S="${WORKDIR}/${PN}-${P}" + +DOCS=(AUTHORS BUGS Changelog README TODO) + +pkg_setup() { + fortran-2_pkg_setup + java-pkg-opt-2_pkg_setup + use python && python-single-r1_pkg_setup +} + +src_prepare() { + java-pkg-opt-2_src_prepare + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + --disable-idl + $(use_enable fortran fortran2003) + $(use_enable java) + $(use_enable lua) + $(use_enable perl) + $(use_enable python) + $(use_enable python python-integration) + ) + autotools-utils_src_configure +} + +src_compile() { + # see https://github.com/tschoonj/xraylib/issues/11 + if use fortran || use java; then + MAKEOPTS+=" -j1" + fi + autotools-utils_src_compile +} + +src_install() { + autotools-utils_src_install + + if use examples; then + insinto /usr/share/doc/${PF}/examples + doins example/*.c example/*.cpp + use java && doins example/*.java + use lua && doins example/*.lua + use perl && doins example/*.pl + use python && doins example/*.py + docompress -x /usr/share/doc/${PF}/examples # Don't compress examples + fi + + use java && java-pkg_regso /usr/share/xraylib/java/libxraylib.so +} diff --git a/sci-libs/zarja/ChangeLog b/sci-libs/zarja/ChangeLog index 173c5ec59..8028e709c 100644 --- a/sci-libs/zarja/ChangeLog +++ b/sci-libs/zarja/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/zarja -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-libs/zarja: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> zarja-1.1.1.ebuild, metadata.xml: Move to EAPI=5; fix slot for fftw dep; move to virtual/pkgconfig; clean @@ -12,4 +15,3 @@ 16 Apr 2009; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml, +zarja-1.1.1.ebuild: Initial import to science overlay - bug #254832 - Thanks Hynek Lavička - diff --git a/sci-libs/zarja/metadata.xml b/sci-libs/zarja/metadata.xml index 65dfd5ca8..a5548374a 100644 --- a/sci-libs/zarja/metadata.xml +++ b/sci-libs/zarja/metadata.xml @@ -7,4 +7,7 @@ simulations on graphs. Its functionality was proved in Classical or Quantum mechanical models. </longdescription> + <upstream> + <remote-id type="sourceforge">zarja</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild index 0a517199c..81825a337 100644 --- a/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild +++ b/sci-mathematics/Macaulay2/Macaulay2-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit autotools elisp-common eutils flag-o-matic git-r3 python-single-r1 toolchain-funcs diff --git a/sci-mathematics/acl2/ChangeLog b/sci-mathematics/acl2/ChangeLog index 995db6561..108ca3f59 100644 --- a/sci-mathematics/acl2/ChangeLog +++ b/sci-mathematics/acl2/ChangeLog @@ -1,7 +1,23 @@ # ChangeLog for sci-mathematics/acl2 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*acl2-7.1 (16 Jun 2015) + + 16 Jun 2015; zcj <ustcscgy@163.com> +acl2-7.1.ebuild, -acl2-7.0.ebuild, + metadata.xml: + sci-mathematics/acl2: sci-mathematics/acl2: Version bump; Upstream url + changes. + + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/acl2: Add github to remote-id in metadata.xml + +*acl2-7.0 (25 Mar 2015) + + 25 Mar 2015; zcj <ustcscgy@163.com> +acl2-7.0.ebuild, -acl2-6.3.ebuild, + -files/set-booksdir.patch, metadata.xml: + sci-mathematics/acl2: sci-mathematics/acl2 version bump, drop old + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> -acl2-4.2.ebuild, -acl2-4.3.ebuild: Drop old @@ -28,4 +44,3 @@ 12 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> +acl2-4.2.ebuild +ChangeLog +metadata.xml : Initial import. #49316 - diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest index 4cdd06d66..1444f00a9 100644 --- a/sci-mathematics/acl2/Manifest +++ b/sci-mathematics/acl2/Manifest @@ -1,3 +1 @@ -DIST acl2-6.3.tar.gz 7068895 SHA256 ee7ca85232c36068516e8852a5b31fcd8f38cb2596ce8d4d7934009e28400bb9 SHA512 e79c7da62b7edf7d02080a750f767c2d71a8565b2ff54c4421ab48a6df0c191bc29e54b7496b63ea025980bbcf790a5fc6a7211ce5c639537dda4127296fc529 WHIRLPOOL 1b2d669c6ff4369ed5a32ac1e9a8802218814f12e04312dbdea90b3d704edefcaf4f795fdc5b98a67fd47ca9b2bcee3d35ea16bc71e1c7656e7fc70002d9b03d -DIST books-6.3.tar.gz 13598991 SHA256 29f9c5b1de6131695b01153f337bb107869e9ae0c1b506e46a3de9373bbd1bfa SHA512 5bde2d2118bd67c3efcff79e22d43513cf6545fc0c7143bdfb70aec6a018f06eb995df29ed1d67d81ce24f61dc8f7fa900874e1f64f25ed05346bfa508ebc21f WHIRLPOOL 28e371556dd24362daaa7906a70dfe9c5f9a88d2b2d5b78b1b8c91c0cf2e6674ac09b78fa433286cba34bf4cd324d902053e3894b50bccd19fed703659b0dbf5 -DIST workshops-6.3.tar.gz 29675655 SHA256 203a65d8d8b42d41a202c34255cf2603fcb5d6b568938550603bdd48e5248164 SHA512 3b6016780ae4310287c859907350905f9e531b33f4b4e29c23462e09caa6ec8720f4923eb6b61f4d9ac2789c8e9109b5943f2bd9ad9c3da70b560bdcf5d27a26 WHIRLPOOL d0868690981c464fc1900173c073180c5c47c424a1ef16a7081dbd42d10f4b7f66767d5b8f5c0336e13eeb14bfcb00633f2f572a63f99b750bbbf069374482a2 +DIST acl2-7.1.tar.gz 63345284 SHA256 1a8503095a4e1deb6a6b0f3bc51823ba65cad38466def8d6845f193d73338f9d SHA512 5875b88615930fc841cd1d7ed30ada7c04b241a391eeee22184b4e3630e57cc6304a51e445e33ca1284576c2b4110c269f9eb59c47bd2eb47659134450151e27 WHIRLPOOL 632012e3d8998c67f70cd19b8fa7c7ff8000dbdba2d87dfdd56d5b4b39ebb390503d243e051c308c8a5aea0097bb48fa4e5c510b24478886a4a8bfca2c8d0645 diff --git a/sci-mathematics/acl2/acl2-6.3.ebuild b/sci-mathematics/acl2/acl2-6.3.ebuild deleted file mode 100644 index 5302b3c55..000000000 --- a/sci-mathematics/acl2/acl2-6.3.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="ACL2 industrial strength theorem prover" -HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI=" - http://www.cs.utexas.edu/users/moore/${PN}/v${PV/\./-}/distrib/${PN}.tar.gz -> ${P}.tar.gz - books? ( https://acl2-books.googlecode.com/files/books-${PV}.tar.gz - workshops? ( http://acl2-books.googlecode.com/files/workshops-${PV}.tar.gz ) )" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="+books workshops html" - -REQUIRED_USE="workshops? ( books )" - -DEPEND=" - dev-lisp/sbcl - books? ( dev-lang/perl )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}-sources" - -src_unpack() { - default - if use books; then - mv "${WORKDIR}/books" "${S}"/ || die - if use workshops; then - mv "${WORKDIR}/workshops" "${S}/books/" || die - fi - fi -} - -src_compile() { - emake LISP="sbcl --noinform --noprint" - - if use books; then - echo - einfo "Building certificates ..." - einfo "(this may take hours to finish)" - emake regression - fi -} - -src_install() { - sed -e "s:${S}:/usr/share/acl2:g" -i saved_acl2 || die - if use books; then - sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i saved_acl2 || die - fi - dobin saved_acl2 - - insinto /usr/share/acl2 - doins TAGS saved_acl2.core - if use books; then - doins -r books - fi - - if use html; then - dohtml -r doc/HTML - fi - doinfo doc/EMACS/* -} diff --git a/sci-mathematics/acl2/acl2-7.1.ebuild b/sci-mathematics/acl2/acl2-7.1.ebuild new file mode 100644 index 000000000..8378eafb5 --- /dev/null +++ b/sci-mathematics/acl2/acl2-7.1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="Industrial strength theorem prover" +HOMEPAGE="http://www.cs.utexas.edu/users/moore/acl2/" +MY_PN=${PN}-devel +SRC_URI="https://github.com/${MY_PN}/${MY_PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +IUSE="books" + +DEPEND=" + dev-lisp/sbcl:= + books? ( dev-lang/perl )" +RDEPEND="${DEPEND}" +S="${WORKDIR}/${MY_PN}-${PV}" + +src_compile() { + emake LISP="sbcl --noinform --noprint \ + --no-sysinit --no-userinit --disable-debugger" + + if use books; then + echo + einfo "Building certificates ..." + einfo "(this may take hours to finish)" + emake certify-books + fi +} + +src_install() { + SAVED_NAME=saved_acl2 + sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die + if use books; then + sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ + -i ${SAVED_NAME} || die + fi + dobin ${SAVED_NAME} + + insinto /usr/share/acl2 + doins TAGS ${SAVED_NAME}.core + if use books; then + doins -r books + fi +} diff --git a/sci-mathematics/acl2/files/set-booksdir.patch b/sci-mathematics/acl2/files/set-booksdir.patch deleted file mode 100644 index 4f4d4334a..000000000 --- a/sci-mathematics/acl2/files/set-booksdir.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/books/Makefile-generic 2011-04-12 14:42:17.790165650 -0400 -+++ b/books/Makefile-generic 2011-04-12 14:55:54.436829607 -0400 -@@ -55,7 +55,7 @@ - # Determine the location of this Makefile-generic. NOTE: We have - # tried $(realpath $(dir ...)) and similarly for abspath, but they - # have returned the empty string, presumably an error. --BOOKS_DIR := $(dir $(word $(words $(MAKEFILE_LIST)),$(MAKEFILE_LIST))) -+BOOKS_DIR := /usr/share/acl2/books/ - - # and use that to determine the default location of ACL2. To override, - # set the ACL2 variable on the command line or in the environment. diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml index d0675a2ec..0782df404 100644 --- a/sci-mathematics/acl2/metadata.xml +++ b/sci-mathematics/acl2/metadata.xml @@ -1,29 +1,24 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-mathematics</herd> - <maintainer> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>ACL2 industrial strength theorem prover</description> - </maintainer> - <longdescription> -ACL2 is both a programming language in which you can model computer systems and -a tool to help you prove properties of those models. ACL2 is part of the -Boyer-Moore family of provers, for which its authors have received the 2005 ACM + <herd>sci-mathematics</herd> + <maintainer> + <email>dongxuli2011@gmail.com</email> + <name>Dongxu Li</name> + <description>Industrial strength theorem prover</description> + </maintainer> + <longdescription> +ACL2 is both a programming language in which you can model computer systems and +a tool to help you prove properties of those models. ACL2 is part of the +Boyer-Moore family of provers, for which its authors have received the 2005 ACM Software System Award. -</longdescription> - <use> - <flag name="books"> + </longdescription> + <use> + <flag name="books"> build community books, the canonical collection of open-source libraries -</flag> - </use> - <use> - <flag name="html"> Install HTML documentation</flag> - </use> - <use> - <flag name="workshops"> - build community books from ACL2 community workshops -</flag> - </use> + </flag> + </use> + <upstream> + <remote-id type="github">acl2-devel/acl2-devel</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/burrtools/ChangeLog b/sci-mathematics/burrtools/ChangeLog index bec5130ec..25b103241 100644 --- a/sci-mathematics/burrtools/ChangeLog +++ b/sci-mathematics/burrtools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/burrtools -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/burrtools: Updating remote-id in metadata.xml + 05 Apr 2011; Justin Lecher <jlec@gentoo.org> burrtools-0.5.2-r1.ebuild: Corrected Slot of fltk to 1 @@ -16,4 +19,3 @@ 13 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +burrtools-0.5.2.ebuild, +metadata.xml: Initial import. Ebuild initially submitted by Andreas Röver, bug #171816 - diff --git a/sci-mathematics/burrtools/metadata.xml b/sci-mathematics/burrtools/metadata.xml index cd544f35c..aff4a5140 100644 --- a/sci-mathematics/burrtools/metadata.xml +++ b/sci-mathematics/burrtools/metadata.xml @@ -1,11 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription lang='en'> + <herd>sci-mathematics</herd> + <longdescription lang="en"> This (set of) program(s) will help you solve a certain kind of puzzle. Namely puzzles that are made out of square or dice shaped units, spheres or prisms with an equilateral triangle as base and where the pieces are also aligned along those grids in the solutions. </longdescription> + <upstream> + <remote-id type="sourceforge">burrtools</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/cdfplayer/ChangeLog b/sci-mathematics/cdfplayer/ChangeLog index fff3a0ad2..41635cb40 100644 --- a/sci-mathematics/cdfplayer/ChangeLog +++ b/sci-mathematics/cdfplayer/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/cdfplayer -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*cdfplayer-10.0.2 (08 Mar 2015) + + 08 Mar 2015; zcj <ustcscgy@163.com> +cdfplayer-10.0.2.ebuild, + -cdfplayer-9.0.1.ebuild, -files/cdfplayer-9.0.1-installer.patch: + sci-mathematics/cdfplayer: Version bump; Patch is not needed. + *cdfplayer-9.0.1 (11 Mar 2013) 11 Mar 2013; Jauhien Piatlicki (jauhien) <piatlicki@gmail.com> @@ -22,4 +28,3 @@ +cdfplayer-8.0.4.ebuild, +files/cdfplayer-8.0.4-installer.patch, +metadata.xml: initial commit for bug #421019 - diff --git a/sci-mathematics/cdfplayer/Manifest b/sci-mathematics/cdfplayer/Manifest index 571c6ebcb..081ad1bdf 100644 --- a/sci-mathematics/cdfplayer/Manifest +++ b/sci-mathematics/cdfplayer/Manifest @@ -1 +1 @@ -DIST CDFPlayer_9.0.1_LINUX.sh 626338589 SHA256 fff328f92df33b502a7b3f90869ce48d61ae862a0ad404fb1a7e0f44d7514499 SHA512 74692895b8f463ee85b8da52458d05b8eabe015895fb5dac2b5f9fbac3a96aaaac6ae904e3238d3aa5201bb9fd83d5c8b2715ae9f4e334f871c2c5e375b6f33e WHIRLPOOL 162ee5bc00d8edaa3e346af37b9a8671265329b9b574031268db794af6b19b6e375daa9a80089fcdccd9f4f28eee6070878dcacfb7b7619e5cf571b21d852cd4 +DIST CDFPlayer_10.0.2_LINUX.sh 940706589 SHA256 e6e7f950c68a076a9e1bbe35f90fa24e4a60043d87883730e1641fc486c98219 SHA512 c1117ef746500a3befa3744a30c1914624ad7b624a2a4a0a2ac2a9e80776dc3732af6f03690fef37dee4a7f935fb94a11d0dea09f8b62f448cfbfb90e115e9b4 WHIRLPOOL 150a933303d5e1455d54fe0f5662b49a740902ab3cb987d33756d5907649cdb5f28ea6f0644bd1615afaaf13ca8a77ec020aa7c1b1cf9b236681bef4f26f620f diff --git a/sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild b/sci-mathematics/cdfplayer/cdfplayer-10.0.2.ebuild index b2052117e..231397f7e 100644 --- a/sci-mathematics/cdfplayer/cdfplayer-9.0.1.ebuild +++ b/sci-mathematics/cdfplayer/cdfplayer-10.0.2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -7,7 +7,7 @@ EAPI=5 inherit eutils MY_SCRIPT=CDFPlayer_${PV}_LINUX.sh -MY_DESKTOPFILE=${ED}/opt/wolfram/SystemFiles/Installation/wolfram-cdf9.desktop +MY_DESKTOPFILE=${ED}/opt/wolfram/SystemFiles/Installation/wolfram-cdf10.desktop DESCRIPTION="Player for Wolfram CDF" HOMEPAGE="http://www.wolfram.com/cdf-player/" @@ -30,12 +30,8 @@ src_unpack() { chmod u+x "${S}/${MY_SCRIPT}" || die } -src_prepare() { - epatch "${FILESDIR}/${P}-installer.patch" -} - src_install() { - "${S}/${MY_SCRIPT}" --target "${S}/${P}" -- -auto -verbose -createdir=y \ + "${S}/${MY_SCRIPT}" --target "${S}/${P}" --nox11 -- -auto -verbose -createdir=y \ -targetdir="${ED}/opt/wolfram" -execdir="${ED}/usr/bin" || die find "${ED}" -name '*.desktop' -exec \ sed -i "s%${ED}%/%g" {} \; || die diff --git a/sci-mathematics/cdfplayer/files/cdfplayer-9.0.1-installer.patch b/sci-mathematics/cdfplayer/files/cdfplayer-9.0.1-installer.patch deleted file mode 100644 index 1ec036b14..000000000 --- a/sci-mathematics/cdfplayer/files/cdfplayer-9.0.1-installer.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- CDFPlayer_9.0.1_LINUX.sh -+++ CDFPlayer_9.0.1_LINUX.sh -@@ -261,11 +261,11 @@ - fi - done - chmod a+x $0 || echo Please add execution rights on $0 -- if test `echo "$0" | cut -c1` = "/"; then # Spawn a terminal! -- exec $XTERM -title "$label" -e "$0" --xwin "$@" -- else -- exec $XTERM -title "$label" -e "./$0" --xwin "$@" -- fi -+ #if test `echo "$0" | cut -c1` = "/"; then # Spawn a terminal! -+ # exec $XTERM -title "$label" -e "$0" --xwin "$@" -+ #else -+ # exec $XTERM -title "$label" -e "./$0" --xwin "$@" -+ #fi - fi - fi - fi diff --git a/sci-mathematics/cipi/ChangeLog b/sci-mathematics/cipi/ChangeLog index 523a1f16f..5e2475db6 100644 --- a/sci-mathematics/cipi/ChangeLog +++ b/sci-mathematics/cipi/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/cipi -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/cipi: Add github to remote-id in metadata.xml + 06 Jan 2014; Justin Lecher <jlec@gentoo.org> cipi-1.0.ebuild, metadata.xml: Use tarball instead of git pull @@ -15,4 +18,3 @@ 20 Jul 2010; Thomas Kahle <tom111@gmx.de> +cipi-1.0.ebuild, +metadata.xml: initial upload for bug 329169 - diff --git a/sci-mathematics/cipi/metadata.xml b/sci-mathematics/cipi/metadata.xml index ff77aadc4..bc37ee723 100644 --- a/sci-mathematics/cipi/metadata.xml +++ b/sci-mathematics/cipi/metadata.xml @@ -10,4 +10,7 @@ cipi is a threaded implementation of iterative proportional fitting. It is used to compute information projections iteratively. </longdescription> + <upstream> + <remote-id type="github">tom111/cipi</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/dolfin/ChangeLog b/sci-mathematics/dolfin/ChangeLog index 980a24abe..f5a0b74b1 100644 --- a/sci-mathematics/dolfin/ChangeLog +++ b/sci-mathematics/dolfin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/dolfin -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/dolfin: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> dolfin-0.9.9.ebuild, metadata.xml: Bump EAPI to 5; Bump to python-single-r1 eclass @@ -19,4 +22,3 @@ +dolfin-0.9.9.ebuild, +files/dolfin-0.9.9-find-armadillo.patch, +metadata.xml: Initial import. - diff --git a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild b/sci-mathematics/dolfin/dolfin-0.9.9.ebuild index 1303d4bde..c54704334 100644 --- a/sci-mathematics/dolfin/dolfin-0.9.9.ebuild +++ b/sci-mathematics/dolfin/dolfin-0.9.9.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils eutils python-single-r1 diff --git a/sci-mathematics/dolfin/metadata.xml b/sci-mathematics/dolfin/metadata.xml index 9c1b5e566..c3247869e 100644 --- a/sci-mathematics/dolfin/metadata.xml +++ b/sci-mathematics/dolfin/metadata.xml @@ -12,4 +12,7 @@ DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Proble <flag name="scotch">Adds support for graph partitioning with <pkg>sci-libs/scotch</pkg></flag> <flag name="umfpack">Adds support for sparse solving with <pkg>sci-libs/umfpack</pkg></flag> </use> + <upstream> + <remote-id type="launchpad">dolfin</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/freefem++/ChangeLog b/sci-mathematics/freefem++/ChangeLog index 616b17ad2..784ad0699 100644 --- a/sci-mathematics/freefem++/ChangeLog +++ b/sci-mathematics/freefem++/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/freefem++ -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 19 Feb 2015; Marius Brehler <marbre@linux.sungazer.de> freefem++-3.8.ebuild: + Fix SRC_URI and SLOT operators + 15 Nov 2014; Christoph Junghans <ottxor@gentoo.org> freefem++-3.8.ebuild: fixed latex dep diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest index a7b3c4eae..7defda7a2 100644 --- a/sci-mathematics/freefem++/Manifest +++ b/sci-mathematics/freefem++/Manifest @@ -1 +1 @@ -DIST freefem++-3.8.tar.gz 21848854 SHA256 4ea6d754eb3914f20b1fe7620d562e95461b7206f289108e2fc803baecf70e6c +DIST freefem++-3.8.tar.gz 21848854 SHA256 4ea6d754eb3914f20b1fe7620d562e95461b7206f289108e2fc803baecf70e6c SHA512 357dbbe1d5598da43ce2d6071bc939daac4c2b2f700879e8f9b47e68a15c95be030b69da48d49a097b02814d6596250cc5c2e50417bef23c2db2da6222909519 WHIRLPOOL 0c48961b27b677f9b3f050ce84dc9430f051819da2a4d2fed2169eb9cbf8364f42467bdd73ecff708bb5ec58ec71ea3b0925c326977f928dbc247e72e5e65d27 diff --git a/sci-mathematics/freefem++/freefem++-3.8.ebuild b/sci-mathematics/freefem++/freefem++-3.8.ebuild index 4163738fb..04c845192 100644 --- a/sci-mathematics/freefem++/freefem++-3.8.ebuild +++ b/sci-mathematics/freefem++/freefem++-3.8.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,7 +10,7 @@ MY_PV=$(replace_version_separator 2 '-') DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains" HOMEPAGE="http://www.freefem.org/ff++/" -SRC_URI="http://www.freefem.org/ff%2B%2B/ftp/${PN}-${MY_PV}.tar.gz" +SRC_URI="http://www.freefem.org/ff++/ftp/old-v3/${PN}-${MY_PV}.tar.gz" LICENSE="LGPL-2.1" SLOT="0" @@ -18,7 +18,7 @@ KEYWORDS="~amd64" IUSE="doc examples mpi opengl X" RDEPEND=" - sci-libs/fftw + sci-libs/fftw:3.0 virtual/cblas virtual/lapack sci-libs/umfpack diff --git a/sci-mathematics/gambit/ChangeLog b/sci-mathematics/gambit/ChangeLog index 3d3d1a6d3..6643075ff 100644 --- a/sci-mathematics/gambit/ChangeLog +++ b/sci-mathematics/gambit/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/gambit -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/gambit: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> gambit-0.2010.09.01.ebuild, metadata.xml: Fix header and move to EAPI=5 @@ -15,4 +18,3 @@ 15 Apr 2011; Dongxu Li <dongxuli2011@gmail.com> +gambit-0.2010.09.01.ebuild +Manifest +metadata.html +ChangeLog: Initial port. #47670 - diff --git a/sci-mathematics/gambit/metadata.xml b/sci-mathematics/gambit/metadata.xml index 917e7fd9e..63f1ab756 100644 --- a/sci-mathematics/gambit/metadata.xml +++ b/sci-mathematics/gambit/metadata.xml @@ -11,4 +11,7 @@ Enable gui support using wxWidgets. </flag> </use> + <upstream> + <remote-id type="sourceforge">gambit</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/kayali/ChangeLog b/sci-mathematics/kayali/ChangeLog index 293899f57..ae495b18d 100644 --- a/sci-mathematics/kayali/ChangeLog +++ b/sci-mathematics/kayali/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/kayali -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/kayali: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> kayali-0.3.2.ebuild, metadata.xml: Bump EAPI to 5; Bump to python-single-r1 eclass diff --git a/sci-mathematics/kayali/kayali-0.3.2.ebuild b/sci-mathematics/kayali/kayali-0.3.2.ebuild index 4910db2df..daeaff37a 100644 --- a/sci-mathematics/kayali/kayali-0.3.2.ebuild +++ b/sci-mathematics/kayali/kayali-0.3.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit eutils python-single-r1 diff --git a/sci-mathematics/kayali/metadata.xml b/sci-mathematics/kayali/metadata.xml index 82fef4f2e..4be31a565 100644 --- a/sci-mathematics/kayali/metadata.xml +++ b/sci-mathematics/kayali/metadata.xml @@ -8,4 +8,7 @@ used as an advanced replacement for KDE KCalc. It is essentially a front end GUI forMaxima (and is easily extended to other CAS back-ends) and Gnuplot. </longdescription> + <upstream> + <remote-id type="sourceforge">kayali</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/lie/ChangeLog b/sci-mathematics/lie/ChangeLog index 581a3da02..fbed4ec9e 100644 --- a/sci-mathematics/lie/ChangeLog +++ b/sci-mathematics/lie/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-mathematics/lie -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 May 2015; François Bissey <francois.bissey@canterbury.ac.nz> + lie-2.2.2.ebuild: + Cosmetic fixes requested by jlec + + 18 May 2015; François Bissey <francois.bissey@canterbury.ac.nz> + lie-2.2.2.ebuild: + Update upstream homepage and source location. Migrate to EAPI 5. + 22 Aug 2010; François Bissey <f.r.bissey@massey.ac.nz> lie-2.2.2.ebuild: Keyword lie ~amd64 @@ -26,4 +34,3 @@ 03 Apr 2009; Francois Bissey <f.r.bissey@massey.ac.nz> ChangeLog: Initial import for the science overlay. - diff --git a/sci-mathematics/lie/Manifest b/sci-mathematics/lie/Manifest index bd90c7fa0..2cd411903 100644 --- a/sci-mathematics/lie/Manifest +++ b/sci-mathematics/lie/Manifest @@ -1 +1 @@ -DIST conLiE.tar.gz 361170 SHA256 6eac244471abb730811a05c8cb0b36eb7f8285cd18a03b956dadcf80ef1f0961 +DIST lie-2.2.2.tar.gz 361073 SHA256 c4d6f67fa17d2bc77c875a5b2ad2b42ffc5cadf30e7d1c64c097648ccb918b1e SHA512 a7d9a4471fe30d1d3d402f4bed3b15462c241e3cfba9483e2835f00f85919ffea3b864eed3daef13d1c7bb063603b4b1f4b8d267ccc333c148e8a4c10e3e91e1 WHIRLPOOL 25c9d8cd2ae99dd25c04aa178a5e13cf79917d63a7f7778ffdae628ae70b9dc7412442a1eb2f59329e36ce009b99e527352bfd0d3a4c70abe4770498cb1fea7c diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild index b31b6f808..856ebd187 100644 --- a/sci-mathematics/lie/lie-2.2.2.ebuild +++ b/sci-mathematics/lie/lie-2.2.2.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 inherit eutils toolchain-funcs DESCRIPTION="A Computer algebra package for Lie group computations" -HOMEPAGE="http://young.sp2mi.univ-poitiers.fr/~marc/LiE" -SRC_URI="http://young.sp2mi.univ-poitiers.fr/~marc/LiE/conLiE.tar.gz" +HOMEPAGE="http://www-math.univ-poitiers.fr/~maavl/LiE/" +SRC_URI="http://wwwmathlabo.univ-poitiers.fr/~maavl/LiE/conLiE.tar.gz -> ${P}.tar.gz" #### Remove the following line when moving this ebuild to the main tree! RESTRICT="mirror" @@ -19,24 +19,24 @@ SLOT="0" KEYWORDS="~x86 ~amd64" IUSE="doc" DEPEND="sys-devel/bison - sys-libs/readline + sys-libs/readline:= sys-libs/ncurses" -RDEPEND="sys-libs/readline +RDEPEND="sys-libs/readline:= sys-libs/ncurses" S="${WORKDIR}/LiE" src_prepare() { - epatch "${FILESDIR}/${P}-make.patch" - epatch "${FILESDIR}/parrallelmake-${P}.patch" + epatch "${FILESDIR}"/${P}-make.patch \ + "${FILESDIR}"/parrallelmake-${P}.patch } src_compile() { - emake CC=$(tc-getCC) || die "failed to compile" + emake CC=$(tc-getCC) } src_install() { - emake DESTDIR="${ED}" install || die + emake DESTDIR="${ED}" install use doc && dodoc "${S}"/manual/* dodoc README } diff --git a/sci-mathematics/mdp/mdp-9999.ebuild b/sci-mathematics/mdp/mdp-9999.ebuild index 7a28e1336..dec960fe2 100644 --- a/sci-mathematics/mdp/mdp-9999.ebuild +++ b/sci-mathematics/mdp/mdp-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_7,3_3} ) inherit distutils-r1 git-r3 diff --git a/sci-mathematics/netgen/ChangeLog b/sci-mathematics/netgen/ChangeLog index f8dc833ac..4484817eb 100644 --- a/sci-mathematics/netgen/ChangeLog +++ b/sci-mathematics/netgen/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/netgen -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/netgen: Updating remote-id in metadata.xml + + 26 Apr 2015; Marius Brehler <marbre@linux.sungazer.de> netgen-5.0.0.ebuild: + Bump to EAPI=5; Update Manifest (Bug #407) + 14 Mar 2011; Justin Lecher <jlec@gentoo.org> netgen-4.9.13.ebuild: Moved media-libs/jpeg -> virtual/jpeg @@ -52,4 +58,3 @@ Initial import. See bug #155424 for anything relating the building process. Ebuild from Daniel Tourde <daniel.tourde@caelae.se> and Oliver Borm <oli.borm@web.de>. - diff --git a/sci-mathematics/netgen/Manifest b/sci-mathematics/netgen/Manifest index 0b262a928..0bc56e762 100644 --- a/sci-mathematics/netgen/Manifest +++ b/sci-mathematics/netgen/Manifest @@ -1,2 +1,2 @@ DIST netgen-4.9.13.tar.gz 1829916 SHA256 a5f188bb0fafc0536389314efb8fe6d294b93512b54f2b67c9a3e5431c3b0412 SHA512 6cfe6ea799f37a35dc74112f5c370fd369277a55965769649c00632eba308061901fd7563fe7eb4b427b0702d39f4f004854da9f02f2e6f11ccd3a72e6b6afa3 WHIRLPOOL e4a0dc3ca74241f77d3c389b30944ea59fe7b0035af18f343499f4f7f644568fd5b687590b249b25121614508496ff8270ca52e91c8a2997ac2792f301533b4c -DIST netgen-5.0.0.tar.gz 1835590 SHA256 c8b9a3bd93b0502436af172b40ea698e3dcc0ed14cefebf2ae2ac18f7682cb81 SHA512 bafa6ee4eb36065d3f783d2e7140ec024d9ae4827fc1de22ecb8becd90e96dee0f38d10f74437257b0fd5d4ad38b99e609a00020fa9fbbe9072b88d12e146e4c WHIRLPOOL f6e2bfa5e090a4f898281137edc0e26e8b253ab2fc8bb5413386e18ffc2ba6883f56ebb9bc1283f0349098957b1b04dd5424d23627cb84698521b5b622937636 +DIST netgen-5.0.0.tar.gz 1835004 SHA256 c122aa41fe6cc7c491df5df40c1c2a5633ee96a36d363a630ff1c5c4e4921419 SHA512 27f46feaa1cf9d269c4898c093cca404fdc5e5fbfc8c9684d0d2f2ec2f2f9af85dd8b3d3372044f63fca08e1a079fd042fbcdc7b9ca881c38a3cfe67586b34b4 WHIRLPOOL 98a1eb2455d767929a808145e2e55d7064a99e0e6e2c80e464736b6b30df750d03069fc6f04a2e3e0d876f5664b6a2138e5ea5e3a9ac99294756ba4187710963 diff --git a/sci-mathematics/netgen/metadata.xml b/sci-mathematics/netgen/metadata.xml index 450140bdd..a4ba975d8 100644 --- a/sci-mathematics/netgen/metadata.xml +++ b/sci-mathematics/netgen/metadata.xml @@ -1,8 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> - <use> - <flag name="opencascade"> Enable OpenCASCADE support</flag> - </use> + <herd>sci-mathematics</herd> + <use> + <flag name="opencascade"> Enable OpenCASCADE support</flag> + </use> + <upstream> + <remote-id type="sourceforge">netgen-mesher</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/netgen/netgen-5.0.0.ebuild b/sci-mathematics/netgen/netgen-5.0.0.ebuild index 2e8a7a466..8bfb5132e 100644 --- a/sci-mathematics/netgen/netgen-5.0.0.ebuild +++ b/sci-mathematics/netgen/netgen-5.0.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="2" +EAPI=5 inherit autotools eutils flag-o-matic multilib versionator @@ -24,7 +24,7 @@ DEPEND="dev-tcltk/tix opencascade? ( sci-libs/opencascade ) ffmpeg? ( media-video/ffmpeg ) jpeg? ( virtual/jpeg ) - mpi? ( virtual/mpi ) " + mpi? ( virtual/mpi ( || ( sci-libs/parmetis sci-libs/metis ) ) ) " RDEPEND="${DEPEND}" # Note, MPI has not be tested. @@ -46,11 +46,12 @@ src_configure() { myconf="${myconf} --enable-occ --with-occ=$CASROOT" append-ldflags -L$CASROOT/lin/$(get_libdir) fi - - use mpi && myconf="${myconf} --enable-parallel" + if use mpi; then + myconf="${myconf} --enable-parallel" + append-cppflags -I/usr/include/metis + fi use ffmpeg && myconf="${myconf} --enable-ffmpeg" use jpeg && myconf="${myconf} --enable-jpeglib" - append-cppflags -I/usr/include/togl-1.7 econf \ @@ -71,12 +72,12 @@ src_install() { echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl1.7" > ./99netgen doenvd 99netgen - emake DESTDIR="${D}" install || die "make install failed" - mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" + emake DESTDIR="${D}" install + mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die # Install icon and .desktop for menu entry - doicon "${FILESDIR}"/${PN}.png || die "doicon failed" - domenu "${FILESDIR}"/${PN}.desktop || die "domenu failed" + doicon "${FILESDIR}"/${PN}.png + domenu "${FILESDIR}"/${PN}.desktop } pkg_postinst() { diff --git a/sci-mathematics/open-axiom/ChangeLog b/sci-mathematics/open-axiom/ChangeLog index ad2fb6847..71aa09fd0 100644 --- a/sci-mathematics/open-axiom/ChangeLog +++ b/sci-mathematics/open-axiom/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/open-axiom -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/open-axiom: Updating remote-id in metadata.xml + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> open-axiom-1.4.2.ebuild, metadata.xml: Drop src_install in favour of default and use DOCS @@ -11,4 +14,3 @@ 22 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> +open-axiom-1.3.0.ebuild, +metadata.xml: Initial experimental ebuild of open-axiom - diff --git a/sci-mathematics/open-axiom/metadata.xml b/sci-mathematics/open-axiom/metadata.xml index 7485722c6..123d02826 100644 --- a/sci-mathematics/open-axiom/metadata.xml +++ b/sci-mathematics/open-axiom/metadata.xml @@ -8,4 +8,7 @@ programming language, a compiler, a large set of mathematical libraries of interest to researchers and practitioners of computational sciences. </longdescription> + <upstream> + <remote-id type="sourceforge">open-axiom</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/petsc/ChangeLog b/sci-mathematics/petsc/ChangeLog index a3aabff32..a29efad6d 100644 --- a/sci-mathematics/petsc/ChangeLog +++ b/sci-mathematics/petsc/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-mathematics/petsc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*petsc-3.5.3 (13 Mar 2015) + + 13 Mar 2015; Matthias Maier <tamiko@gentoo.org> + +files/petsc-3.5.3-disable-rpath.patch, +petsc-3.5.3.ebuild: + version bump + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> petsc-3.4.2.ebuild: remove whitespace diff --git a/sci-mathematics/petsc/Manifest b/sci-mathematics/petsc/Manifest index 5b82aa1b8..ee294a873 100644 --- a/sci-mathematics/petsc/Manifest +++ b/sci-mathematics/petsc/Manifest @@ -1,2 +1,3 @@ DIST petsc-3.4.2.tar.gz 18658689 SHA256 f13b0dc978fe0dcc1df032f8142a2fd345217f02b9967936d9aac26ce4b2b52e SHA512 f839e4cfadbee720e53993eb8de74a2d82bfe2a46a418f528b4cdb2e9245b8ecafbc02d6d1718034cfe80d291095187b0946ebe237c8f985e4213c4c35bc345b WHIRLPOOL a00f4340e5dc151c57d9f5e2b764a609a508490756d8337d52bec4712fb26b8c06edf46293ed838f08ff34e1c068549ea9680657b7282cb884df4c1314c58cdb DIST petsc-3.5.1.tar.gz 20099475 SHA256 199af205f62dcc572728600670c7d4c8cb0d4efc4172c26f02b895d9dd1df245 SHA512 6c7285ad4d89de39b8ff0e73c65e6caeaed7dc7797c21f56caaca75f53550459cb76962c98d345748e1aae96c3daf57c8c20340a2b3233352022910ec5f08010 WHIRLPOOL 04f18580559b64f294237c6f4b2987f11b9b53ab86f20a0114a39c903f676e73753d6c782e9360b68225b72e42558d64e401f5d661708242f29fca959fa396e0 +DIST petsc-3.5.3.tar.gz 20729341 SHA256 68e6a42f5ec75bad87f74d4df8f55ad63f0c4d996f162da6713cb3d6f566830d SHA512 7455e9a67e5bbefce8f51eeb85418cdca2b14c50c85c8f9e91c0c53744a30954915a5a3aa141969d123daf54513610502cc52051a36a2a2da82410110f7421f8 WHIRLPOOL f473eb4a4136fb74114a51e3fa4a7ff60600c77b029a600360eca0418f6412ea653a6a8d6c72f750711d9d961982aad4b4e55332661dc2c203bb8c9344e0cca4 diff --git a/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch b/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch new file mode 100644 index 000000000..7fe3760c9 --- /dev/null +++ b/sci-mathematics/petsc/files/petsc-3.5.3-disable-rpath.patch @@ -0,0 +1,18 @@ +diff --git a/config/BuildSystem/config/setCompilers.py b/config/BuildSystem/config/setCompilers.py +index 8e0d2ee..ce53ad0 100644 +--- a/config/BuildSystem/config/setCompilers.py ++++ b/config/BuildSystem/config/setCompilers.py +@@ -1326,12 +1326,7 @@ class Configure(config.base.Configure): + for language in languages: + flag = '-L' + self.pushLanguage(language) +- # test '-R' before '-rpath' as sun compilers [c,fortran] don't give proper errors with wrong options. +- if not Configure.isDarwin(): +- testFlags = ['-Wl,-rpath,', '-R','-rpath ' , '-Wl,-R,'] +- else: +- testFlags = [] +- # test '-R' before '-Wl,-rpath' for SUN compilers [as cc on linux accepts -Wl,-rpath, but f90 & CC do not. ++ testFlags = [] + if self.isSun(self.framework.getCompiler()): + testFlags.insert(0,'-R') + for testFlag in testFlags: diff --git a/sci-mathematics/petsc/petsc-3.5.3.ebuild b/sci-mathematics/petsc/petsc-3.5.3.ebuild new file mode 100644 index 000000000..09e5bfb1a --- /dev/null +++ b/sci-mathematics/petsc/petsc-3.5.3.ebuild @@ -0,0 +1,243 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs versionator + +MY_P="${PN}-$(replace_version_separator _ -)" + +DESCRIPTION="Portable, Extensible Toolkit for Scientific Computation" +HOMEPAGE="http://www.mcs.anl.gov/petsc/" +SRC_URI="http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${MY_P}.tar.gz" + +LICENSE="petsc" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="afterimage boost complex-scalars cxx debug doc fftw + fortran hdf5 hypre mpi mumps scotch sparse superlu threads X" +# Failed: imagemagick metis + +# hypre and superlu curretly exclude each other due to missing linking to hypre +# if both are enabled +REQUIRED_USE=" + afterimage? ( X ) + hdf5? ( mpi ) + hypre? ( cxx mpi ) + mumps? ( mpi scotch ) + scotch? ( mpi ) + ^^ ( hypre superlu ) +" +# imagemagick? ( X ) + +RDEPEND=" + virtual/blas + virtual/lapack + afterimage? ( media-libs/libafterimage ) + boost? ( dev-libs/boost ) + fftw? ( sci-libs/fftw[mpi?] ) + hdf5? ( sci-libs/hdf5[mpi?] ) + hypre? ( >=sci-libs/hypre-2.8.0b[mpi?] ) + mpi? ( virtual/mpi[cxx?,fortran?] ) + mumps? ( sci-libs/mumps[mpi?] sci-libs/scalapack ) + scotch? ( sci-libs/scotch[mpi?] ) + sparse? ( sci-libs/suitesparse >=sci-libs/cholmod-1.7.0 ) + superlu? ( sci-libs/superlu ) + X? ( x11-libs/libX11 ) +" +# metis? ( sci-libs/parmetis ) +# imagemagick? ( media-gfx/imagemagick ) + +DEPEND="${RDEPEND} + ${PYTHON_DEPS} + virtual/pkgconfig + dev-util/cmake +" +# cmake is used for parallel building +# in some configuration setups, legacy build is used (slow) + +# +# PETSc does not want its Makefiles to be invoked with anything higher than +# -j1. The underlying build system does automatically invoke a parallel +# build. This might not be what you want, but *hey* not your choice. +# +MAKEOPTS="${MAKEOPTS} -j1" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + epatch "${FILESDIR}"/${P%_*}-disable-rpath.patch + sed -i -e 's%/usr/bin/env python%/usr/bin/env python2%' configure || die +} + +src_configure() { + # petsc uses --with-blah=1 and --with-blah=0 to en/disable options + petsc_enable() { + use "$1" && echo "--with-${2:-$1}=1" || echo "--with-${2:-$1}=0" + } + # add external library: + # petsc_with use_flag libname libdir + # petsc_with use_flag libname include linking_libs + petsc_with() { + local myuse p=${2:-${1}} + if use ${1}; then + myuse="--with-${p}=1" + if [[ $# -ge 4 ]]; then + myuse="${myuse} --with-${p}-include=${EPREFIX}${3}" + shift 3 + myuse="${myuse} --with-${p}-lib=$@" + else + myuse="${myuse} --with-${p}-dir=${EPREFIX}${3:-/usr}" + fi + else + myuse="--with-${p}=0" + fi + echo ${myuse} + } + + # select between configure options depending on use flag + petsc_select() { + use "$1" && echo "--with-$2=$3" || echo "--with-$2=$4" + } + + local mylang + local myopt + + use cxx && mylang="cxx" || mylang="c" + use debug && myopt="debug" || myopt="opt" + + # environmental variables expected by petsc during build + export PETSC_DIR="${S}" + export PETSC_ARCH="linux-gnu-${mylang}-${myopt}" + + if use debug; then + strip-flags + filter-flags -O* + fi + + # C Support on Cxx builds is enabled if possible + # i.e. when not using complex scalars + # (no complex type for both available at the same time) + + # run petsc configure script + econf \ + scrollOutput=1 \ + CFLAGS="${CFLAGS}" \ + CXXFLAGS="${CXXFLAGS}" \ + LDFLAGS="${LDFLAGS}" \ + --with-shared-libraries \ + --with-single-library \ + --with-clanguage=${mylang} \ + $(use cxx && ! use complex-scalars && echo "with-c-support=1") \ + --with-petsc-arch=${PETSC_ARCH} \ + --with-precision=double \ + --with-gnu-compilers \ + --with-blas-lapack-lib="$($(tc-getPKG_CONFIG) --libs lapack)" \ + $(petsc_enable debug debugging) \ + $(petsc_enable mpi) \ + $(petsc_select mpi cc mpicc $(tc-getCC)) \ + $(petsc_select mpi cxx mpicxx $(tc-getCXX)) \ + $(petsc_enable fortran) \ + $(use fortran && echo "$(petsc_select mpi fc mpif77 $(tc-getF77))") \ + $(petsc_enable mpi mpi-compilers) \ + $(petsc_select complex-scalars scalar-type complex real) \ + --with-windows-graphics=0 \ + --with-matlab=0 \ + --with-cmake=cmake \ + $(petsc_enable threads pthread) \ + $(petsc_with afterimage afterimage \ + /usr/include/libAfterImage -lAfterImage) \ + $(petsc_with hdf5) \ + $(petsc_with hypre hypre \ + /usr/include/hypre -lHYPRE) \ + $(petsc_with sparse suitesparse) \ + $(petsc_with superlu superlu \ + /usr/include/superlu -lsuperlu) \ + $(petsc_with X x) \ + $(petsc_with X x11) \ + $(petsc_with scotch ptscotch \ + /usr/include/scotch \ + [-lptesmumps,-lptscotch,-lptscotcherr,-lscotch,-lscotcherr]) \ + $(petsc_with mumps scalapack \ + /usr/include/scalapack -lscalapack) \ + $(petsc_with mumps mumps \ + /usr/include \ + [-lcmumps,-ldmumps,-lsmumps,-lzmumps,-lmumps_common,-lpord]) \ + --with-imagemagick=0 \ + --with-python=0 \ + $(petsc_with boost) \ + $(petsc_with fftw) + +# not yet tested: +# python bindings, netcdf, fftw + +# failed dependencies, perhaps fixed in upstream soon: +# $(petsc_with metis parmetis) \ # needs metis too (>=5.0.2) +# $(petsc_with imagemagick imagemagick \ +# /usr/include/ImageMagick $($(tc-getPKG_CONFIG) --libs MagickCore)) \ +# $(petsc_enable threads pthreadclasses) \ +} + +src_install() { + # petsc install structure is very different from + # installing headers to /usr/include/petsc and lib to /usr/lib + # it also installs many unneeded executables and scripts + # so manual install is easier than cleanup after "emake install" + insinto /usr/include/${PN} + doins include/*.h* + insinto /usr/include/${PN}/${PETSC_ARCH}/include + doins ${PETSC_ARCH}/include/* + if use fortran; then + insinto /usr/include/${PN}/finclude + doins -r include/finclude/* + fi + if ! use mpi ; then + insinto /usr/include/${PN}/mpiuni + doins include/mpiuni/*.h + fi + insinto /usr/include/${PN}/conf + doins conf/{variables,rules,test} + insinto /usr/include/${PN}/${PETSC_ARCH}/conf + doins ${PETSC_ARCH}/conf/{petscrules,petscvariables,RDict.db} + insinto /usr/include/${PN}/petsc-private + doins include/petsc-private/*.h + + # fix configuration files: replace "${S}" by installed location + sed -i \ + -e "s:"${S}"::g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die + sed -i \ + -e "s:-I/include:-I${EPREFIX}/usr/include/${PN}:g" \ + -e "s:-I/linux-gnu-cxx-opt/include:-I${EPREFIX}/usr/include/${PN}/${PETSC_ARCH}/include/:g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/conf/petscvariables || die + sed -i \ + -e "s:usr/lib:usr/$(get_libdir):g" \ + "${ED}"/usr/include/${PN}/${PETSC_ARCH}/include/petscconf.h || die + + # add information about installation directory and + # PETSC_ARCH to environmental variables + cat >> 99petsc <<- EOF + PETSC_ARCH=${PETSC_ARCH} + PETSC_DIR=${EPREFIX}/usr/include/${PN} + EOF + doenvd 99petsc + + dolib.so ${PETSC_ARCH}/lib/*.so + dolib.so ${PETSC_ARCH}/lib/*.so.* + + if use doc ; then + einfo "installing documentation (this could take a while)" + dodoc docs/manual.pdf + dohtml -r docs/*.html docs/changes docs/manualpages + fi +} + +pkg_postinst() { + elog "The petsc ebuild is still under development." + elog "Help us improve the ebuild in:" + elog "http://bugs.gentoo.org/show_bug.cgi?id=53386" +} diff --git a/sci-mathematics/pulp/ChangeLog b/sci-mathematics/pulp/ChangeLog index 83a1448a6..49df6c4a4 100644 --- a/sci-mathematics/pulp/ChangeLog +++ b/sci-mathematics/pulp/ChangeLog @@ -4,7 +4,7 @@ 09 Apr 2014; Justin Lecher <jlec@gentoo.org> -pulp-1.5.3.ebuild, +pulp-1.5.6.ebuild: - Version BUmp; fix distutils-r1 eclass usage + Version Bump; fix distutils-r1 eclass usage *pulp-1.5.3 (14 Jan 2013) diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml index 897aa2e6b..fda7a636f 100644 --- a/sci-mathematics/pulp/metadata.xml +++ b/sci-mathematics/pulp/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="pypi">PuLP</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/pulp/pulp-1.5.6.ebuild b/sci-mathematics/pulp/pulp-1.5.6.ebuild index a3d76e6cb..affd775b9 100644 --- a/sci-mathematics/pulp/pulp-1.5.6.ebuild +++ b/sci-mathematics/pulp/pulp-1.5.6.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3,3_4} pypy ) +PYTHON_COMPAT=( python{2_7,3_3,3_4} pypy ) inherit distutils-r1 diff --git a/sci-mathematics/scilab/ChangeLog b/sci-mathematics/scilab/ChangeLog index 4a619b97b..f6c4a459d 100644 --- a/sci-mathematics/scilab/ChangeLog +++ b/sci-mathematics/scilab/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*scilab-5.5.2 (03 Apr 2015) + + 03 Apr 2015; Guillaume Horel <guillaume.horel@gmail.com> + +files/scilab-5.5.2-accessviolation.patch, + +files/scilab-5.5.2-fix-random-runtime-failure.patch, + +files/scilab-5.5.2-followlinks.patch, +files/scilab-5.5.2-gluegen.patch, + +files/scilab-5.5.2-java-heap.patch, +files/scilab-5.5.2-missinglib.patch, + +files/scilab-5.5.2-nogui.patch, +scilab-5.5.2.ebuild: + sci-mathematics/scilab: version bump + 01 Feb 2015; Guillaume Horel <guillaume.horel@gmail.com> scilab-5.5.1.ebuild: sci-mathematics/scilab: more precise dependencies diff --git a/sci-mathematics/scilab/Manifest b/sci-mathematics/scilab/Manifest index bb446c092..59ce40909 100644 --- a/sci-mathematics/scilab/Manifest +++ b/sci-mathematics/scilab/Manifest @@ -1,2 +1,3 @@ DIST scilab-5.5.0-src.tar.gz 68627863 SHA256 7896ef914e40f6c7ce93dd106e091c552b1822190a3986795ee8b412a53aa5c3 SHA512 b8c061fdb8ef4bd18b332c735b0b4fb91a3aaa35edbe06d69ff4e3f360feae0be9fa3982e5f968ee3f7f0c94f115d25ec34ee3416339d38cbc4a8efa19f7b367 WHIRLPOOL 4e995b43477468d70a392214d155fd173dc22fa06ca045a84d22d7d486b26ad432a2670a7e938b6256b7e91b9540c47f60b1eac1c82e11adb5bf3f72d1b0265d DIST scilab-5.5.1-src.tar.gz 69538169 SHA256 c056223e12f17434a17ce881d13651bdb1b79a793bde028a978ea8dc20806729 SHA512 8906e916edef2068578e55fd01d4978ce58cb3431f0b7e9574bdd7f88667bcb74f10703a0391633e2b4fcc9ba2506c385338273b48f0f802267257f07e34d974 WHIRLPOOL 5d9d8b270ba9a814957f96d4084ff87abc5343bbc63d4ca21ae07f630be91658a4f5d9ff457c24d8bd26b90fc7ac6dfae99643f67ac75c9763e67479f1f8279a +DIST scilab-5.5.2-src.tar.gz 69626327 SHA256 a734519de96d35b8f081768a5584086e46db089ab11c021744897b22ec4d0f5e SHA512 7f00ac837e36b5524a9c9a3106bdaefebb71559eb2932b2a16e4fac53fa1f9e66b87eabf98b3006ede25f8ab1d16d6ef1c7561ed29b67ddb42c98610fa72fe79 WHIRLPOOL 6f2fbe086fe7bff8364f85ea3d63cddd607bf63a2273bfbde7b1f18d96bda54d0e7f5bd9982616643014edc69d6a337887f0d4aef3f4a3d4b8f03e756a705fdf diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch b/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch new file mode 100644 index 000000000..a84de9a2b --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-accessviolation.patch @@ -0,0 +1,21 @@ +diff -urN scilab-5.5.0-orig/bin/scilab scilab-5.5.0/bin/scilab +--- scilab-5.5.0-orig/bin/scilab 2014-07-12 15:24:17.105686656 -0400 ++++ scilab-5.5.0/bin/scilab 2014-07-12 15:25:29.307725409 -0400 +@@ -647,17 +647,6 @@ + GTK_MODULES=$(echo $GTK_MODULES | sed s/gnomebreakpad//g) + export GTK_MODULES + +-# libEGL may be partially supported by the closed-source NVIDIA driver. +-# Until they release an EGL driver, we force the egl_glx driver. +-# http://bugzilla.scilab.org/show_bug.cgi?id=12940 +-if test -x /usr/bin/glxinfo; then +- NVIDIA_GLX_VENDOR=$(/usr/bin/glxinfo |grep "NVIDIA Corporation") +- if test ! -z "$NVIDIA_GLX_VENDOR"; then +- EGL_DRIVER=egl_glx +- export EGL_DRIVER +- fi +-fi +- + if test $SCIVERBOSE -ne 0; then + echo "SCI : $SCI" + echo "SCIBIN : $SCIBIN" diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch b/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch new file mode 100644 index 000000000..92ac45339 --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-fix-random-runtime-failure.patch @@ -0,0 +1,12 @@ +diff -urN scilab-orig/modules/api_scilab/src/cpp/api_double.cpp scilab/modules/api_scilab/src/cpp/api_double.cpp +--- scilab-orig/modules/api_scilab/src/cpp/api_double.cpp 2012-08-06 23:26:31.342617365 -0400 ++++ scilab/modules/api_scilab/src/cpp/api_double.cpp 2012-08-06 23:27:34.838621420 -0400 +@@ -497,7 +497,7 @@ + /*--------------------------------------------------------------------------*/ + int createScalarDouble(void* _pvCtx, int _iVar, double _dblReal) + { +- return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, NULL); ++ return createCommonScalarDouble(_pvCtx, _iVar, 0, _dblReal, 0); + } + /*--------------------------------------------------------------------------*/ + int createScalarComplexDouble(void* _pvCtx, int _iVar, double _dblReal, double _dblImg) diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch b/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch new file mode 100644 index 000000000..fd6aa7bae --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-followlinks.patch @@ -0,0 +1,11 @@ +--- m4/java.m4.orig 2014-02-11 23:43:03.030430258 -0500 ++++ m4/java.m4 2014-02-11 23:43:54.008428766 -0500 +@@ -839,7 +839,7 @@ + for jar in "$jardir/$1.jar" "$jardir/lib$1.jar" "$jardir/lib$1-java.jar" "$jardir/$1*.jar"; do + + # TODO check the behaviour when spaces +- jars_resolved=`ls $jar 2>/dev/null` ++ jars_resolved=$(realpath $(ls $jar 2>/dev/null) 2>/dev/null) + for jar_resolved in $jars_resolved; do # If several jars matches + if test -e "$jar_resolved"; then + export ac_java_classpath="$jar_resolved:$ac_java_classpath" diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch b/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch new file mode 100644 index 000000000..151443926 --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-gluegen.patch @@ -0,0 +1,11 @@ +--- scilab/modules/gui/src/java/org/scilab/modules/gui/SwingView.java.orig 2014-03-24 22:38:00.928934500 -0400 ++++ scilab/modules/gui/src/java/org/scilab/modules/gui/SwingView.java 2014-03-24 22:37:33.947567043 -0400 +@@ -157,7 +157,7 @@ + + static { + try { +- System.loadLibrary("gluegen2-rt"); ++ System.loadLibrary("gluegen-rt"); + } catch (Exception e) { + System.err.println(e); + } diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch b/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch new file mode 100644 index 000000000..31060d75a --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-java-heap.patch @@ -0,0 +1,11 @@ +--- etc/jvm_options.xml.orig 2014-02-12 00:05:34.323390688 -0500 ++++ etc/jvm_options.xml 2014-02-12 00:05:53.977390112 -0500 +@@ -22,7 +22,7 @@ + <!-- ENABLE Just In Time java compiler --> + <option value="-Djava.compiler=JIT"/> + <!-- Set Java Heap space to 256mb --> +- <option value="-Xmx256m"/> ++ <option value="-Xmx512m"/> + <!-- Avoid jvm to handle sigint (& other signals) --> + <option value="-Xrs"/> + diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch b/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch new file mode 100644 index 000000000..7f88068c5 --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-missinglib.patch @@ -0,0 +1,11 @@ +diff -urN scilab-5.5.1-orig/Makefile.am scilab-5.5.1/Makefile.am +--- scilab-5.5.1-orig/Makefile.am 2014-10-09 18:22:21.994610695 -0400 ++++ scilab-5.5.1/Makefile.am 2014-10-09 18:24:28.208333575 -0400 +@@ -74,6 +74,7 @@ + if NEED_JAVA + scilab_bin_LDADD += \ + $(top_builddir)/modules/console/libsciconsole.la \ ++ $(top_builddir)/modules/console/libsciconsole-minimal.la \ + $(top_builddir)/modules/jvm/libscijvm.la \ + $(top_builddir)/modules/commons/libscicommons.la + else diff --git a/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch b/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch new file mode 100644 index 000000000..60cee5a45 --- /dev/null +++ b/sci-mathematics/scilab/files/scilab-5.5.2-nogui.patch @@ -0,0 +1,13 @@ +--- Makefile.in.orig 2014-01-09 22:29:06.534469383 -0500 ++++ Makefile.in 2014-01-09 22:29:40.368471544 -0500 +@@ -2247,8 +2247,8 @@ + @BUILD_HELP_TRUE@ done; \ + @BUILD_HELP_TRUE@ fi + # Also install scirenderer.jar +-@EXTERNAL_SCIRENDERER_FALSE@ $(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER) +-@EXTERNAL_SCIRENDERER_FALSE@ $(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/ ++@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@ $(mkinstalldirs) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER) ++@EXTERNAL_SCIRENDERER_FALSE@@NEED_JAVA_TRUE@ $(INSTALL_DATA) $(top_builddir)/$(PATHTOSCIRENDERER)/$(SCIRENDERERJAR) $(DESTDIR)$(pkgdatadir)/$(PATHTOSCIRENDERER)/ + + .PHONY: macros localization doc + diff --git a/sci-mathematics/scilab/scilab-5.5.2.ebuild b/sci-mathematics/scilab/scilab-5.5.2.ebuild new file mode 100644 index 000000000..095281a0c --- /dev/null +++ b/sci-mathematics/scilab/scilab-5.5.2.ebuild @@ -0,0 +1,261 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +RESTRICT="test" + +JAVA_PKG_OPT_USE="gui" +VIRTUALX_REQUIRED="manual" + +inherit eutils autotools bash-completion-r1 check-reqs fdo-mime flag-o-matic \ + fortran-2 java-pkg-opt-2 toolchain-funcs virtualx + +DESCRIPTION="Scientific software package for numerical computations" +HOMEPAGE="http://www.scilab.org/" +SRC_URI="http://www.scilab.org/download/${PV}/${P}-src.tar.gz" + +LICENSE="CeCILL-2.1" +SLOT="0" +KEYWORDS="~x86 ~amd64" +IUSE="bash-completion debug doc emf fftw +gui +matio mpi nls openmp + static-libs test tk +umfpack +xcos" +REQUIRED_USE="xcos? ( gui ) doc? ( gui )" + +LINGUAS="fr_FR zh_CN zh_TW ru_RU ca_ES de_DE es_ES pt_BR ja_JP it_IT uk_UA pl_PL cs_CZ" +LINGUAS_DOC="fr_FR pt_BR ja_JP ru_RU" + +for l in ${LINGUAS}; do + IUSE="${IUSE} linguas_${l}" +done + +CDEPEND="dev-libs/libpcre + dev-libs/libxml2:2 + sci-libs/hdf5[mpi=] + >=sci-libs/arpack-3 + sys-devel/gettext + sys-libs/ncurses + sys-libs/readline:0 + virtual/lapack + emf? ( dev-java/freehep-graphicsio + dev-java/freehep-graphicsio-emf + dev-java/freehep-graphics2d + dev-java/freehep-io + dev-java/freehep-util ) + fftw? ( sci-libs/fftw:3.0 ) + gui? ( + dev-java/avalon-framework:4.2 + dev-java/commons-io:1 + dev-java/commons-logging:0 + >=dev-java/flexdock-1.2.4:0 + dev-java/fop:0 + =dev-java/gluegen-2.2.4:2.2 + dev-java/javahelp:0 + dev-java/jeuclid-core:0 + dev-java/jgoodies-looks:2.6 + >=dev-java/jlatexmath-1.0.3:1 + >=dev-java/jlatexmath-fop-1.0.3:1 + =dev-java/jogl-2.2.4:2.2 + >=dev-java/jrosetta-1.0.4:0 + dev-java/skinlf:0 + dev-java/xmlgraphics-commons:1.5 + virtual/opengl + xcos? ( dev-java/jgraphx:2.5 ) + ) + matio? ( >=sci-libs/matio-1.5 ) + tk? ( dev-lang/tk:0 ) + umfpack? ( sci-libs/umfpack )" + +RDEPEND="${CDEPEND} + gui? ( >=virtual/jre-1.5 )" + +DEPEND="${CDEPEND} + virtual/pkgconfig + debug? ( dev-util/lcov ) + gui? ( + >=virtual/jdk-1.5 + doc? ( dev-java/batik:1.7 + app-text/docbook-xsl-stylesheets + dev-java/xml-commons-external:1.4 + dev-java/saxon:9 ) + xcos? ( dev-lang/ocaml ) + ) + test? ( + dev-java/junit:4 + gui? ( ${VIRTUALX_DEPEND} ) )" + +DOCS=( "ACKNOWLEDGEMENTS" "README_Unix" "Readme_Visual.txt" ) + +pkg_pretend() { + use doc && CHECKREQS_MEMORY="512M" check-reqs_pkg_pretend +} + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCC) == *gcc* ]] && ! tc-has-openmp; then + ewarn "You are using a gcc without OpenMP capabilities" + die "Need an OpenMP capable compiler" + fi + FORTRAN_NEED_OPENMP=1 + fi + FORTRAN_STANDARD="77 90" + fortran-2_pkg_setup + #bug 8053 + unset F77 + java-pkg-opt-2_pkg_setup + + ALL_LINGUAS="en_US" + ALL_LINGUAS_DOC="en_US" + for l in ${LINGUAS}; do + use linguas_${l} && ALL_LINGUAS="${ALL_LINGUAS} ${l}" + done + for l in ${LINGUAS_DOC}; do + use linguas_${l} && ALL_LINGUAS_DOC="${ALL_LINGUAS_DOC} ${l}" + done + export ALL_LINGUAS ALL_LINGUAS_DOC +} + +src_prepare() { + epatch \ + "${FILESDIR}/${P}-followlinks.patch" \ + "${FILESDIR}/${P}-gluegen.patch" \ + "${FILESDIR}/${P}-fix-random-runtime-failure.patch" \ + "${FILESDIR}/${P}-accessviolation.patch" \ + "${FILESDIR}/${P}-missinglib.patch" + + # works for me on x86, but users are having + # trouble without see #282 on github + append-ldflags $(no-as-needed) + + # increases java heap to 512M when building docs (sync with cheqreqs above) + use doc && epatch "${FILESDIR}/${P}-java-heap.patch" + + # use the LINGUAS variable that we set + sed -i -e "/^ALL_LINGUAS=/d" -e "/^ALL_LINGUAS_DOC=/d" -i configure.ac ||die + + # make sure the DOCBOOK_ROOT variable is set + sed -i -e "s/xsl-stylesheets-\*/xsl-stylesheets/g" bin/scilab* || die + + #add specific gentoo java directories + if use gui; then + sed -i -e "s|/usr/lib/jogl2|/usr/lib/jogl-2.2|" \ + -e "s|/usr/lib64/jogl2|/usr/lib64/jogl-2.2|" configure.ac || die + sed -i -e "s|/usr/lib/gluegen2|/usr/lib/gluegen-2.2|" \ + -e "s|/usr/lib64/gluegen2|/usr/lib64/gluegen-2.2|" \ + -e "s|AC_CHECK_LIB(\[gluegen2-rt|AC_CHECK_LIB([gluegen-rt|" \ + configure.ac || die + + sed -i -e "s/jogl2/jogl-2.2/" -e "s/gluegen2/gluegen-2.2/" \ + etc/librarypath.xml || die + fi + + mkdir jar || die + pushd jar >/dev/null + if use gui; then + java-pkg_jar-from jlatexmath-1,flexdock,skinlf + java-pkg_jar-from jgoodies-looks-2.6,jrosetta + java-pkg_jar-from avalon-framework-4.2,jeuclid-core + java-pkg_jar-from xmlgraphics-commons-1.5,commons-io-1 + java-pkg_jar-from jogl-2.2 jogl-all.jar jogl2.jar + java-pkg_jar-from gluegen-2.2 gluegen-rt.jar gluegen2-rt.jar + java-pkg_jar-from fop fop.jar + java-pkg_jar-from javahelp jhall.jar + java-pkg_jar-from jlatexmath-fop-1 + use xcos && java-pkg_jar-from jgraphx-2.5 + if use doc; then + java-pkg_jar-from --build-only batik-1.7 batik-all.jar + java-pkg_jar-from --build-only saxon-9 saxon.jar saxon9he.jar + java-pkg_jar-from --build-only xml-commons-external-1.4 xml-apis-ext.jar + fi + fi + if use emf; then + java-pkg_jar-from freehep-graphicsio-emf,freehep-graphics2d + java-pkg_jar-from freehep-graphicsio,freehep-io,freehep-util + fi + if use test; then + java-pkg_jar-from junit-4 junit.jar junit4.jar + java-pkg_jar-from ant-junit + fi + popd + + java-pkg-opt-2_src_prepare + eautoconf +} + +src_configure() { + if use gui; then + export JAVA_HOME="$(java-config -O)" + else + unset JAVAC + fi + + export BLAS_LIBS="$($(tc-getPKG_CONFIG) --libs blas)" + export LAPACK_LIBS="$($(tc-getPKG_CONFIG) --libs lapack)" + export F77_LDFLAGS="${LDFLAGS}" + + econf \ + --enable-relocatable \ + --disable-rpath \ + --with-docbook="${EPREFIX}/usr/share/sgml/docbook/xsl-stylesheets" \ + --disable-static-system-lib \ + $(use_enable debug) \ + $(use_enable debug code-coverage) \ + $(use_enable debug debug-C) \ + $(use_enable debug debug-CXX) \ + $(use_enable debug debug-fortran) \ + $(use_enable debug debug-java) \ + $(use_enable debug debug-linker) \ + $(use_enable doc build-help) \ + $(use_enable nls) \ + $(use_enable nls build-localization) \ + $(use_enable static-libs static) \ + $(use_enable test compilation-tests) \ + $(use_with emf) \ + $(use_with fftw) \ + $(use_with gui) \ + $(use_with gui javasci) \ + $(use_with matio) \ + $(use_with openmp) \ + $(use_with tk) \ + $(use_with umfpack) \ + $(use_with xcos) \ + $(use_with xcos modelica) \ + $(use_with mpi) +} + +src_compile() { + addpredict /proc/mtrr + emake + use doc && emake doc +} + +src_test() { + if use gui; then + Xemake check + else + emake check + fi +} + +src_install() { + default + prune_libtool_files --all + rm -rf "${D}"/usr/share/scilab/modules/*/tests ||die + use bash-completion && newbashcomp "${FILESDIR}"/"${PN}".bash_completion "${PN}" + echo "SEARCH_DIRS_MASK=${EPREFIX}/usr/$(get_libdir)/scilab" \ + > 50-"${PN}" + insinto /etc/revdep-rebuild && doins "50-${PN}" +} + +pkg_postinst() { + fdo-mime_mime_database_update + einfo "If you are using the NVIDIA binary drivers, and run into graphics" + einfo "crashes, you may try to run scilab as follows:" + einfo "EGL_DRIVER=egl_glx scilab" + einfo "See upstream http://bugzilla.scilab.org/show_bug.cgi?id=12940" +} + +pkg_postrm() { + fdo-mime_mime_database_update +} diff --git a/sci-mathematics/singular/ChangeLog b/sci-mathematics/singular/ChangeLog deleted file mode 100644 index e275fd857..000000000 --- a/sci-mathematics/singular/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sci-mathematics/singular -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*singular-4.0.0_p2 (09 May 2014) - - 09 May 2014; Thomas Kahle <tomka@gentoo.org> +files/60singular-gentoo.el, - +files/singular-4.0.0-fix-omalloc-ar-detection.patch, - +files/singular-4.0.0-gentoo.patch, +metadata.xml, +singular-4.0.0_p2.ebuild: - Experimental bump to 4.0.0 diff --git a/sci-mathematics/singular/Manifest b/sci-mathematics/singular/Manifest deleted file mode 100644 index 975d6efd8..000000000 --- a/sci-mathematics/singular/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST singular-4.0.0.p2.tar.gz 9192414 SHA256 cfd768bd024497a4f5c8ae7d3a38cd39f7cf9678e0193975444074291ecd7db3 SHA512 0a22f42c216684236e3fb916391f55430f26cca7ec49d257bc8b673ce6f889cd0fa93d59bad63e2336076e80e891537f9e39d9158d3a5d46b16f98ef15b6bbde WHIRLPOOL a37021bf442773dfbe3988bece834baf8d5870333fe19713e7f26815d8329200d3e8270bd34f6523af7787904645cd740d5894963f9a72c4f9c8ee45ea5068f9 diff --git a/sci-mathematics/singular/files/60singular-gentoo.el b/sci-mathematics/singular/files/60singular-gentoo.el deleted file mode 100644 index 7be8c08ef..000000000 --- a/sci-mathematics/singular/files/60singular-gentoo.el +++ /dev/null @@ -1,10 +0,0 @@ - -;; site-file for sci-mathematics/singular - -(add-to-list 'load-path "@SITELISP@") -(autoload 'singular "singular" - "Start Singular using default values." t) -(autoload 'singular-other "singular" - "Ask for arguments and start Singular." t) - -(add-to-list 'auto-mode-alist '("\\.sing\\'" . c++-mode)) diff --git a/sci-mathematics/singular/files/singular-4.0.0-fix-omalloc-ar-detection.patch b/sci-mathematics/singular/files/singular-4.0.0-fix-omalloc-ar-detection.patch deleted file mode 100644 index 87b44234a..000000000 --- a/sci-mathematics/singular/files/singular-4.0.0-fix-omalloc-ar-detection.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -U 3 -dHrN singular-4.0.0.orig/omalloc/configure.ac singular-4.0.0/omalloc/configure.ac ---- singular-4.0.0.orig/omalloc/configure.ac 2014-03-06 18:07:49.000000000 +0100 -+++ singular-4.0.0/omalloc/configure.ac 2014-05-09 15:41:19.755097185 +0200 -@@ -117,7 +117,7 @@ - dnl check for programs - dnl - AC_CHECK_PROG(AR, ar, ar, :) --if test "$ac_cv_prog_AR" != ar; then -+if test "$ac_cv_prog_AR" = no; then - AC_MSG_ERROR(*** ar program not found) - fi - AC_CHECK_PROGS(PERL, perl, "no") diff --git a/sci-mathematics/singular/files/singular-4.0.0-gentoo.patch b/sci-mathematics/singular/files/singular-4.0.0-gentoo.patch deleted file mode 100644 index ba7b841c9..000000000 --- a/sci-mathematics/singular/files/singular-4.0.0-gentoo.patch +++ /dev/null @@ -1,65 +0,0 @@ ---- resources/feResource.cc.orig 2010-04-30 10:20:14.000000000 +0000 -+++ resources/feResource.cc 2010-10-11 09:19:01.431179334 +0000 -@@ -41,7 +41,7 @@ - #define SINGULAR_DEFAULT_DIR "/usr/local/Singular/"S_VERSION1 - #endif - #else // ! defined(MAKE_DISTRIBUTION) --#define SINGULAR_DEFAULT_DIR S_ROOT_DIR -+#define SINGULAR_DEFAULT_DIR "@GENTOO_PORTAGE_EPREFIX@/usr" - #endif // defined(MAKE_DISTRIBUTION) - - /***************************************************************** -@@ -73,33 +73,31 @@ - { - {"SearchPath", 's', feResPath, NULL, - "$SINGULARPATH;" -- "%b/LIB;" -- "%b/MOD;" -+ "%r/share/singular/MOD;" - "%r/LIB;" -- "%r/../LIB;" -+ "%r/share/singular/LIB;" - "%d/LIB;" -- "%d/../LIB" - ""}, -- {"Singular", 'S', feResBinary,"SINGULAR_EXECUTABLE", "%d/"S_UNAME"/Singular",(char *)""}, -- {"BinDir", 'b', feResDir, "SINGULAR_BIN_DIR", "%d/"S_UNAME, (char *)""}, -- {"RootDir", 'r', feResDir, "SINGULAR_ROOT_DIR", "%b/..", (char *)""}, -+ {"Singular", 'S', feResBinary,"SINGULAR_EXECUTABLE", "%d/bin/Singular",(char *)""}, -+ {"BinDir", 'b', feResDir, "SINGULAR_BIN_DIR", "%d/bin", (char *)""}, -+ {"RootDir", 'r', feResDir, "SINGULAR_ROOT_DIR", "%d", (char *)""}, - {"DefaultDir",'d', feResDir, "SINGULAR_DEFAULT_DIR", SINGULAR_DEFAULT_DIR, (char *)""}, -- {"InfoFile", 'i', feResFile, "SINGULAR_INFO_FILE", "%r/info/singular.hlp", (char *)""}, -- {"IdxFile", 'x', feResFile, "SINGULAR_IDX_FILE", "%r/doc/singular.idx", (char *)""}, -- {"HtmlDir", 'h', feResDir, "SINGULAR_HTML_DIR", "%r/html", (char *)""}, -+ {"InfoFile", 'i', feResFile, "SINGULAR_INFO_FILE", "%r/share/info/singular.info.bz2", (char *)""}, -+ {"IdxFile", 'x', feResFile, "SINGULAR_IDX_FILE", "%r/share/singular/singular.idx", (char *)""}, -+ {"HtmlDir", 'h', feResDir, "SINGULAR_HTML_DIR", "%r/share/doc/PFSUBST/html", (char *)""}, - #ifdef ix86_Win - {"HtmlHelpFile",'C', feResFile, "SINGULAR_CHM_FILE", "%r/doc/Manual.chm", (char *)""}, - #endif - {"ManualUrl", 'u', feResUrl, "SINGULAR_URL", "http://www.singular.uni-kl.de/Manual/"S_VERSION1, (char *)""}, -- {"ExDir", 'm', feResDir, "SINGULAR_EXAMPLES_DIR","%r/examples", (char *)""}, -+ {"ExDir", 'm', feResDir, "SINGULAR_EXAMPLES_DIR","%r/share/doc/PFSUBST/examples", (char *)""}, - {"Path", 'p', feResPath, NULL, "%b;$PATH", (char *)""}, - - #ifdef ESINGULAR - {"emacs", 'E', feResBinary,"ESINGULAR_EMACS", "%b/emacs", (char *)""}, - {"xemacs", 'A', feResBinary,"ESINGULAR_EMACS", "%b/xemacs", (char *)""}, - {"SingularEmacs",'M', feResBinary,"ESINGULAR_SINGULAR", "%b/Singular", (char *)""}, -- {"EmacsLoad", 'l', feResFile, "ESINGULAR_EMACS_LOAD", "%e/.emacs-singular", (char *)""}, -- {"EmacsDir", 'e', feResDir, "ESINGULAR_EMACS_DIR", "%r/emacs", (char *)""}, -+ {"EmacsLoad", 'l', feResFile, "ESINGULAR_EMACS_LOAD", "%r/share/emacs/site-lisp/singular/.emacs-singular", (char *)""}, -+ {"EmacsDir", 'e', feResDir, "ESINGULAR_EMACS_DIR", "%r/share/emacs/site-lisp/singular", (char *)""}, - #elif defined(TSINGULAR) - {"SingularXterm",'M', feResBinary,"TSINGULAR_SINGULAR", "%b/Singular", (char *)""}, - #ifdef ix86_Win -@@ -108,7 +106,7 @@ - {"xterm", 'X', feResBinary,"XTERM", "%b/xterm", (char *)""}, - #endif - #else -- {"EmacsDir", 'e', feResDir, "SINGULAR_EMACS_DIR", "%r/emacs", (char *)""}, -+ {"EmacsDir", 'e', feResDir, "SINGULAR_EMACS_DIR", "%r/share/emacs/site-lisp/singular", (char *)""}, - #endif - {NULL, 0, feResUndef, NULL, NULL, NULL}, // must be the last record - }; diff --git a/sci-mathematics/singular/metadata.xml b/sci-mathematics/singular/metadata.xml deleted file mode 100644 index 936baecd7..000000000 --- a/sci-mathematics/singular/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<maintainer> - <email>tomka@gentoo.org</email> - <name>Thomas Kahle</name> -</maintainer> -<herd>sci-mathematics</herd> -<use> - <flag name='boost'>Compile against external boost headers (<pkg>dev-libs/boost</pkg>)</flag> -</use> -</pkgmetadata> diff --git a/sci-mathematics/singular/singular-4.0.0_p2.ebuild b/sci-mathematics/singular/singular-4.0.0_p2.ebuild deleted file mode 100644 index 1ec80b4f3..000000000 --- a/sci-mathematics/singular/singular-4.0.0_p2.ebuild +++ /dev/null @@ -1,147 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-mathematics/singular/singular-3.1.4-r1.ebuild,v 1.4 2012/06/23 10:50:20 xarthisius Exp $ - -EAPI=5 - -inherit autotools eutils elisp-common flag-o-matic multilib prefix versionator - -MY_PN=Singular -MY_PV=$(replace_all_version_separators '.') -# Consistency is different... -MY_DIR2=$(get_version_component_range 1-3 ${PV}) -MY_DIR=$(replace_all_version_separators '-' ${MY_DIR2}) - -DESCRIPTION="Computer algebra system for polynomial computations" -HOMEPAGE="http://www.singular.uni-kl.de/" -SRC_URI="http://www.mathematik.uni-kl.de/ftp/pub/Math/${MY_PN}/SOURCES/${MY_DIR}/${PN}-${MY_PV}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~x86-linux ~x86-macos" -IUSE="boost doc emacs examples python +readline" - -RDEPEND="dev-libs/gmp - >=dev-libs/ntl-5.5.1 - emacs? ( >=virtual/emacs-22 )" - -DEPEND="${RDEPEND} - dev-lang/perl - boost? ( dev-libs/boost ) - readline? ( sys-libs/readline )" - -SITEFILE=60${PN}-gentoo.el - -S="${WORKDIR}/${PN}-${MY_DIR2}" - -pkg_setup() { - append-flags "-fPIC" - append-ldflags "-fPIC" - tc-export AR CC CPP CXX - - # Ensure that >=emacs-22 is selected - if use emacs; then - elisp-need-emacs 22 || die "Emacs version too low" - fi -} - -src_prepare () { - # Need to do something about resources later... - # epatch "${FILESDIR}"/${PN}-4.0.0-gentoo.patch - - # omalloc's old configure will fail if ar is not exactly 'ar'. - epatch "${FILESDIR}"/${PN}-4.0.0-fix-omalloc-ar-detection.patch - - cd "${S}"/omalloc || die "failed to cd into omalloc directory" - eautoreconf -} - -src_configure() { - econf \ -# --prefix="${S}"/build \ -# --exec-prefix="${S}"/build \ -# --bindir="${S}"/build/bin \ -# --libdir="${S}"/build/lib \ -# --libexecdir="${S}"/build/lib \ -# --includedir="${S}"/build/include \ - --with-gmp="${EPREFIX}"/usr \ - --with-ntl \ - --disable-debug \ - --disable-doc \ - --enable-factory \ - --enable-libfac \ - --enable-IntegerProgramming \ -# --enable-Singular \ - $(use_with python python embed) \ - $(use_with boost Boost) \ - $(use_enable emacs) \ - $(use_with readline) || die "configure failed" -} - -src_compile() { - emake || die "emake failed" - - if use emacs; then - cd "${WORKDIR}"/${MY_PN}/${MY_SHARE_DIR}/emacs/ - elisp-compile *.el || die "elisp-compile failed" - fi -} - -src_test() { - emake test || die "tests failed" -} - -# src_install () { -# dodoc README -# # execs and libraries -# cd "${S}"/build/bin -# dobin ${MY_PN}* gen_test change_cost solve_IP toric_ideal LLL \ -# || die "failed to install binaries" -# insinto /usr/$(get_libdir)/${PN} -# doins *.so || die "failed to install libraries" -# -# dosym ${MY_PN}-${MY_DIR} /usr/bin/${MY_PN} \ -# || die "failed to create symbolic link" -# -# # stuff from the share tar ball -# cd "${WORKDIR}"/${MY_PN}/${MY_SHARE_DIR} -# insinto /usr/share/${PN} -# doins -r LIB || die "failed to install lib files" -# if use examples; then -# insinto /usr/share/doc/${PF} -# doins -r examples || die "failed to install examples" -# fi -# if use doc; then -# dohtml -r html/* || die "failed to install html docs" -# insinto /usr/share/${PN} -# doins doc/singular.idx || die "failed to install idx file" -# cp info/${PN}.hlp info/${PN}.info && -# doinfo info/${PN}.info \ -# || die "failed to install info files" -# fi -# if use emacs; then -# elisp-install ${PN} emacs/*.el emacs/*.elc emacs/.emacs* \ -# || die "elisp-install failed" -# elisp-site-file-install "${FILESDIR}/${SITEFILE}" -# fi -# } - -pkg_postinst() { - einfo "The authors ask you to register as a SINGULAR user." - einfo "Please check the license file for details." - - if use emacs; then - echo - ewarn "Please note that the ESingular emacs wrapper has been" - ewarn "removed in favor of full fledged singular support within" - ewarn "Gentoo's emacs infrastructure; i.e. just fire up emacs" - ewarn "and you should be good to go! See bug #193411 for more info." - echo - fi - - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/ufc/ChangeLog b/sci-mathematics/ufc/ChangeLog index 3e9549b60..fefc01844 100644 --- a/sci-mathematics/ufc/ChangeLog +++ b/sci-mathematics/ufc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/ufc -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/ufc: Add bitbucket to remote-id in metadata.xml + 16 Jul 2014; Andrew Reisner <andrew@reisner.co> ufc-2.3.0.ebuild: added keyword diff --git a/sci-mathematics/ufc/metadata.xml b/sci-mathematics/ufc/metadata.xml index 132ec13b6..497df0887 100644 --- a/sci-mathematics/ufc/metadata.xml +++ b/sci-mathematics/ufc/metadata.xml @@ -1,9 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-mathematics</herd> -<longdescription lang="en"> + <herd>sci-mathematics</herd> + <longdescription lang="en"> UFC (Unified Form-assembly Code) is a unified framework for finite element assembly. More precisely, it defines a fixed interface for communicating low level routines (functions) for evaluating and assembling finite element variational forms. The UFC interface consists of a single header file ufc.h that specifies a C++ interface that must be implemented by code that complies with the UFC specification. </longdescription> + <upstream> + <remote-id type="bitbucket">fenics-project/ufc-deprecated</remote-id> + </upstream> </pkgmetadata> - diff --git a/sci-mathematics/yorick/ChangeLog b/sci-mathematics/yorick/ChangeLog index cadcebccc..2d5679755 100644 --- a/sci-mathematics/yorick/ChangeLog +++ b/sci-mathematics/yorick/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/yorick -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-mathematics/yorick: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> yorick-2.1.06.ebuild, metadata.xml: Move to EAPI=5; add missing multilib.eclass diff --git a/sci-mathematics/yorick/metadata.xml b/sci-mathematics/yorick/metadata.xml index 754d00e96..5770e5a45 100644 --- a/sci-mathematics/yorick/metadata.xml +++ b/sci-mathematics/yorick/metadata.xml @@ -11,4 +11,7 @@ Yorick is a language for scientific computing and rapid prototyping, similar to matlab. It can easily call C functions and libraries, has multidimensional arrays and built-in plot functions. </longdescription> + <upstream> + <remote-id type="sourceforge">yorick</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/z3/ChangeLog b/sci-mathematics/z3/ChangeLog index ea8b48b40..0df768f57 100644 --- a/sci-mathematics/z3/ChangeLog +++ b/sci-mathematics/z3/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/z3 -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 29 Mar 2015; Justin Lecher <jlec@gentoo.org> z3-4.3.1.ebuild, z3-9999.ebuild: + sci-mathematics/z3: Correct license to MIT, thanks Daniel GOUJOT + 06 Mar 2014; Justin Lecher <jlec@gentoo.org> z3-9999.ebuild: Adopt to recent changes in git-r3.eclass @@ -13,4 +16,3 @@ Make build verbose; respect CXX, CXXFLAGS, LDFLAGS; use EPYTHON instead of a direct python call; check for openmp compatibility of the c++ compiler; add USE=gmp; drop unnecessary eclass; add missing metadata.xml - diff --git a/sci-mathematics/z3/z3-4.3.1.ebuild b/sci-mathematics/z3/z3-4.3.1.ebuild index 041a2c2d8..d4a1523bd 100644 --- a/sci-mathematics/z3/z3-4.3.1.ebuild +++ b/sci-mathematics/z3/z3-4.3.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -13,14 +13,14 @@ HOMEPAGE="http://z3.codeplex.com/" SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" SLOT="0" -LICENSE="MSR-LA" +LICENSE="MIT" KEYWORDS="~amd64 ~x86" IUSE="gmp" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND="${PYTHON_DEPS} - gmp? ( dev-libs/gmp )" + gmp? ( dev-libs/gmp:0 )" DEPEND="${RDEPEND}" pkg_setup() { diff --git a/sci-mathematics/z3/z3-9999.ebuild b/sci-mathematics/z3/z3-9999.ebuild index a9b9d9080..590ef54be 100644 --- a/sci-mathematics/z3/z3-9999.ebuild +++ b/sci-mathematics/z3/z3-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -15,14 +15,14 @@ EGIT_REPO_URI="https://git01.codeplex.com/z3" EGIT_MIN_CLONE_TYPE=single SLOT="0" -LICENSE="MSR-LA" +LICENSE="MIT" KEYWORDS="" IUSE="gmp" REQUIRED_USE="${PYTHON_REQUIRED_USE}" RDEPEND="${PYTHON_DEPS} - gmp? ( dev-libs/gmp )" + gmp? ( dev-libs/gmp:0 )" # A new curl is needed because codeplex has a bug and early version of libcurl # will cause a failed git clone. DEPEND="${RDEPEND} diff --git a/sci-misc/elmer-gui/elmer-gui-9999.ebuild b/sci-misc/elmer-gui/elmer-gui-9999.ebuild index c1ff9722c..a150a4fd3 100644 --- a/sci-misc/elmer-gui/elmer-gui-9999.ebuild +++ b/sci-misc/elmer-gui/elmer-gui-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit autotools eutils qt4-r2 subversion python-single-r1 versionator diff --git a/sci-misc/hfst/ChangeLog b/sci-misc/hfst/ChangeLog index 550fcb04d..7ef0a3c11 100644 --- a/sci-misc/hfst/ChangeLog +++ b/sci-misc/hfst/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/hfst -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/hfst: Updating remote-id in metadata.xml + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> hfst-3.0.2.ebuild, hfst-3.3.12.ebuild, metadata.xml: Add ~amd64 or ~x86 keywords for revdeps @@ -28,4 +31,3 @@ 17 Nov 2009; <flammie@gentoo.org> +hfst-2.2.ebuild, +metadata.xml: Initial ebuild for HFST - diff --git a/sci-misc/hfst/metadata.xml b/sci-misc/hfst/metadata.xml index 1e603324b..4be3eac8d 100644 --- a/sci-misc/hfst/metadata.xml +++ b/sci-misc/hfst/metadata.xml @@ -1,28 +1,31 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> + <longdescription lang="en"> Open Source API for FSTs, a set of command line tools, and clones of traditional FST-based linguistic morphology tools. </longdescription> - <use> - <flag name="openfst"> + <use> + <flag name="openfst"> Add optional support for openfst backend library (<pkg>sci-misc/openfst</pkg>) </flag> - <flag name="foma"> + <flag name="foma"> Add optional support for foma backend library (<pkg>sci-misc/foma</pkg>)</flag> - <flag name="sfst"> + <flag name="sfst"> Add optional support for sfst backend library (<pkg>sci-misc/sfst</pkg>) </flag> - <flag name="glib"> + <flag name="glib"> Parse UTF-8 and collate unicode using glib instead of homebrewn methods </flag> - <flag name="xml"> + <flag name="xml"> Include parsers for grammars and formats that require XML support </flag> - </use> + </use> + <upstream> + <remote-id type="sourceforge">hfst</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/irstlm/ChangeLog b/sci-misc/irstlm/ChangeLog index c7329528a..36a33d004 100644 --- a/sci-misc/irstlm/ChangeLog +++ b/sci-misc/irstlm/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-misc/irstlm -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/irstlm: Updating remote-id in metadata.xml + +*irstlm-5.80.08 (28 Feb 2015) + + 28 Feb 2015; Pavel Denisov <pavel.a.denisov@gmail.com> + -irstlm-5.80.03.ebuild, -irstlm-5.80.06.ebuild, +irstlm-5.80.08.ebuild: + Version bump. + *irstlm-5.80.06 (22 Oct 2014) 22 Oct 2014; Pavel Denisov <pavel.a.denisov@gmail.com> diff --git a/sci-misc/irstlm/Manifest b/sci-misc/irstlm/Manifest index bf20b8062..af5f2b25c 100644 --- a/sci-misc/irstlm/Manifest +++ b/sci-misc/irstlm/Manifest @@ -1,2 +1 @@ -DIST irstlm-5.80.03.tgz 146287 SHA256 500c64e90cae73c2f06ed34ad078423cc100f4e16e6dd98a9e466b17367d31e7 SHA512 0a8ef2bb565a258340a13e5ac8533b31f261b6ec522116fa82b4e005c5253653ea04f7b95c492a1f48fd44035eab6646956e700ce509851b721b9df80f29b8ac WHIRLPOOL 8d4e796c4b56e0fc57041c686dd8edae39fde294d59209ade2090107b1b8210112815dc82fe52a71e78ee9fb051952b49dee8ff0decf23c49fdf9f420faf81ad -DIST irstlm-5.80.06.tgz 9564608 SHA256 d3d7f1183e1b43636efc555802d012e848542910f5b94fc0a7bb10e4396efe29 SHA512 2fcc667475b8d5ea2944c369fb3db00414dced197dbee64db01f66ebd69eeb50a5a0e327d8c7744590c6773e2c0a8bb3dc2b7e17f8513dac31b3e536e6fe3aca WHIRLPOOL f480926a08a81038a823e992151da98d16a738071d066f2e8c47e6c22dff96dae0dd750deb84fb0654bdb8510c156dbfa53cfe0613453bb309dc0d4f1edb5cbc +DIST irstlm-5.80.08.tgz 11590533 SHA256 4d1eee217ee70f8abb08d2509c438d034772922b2fc7f90b6084629d7f8d0d7e SHA512 c337723b597275bf6e6db693d97271cbb3d833a6c71e855edeae73cee51fd804e51e7883acabdefd4221d4a4a5769019a96c54945ac7e778c985b92482407b01 WHIRLPOOL 72fcc15b479065a996a05750145678e8d5302e0c41dc63a881262cb84ad757ec5a25087a1ceb9e163ee51d99587621ca04937884f73d9821520ef21980bf7004 diff --git a/sci-misc/irstlm/irstlm-5.80.03.ebuild b/sci-misc/irstlm/irstlm-5.80.03.ebuild deleted file mode 100644 index 71932f36b..000000000 --- a/sci-misc/irstlm/irstlm-5.80.03.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="5" - -inherit autotools - -DESCRIPTION="A tool for the estimation, representation, and computation of statistical language models" -HOMEPAGE="http://hlt.fbk.eu/en/irstlm" -SRC_URI="mirror://sourceforge/${PN}/${P}.tgz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -src_prepare() { - eautoreconf -} diff --git a/sci-misc/irstlm/irstlm-5.80.06.ebuild b/sci-misc/irstlm/irstlm-5.80.08.ebuild index 98bc74866..f82fc8955 100644 --- a/sci-misc/irstlm/irstlm-5.80.06.ebuild +++ b/sci-misc/irstlm/irstlm-5.80.08.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ diff --git a/sci-misc/irstlm/metadata.xml b/sci-misc/irstlm/metadata.xml index 5d16554ed..e74038ce8 100644 --- a/sci-misc/irstlm/metadata.xml +++ b/sci-misc/irstlm/metadata.xml @@ -1,14 +1,17 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>pavel.a.denisov@gmail.com</email> - </maintainer> - <longdescription lang="en"> + <maintainer> + <email>pavel.a.denisov@gmail.com</email> + </maintainer> + <longdescription lang="en"> The IRST Language Modeling Toolkit features algorithms and data structures suitable to estimate, store, and access very large LMs. The software has been integrated into a popular open source Statistical Machine Translation decoder called Moses, and is compatible with language models created with other tools, such as the SRILM Tooolkit. </longdescription> + <upstream> + <remote-id type="sourceforge">irstlm</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/jwnl/ChangeLog b/sci-misc/jwnl/ChangeLog index 9a050012b..4e38184d2 100644 --- a/sci-misc/jwnl/ChangeLog +++ b/sci-misc/jwnl/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/jwnl -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/jwnl: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> jwnl-1.3_rc3.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/jwnl/metadata.xml b/sci-misc/jwnl/metadata.xml index faf15b461..dc7c73e44 100644 --- a/sci-misc/jwnl/metadata.xml +++ b/sci-misc/jwnl/metadata.xml @@ -8,4 +8,7 @@ Java based programming interface for accessing wordnet style dictionary data. </longdescription> + <upstream> + <remote-id type="sourceforge">jwordnet</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/kaldi/ChangeLog b/sci-misc/kaldi/ChangeLog index f7406faf9..6639e7e5a 100644 --- a/sci-misc/kaldi/ChangeLog +++ b/sci-misc/kaldi/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*kaldi-0_p20150301 (01 Mar 2015) + + 01 Mar 2015; Pavel Denisov <pavel.a.denisov@gmail.com> + -kaldi-0_p20150101.ebuild, +kaldi-0_p20150301.ebuild, files/Makefile.patch, + files/configure.patch, files/default_rules.mk.patch: + Version bump. + *kaldi-0_p20150101 (11 Jan 2015) 11 Jan 2015; Pavel Denisov <pavel.a.denisov@gmail.com> +files/Makefile.patch, diff --git a/sci-misc/kaldi/files/Makefile.patch b/sci-misc/kaldi/files/Makefile.patch index 07302d6d4..ef1a60640 100644 --- a/sci-misc/kaldi/files/Makefile.patch +++ b/sci-misc/kaldi/files/Makefile.patch @@ -1,19 +1,57 @@ ---- Makefile.orig 2015-01-01 21:51:30.999356027 -0400 -+++ Makefile 2015-01-04 16:54:02.527824499 -0400 -@@ -131,6 +131,16 @@ - ext_depend: check_portaudio - -for x in $(EXT_SUBDIRS); do $(MAKE) -C $$x depend; done - -+print-binfiles: $(addsuffix /print-binfiles, $(SUBDIRS)) -+ -+%/print-binfiles: -+ @$(MAKE) --no-print-directory -C $(dir $@) print-binfiles -+ -+print-libfiles: $(addsuffix /print-libfiles, $(SUBDIRS)) -+ -+%/print-libfiles: -+ @$(MAKE) --no-print-directory -C $(dir $@) print-libfiles -+ - - .PHONY: $(SUBDIRS) - $(SUBDIRS) : mklibdir +*** Makefile.orig 2015-02-28 16:31:57.377401743 -0400 +--- Makefile 2015-02-28 16:48:58.153175376 -0400 +*************** +*** 30,36 **** + + # Reset the default goal, so that the all target will become default + .DEFAULT_GOAL := +! all: checkversion test_dependencies kaldi.mk mklibdir $(SUBDIRS) + -echo Done + + mklibdir: +--- 30,36 ---- + + # Reset the default goal, so that the all target will become default + .DEFAULT_GOAL := +! all: checkversion kaldi.mk mklibdir $(SUBDIRS) + -echo Done + + mklibdir: +*************** +*** 88,103 **** + ext: test_dependencies ext_depend $(SUBDIRS) $(EXT_SUBDIRS) + -echo Done + +- ifndef OPENFST_VER +- $(error Please rerun configure: OPENFST_VER is not defined, likely kaldi.mk was produced by older configure script.) +- endif +- # Note: OPENFST_VER is determined by configure and added to kaldi.mk +- OPENFST_VER_NUM := $(shell echo $(OPENFST_VER) | sed 's/\./ /g' | xargs printf "%d%02d%02d") +- test_dependencies: +- ifeq ("$(shell expr $(OPENFST_VER_NUM) \< 10302)","1") +- $(error OpenFst $(OPENFST_VER) is not supported. You now need OpenFst >= 1.3.2.) +- endif +- + check_portaudio: + @[ -d ../tools/portaudio ] || ( cd ../tools; ./install_portaudio.sh ) + +--- 88,93 ---- +*************** +*** 131,136 **** +--- 121,136 ---- + ext_depend: check_portaudio + -for x in $(EXT_SUBDIRS); do $(MAKE) -C $$x depend; done + ++ print-binfiles: $(addsuffix /print-binfiles, $(SUBDIRS)) ++ ++ %/print-binfiles: ++ @$(MAKE) --no-print-directory -C $(dir $@) print-binfiles ++ ++ print-libfiles: $(addsuffix /print-libfiles, $(SUBDIRS)) ++ ++ %/print-libfiles: ++ @$(MAKE) --no-print-directory -C $(dir $@) print-libfiles ++ + + .PHONY: $(SUBDIRS) + $(SUBDIRS) : mklibdir diff --git a/sci-misc/kaldi/files/configure.patch b/sci-misc/kaldi/files/configure.patch index 07d663e93..f6086fc3c 100644 --- a/sci-misc/kaldi/files/configure.patch +++ b/sci-misc/kaldi/files/configure.patch @@ -1,71 +1,93 @@ ---- configure.orig 2015-01-01 21:51:05.611960184 -0400 -+++ configure 2015-01-01 22:06:11.027064734 -0400 -@@ -45,15 +45,6 @@ - fi - } - -- -- --## First do some checks. These verify that all the things are --## here that should be here. --if [ "`basename $PWD`" != "src" ]; then -- echo 'You must run "configure" from the src/ directory.' -- exit 1 --fi -- - ## Default locations for FST and linear algebra libraries. - MATHLIB='ATLAS' - ATLASROOT=`rel2abs ../tools/ATLAS/` -@@ -473,6 +464,23 @@ - exit_success; - } - -+function linux_configure_gentoo { -+ m=$1 # 64 or empty. -+ ATLASLIBS="/usr/lib$m/libatlas.so.3 /usr/lib$m/libf77blas.so.3 /usr/lib$m/libatlcblas.so.3 /usr/lib$m/libatlclapack.so.3" -+ for f in $ATLASLIBS; do -+ [ ! -f $f ] && return 1; -+ done -+ libdir=$(dirname $(echo $ATLASLIBS | awk '{print $1}')) -+ [ -z "$libdir" ] && echo "Error getting libdir in linux_configure_gentoo" && exit 1; -+ echo ATLASINC = $ATLASROOT >> kaldi.mk -+ echo ATLASLIBS = $ATLASLIBS -Wl,-rpath=$libdir >> kaldi.mk -+ echo -+ cat makefiles/linux_atlas.mk >> kaldi.mk -+ fix_cxx_flag -+ echo "Successfully configured for gentoo [dynamic libraries] with ATLASLIBS =$ATLASLIBS" -+ $use_cuda && linux_configure_cuda -+ exit_success; -+} - - function linux_configure_static { - if $threaded_atlas; then pt=pt; else pt=""; fi -@@ -716,8 +724,8 @@ - - echo "On Linux: Checking for linear algebra header files ..." - if [ "$MATHLIB" == "ATLAS" ]; then -- if [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ; then -- failure "Could not find required header files cblas.h or clapack.h in ATLAS dir '$ATLASROOT/include'" -+ if ( [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ) && ( [ ! -f $ATLASROOT/cblas.h ] || [ ! -f $ATLASROOT/clapack.h ] ) ; then -+ failure "Could not find required header files cblas.h or clapack.h in ATLAS dirs '$ATLASROOT/include' or '$ATLASROOT'" - fi - echo "Using ATLAS as the linear algebra library." - -@@ -741,6 +749,8 @@ - linux_configure_debian7 || \ - linux_configure_redhat 64 || \ - linux_configure_redhat || \ -+ linux_configure_gentoo 64 || \ -+ linux_configure_gentoo || \ - linux_atlas_failure "Failed to configure ATLAS lbiraries"; - else - # Prefer dynamic to static math. -@@ -751,6 +761,8 @@ - linux_configure_debian7 || \ - linux_configure_redhat 64 || \ - linux_configure_redhat || \ -+ linux_configure_gentoo 64 || \ -+ linux_configure_gentoo || \ - linux_atlas_failure "Failed to configure ATLAS lbiraries"; - fi - +*** configure.orig 2015-02-28 16:31:35.568045409 -0400 +--- configure 2015-02-28 17:21:58.477634475 -0400 +*************** +*** 46,60 **** + fi + } + +- +- +- ## First do some checks. These verify that all the things are +- ## here that should be here. +- if [ "`basename $PWD`" != "src" ]; then +- echo 'You must run "configure" from the src/ directory.' +- exit 1 +- fi +- + ## Default locations for FST and linear algebra libraries. + MATHLIB='ATLAS' + ATLASROOT=`rel2abs ../tools/ATLAS/` +--- 46,51 ---- +*************** +*** 522,527 **** +--- 513,535 ---- + exit_success; + } + ++ function linux_configure_gentoo { ++ m=$1 # 64 or empty. ++ ATLASLIBS="/usr/lib$m/libatlas.so.3 /usr/lib$m/libf77blas.so.3 /usr/lib$m/libatlcblas.so.3 /usr/lib$m/libatlclapack.so.3" ++ for f in $ATLASLIBS; do ++ [ ! -f $f ] && return 1; ++ done ++ libdir=$(dirname $(echo $ATLASLIBS | awk '{print $1}')) ++ [ -z "$libdir" ] && echo "Error getting libdir in linux_configure_gentoo" && exit 1; ++ echo ATLASINC = $ATLASROOT >> kaldi.mk ++ echo ATLASLIBS = $ATLASLIBS -Wl,-rpath=$libdir >> kaldi.mk ++ echo ++ cat makefiles/linux_atlas.mk >> kaldi.mk ++ fix_cxx_flag ++ echo "Successfully configured for gentoo [dynamic libraries] with ATLASLIBS =$ATLASLIBS" ++ $use_cuda && linux_configure_cuda ++ exit_success; ++ } + + function linux_configure_static { + if $threaded_atlas; then pt=pt; else pt=""; fi +*************** +*** 682,688 **** + echo "FSTROOT = $FSTROOT" >> kaldi.mk + + # Check installed OpenFst version and add C++11 flags if OpenFst >= 1.4 +! OPENFST_VER=`grep 'PACKAGE_VERSION' $FSTROOT/Makefile | sed -e 's:.*= ::'` + echo "OPENFST_VER = $OPENFST_VER" >> kaldi.mk + OPENFST_VER_NUM=`echo $OPENFST_VER | sed 's/\./ /g' | xargs printf "%d%02d%02d"` + if [ $OPENFST_VER_NUM -ge 10400 ]; then +--- 690,696 ---- + echo "FSTROOT = $FSTROOT" >> kaldi.mk + + # Check installed OpenFst version and add C++11 flags if OpenFst >= 1.4 +! OPENFST_VER="1.4.1" + echo "OPENFST_VER = $OPENFST_VER" >> kaldi.mk + OPENFST_VER_NUM=`echo $OPENFST_VER | sed 's/\./ /g' | xargs printf "%d%02d%02d"` + if [ $OPENFST_VER_NUM -ge 10400 ]; then +*************** +*** 765,772 **** + + echo "On Linux: Checking for linear algebra header files ..." + if [ "$MATHLIB" == "ATLAS" ]; then +! if [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ; then +! failure "Could not find required header files cblas.h or clapack.h in ATLAS dir '$ATLASROOT/include'" + fi + echo "Using ATLAS as the linear algebra library." + +--- 773,780 ---- + + echo "On Linux: Checking for linear algebra header files ..." + if [ "$MATHLIB" == "ATLAS" ]; then +! if ( [ ! -f $ATLASROOT/include/cblas.h ] || [ ! -f $ATLASROOT/include/clapack.h ] ) && ( [ ! -f $ATLASROOT/cblas.h ] || [ ! -f $ATLASROOT/clapack.h ] ) ; then +! failure "Could not find required header files cblas.h or clapack.h in ATLAS dirs '$ATLASROOT/include' or '$ATLASROOT'" + fi + echo "Using ATLAS as the linear algebra library." + +*************** +*** 797,802 **** +--- 805,812 ---- + else + # Prefer dynamic to static math. + linux_configure_debian_ubuntu3 || \ ++ linux_configure_gentoo 64 || \ ++ linux_configure_gentoo || \ + linux_configure_dynamic || \ + linux_configure_static || \ + linux_configure_debian_ubuntu 64 || \ diff --git a/sci-misc/kaldi/files/default_rules.mk.patch b/sci-misc/kaldi/files/default_rules.mk.patch index 26c7f3616..60e34307b 100644 --- a/sci-misc/kaldi/files/default_rules.mk.patch +++ b/sci-misc/kaldi/files/default_rules.mk.patch @@ -1,20 +1,47 @@ ---- makefiles/default_rules.mk.orig 2015-01-10 19:56:03.918751769 -0400 -+++ makefiles/default_rules.mk 2015-01-11 13:34:14.596055674 -0400 -@@ -14,7 +14,7 @@ - LIBFILE = lib$(LIBNAME).so - #LDLIBS += -l$(LIBNAME) - endif -- LDFLAGS += -Wl,-rpath=$(shell readlink -f $(KALDILIBDIR)) -L. -+ LDFLAGS += -L. - LDFLAGS += $(foreach dep,$(ADDLIBS), -L$(dir $(dep)) ) - XDEPENDS = $(foreach dep,$(ADDLIBS), $(dir $(dep))/lib$(notdir $(basename $(dep))).so ) - else # Platform not supported -@@ -84,3 +84,8 @@ - #.depend.mk: depend - -include .depend.mk - -+print-binfiles: -+ @echo $(addprefix $(shell pwd)/, $(BINFILES)) -+ -+print-libfiles: -+ @echo $(addsuffix .so, $(addprefix $(shell pwd)/lib, $(LIBNAME))) +*** makefiles/default_rules.mk.orig 2015-02-28 16:32:00.830458169 -0400 +--- makefiles/default_rules.mk 2015-02-28 19:10:50.692172138 -0400 +*************** +*** 14,20 **** + LIBFILE = lib$(LIBNAME).so + #LDLIBS += -l$(LIBNAME) + endif +! LDFLAGS += -Wl,-rpath=$(shell readlink -f $(KALDILIBDIR)) -L. + LDFLAGS += $(foreach dep,$(ADDLIBS), -L$(dir $(dep)) ) + XDEPENDS = $(foreach dep,$(ADDLIBS), $(dir $(dep))/lib$(notdir $(basename $(dep))).so ) + else # Platform not supported +--- 14,20 ---- + LIBFILE = lib$(LIBNAME).so + #LDLIBS += -l$(LIBNAME) + endif +! LDFLAGS += -L. + LDFLAGS += $(foreach dep,$(ADDLIBS), -L$(dir $(dep)) ) + XDEPENDS = $(foreach dep,$(ADDLIBS), $(dir $(dep))/lib$(notdir $(basename $(dep))).so ) + else # Platform not supported +*************** +*** 72,78 **** + test_compile: $(TESTFILES) + + test: test_compile +! @result=0; for x in $(TESTFILES); do printf "Running $$x ..."; ./$$x >/dev/null 2>&1; if [ $$? -ne 0 ]; then echo "... FAIL $$x"; result=1; else echo "... SUCCESS"; fi; done; exit $$result + + .valgrind: $(BINFILES) $(TESTFILES) + +--- 72,78 ---- + test_compile: $(TESTFILES) + + test: test_compile +! @result=0; for x in $(TESTFILES); do printf "Running $$x ..."; LD_LIBRARY_PATH=$(KALDILIBDIR):${LD_LIBRARY_PATH} ./$$x >/dev/null 2>&1; if [ $$? -ne 0 ]; then echo "... FAIL $$x"; result=1; else echo "... SUCCESS"; fi; done; exit $$result + + .valgrind: $(BINFILES) $(TESTFILES) + +*************** +*** 84,86 **** +--- 84,91 ---- + #.depend.mk: depend + -include .depend.mk + ++ print-binfiles: ++ @echo $(addprefix $(shell pwd)/, $(BINFILES)) ++ ++ print-libfiles: ++ @echo $(addsuffix .so, $(addprefix $(shell pwd)/lib, $(LIBNAME))) diff --git a/sci-misc/kaldi/kaldi-0_p20150101.ebuild b/sci-misc/kaldi/kaldi-0_p20150301.ebuild index 9ef57039e..8ba100db8 100644 --- a/sci-misc/kaldi/kaldi-0_p20150101.ebuild +++ b/sci-misc/kaldi/kaldi-0_p20150301.ebuild @@ -8,7 +8,7 @@ inherit eutils flag-o-matic subversion DESCRIPTION="A toolkit for speech recognition" HOMEPAGE="http://kaldi.sourceforge.net/" -ESVN_REPO_URI="https://svn.code.sf.net/p/kaldi/code/trunk/src@4735" +ESVN_REPO_URI="https://svn.code.sf.net/p/kaldi/code/trunk/src@4927" LICENSE="Apache-2.0" SLOT="0" @@ -18,7 +18,7 @@ KEYWORDS="" RDEPEND=" media-libs/speex sci-libs/atlas[lapack,threads=] - ~sci-misc/openfst-1.3.4" + >=sci-misc/openfst-1.4.1" DEPEND="${RDEPEND} doc? ( app-doc/doxygen )" @@ -41,7 +41,6 @@ src_configure() { use test || append-cxxflags -DNDEBUG sed -i \ - -e 's/OPENFST_VER =/OPENFST_VER = 1.3.4#/' \ -e "s:-g :-DHAVE_SPEEX ${CXXFLAGS} :" \ -e "s:-lm -lpthread -ldl:-lm -lpthread -ldl -lspeex ${LDFLAGS}:" \ kaldi.mk || die "sed unix/kaldi.mk failed" diff --git a/sci-misc/nltk/ChangeLog b/sci-misc/nltk/ChangeLog index 613b269e1..d91ac2a39 100644 --- a/sci-misc/nltk/ChangeLog +++ b/sci-misc/nltk/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/nltk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/nltk: Add github to remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> -nltk-2.0.1_rc1.ebuild, +nltk-2.0.4.ebuild, metadata.xml: Version Bump; Bump to distutils-r1 eclass diff --git a/sci-misc/nltk/metadata.xml b/sci-misc/nltk/metadata.xml index eefdbc160..8cf6c1d55 100644 --- a/sci-misc/nltk/metadata.xml +++ b/sci-misc/nltk/metadata.xml @@ -8,4 +8,7 @@ NLTK is collection of natural language tools written in python language. It also contains huge corpora. </longdescription> + <upstream> + <remote-id type="github">nltk/nltk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/nltk/nltk-2.0.4.ebuild b/sci-misc/nltk/nltk-2.0.4.ebuild index 36801f201..dea67d7c5 100644 --- a/sci-misc/nltk/nltk-2.0.4.ebuild +++ b/sci-misc/nltk/nltk-2.0.4.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) PYTHON_REQ_USE="tk" inherit distutils-r1 diff --git a/sci-misc/openfst/ChangeLog b/sci-misc/openfst/ChangeLog index 47bb94e86..4278e322a 100644 --- a/sci-misc/openfst/ChangeLog +++ b/sci-misc/openfst/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-misc/openfst -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*openfst-1.4.1 (28 Feb 2015) + + 28 Feb 2015; Pavel Denisov <pavel.a.denisov@gmail.com> +openfst-1.4.1.ebuild, + +files/kaldi-openfst-1.4.1.patch: + Version bump. + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> -openfst-1.2.7.ebuild: Drop old diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest index ad46d23ff..7312addb8 100644 --- a/sci-misc/openfst/Manifest +++ b/sci-misc/openfst/Manifest @@ -1 +1,2 @@ DIST openfst-1.3.4.tar.gz 769158 SHA256 e95fa96674e1c9d6866bbf79b9cd755c5121ad165b76224c7c6bbfa139399a61 SHA512 6ed87cbb949776b8702545a51d129e03f33428369b20255d637191e054ce04e529969aef49549b098b144cfde45cd9b741e6cba6680f815c04ad5717fdb0cbd9 WHIRLPOOL 593fd22668044f9ec8df70c274ee910f9da85a48fcd33c73993e54afd21298208d69804342b4e3a5d36e59aa92e853e84d95d1623c3708e7e1fc70e42916949f +DIST openfst-1.4.1.tar.gz 824020 SHA256 e671bf6bd4425a1fed4e7543a024201b74869bfdd029bdf9d10c53a3c2818277 SHA512 8cb3b3e83155d1b2bd0075bab4fcf5d7160b427af87a2c03217a614a9dd1f9d7d1a67d404d897ad8659532686a7ad2fd20270de7cf838c6f38d4ae807369c51f WHIRLPOOL b9ae3562e2c7b2d651852d35e56ed7e678a990b46c7f720ac3a8e80cc7edee786bff3e1ab34aa6d5e9d33ec0821dbff8d6a5b6ea97c32ced40474891bfe4a4a3 diff --git a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch b/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch new file mode 100644 index 000000000..140ea4e24 --- /dev/null +++ b/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch @@ -0,0 +1,269 @@ +diff -crB openfst-1.4.1.orig/src/include/fst/lock.h openfst-1.4.1/src/include/fst/lock.h +*** openfst-1.4.1.orig/src/include/fst/lock.h 2012-04-25 19:43:47.000000000 -0400 +--- openfst-1.4.1/src/include/fst/lock.h 2015-02-28 14:12:29.009385600 -0400 +*************** +*** 78,85 **** + RefCounter() : count_(1) {} + + int count() const { return count_; } +! int Incr() const { return ++count_; } +! int Decr() const { return --count_; } + + private: + mutable int count_; +--- 78,93 ---- + RefCounter() : count_(1) {} + + int count() const { return count_; } +! +! // below lines are modifications of openfst for multi-thrads support, +! // from tools/extras/openfst_gcc41up.patch, applied by tools/Makefile, +! // applicable to gcc 4.1 or above +! // int Incr() const { return ++count_; } +! // int Decr() const { return --count_; } +! +! int Incr() const { return __sync_add_and_fetch(&count_, 1); } +! int Decr() const { return __sync_sub_and_fetch(&count_, 1); } +! // end modifications + + private: + mutable int count_; +diff -crB openfst-1.4.1.orig/src/include/fst/minimize.h openfst-1.4.1/src/include/fst/minimize.h +*** openfst-1.4.1.orig/src/include/fst/minimize.h 2014-04-29 18:15:17.000000000 -0400 +--- openfst-1.4.1/src/include/fst/minimize.h 2015-02-28 14:11:39.270566070 -0400 +*************** +*** 134,140 **** + typedef typename A::Weight Weight; + typedef ReverseArc<A> RevA; + +! CyclicMinimizer(const ExpandedFst<A>& fst) { + Initialize(fst); + Compute(fst); + } +--- 134,147 ---- + typedef typename A::Weight Weight; + typedef ReverseArc<A> RevA; + +! CyclicMinimizer(const ExpandedFst<A>& fst): +! // tell the Partition data-member to expect multiple repeated +! // calls to SplitOn with the same element if we are non-deterministic. +! P_(fst.Properties(kIDeterministic, true) == 0) { +! if(fst.Properties(kIDeterministic, true) == 0) +! CHECK(Weight::Properties() & kIdempotent); // this minimization +! // algorithm for non-deterministic FSTs can only work with idempotent +! // semirings. + Initialize(fst); + Compute(fst); + } +*************** +*** 315,321 **** + typedef typename A::StateId ClassId; + typedef typename A::Weight Weight; + +! AcyclicMinimizer(const ExpandedFst<A>& fst) { + Initialize(fst); + Refine(fst); + } +--- 322,334 ---- + typedef typename A::StateId ClassId; + typedef typename A::Weight Weight; + +! AcyclicMinimizer(const ExpandedFst<A>& fst): +! // tell the Partition data-member to expect multiple repeated +! // calls to SplitOn with the same element if we are non-deterministic. +! partition_(fst.Properties(kIDeterministic, true) == 0) { +! if(fst.Properties(kIDeterministic, true) == 0) +! CHECK(Weight::Properties() & kIdempotent); // minimization for +! // non-deterministic FSTs can only work with idempotent semirings. + Initialize(fst); + Refine(fst); + } +*************** +*** 531,543 **** + void Minimize(MutableFst<A>* fst, + MutableFst<A>* sfst = 0, + float delta = kDelta) { +! uint64 props = fst->Properties(kAcceptor | kIDeterministic| +! kWeighted | kUnweighted, true); +! if (!(props & kIDeterministic)) { +! FSTERROR() << "FST is not deterministic"; +! fst->SetProperties(kError, kError); +! return; +! } + + if (!(props & kAcceptor)) { // weighted transducer + VectorFst< GallicArc<A, GALLIC_LEFT> > gfst; +--- 544,550 ---- + void Minimize(MutableFst<A>* fst, + MutableFst<A>* sfst = 0, + float delta = kDelta) { +! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true); + + if (!(props & kAcceptor)) { // weighted transducer + VectorFst< GallicArc<A, GALLIC_LEFT> > gfst; +diff -crB openfst-1.4.1.orig/src/include/fst/partition.h openfst-1.4.1/src/include/fst/partition.h +*** openfst-1.4.1.orig/src/include/fst/partition.h 2014-04-29 18:15:17.000000000 -0400 +--- openfst-1.4.1/src/include/fst/partition.h 2015-02-28 14:11:39.271566087 -0400 +*************** +*** 43,50 **** + friend class PartitionIterator<T>; + + struct Element { +! Element() : value(0), next(0), prev(0) {} +! Element(T v) : value(v), next(0), prev(0) {} + + T value; + Element* next; +--- 43,50 ---- + friend class PartitionIterator<T>; + + struct Element { +! Element() : value(0), next(0), prev(0) {} +! Element(T v) : value(v), next(0), prev(0) {} + + T value; + Element* next; +*************** +*** 52,60 **** + }; + + public: +! Partition() {} + +! Partition(T num_states) { + Initialize(num_states); + } + +--- 52,62 ---- + }; + + public: +! Partition(bool allow_repeated_split): +! allow_repeated_split_(allow_repeated_split) {} + +! Partition(bool allow_repeated_split, T num_states): +! allow_repeated_split_(allow_repeated_split) { + Initialize(num_states); + } + +*************** +*** 137,152 **** + if (class_size_[class_id] == 1) return; + + // first time class is split +! if (split_size_[class_id] == 0) + visited_classes_.push_back(class_id); +! + // increment size of split (set of element at head of chain) + split_size_[class_id]++; +! + // update split point +! if (class_split_[class_id] == 0) +! class_split_[class_id] = classes_[class_id]; +! if (class_split_[class_id] == elements_[element_id]) + class_split_[class_id] = elements_[element_id]->next; + + // move to head of chain in same class +--- 139,154 ---- + if (class_size_[class_id] == 1) return; + + // first time class is split +! if (split_size_[class_id] == 0) { + visited_classes_.push_back(class_id); +! class_split_[class_id] = classes_[class_id]; +! } + // increment size of split (set of element at head of chain) + split_size_[class_id]++; +! + // update split point +! if (class_split_[class_id] != 0 +! && class_split_[class_id] == elements_[element_id]) + class_split_[class_id] = elements_[element_id]->next; + + // move to head of chain in same class +*************** +*** 157,165 **** + // class indices of the newly created class. Returns the new_class id + // or -1 if no new class was created. + T SplitRefine(T class_id) { + // only split if necessary +! if (class_size_[class_id] == split_size_[class_id]) { +! class_split_[class_id] = 0; + split_size_[class_id] = 0; + return -1; + } else { +--- 159,169 ---- + // class indices of the newly created class. Returns the new_class id + // or -1 if no new class was created. + T SplitRefine(T class_id) { ++ ++ Element* split_el = class_split_[class_id]; + // only split if necessary +! //if (class_size_[class_id] == split_size_[class_id]) { +! if(split_el == NULL) { // we split on everything... + split_size_[class_id] = 0; + return -1; + } else { +*************** +*** 163,180 **** + split_size_[class_id] = 0; + return -1; + } else { +- + T new_class = AddClass(); + size_t remainder = class_size_[class_id] - split_size_[class_id]; + if (remainder < split_size_[class_id]) { // add smaller +- Element* split_el = class_split_[class_id]; + classes_[new_class] = split_el; +- class_size_[class_id] = split_size_[class_id]; +- class_size_[new_class] = remainder; + split_el->prev->next = 0; + split_el->prev = 0; + } else { +- Element* split_el = class_split_[class_id]; + classes_[new_class] = classes_[class_id]; + class_size_[class_id] = remainder; + class_size_[new_class] = split_size_[class_id]; +--- 167,189 ---- + split_size_[class_id] = 0; + return -1; + } else { + T new_class = AddClass(); ++ ++ if(allow_repeated_split_) { // split_size_ is possibly ++ // inaccurate, so work it out exactly. ++ size_t split_count; Element *e; ++ for(split_count=0,e=classes_[class_id]; ++ e != split_el; split_count++, e=e->next); ++ split_size_[class_id] = split_count; ++ } + size_t remainder = class_size_[class_id] - split_size_[class_id]; + if (remainder < split_size_[class_id]) { // add smaller + classes_[new_class] = split_el; + split_el->prev->next = 0; + split_el->prev = 0; ++ class_size_[class_id] = split_size_[class_id]; ++ class_size_[new_class] = remainder; + } else { + classes_[new_class] = classes_[class_id]; + class_size_[class_id] = remainder; + class_size_[new_class] = split_size_[class_id]; +*************** +*** 245,254 **** +--- 254,269 ---- + vector<T> class_size_; + + // size of split for each class ++ // in the nondeterministic case, split_size_ is actually an upper ++ // bound on the size of split for each class. + vector<T> split_size_; + + // set of visited classes to be used in split refine + vector<T> visited_classes_; ++ ++ // true if input fst was deterministic: we can make ++ // certain assumptions in this case that speed up the algorithm. ++ bool allow_repeated_split_; + }; + + diff --git a/sci-misc/openfst/openfst-1.4.1.ebuild b/sci-misc/openfst/openfst-1.4.1.ebuild new file mode 100644 index 000000000..a3eb530d5 --- /dev/null +++ b/sci-misc/openfst/openfst-1.4.1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI="5" + +inherit eutils + +DESCRIPTION="Finite State Transducer tools by Google et al." +HOMEPAGE="http://www.openfst.org" +SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_prepare() { + epatch "${FILESDIR}/kaldi-${P}.patch" +} diff --git a/sci-misc/opennlp-maxent/ChangeLog b/sci-misc/opennlp-maxent/ChangeLog index 388545bd0..f38888dba 100644 --- a/sci-misc/opennlp-maxent/ChangeLog +++ b/sci-misc/opennlp-maxent/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/opennlp-maxent -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/opennlp-maxent: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> opennlp-maxent-2.4.0.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/opennlp-maxent/metadata.xml b/sci-misc/opennlp-maxent/metadata.xml index a9988e63d..74e102484 100644 --- a/sci-misc/opennlp-maxent/metadata.xml +++ b/sci-misc/opennlp-maxent/metadata.xml @@ -8,4 +8,7 @@ Implementation of statistical classification using maximum entropy models in opennlp framework. </longdescription> + <upstream> + <remote-id type="sourceforge">maxent</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/opennlp-tools/ChangeLog b/sci-misc/opennlp-tools/ChangeLog index 717e1908c..ea33a006b 100644 --- a/sci-misc/opennlp-tools/ChangeLog +++ b/sci-misc/opennlp-tools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/opennlp-tools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/opennlp-tools: Updating remote-id in metadata.xml + 12 Nov 2014; Justin Lecher <jlec@gentoo.org> opennlp-tools-1.3.0.ebuild, metadata.xml: Bump to EAPI=5 diff --git a/sci-misc/opennlp-tools/metadata.xml b/sci-misc/opennlp-tools/metadata.xml index 3d05bed34..8a0ae8ca7 100644 --- a/sci-misc/opennlp-tools/metadata.xml +++ b/sci-misc/opennlp-tools/metadata.xml @@ -11,4 +11,7 @@ <use> <flag name="models">Automatically generated description for models</flag> </use> + <upstream> + <remote-id type="sourceforge">opennlp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/pywordnet/ChangeLog b/sci-misc/pywordnet/ChangeLog index e1b6547ae..9a7ca7d64 100644 --- a/sci-misc/pywordnet/ChangeLog +++ b/sci-misc/pywordnet/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/pywordnet -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/pywordnet: Updating remote-id in metadata.xml + 04 Dec 2013; Justin Lecher <jlec@gentoo.org> pywordnet-2.0.1.ebuild, metadata.xml: Bump to distutils-r1 eclass diff --git a/sci-misc/pywordnet/metadata.xml b/sci-misc/pywordnet/metadata.xml index 822a0ca76..41b4345f3 100644 --- a/sci-misc/pywordnet/metadata.xml +++ b/sci-misc/pywordnet/metadata.xml @@ -7,4 +7,7 @@ <longdescription> Pywordnet contains python bindings to handle wordnet databases. </longdescription> + <upstream> + <remote-id type="sourceforge">pywordnet</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/pywordnet/pywordnet-2.0.1.ebuild b/sci-misc/pywordnet/pywordnet-2.0.1.ebuild index 641fd174a..b2b8ffaea 100644 --- a/sci-misc/pywordnet/pywordnet-2.0.1.ebuild +++ b/sci-misc/pywordnet/pywordnet-2.0.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sci-misc/simx/ChangeLog b/sci-misc/simx/ChangeLog index 1907c83c6..2ac2ee578 100644 --- a/sci-misc/simx/ChangeLog +++ b/sci-misc/simx/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-misc/simx -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-misc/simx: Add github to remote-id in metadata.xml + *simx-0.2 (07 Feb 2014) 07 Feb 2014; Christoph Junghans <ottxor@gentoo.org> +simx-0.2.ebuild, diff --git a/sci-misc/simx/metadata.xml b/sci-misc/simx/metadata.xml index 897aa2e6b..6e9c32417 100644 --- a/sci-misc/simx/metadata.xml +++ b/sci-misc/simx/metadata.xml @@ -2,4 +2,7 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <upstream> + <remote-id type="github">sim-x</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-misc/simx/simx-0.2.ebuild b/sci-misc/simx/simx-0.2.ebuild index b53d77911..6f4d02e95 100644 --- a/sci-misc/simx/simx-0.2.ebuild +++ b/sci-misc/simx/simx-0.2.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils distutils-r1 diff --git a/sci-misc/simx/simx-9999.ebuild b/sci-misc/simx/simx-9999.ebuild index b53d77911..6f4d02e95 100644 --- a/sci-misc/simx/simx-9999.ebuild +++ b/sci-misc/simx/simx-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit cmake-utils distutils-r1 diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog index a2b5e94b6..3b70d8d3d 100644 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-physics/abinit -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*abinit-7.10.4 (22 Apr 2015) + + 22 Apr 2015; Honza Macháček <Hloupy.Honza@centrum.cz> + +abinit-7.10.4.ebuild, +files/7.10.4-libabinit_options.patch, + +files/7.10.4-syntax.patch: + Version bump to sci-physics/abinit-7.10.4, dependency for USE=bigdft changed + in the new version from sci-libs/bigdft-abi to <sci-physics/bigdft-1.7.5 + *abinit-7.6.4-r1 (10 Dec 2014) *abinit-7.4.2-r1 (10 Dec 2014) diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest index 00f95861e..86578760b 100644 --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@ -1,2 +1,3 @@ +DIST abinit-7.10.4.tar.gz 69930222 SHA256 ebd0a3abd01db4374beda092d1f16c9e00d327712b1ed389bb32e1c80f37c6ef SHA512 32e98a721c56731d9f45f24359c3dd967fdf2f9f3d9fd0328e82a037a25abb789a2b483174a1347d965b71799118d6c26911beee9d0ec833324d36116e8e5b4a WHIRLPOOL 6d292940ee5168563d2ad4114141d272cc84956209d35c49ebd9e0508a3080206fd6e096a49cd63bebd0b9ffab85efac9a3e3d6946e949f3cb306eb597dbc310 DIST abinit-7.4.2.tar.gz 69150549 SHA256 26fcc60e18071b7579843f43cbe44e79db50466dbaae8b862ad96a8986733f63 SHA512 55132cfbfb26bf22ae486ada7e721188bd436a48299da3a386928776f6d0652d8a19a5e5b70261b84afc6cb6b058fe711171fa09aff637bdb2da11e8df032543 WHIRLPOOL add34b50d2c6843064254a3caffbfa4d9fef644ae98513a1b7681ffb8f2c0f4d31b5b995920a97fa656d82a38aeec313f98e1f91c06166ea83ed6ba87192292d DIST abinit-7.6.4.tar.gz 71821245 SHA256 1fa532ca156d2fad1bf3af86edfc8b6695917c8cbcf25084c7bf9b1749812ff7 SHA512 b86dcc26d8e38a8d0f1b4a470dc0bc2bd5363f25dbc1bd954e83ffe8694ce23b85ddf3d411c4b3121d833f65c4d55899cf02054b27e060d2465407a6c110602a WHIRLPOOL b1580f3e8c99148632f0cacd566a3e958c0e7a9b14ec7b1bb20c930a5131491401938d29ab41944411ae82676753bdf0f2294a137aaa267226cc2ac3db43c2fd diff --git a/sci-physics/abinit/abinit-7.10.4.ebuild b/sci-physics/abinit/abinit-7.10.4.ebuild new file mode 100644 index 000000000..40d7fadd0 --- /dev/null +++ b/sci-physics/abinit/abinit-7.10.4.ebuild @@ -0,0 +1,390 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_5,2_6,2_7} ) + +inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs + +DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" +HOMEPAGE="http://www.abinit.org/" +SRC_URI="http://ftp.abinit.org/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="atompaw bigdft cuda cuda-double -debug +etsf_io +fftw fftw-mpi +fftw-threads +fox gsl +hdf5 levmar -libabinit libxc -lotf mpi +netcdf openmp python scalapack scripts -test +threads wannier" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" +#" scalapack? ( !bigdft )" + +RDEPEND="virtual/blas + virtual/lapack + ${PYTHON_DEPS} + dev-python/numpy + atompaw? ( >=sci-physics/atompaw-4.0.0.10[libxc?] ) + bigdft? ( >=sci-physics/bigdft-1.7.0.93[scalapack?] + <sci-physics/bigdft-1.7.5 ) + cuda? ( dev-util/nvidia-cuda-sdk ) + etsf_io? ( >=sci-libs/etsf_io-1.0.4 ) + fftw? ( + sci-libs/fftw:3.0 + fftw-threads? ( + openmp? ( sci-libs/fftw:3.0[openmp] ) + !openmp? ( sci-libs/fftw:3.0[threads] ) + ) + fftw-mpi? ( + sci-libs/fftw:3.0[mpi] + openmp? ( sci-libs/fftw:3.0[openmp] ) + !openmp? ( sci-libs/fftw:3.0[threads] ) + ) + ) + fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) + gsl? ( sci-libs/gsl ) + hdf5? ( sci-libs/hdf5[fortran] ) + levmar? ( sci-libs/levmar ) + libxc? ( >=sci-libs/libxc-2.0.3[fortran] + <sci-libs/libxc-2.2 ) + netcdf? ( + sci-libs/netcdf[hdf5?] + || ( + sci-libs/netcdf[fortran] + sci-libs/netcdf-fortran + ) + ) + mpi? ( virtual/mpi ) + scalapack? ( virtual/scalapack ) + scripts? ( dev-python/PyQt4 ) + wannier? ( >=sci-libs/wannier90-1.2-r1 )" +DEPEND="${RDEPEND} + virtual/pkgconfig + dev-perl/Text-Markdown" + +S=${WORKDIR}/${P%[a-z]} + +DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING + README README.ChangeLog README.GPU README.xlf RELNOTES THANKS ) + +FORTRAN_STANDARD=90 + +pkg_setup() { + # Doesn't compile with gcc-4.0, only >=4.1 + if [[ $(tc-getFC) == *gfortran ]]; then + if [[ $(gcc-major-version) -eq 4 ]] \ + && [[ $(gcc-minor-version) -lt 1 ]]; then + die "Requires gcc-4.1 or newer" + fi + fi + + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + export CXX="mpic++" + else + tc-export FC F77 CC CXX + fi + + # Preprocesor macross can make some lines really long + append-fflags -ffree-line-length-none + + # This should be correct: + # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. + # Should a bug be filed against toolchain-funcs.eclass? + # if use openmp; then + # tc-has-openmp || \ + # die "Please select an openmp capable compiler like gcc[openmp]" + # fi + # + # This is completely wrong: + # If other compilers than Gnu Compiler Collection can be used by portage, + # their support of OpenMP should be properly tested. This code limits the test + # to gcc, and blindly supposes that other compilers do support OpenMP. + # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + # die "Please select an openmp capable compiler like gcc[openmp]" + # fi + # + # Luckily Abinit is a fortran package. + # fortran-2.eclass has its own test for OpenMP support, + # more general than toolchain-funcs.eclass + # The test itself proceeds inside fortran-2_pkg_setup + if use openmp; then FORTRAN_NEED_OPENMP=1; fi + + fortran-2_pkg_setup + + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local code=ebuild-openmp-flags + local ret + local openmp + + pushd "${T}" + cat <<- EOF > "${code}.c" + # include <omp.h> + main () { + int nthreads; + nthreads=omp_get_num_threads(); + } + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log + ret=$? + (( ${ret} )) || break + done + + rm -f "${code}.*" + popd + + if (( ${ret} )); then + die "Please switch to an openmp compatible C compiler" + else + export CC="${CC} ${openmp}" + export CXX="${CXX} ${openmp}" + fi + + pushd "${T}" + cat <<- EOF > "${code}.f" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log + ret=$? + (( ${ret} )) || break + done + + rm -f "${code}.*" + popd + + if (( ${ret} )); then + die "Please switch to an openmp compatible fortran compiler." + else + export FC="${FC} ${openmp}" + export F77="${F77} ${openmp}" + fi + fi + + # Sort out some USE options + if use fftw-threads && ! use fftw; then + ewarn "fftw-threads set but fftw not used, ignored." + fi + if use fftw-mpi; then + if ! use fftw; then + ewarn "fftw-mpi set but fftw not used, ignored." + elif ! use mpi; then + ewarn "fftw-mpi set but mpi not used, ignored." + elif ! use fftw-threads; then + ewarn "fftw-mpi set but fftw-threads not. Will use a threaded fftw nevertheless, required with MPI." + fi + fi + if use cuda-double && ! use cuda; then + ewarn "cuda-double set but cuda not used, ignored" + fi + + python-single-r1_pkg_setup + +} + +src_prepare() { + epatch \ + "${FILESDIR}"/6.2.2-change-default-directories.patch \ + "${FILESDIR}"/6.12.1-autoconf.patch \ + "${FILESDIR}"/6.12.1-xmalloc.patch \ + "${FILESDIR}"/7.10.4-libabinit_options.patch \ + "${FILESDIR}"/7.4.2-levmar_diag_scaling.patch \ + "${FILESDIR}"/7.4.2-cuda_link_stdc++.patch \ + "${FILESDIR}"/7.6.4-cuda_header.patch \ + "${FILESDIR}"/7.10.4-syntax.patch + eautoreconf + sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure || ewarn "sed on configure failed" + python_fix_shebang "${S}" +} + +src_configure() { + local modules="$(FoX-config --sax --fcflags)" + local FoX_libs="$(FoX-config --sax --libs)" + + local trio_flavor="" + use etsf_io && trio_flavor="${trio_flavor}+etsf_io" + use fox && trio_flavor="${trio_flavor}+fox" + use netcdf && trio_flavor="${trio_flavor}+netcdf" + test "no${trio_flavor}" = "no" && trio_flavor="none" + + local netcdff_libs="-lnetcdff" + use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" + +# local linalg_flavor="atlas" + local linalg_flavor="custom" + local mylapack="lapack" + use scalapack && mylapack="scalapack" && linalg_flavor="${linalg_flavor}+scalapack" + + local dft_flavor="" + use atompaw && dft_flavor="${dft_flavor}+atompaw" + use bigdft && dft_flavor="${dft_flavor}+bigdft" + use libxc && dft_flavor="${dft_flavor}+libxc" + use wannier && dft_flavor="${dft_flavor}+wannier90" + test "no${dft_flavor}" = "no" && dft_flavor="none" + + local fft_flavor="fftw3" + local fft_libs="" + # The fftw threads support is protected by black magick. + # Anybody removes it, dies. + # New USE flag "fftw-threads" was added to control usage + # of the threaded fftw variant. Since fftw-3.3 has expanded + # the paralel options by MPI and OpenMP support, analogical + # USE flags should be added to select them in future; + # unusable with previous FFTW versions, they are postponed + # for now. + if use mpi && use fftw-mpi; then + fft_flavor="fftw3-mpi" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_mpi)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_mpi)" + if use openmp; then + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" + else + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" + fi + elif use fftw-threads; then + fft_flavor="fftw3-threads" + if use openmp; then + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_omp)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_omp)" + else + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3_threads)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f_threads)" + fi + else + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3)" + fft_libs+="$($(tc-getPKG_CONFIG) --libs fftw3f)" + fi + + local gpu_flavor="none" + if use cuda; then + gpu_flavor="cuda-single" + if use cuda-double; then + gpu_flavor="cuda-double" + fi + fi + + local myeconfargs=( + --enable-clib + --enable-exports + $(use_enable debug debug enhanced) + $(use_enable mpi) + $(use_enable mpi mpi-io) + $(use_enable openmp) + $(use_enable lotf) + $(use_enable cuda gpu) + "$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")" + "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" + "$(use gsl && echo "--with-math-flavor=gsl")" + "$(use gsl && echo "--with-math-incs=$($(tc-getPKG_CONFIG) --cflags gsl)")" + "$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")" + "$(use levmar && echo "--with-algo-flavor=levmar")" + "$(use levmar && echo "--with-algo-libs=-llevmar")" + --with-linalg-flavor="${linalg_flavor}" + --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs "${mylapack}")" + --with-trio-flavor="${trio_flavor}" + "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" + "$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" + "$(use fox && echo "--with-fox-incs=${modules}")" + "$(use fox && echo "--with-fox-libs=${FoX_libs}")" + "$(use etsf_io && echo "--with-etsf-io-incs=${modules}")" + "$(use etsf_io && echo "--with-etsf-io-libs=-letsf_io -letsf_io_utils -letsf_io_low_level")" + --with-dft-flavor="${dft_flavor}" + "$(use atompaw && echo "--with-atompaw-incs=${modules}")" + "$(use atompaw && echo "--with-atompaw-libs=-latompaw")" + "$(use bigdft && echo "--with-bigdft-incs=${modules}")" + "$(use bigdft && echo "--with-bigdft-libs=$($(tc-getPKG_CONFIG) --libs bigdft)")" + "$(use libxc && echo "--with-libxc-incs=${modules}")" + "$(use libxc && echo "--with-libxc-libs=$($(tc-getPKG_CONFIG) --libs libxc)")" + "$(use wannier && echo "--with-wannier90-bins=/usr/bin")" + "$(use wannier && echo "--with-wannier90-incs=${modules}")" + "$(use wannier && echo "--with-wannier90-libs=-lwannier $($(tc-getPKG_CONFIG) --libs blas lapack)")" + "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" + "$(use fftw && echo "--with-fft-incs=-I/usr/include")" + "$(use fftw && echo "--with-fft-libs=${fft_libs}")" + --with-timer-flavor="abinit" + LD="$(tc-getLD)" + FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${modules} -I/usr/include" + ) + + MARKDOWN=Markdown.pl autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + + # Apparently libabinit.a is not built by default + # Used by BigDFT. Should probably be built separately, + # as a package of its own: BigDFT used by Abinit. + # Does libabinit.a depend on BigDFT, if used? + # Can Abinit use external libabinit.a? + use libabinit && autotools-utils_src_compile libabinit.a + + sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc || ewarn "sed on config.pc failed" +} + +src_test() { + einfo "The complete tests take quite a while, easily several hours or even days." + # autotools-utils_src_test expanded and modified + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + + einfo "Running the internal tests." + emake tests_in || ewarn 'The internal tests failed.' + + einfo "Running the thorough tests. Be patient, please." + "${S}"/tests/runtests.py || ewarn "The package has not passed the thorough tests." + + popd > /dev/null || die +} + +src_install() { + #autotools-utils_src_install() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + emake DESTDIR="${D}" install || die "make install failed" + + use libabinit && dolib libabinit.a + + if use test; then + for dc in results.tar.gz results.txt suite_report.html; do + test -e Test_suite/"${dc}" && dodoc Test_suite/"${dc}" || ewarn "Copying tests results ${dc} failed" + done + fi + + popd > /dev/null + + # XXX: support installing them from builddir as well!!! + if [[ ${DOCS} ]]; then + dodoc "${DOCS[@]}" || die "dodoc failed" + else + local f + # same list as in PMS + for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \ + THANKS BUGS FAQ CREDITS CHANGELOG; do + if [[ -s ${f} ]]; then + dodoc "${f}" || ewarn "(default) dodoc ${f} failed" + fi + done + fi + if [[ ${HTML_DOCS} ]]; then + dohtml -r "${HTML_DOCS[@]}" || ewarn "dohtml failed" + fi + + if use scripts; then + insinto /usr/share/"${P}" + doins -r scripts + fi + + # Remove libtool files and unnecessary static libs + prune_libtool_files +} diff --git a/sci-physics/abinit/abinit-7.6.4-r1.ebuild b/sci-physics/abinit/abinit-7.6.4-r1.ebuild index 50a03fa89..f2309441c 100644 --- a/sci-physics/abinit/abinit-7.6.4-r1.ebuild +++ b/sci-physics/abinit/abinit-7.6.4-r1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_5,2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit autotools-utils eutils flag-o-matic fortran-2 multilib python-single-r1 toolchain-funcs diff --git a/sci-physics/abinit/files/7.10.4-libabinit_options.patch b/sci-physics/abinit/files/7.10.4-libabinit_options.patch new file mode 100644 index 000000000..09c61419a --- /dev/null +++ b/sci-physics/abinit/files/7.10.4-libabinit_options.patch @@ -0,0 +1,82 @@ +diff -Naurp abinit-7.10.4.orig/Makefile.am abinit-7.10.4/Makefile.am +--- abinit-7.10.4.orig/Makefile.am 2015-03-12 06:28:38.000000000 +0100 ++++ abinit-7.10.4/Makefile.am 2015-04-07 12:14:39.816276230 +0200 +@@ -2878,7 +2878,9 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a ++if DO_BUILD_15_GPU_TOOLBOX + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a ++endif + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a +@@ -2898,7 +2900,9 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a ++if DO_BUILD_52_MANAGE_CUDA + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a ++endif + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/54_abiutil/lib54_abiutil.a +@@ -2917,15 +2921,19 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a ++if DO_BUILD_65_LOTF_BASE + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a ++endif + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_fock/lib66_fock.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a ++if DO_BUILD_68_LOTF + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a ++endif + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a +diff -Naurp abinit-7.10.4.orig/Makefile.in abinit-7.10.4/Makefile.in +--- abinit-7.10.4.orig/Makefile.in 2015-03-12 06:28:51.000000000 +0100 ++++ abinit-7.10.4/Makefile.in 2015-04-07 12:14:39.816276230 +0200 +@@ -3803,7 +3803,7 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/11_qespresso_ext/lib11_qespresso_ext.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a +- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a ++@DO_BUILD_15_GPU_TOOLBOX_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/21_psiesta_noabirule/lib21_psiesta_noabirule.a +@@ -3823,7 +3823,7 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a +- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a ++@DO_BUILD_52_MANAGE_CUDA_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/54_abiutil/lib54_abiutil.a +@@ -3842,15 +3842,15 @@ libabinit.a: + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/62_wvl_wfs/lib62_wvl_wfs.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/63_bader/lib63_bader.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/64_atompaw/lib64_atompaw.a +- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a ++@DO_BUILD_65_LOTF_BASE_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_lotf_base/lib65_lotf_base.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_nonlocal/lib65_nonlocal.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/65_psp/lib65_psp.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_fock/lib66_fock.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_paw/lib66_paw.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/66_wfs/lib66_wfs.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/67_common/lib67_common.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_dmft/lib68_dmft.a +- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a ++@DO_BUILD_68_LOTF_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_lotf/lib68_lotf.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_recursion/lib68_recursion.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/68_rsprc/lib68_rsprc.a + cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/69_wfdesc/lib69_wfdesc.a diff --git a/sci-physics/abinit/files/7.10.4-syntax.patch b/sci-physics/abinit/files/7.10.4-syntax.patch new file mode 100644 index 000000000..bfb915e71 --- /dev/null +++ b/sci-physics/abinit/files/7.10.4-syntax.patch @@ -0,0 +1,12 @@ +diff -Naurp abinit-7.10.4.orig/src/98_main/mrgscr.F90 abinit-7.10.4/src/98_main/mrgscr.F90 +--- abinit-7.10.4.orig/src/98_main/mrgscr.F90 2015-03-12 06:24:36.000000000 +0100 ++++ abinit-7.10.4/src/98_main/mrgscr.F90 2015-04-07 13:00:01.166355853 +0200 +@@ -2312,7 +2312,7 @@ program mrgscr + + !!OMP *** OPENMP SECTION *** Added by MS + !$OMP PARALLEL SHARED(Hscr_file,epsm1,nfreqre,epsm1_pole, & +-!$OMP is_scr,npoles,std_out,iqibz,one) & ++!$OMP is_scr,npoles,std_out,iqibz) & + !$OMP PRIVATE(ig1,ig2,refval,imfval,phase) + !!OMP write(std_out,'(a,i0)') ' Entering openmp loop. Number of threads: ',omp_get_num_threads() + ABI_MALLOC(refval,(Hscr_file(1)%nomega)) diff --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog index 8e43d46c9..700368c77 100644 --- a/sci-physics/bigdft/ChangeLog +++ b/sci-physics/bigdft/ChangeLog @@ -1,7 +1,20 @@ # ChangeLog for sci-physics/bigdft -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/bigdft: Updating remote-id in metadata.xml + +*bigdft-1.7.6 (22 Apr 2015) +*bigdft-1.7.1 (22 Apr 2015) + + 22 Apr 2015; Honza Macháček <Hloupy.Honza@centrum.cz> +bigdft-1.7.1.ebuild, + -bigdft-1.7.5.ebuild, +bigdft-1.7.6.ebuild, + +files/bigdft-1.7.1-longline.patch, +files/bigdft-1.7.1-pkgconfig.patch, + -files/bigdft-1.7.5-pkgconfig.patch: + Version bump to sci-physics/bigdft-1.7.6, added sci-physics/bigdft-1.7.1 for + the use by sci-physics/abinit-7.10.4 + 16 Sep 2014; Christoph Junghans <ottxor@gentoo.org> bigdft-1.7.5.ebuild: remove blank line diff --git a/sci-physics/bigdft/Manifest b/sci-physics/bigdft/Manifest index 09a312969..776934470 100644 --- a/sci-physics/bigdft/Manifest +++ b/sci-physics/bigdft/Manifest @@ -1 +1,2 @@ -DIST bigdft-1.7.5.tar.xz 10182428 SHA256 7a96ff161ae9c2da576042fe05b7daf2f376c784d0b7420ba8a1bb013df307d5 SHA512 e187b0f6898d5ca08121168496b7993c59abb5f2bceb5873ccc40539f3cca99ec6bb62ce971ad8aa3f9900a02c6ee2299427cf2cdd325c40de7227d2030e5528 WHIRLPOOL 72512db4bc5efa87f0519f6cc0b0703857c1bba0dc8c60db2e9556569ce56bd78d74e08b5a85805a342e8ae05521eec77528e516f4630e479a49501b2527d520 +DIST bigdft-1.7.1.tar.bz2 12028799 SHA256 3f565f66b423a03d048ac2468f941c7fb1ef1fd6c61315fa05ff5b94bb2338c5 SHA512 e26abe7743106764ea6779e29d85da8a7d9272fa3ebd10f668d74c6ef196ff52283e38669fc815ce9409f1ff245ba74d56b2d300a309f5a69baf445317aafd2e WHIRLPOOL 513c1af5b88752b3550a6c52fa22ae044ef4f21b4f65e7443ef23a680e275f5497cb1dc39c58d4a7544b6fe16a2ace38a68cae80115d8d8226a11b8ee2e08baa +DIST bigdft-1.7.6.tar.xz 10399604 SHA256 cdb443380540eb3238c5393413f031dfa3a649c18edf5212433a06e19b03929c SHA512 cdadda8e9105355e48a9f301ac5d8178955fff90593935143db5219de867f1461bfb7c934a9fe0dcbb7af7c77bb0aedfc5f1d078d1eeeeca76c3e868ee8d3919 WHIRLPOOL 779c5fe8beab1dc268de615e50fe7373db56a229ed1838bc42db8e9dff26698da93be69c64dd15f54e6292f762597050d89b13588db5ff2864c7ccaeec9b629b diff --git a/sci-physics/bigdft/bigdft-1.7.5.ebuild b/sci-physics/bigdft/bigdft-1.7.1.ebuild index 48ae402b2..1871396f2 100644 --- a/sci-physics/bigdft/bigdft-1.7.5.ebuild +++ b/sci-physics/bigdft/bigdft-1.7.1.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -10,7 +10,7 @@ inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-fu DESCRIPTION="A DFT electronic structure code using a wavelet basis set" HOMEPAGE="http://bigdft.org/" -SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.xz" +SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.bz2" LICENSE="GPL-3" SLOT="0" @@ -18,7 +18,8 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux" IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test" RDEPEND=" - >=sci-libs/libxc-1.2.0-r1[fortran] + ( >=sci-libs/libxc-1.2.0-r1[fortran] + <sci-libs/libxc-2.2 ) virtual/blas virtual/fortran virtual/lapack @@ -27,7 +28,7 @@ RDEPEND=" cuda? ( dev-util/nvidia-cuda-sdk ) opencl? ( virtual/opencl ) glib? ( >=dev-libs/glib-2.22 ) - etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) + etsf_io? ( >=sci-libs/etsf_io-1.0.4[pic] ) netcdf? ( || ( sci-libs/netcdf[fortran] sci-libs/netcdf-fortran @@ -91,7 +92,7 @@ pkg_setup() { src_prepare() { epatch \ "${FILESDIR}"/"${P}"-pkgconfig.patch \ - "${FILESDIR}"/"${P}"-dynamic_memory.patch + "${FILESDIR}"/"${P}"-longline.patch eautoreconf } @@ -168,11 +169,4 @@ src_test() { src_install() { autotools-utils_src_install - if use test; then - _check_build_dir - pushd "${BUILD_DIR}" > /dev/null || die - insinto /usr/share/"${P}" - doins -r tests - popd > /dev/null - fi } diff --git a/sci-physics/bigdft/bigdft-1.7.6.ebuild b/sci-physics/bigdft/bigdft-1.7.6.ebuild new file mode 100644 index 000000000..85e9187df --- /dev/null +++ b/sci-physics/bigdft/bigdft-1.7.6.ebuild @@ -0,0 +1,172 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_5 python2_6 python2_7 ) + +inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs + +DESCRIPTION="A DFT electronic structure code using a wavelet basis set" +HOMEPAGE="http://bigdft.org/" +SRC_URI="http://launchpad.net/${PN}/${PV%.*}/${PV}/+download/${P}.tar.xz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="cuda doc etsf_io glib mpi netcdf openmp opencl scalapack test" + +RDEPEND=" + ( >=sci-libs/libxc-2.0[fortran] + <sci-libs/libxc-2.2 ) + virtual/blas + virtual/fortran + virtual/lapack + dev-libs/libyaml + mpi? ( virtual/mpi ) + cuda? ( dev-util/nvidia-cuda-sdk ) + opencl? ( virtual/opencl ) + glib? ( >=dev-libs/glib-2.22 ) + etsf_io? ( >=sci-libs/etsf_io-1.0.4[pic] ) + netcdf? ( || ( + sci-libs/netcdf[fortran] + sci-libs/netcdf-fortran + ) + ) + scalapack? ( virtual/scalapack )" +DEPEND="${RDEPEND} + virtual/pkgconfig + >=sys-devel/autoconf-2.59 + doc? ( virtual/latex-base ) + ${PYTHON_DEPS} + dev-python/pyyaml[libyaml] + dev-util/gdbus-codegen + app-arch/tar + app-arch/gzip" + +DOCS=( README INSTALL ChangeLog AUTHORS NEWS ) + +FORTRAN_STANDARD=90 + +pkg_setup() { + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + export CXX="mpic++" + else + tc-export FC F77 CC CXX + fi + + use openmp && FORTRAN_NEED_OPENMP=1 + + fortran-2_pkg_setup + + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local openmp="" + local fcode=ebuild-openmp-flags.f + local _fc=$(tc-getFC) + + pushd "${T}" + cat <<- EOF > "${fcode}" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + "${_fc}" "${openmp}" "${fcode}" -o "${fcode}.x" && break + done + + rm -f "${fcode}.*" + popd + + append-flags "${openmp}" + fi + + python-any-r1_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/"${PN}"-1.7.1-pkgconfig.patch \ + "${FILESDIR}"/"${PN}"-1.7.5-dynamic_memory.patch + + eautoreconf +} + +src_configure() { + local modules="${EPREFIX}/usr/include" + local netcdff_libs="-lnetcdff" + filter-flags '-m*' '-O*' "-pipe" + local nvcflags="${CFLAGS}" + _filter-var nvcflags '-m*' '-O*' "-pipe" "-W*" + use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*" + local mylapack="lapack" + use scalapack && mylapack="scalapack" + local myeconfargs=( + $(use_enable mpi) + --enable-optimised-convolution + --enable-pseudo + --enable-libbigdft + --enable-binaries + --disable-bindings + --disable-minima-hopping + --disable-internal-libyaml + --enable-internal-libabinit + --with-moduledir="${modules}" + --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l "${mylapack}")" + --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L "${mylapack}")" + --with-libxc="yes" + --disable-internal-libxc + $(use_enable cuda cuda-gpu) + $(use_with cuda cuda-path /opt/cuda) + $(use_with cuda nvcc-flags "${nvcflags}") + $(use_enable opencl) + $(use_with etsf_io etsf-io) + "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" + $(use_with glib gobject) + $(use_with scalapack) + $(use_with scalapack scalapack-path "${EPREFIX}/usr/$(get_libdir)") + $(use_with scalapack blacs) + $(use_with scalapack blacs-path "${EPREFIX}/usr/$(get_libdir)") + PKG_CONFIG="$(tc-getPKG_CONFIG)" + FCFLAGS="${FCFLAGS} -I${modules}" + LD="$(tc-getLD)" + CPP="$(tc-getCPP)" + ) + autotools-utils_src_configure +} + +src_compile() { + #autotools-utils_src_compile() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + emake -j1 + sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc + popd > /dev/null + + #autotools-utils_src_compile + if use doc; then + VARTEXFONTS="${T}/fonts" + autotools-utils_src_compile doc + fi +} + +src_test() { + if use test; then + #autotools-utils_src_test() expanded + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + # Run default src_test as defined in ebuild.sh + cd tests + emake -j1 check + popd > /dev/null + fi +} + +src_install() { + autotools-utils_src_install +} diff --git a/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch b/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch new file mode 100644 index 000000000..29dadb545 --- /dev/null +++ b/sci-physics/bigdft/files/bigdft-1.7.1-longline.patch @@ -0,0 +1,14 @@ +diff -Naurp bigdft-1.7.1.orig/libABINIT/src/16_hideleave/m_errors.F90 bigdft-1.7.1/libABINIT/src/16_hideleave/m_errors.F90 +--- bigdft-1.7.1.orig/libABINIT/src/16_hideleave/m_errors.F90 2013-12-11 09:31:00.000000000 +0000 ++++ bigdft-1.7.1/libABINIT/src/16_hideleave/m_errors.F90 2015-04-21 08:35:18.781370070 +0000 +@@ -777,7 +777,9 @@ subroutine sentinel(level,mode_paral,fun + else if (level==2) then + msg = ' '//TRIM(my_funcname)//' : exit '//ch10 + else +- call die('Wrong level',__FILE__,__LINE__) ++ call die('Wrong level',& ++& __FILE__,& ++& __LINE__) + end if + + call wrtout(std_out,msg,my_mode) diff --git a/sci-physics/bigdft/files/bigdft-1.7.5-pkgconfig.patch b/sci-physics/bigdft/files/bigdft-1.7.1-pkgconfig.patch index fdf5937c8..d1832d280 100644 --- a/sci-physics/bigdft/files/bigdft-1.7.5-pkgconfig.patch +++ b/sci-physics/bigdft/files/bigdft-1.7.1-pkgconfig.patch @@ -6,5 +6,5 @@ diff -Naurp bigdft-1.7.1.orig/bigdft.pc.in bigdft-1.7.1/bigdft.pc.in Requires: Version: @VERSION@ -Libs: -L${libdir} @LIBS_DEPENDENCIES@ @FCLIBS@ -+Libs: -L${libdir} @LIBS_SHORT_DEPS@ @FCLIBS@ ++Libs: -L${libdir} -lbigdft-1 @LIBS_SHORT_DEPS@ @FCLIBS@ Cflags: -I${includedir} diff --git a/sci-physics/bigdft/metadata.xml b/sci-physics/bigdft/metadata.xml index 855d625ca..88bc4b9af 100644 --- a/sci-physics/bigdft/metadata.xml +++ b/sci-physics/bigdft/metadata.xml @@ -27,4 +27,7 @@ BigDFT is a DFT massively parallel electronic structure code (GPL license) using Use ScaLAPACK, a subset of LAPACK routines redesigned for heterogenous computing </flag> </use> + <upstream> + <remote-id type="launchpad">bigdft</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/clip/ChangeLog b/sci-physics/clip/ChangeLog new file mode 100644 index 000000000..0876cda74 --- /dev/null +++ b/sci-physics/clip/ChangeLog @@ -0,0 +1,6 @@ +# ChangeLog for sci-physics/clip +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/clip: Updating remote-id in metadata.xml diff --git a/sci-physics/clip/metadata.xml b/sci-physics/clip/metadata.xml index 8a9f75597..fab4f8637 100644 --- a/sci-physics/clip/metadata.xml +++ b/sci-physics/clip/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <longdescription> @@ -6,4 +6,7 @@ Clip can simulate Laue patterns for arbitrary settings of crystal and detection plane. Moreover it allows to determine the crystal orientation from spots and zones marked on a Laue photograph. </longdescription> + <upstream> + <remote-id type="sourceforge">clip4</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/elk/ChangeLog b/sci-physics/elk/ChangeLog index 9f01d7650..a1e52cc3a 100644 --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-physics/elk -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/elk: Updating remote-id in metadata.xml + *elk-2.1.25 (23 Jul 2013) 23 Jul 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +elk-2.1.25.ebuild, @@ -43,4 +46,3 @@ failed tests miserably, even with a lot of segfaults. Using its internal lapack with USE=-lapack, it looks well. Tested OK with USE="-lapack libxc mpi openmp". - diff --git a/sci-physics/elk/metadata.xml b/sci-physics/elk/metadata.xml index a7ed67ff3..ecc6af8e1 100644 --- a/sci-physics/elk/metadata.xml +++ b/sci-physics/elk/metadata.xml @@ -20,4 +20,7 @@ Elk is an all-electron full-potential linearised augmented-plane wave (FP-LAPW) Install python scripts. </flag> </use> + <upstream> + <remote-id type="sourceforge">elk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/espresso++/ChangeLog b/sci-physics/espresso++/ChangeLog index dd0c03d0f..7a589edd3 100644 --- a/sci-physics/espresso++/ChangeLog +++ b/sci-physics/espresso++/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-physics/espresso++ -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-physics/espresso++: Add github to remote-id in metadata.xml + + 20 Mar 2015; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild: + added test feature + + 01 Mar 2015; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild: + move live version to git + 13 Nov 2014; Christoph Junghans <ottxor@gentoo.org> espresso++-9999.ebuild: sync with gx86 diff --git a/sci-physics/espresso++/espresso++-9999.ebuild b/sci-physics/espresso++/espresso++-9999.ebuild index d21c13398..c1d7f2d53 100644 --- a/sci-physics/espresso++/espresso++-9999.ebuild +++ b/sci-physics/espresso++/espresso++-9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -12,20 +12,20 @@ inherit cmake-utils python-single-r1 DESCRIPTION="extensible, flexible, fast and parallel simulation software for soft matter research" HOMEPAGE="https://www.espresso-pp.de" +MY_PN="${PN//+/p}" if [[ ${PV} = 9999 ]]; then - EHG_REPO_URI="https://bitbucket.org/${PN//+/p}/${PN//+/p}" - inherit mercurial + EGIT_REPO_URI="git://github.com/${MY_PN}/${MY_PN}.git http://github.com/${MY_PN}/${MY_PN}.git" + inherit git-r3 KEYWORDS= else - inherit vcs-snapshot #SRC_URI="https://espressopp.mpip-mainz.mpg.de/Download/${PN//+/p}-${PV}.tgz" - SRC_URI="https://bitbucket.org/${PN//+/p}/${PN//+/p}/get/v${PV}.tar.bz2 -> ${P}.tar.bz2" + SRC_URI="https://github.com/${MY_PN}/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-macos" fi LICENSE="GPL-3" SLOT="0" -IUSE="" +IUSE="test" REQUIRED_USE="${PYTHON_REQUIRED_USE}" diff --git a/sci-physics/espresso++/metadata.xml b/sci-physics/espresso++/metadata.xml index a556ddb82..25acc4649 100644 --- a/sci-physics/espresso++/metadata.xml +++ b/sci-physics/espresso++/metadata.xml @@ -6,4 +6,7 @@ <email>ottxor@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">espressopp/espressopp</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-physics/espresso/ChangeLog b/sci-physics/espresso/ChangeLog index 39f0e5a6f..23a6056ee 100644 --- a/sci-physics/espresso/ChangeLog +++ b/sci-physics/espresso/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-physics/espresso -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Mar 2015; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild: + update git location + 26 Dec 2014; Christoph Junghans <ottxor@gentoo.org> espresso-9999.ebuild: fixed homepage and deps diff --git a/sci-physics/espresso/espresso-9999.ebuild b/sci-physics/espresso/espresso-9999.ebuild index 149a662f0..337e575c0 100644 --- a/sci-physics/espresso/espresso-9999.ebuild +++ b/sci-physics/espresso/espresso-9999.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/espresso/espresso-3.3.0.ebuild,v 1.1 2014/08/11 21:33:08 ottxor Exp $ +# $Header: $ EAPI=5 @@ -12,7 +12,7 @@ DESCRIPTION="Extensible Simulation Package for Research on Soft matter" HOMEPAGE="http://espressomd.org" if [[ ${PV} = 9999 ]]; then - EGIT_REPO_URI="git://git.savannah.nongnu.org/espressomd.git" + EGIT_REPO_URI="git://github.com/espressomd/espresso.git https://github.com/espressomd/espresso.git" EGIT_BRANCH="master" AUTOTOOLS_AUTORECONF=1 inherit git-r3 diff --git a/sci-physics/geant/ChangeLog b/sci-physics/geant/ChangeLog deleted file mode 100644 index 457ebb007..000000000 --- a/sci-physics/geant/ChangeLog +++ /dev/null @@ -1,353 +0,0 @@ -# ChangeLog for sci-physics/geant -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/geant/ChangeLog,v 1.68 2012/12/14 16:51:50 bicatali Exp $ - -*geant-3.21.14-r4 (18 Jan 2013) - - 18 Jan 2013; Sébastien Fabbro <bicatali@gentoo.org> - +geant-3.21.14-r4.ebuild, +metadata.xml: - Introducing virtual/geant:3. Updating debian patch. Ebuild clean. Keyword - amd64-linux, x86-linux - -*geant-4.9.5_p02 (14 Dec 2012) -*geant-4.9.6 (14 Dec 2012) - - 14 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> +geant-4.9.5_p02.ebuild, - +geant-4.9.6.ebuild, -geant-4.9.2_p02.ebuild, -geant-4.9.5-r1.ebuild, - -geant-4.9.5_p01.ebuild, metadata.xml: - Version bumps. Tests are not in tar ball anymore. Might have to re-apply patch - for data environment variables - - 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> geant-3.21.14-r2.ebuild, - geant-3.21.14-r3.ebuild, geant-4.9.2_p02.ebuild, geant-4.9.5-r1.ebuild, - geant-4.9.5_p01.ebuild: - Update dependency after package move from x11-libs/openmotif to - x11-libs/motif. - - 16 Oct 2012; Justin Lecher <jlec@gentoo.org> geant-3.21.14-r2.ebuild, - geant-3.21.14-r3.ebuild, geant-4.9.2_p02.ebuild, geant-4.9.4_p03.ebuild, - geant-4.9.5-r1.ebuild, geant-4.9.5_p01.ebuild: - Remove virtual/fortran and always call fortran-2_pkg_setup as intend by the - updated fortran-2.eclass - - 04 Jul 2012; Jeff Horelick <jdhore@gentoo.org> geant-4.9.4_p03.ebuild: - marked x86 per bug 420295 - - 16 Jun 2012; Agostino Sarubbo <ago@gentoo.org> geant-4.9.4_p03.ebuild: - Stable for amd64, wrt bug #420295 - - 20 May 2012; Benda Xu <heroxbd@gentoo.org> geant-4.9.5-r1.ebuild, - geant-4.9.5_p01.ebuild: - I have massed up the keywords and Changelog with blind rsync with my overlay. - This is just a fix. - - 20 May 2012; Benda Xu <heroxbd@gentoo.org> +geant-4.9.5-r1.ebuild, - +files/geant-4.9.5_p01-scripts-only-dataenv.patch, - files/geant-4.9.5-scripts-only-dataenv.patch: - add back geant-4.9.5-r1.ebuild because geant-python cannot function correctly - with 4.9.5_p01, upstream http://bugzilla-geant4.kek.jp/show_bug.cgi?id=1317 - -*geant-4.9.5_p01 (19 May 2012) - - 19 May 2012; Benda Xu <heroxbd@gentoo.org> +geant-4.9.5_p01.ebuild, - -geant-4.9.5-r1.ebuild, files/geant-4.9.4-zlib.patch, - files/geant-4.9.5-scripts-only-dataenv.patch: - version bump to 4.9.5_p01 - - 19 May 2012; Benda Xu <heroxbd@gentoo.org> geant-4.9.5-r1.ebuild: - delete the wrong sed phrase. - - 18 May 2012; Benda Xu <heroxbd@gentoo.org> - +files/geant-4.9.5-scripts-only-dataenv.patch, geant-4.9.5-r1.ebuild: - keyword amd64-linux and x86-linux; handle data dir via envd; fix clhep linking - - 16 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> -geant-4.9.5.ebuild, - geant-4.9.5-r1.ebuild: - Fix for openinventor to use SGI OpenInventor in portage instead of SoXt, bug - #408187 - -*geant-4.9.5-r1 (13 Mar 2012) - - 13 Mar 2012; Sébastien Fabbro <bicatali@gentoo.org> - files/geant-4.9.4-zlib.patch, +geant-4.9.5-r1.ebuild: - Fixed more zlib issues. The geant3 flag is now only for unit conversion (if - geant3 is needed, geant:3 has to be installed from user). The data is now - fetched (building needs network) to ease maintenance and set up the proper - env variables in the geant4*sh scripts. Removed a use dawn duplicate. Thanks - Marek Szuba for his suggestions (bug #407517 and bug #359673). Added a - message for backward compatibility (bug #360285) - -*geant-4.9.5 (18 Dec 2011) -*geant-4.9.4_p03 (18 Dec 2011) - - 18 Dec 2011; Sébastien Fabbro <bicatali@gentoo.org> - -geant-4.9.3_p02-r1.ebuild, -geant-4.9.4_p01.ebuild, +geant-4.9.4_p03.ebuild, - +files/geant-4.9.4-trajectory.patch, files/geant-4.9.4-zlib.patch, - +geant-4.9.5.ebuild: - Version bumps. Re-introduced some older flags and fixed linking of - zlib. Added patch for source trajectory example (bug #365171), thanks Matthias Nagl. - - 02 Aug 2011; Matt Turner <mattst88@gentoo.org> geant-4.9.2_p02.ebuild, - geant-4.9.3_p02-r1.ebuild: - Renamed x11-libs/Xaw3d to x11-libs/libXaw3d. - -*geant-3.21.14-r3 (21 Jul 2011) - - 21 Jul 2011; Sébastien Fabbro <bicatali@gentoo.org> - +geant-3.21.14-r3.ebuild: - New debian patch set. Switch to EAPI4 - - 28 Jun 2011; Justin Lecher <jlec@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p02-r1.ebuild, geant-4.9.4_p01.ebuild, - metadata.xml: - Fix sed on *FLAGS from : to |, EAPI bump - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p02-r1.ebuild, geant-4.9.4_p01.ebuild: - Add dependency on virtual/fortran - - 21 Jun 2011; Justin Lecher <jlec@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p02-r1.ebuild, geant-4.9.4_p01.ebuild: - Added fortran-2.eclass support - - 07 Jun 2011; Jeroen Roovers <jer@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p02-r1.ebuild, geant-4.9.4_p01.ebuild: - Drop HPPA keywording. - - 22 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> geant-4.9.4_p01.ebuild: - Proper CMake optional use bug #359437 thanks Rafal Lalik - -*geant-4.9.4_p01 (18 Mar 2011) - - 18 Mar 2011; Sébastien Fabbro <bicatali@gentoo.org> -geant-4.9.4.ebuild, - +geant-4.9.4_p01.ebuild: - Version bump. Unm Unmasking. - - 13 Feb 2011; Raúl Porcel <armin76@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p02-r1.ebuild, geant-4.9.4.ebuild: - Drop sparc keywords - - 07 Feb 2011; Sébastien Fabbro <bicatali@gentoo.org> geant-4.9.4.ebuild: - Fixed a forgotten flag, thanks Rafal Lalik bug #353740 - -*geant-4.9.4 (22 Jan 2011) - - 22 Jan 2011; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.3_p02-r1.ebuild, files/geant-4.9.3-zlib.patch, +geant-4.9.4.ebuild, - +files/geant-4.9.4-datadir.patch, +files/geant-4.9.4-libdir.patch, - +files/geant-4.9.4-no-benchmarks.patch, +files/geant-4.9.4-no-examples.patch, - +files/geant-4.9.4-zlib.patch, metadata.xml: - Version bump, switched to cmake. Fixed Qt drivers bug #263450, bug #347279. - Removed G4WORKDIR bug #345855. - -*geant-4.9.3_p02-r1 (07 Nov 2010) - - 07 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> - -geant-4.9.3_p01.ebuild, -geant-4.9.3_p02.ebuild, - +geant-4.9.3_p02-r1.ebuild, +files/geant-4.9.3-respect_flags.patch: - Fix building with --as-needed wrt bug 344119, respect CXX. Drop old. - - 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild, geant-4.9.3_p01.ebuild, geant-4.9.3_p02.ebuild: - Fix openmotif dependency. - -*geant-4.9.3_p02 (29 Sep 2010) - - 29 Sep 2010; Sébastien Fabbro <bicatali@gentoo.org> - +geant-4.9.3_p02.ebuild: - Version bump - - 12 Aug 2010; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.2_p02.ebuild, -geant-4.9.3.ebuild, geant-4.9.3_p01.ebuild: - Change clhep dependency, clhep-2.1 api incompatible - -*geant-4.9.3_p01 (27 Apr 2010) - - 27 Apr 2010; Sébastien Fabbro <bicatali@gentoo.org> - +geant-4.9.3_p01.ebuild: - Version bump. Switched static flag to static-libs - -*geant-4.9.3 (08 Jan 2010) - - 08 Jan 2010; Sébastien Fabbro <bicatali@gentoo.org> - -geant-4.9.2-r2.ebuild, +geant-4.9.3.ebuild, - +files/geant-4.9.3-zlib.patch: - Version bump, thanks Ben Bannier - - 26 Dec 2009; Raúl Porcel <armin76@gentoo.org> geant-4.9.2_p02.ebuild: - sparc stable wrt #294442 - - 10 Dec 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.2_p02.ebuild: - Propagate compiler correctly, bug #296043 - - 07 Dec 2009; Jeroen Roovers <jer@gentoo.org> geant-3.21.14-r2.ebuild, - geant-4.9.2_p02.ebuild: - Stable for HPPA (bug #294442). - - 04 Dec 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-3.21.14-r2.ebuild: - Re-changing to old style patching at least until patch-2.6 is not buggy - and masked - - 26 Nov 2009; Markus Meier <maekke@gentoo.org> geant-4.9.2_p02.ebuild: - amd64 stable, bug #294442 - - 26 Nov 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-3.21.14-r2.ebuild: - Fixing patch application with more recent versions - - 26 Nov 2009; Christian Faulhammer <fauli@gentoo.org> - geant-4.9.2_p02.ebuild: - stable x86, bug 294442 - - 06 Oct 2009; Dominik Kapusta <ayoy@gentoo.org> geant-4.9.2-r2.ebuild, - geant-4.9.2_p02.ebuild: - Removed alternative dependency on Qt metapackage - -*geant-4.9.2_p02 (23 Sep 2009) - - 23 Sep 2009; Sébastien Fabbro <bicatali@gentoo.org> - -geant-4.9.1_p03.ebuild, -geant-4.9.2_p01.ebuild, +geant-4.9.2_p02.ebuild, - metadata.xml: - Version bump. Added aida USE flag, fixed Qt and GDML build options, - hopefully fixing examples compiling (bug #260102), thanks Matej and - Giovanni Fattori for their input - - 05 May 2009; Christian Faulhammer <fauli@gentoo.org> - geant-3.21.14-r2.ebuild, geant-4.9.2-r2.ebuild: - stable x86, bug 245875 - - 17 Apr 2009; Sébastien Fabbro <bicatali@gentoo.org> geant-3.21.14-r2: - Fixed some latex font generation and made ebuild consistent with other - cernlib ebuilds - - 23 Mar 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.2-r2.ebuild: - Added building of opengl qt4 driver, thanks merkel@kph.uni-mainz.de (bug - #263450) for noticing - - 22 Mar 2009; Jeremy Olexa <darkside@gentoo.org> geant-4.9.2-r2.ebuild: - amd64 stable, bug 245875 - - 22 Mar 2009; Jeremy Olexa <darkside@gentoo.org> geant-3.21.14-r2.ebuild: - amd64 stable, bug 245875 - -*geant-4.9.2_p01 (18 Mar 2009) - - 18 Mar 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-3.21.14-r2.ebuild, +geant-4.9.2_p01.ebuild: - Version bump (bug fixes only) - - 05 Mar 2009; Ferris McCormick <fmccor@gentoo.org> geant-4.9.2-r2.ebuild: - Sparc stable, although early. See Bug #245875 --- needed for gcc-4.3 (Bug - #245160). - - 05 Mar 2009; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.2-r2.ebuild: - Fixed linking qt4 libraries, added G4WORKDIR to make it work on paludis - and a bit of ebuild cleaning - - 03 Mar 2009; Ferris McCormick <fmccor@gentoo.org> geant-3.21.14-r2.ebuild: - Sparc stable, part of Bug #245875. - -*geant-4.9.2-r2 (27 Feb 2009) - - 27 Feb 2009; Sébastien Fabbro <bicatali@gentoo.org> -geant-4.9.2.ebuild, - -geant-4.9.2-r1.ebuild, +geant-4.9.2-r2.ebuild: - Adding fixes from Benjamin Bannier to include linking when building - examples, and a syntax error caught by Matej Batic, see bug #260102 - -*geant-4.9.2-r1 (19 Jan 2009) - - 19 Jan 2009; Sébastien Fabbro <bicatali@gentoo.org> - +files/geant-4.9.2-zlib.patch, +geant-4.9.2-r1.ebuild: - Added a patch to avoid linking to G4zlib, closing bug #255017, thanks to - Benjamin Bannier for the hint - -*geant-4.9.2 (10 Jan 2009) - - 10 Jan 2009; Sébastien Fabbro <bicatali@gentoo.org> +geant-4.9.2.ebuild: - Version bump. Switched to EAPI=2, added qt4 support, updated data files, - updated minimum dependencies, and now propagate LDFLAGS. Closing bug #253769. - - 24 Nov 2008; Sébastien Fabbro <bicatali@gentoo.org> - -geant-4.9.1_p02.ebuild, geant-4.9.1_p03.ebuild: - Removed bundled zlib, closing bug #248423 - -*geant-4.9.1_p03 (23 Sep 2008) - - 23 Sep 2008; Sébastien Fabbro <bicatali@gentoo.org> - +geant-4.9.1_p03.ebuild: - Version bump. Closing bug #238132. - - 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: - Add USE flag description to metadata wrt GLEP 56. - - 17 Jul 2008; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.1_p02.ebuild: - Fixed the make global step to not remove previous built granula libaries, - see bug #231314, thanks Benjamin Bannier. - - 15 Jul 2008; Ferris McCormick <fmccor@gentoo.org> geant-4.9.1_p02.ebuild: - Add ~sparc for testing and for sci-physics/root --- Bug #230716 which see - for comments. - - 15 Jul 2008; Ferris McCormick <fmccor@gentoo.org> geant-3.21.14-r2.ebuild: - Add ~sparc for testing, dependency required for Bug #230716. - - 15 Jul 2008; Jeroen Roovers <jer@gentoo.org> geant-4.9.1_p02.ebuild: - Marked ~hppa (bug #230716). - - 14 Jul 2008; Jeroen Roovers <jer@gentoo.org> geant-3.21.14-r2.ebuild: - Marked ~hppa (bug #230716). - - 10 Jul 2008; Sébastien Fabbro <bicatali@gentoo.org> - geant-4.9.1_p02.ebuild: - Fix some global libraries issues, see bug #231314, thanks Benjamin Bannier - for his patch. - - 06 Jul 2008; Jeroen Roovers <jer@gentoo.org> geant-3.21.14-r1.ebuild: - Fix duplicate KEYWORDS definition. - - 06 Jul 2008; Jeroen Roovers <jer@gentoo.org> geant-3.21.14-r2.ebuild: - Fix duplicate KEYWORDS definition. - - 29 Jun 2008; Torsten Veller <tove@gentoo.org> geant-3.21.14-r1.ebuild, - geant-3.21.14-r2.ebuild: - Add missing die: || "..." -> || die "..." - - 27 Jun 2008; Ulrich Mueller <ulm@gentoo.org> geant-3.21.14-r1.ebuild, - geant-3.21.14-r2.ebuild, geant-4.9.1_p02.ebuild: - Change dependency from virtual/motif to x11-libs/openmotif, bug 224749. - -*geant-4.9.1_p02 (06 Jun 2008) -*geant-3.21.14-r2 (06 Jun 2008) - - 06 Jun 2008; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml, - -geant-3.21.14.ebuild, +geant-3.21.14-r2.ebuild, +geant-4.9.1_p02.ebuild: - Added major version bump for geant-4, slotted. Thanks much to Benjamin - Bennier for his work (bug #212221). Now geant-3 is also slotted, and got a - revision bump - -*geant-4.9.1_p02 (06 Jun 2008) -*geant-3.21.14-r2 (06 Jun 2008) - - 06 Jun 2008; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml, - -geant-3.21.14.ebuild, +geant-3.21.14-r2.ebuild, +geant-4.9.1_p02.ebuild: - Added major version bump for geant-4, slotted. Thanks much to Benjamin - Bennier for his work (bug #212221). Now geant-3 is also slotted, and got a - revision bump - -*geant-3.21.14-r1 (11 Mar 2008) - - 11 Mar 2008; Sébastien Fabbro <bicatali@gentoo.org> - +geant-3.21.14-r1.ebuild: - New series of patches from Debian, more compatible with gfortran and better - tests. Much ebuild cleaning. - -*geant-3.21.14 (24 Aug 2007) - - 24 Aug 2007; Sébastien Fabbro <bicatali@gentoo.org> +metadata.xml, - +geant-3.21.14.ebuild: - Initial import. diff --git a/sci-physics/geant/Manifest b/sci-physics/geant/Manifest deleted file mode 100644 index 04c8801c9..000000000 --- a/sci-physics/geant/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST geant321_3.21.14.dfsg-10.diff.gz 46221 SHA256 a148234b0b09c74e7cd2afe3348adfdcce84d7db41fcf483f09fb52443949df2 SHA512 c0b1da38c966e8bff356726afba344cff953e902fff7e728bd5fce9472d7562701fceae482b8d6cba81bc78ccf5027229aee0379e1b59787c957b88b94ce8cb4 WHIRLPOOL ea1ae564f36ffb93ea8c57125ca21f55d640bc7ca03aa4457bfcecebe93500a66e3e63b43d1b28583d40319f52f0093149a1e868717ea1c855ebae12cf0d638d -DIST geant321_3.21.14.dfsg.orig.tar.gz 10922928 SHA256 186fe98a08ad1de39f68698a09a46e7c2f14c37b22f8f990257b0bd66215c5b4 SHA512 733a77e529ecfe17c35d1e0bf44cf9062dbd9f2e3880e12cbfabf7372e6c60ea9690df010574094b44aef6fe306dfd85dfd4f42641b8f03efda3938a50313734 WHIRLPOOL fc2b230e1bf2ae1157cf9c92f474ff72fc1f3158e5db5a8f1a7d4f7c983fae9b886dc1aeb148019cb961bc602abc629d75a1aa728d66b10887daa45de040def6 diff --git a/sci-physics/geant/geant-3.21.14-r4.ebuild b/sci-physics/geant/geant-3.21.14-r4.ebuild deleted file mode 100644 index 6e6bcf9c3..000000000 --- a/sci-physics/geant/geant-3.21.14-r4.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils fortran-2 alternatives-2 - -DEB_PN=geant321 -DEB_PV=${PV}.dfsg -DEB_PR=10 -DEB_P=${DEB_PN}_${DEB_PV} - -DESCRIPTION="CERN's detector description and simulation Tool" -HOMEPAGE="http://wwwasd.web.cern.ch/wwwasd/geant/" -SRC_URI=" - mirror://debian/pool/main/${DEB_PN:0:1}/${DEB_PN}/${DEB_P}.orig.tar.gz - mirror://debian/pool/main/${DEB_PN:0:1}/${DEB_PN}/${DEB_P}-${DEB_PR}.diff.gz" - -SLOT="3" -LICENSE="GPL-2 LGPL-2 BSD" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - x11-libs/motif:0 - dev-lang/cfortran - sci-physics/cernlib - sci-physics/paw - !sci-physics/geant-vmc:3" -DEPEND="${RDEPEND} - virtual/latex-base - x11-misc/imake - x11-misc/makedepend" - -S="${WORKDIR}/${DEB_PN}-${DEB_PV}.orig" - -src_prepare() { - cd "${WORKDIR}" - sed -i -e 's:/tmp/dp.*/cern:cern:g' ${DEB_P}-${DEB_PR}.diff || die - epatch ${DEB_P}-${DEB_PR}.diff - cd "${S}" - cp debian/add-ons/Makefile . || die - export DEB_BUILD_OPTIONS="$(tc-getFC) nostrip nocheck" - sed -i \ - -e "s:/usr/local:${EROOT}/usr:g" \ - Makefile || die "sed'ing the Makefile failed" - einfo "Applying Debian patches" - emake -j1 patch - - # since we depend on cfortran, do not use the one from cernlib - rm src/include/cfortran/cfortran.h || die -} - -src_compile() { - # create local LaTeX cache directory - VARTEXFONTS="${T}"/fonts - emake -j1 cernlib-indep cernlib-arch -} - -src_test_() { - LD_LIBRARY_PATH="${S}"/shlib emake -j1 cernlib-test -} - -src_install() { - default - cd debian - dodoc changelog README.* deadpool.txt NEWS copyright - newdoc add-ons/README README.add-ons -} diff --git a/sci-physics/geant/metadata.xml b/sci-physics/geant/metadata.xml deleted file mode 100644 index c32b134f3..000000000 --- a/sci-physics/geant/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci-physics</herd> -<longdescription lang="en"> - Geant simulates the passage of subatomic particles through matter, for - instance, particle detectors. Geant 3 simulations are performed by - linking Fortran code supplied by the user with the Geant libraries, - then running the resulting executable. This package includes gxint, - the script used to perform this linking step. - Geant 4 is a complete rewrite in C++ with addition of other modern - features and detectors. -</longdescription> -</pkgmetadata> diff --git a/sci-physics/hoomd-blue/ChangeLog b/sci-physics/hoomd-blue/ChangeLog new file mode 100644 index 000000000..20102faf7 --- /dev/null +++ b/sci-physics/hoomd-blue/ChangeLog @@ -0,0 +1,18 @@ +# ChangeLog for sci-physics/hoomd-blue +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 09 Mar 2015; Christoph Junghans <ottxor@gentoo.org> hoomd-blue-9999.ebuild: + switched to ninja + + 06 Mar 2015; Christoph Junghans <ottxor@gentoo.org> hoomd-blue-9999.ebuild: + update live ebuild + + 01 Mar 2015; Christoph Junghans <ottxor@gentoo.org> hoomd-blue-9999.ebuild: + fixed license + +*hoomd-blue-9999 (26 Feb 2015) + + 26 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +hoomd-blue-9999.ebuild, + +metadata.xml: + initial commit diff --git a/sci-physics/hoomd-blue/hoomd-blue-9999.ebuild b/sci-physics/hoomd-blue/hoomd-blue-9999.ebuild new file mode 100644 index 000000000..43f51f7ce --- /dev/null +++ b/sci-physics/hoomd-blue/hoomd-blue-9999.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_7,3_3,3_4} ) +CMAKE_MAKEFILE_GENERATOR="ninja" + +inherit cmake-utils cuda python-single-r1 + +DESCRIPTION="a general-purpose particle simulation toolkit" +HOMEPAGE="http://codeblue.umich.edu/hoomd-blue/" + +if [[ ${PV} = 9999 ]]; then + EGIT_REPO_URI="https://bitbucket.org/glotzer/${PN}.git" + inherit git-r3 + KEYWORDS= +else + inherit vcs-snapshot + SRC_URI="https://bitbucket.org/glotzer/${PN}/get/v${PV}.tar.bz2 -> ${P}.tar.bz2" + KEYWORDS="~amd64" +fi + +LICENSE="hoomd-blue" +SLOT="0" +IUSE="cuda doc test mpi +zlib" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + mpi? ( virtual/mpi ) + cuda? ( dev-util/nvidia-cuda-sdk ) + zlib? ( sys-libs/zlib ) + dev-libs/boost:=[threads,python,mpi,${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +src_prepare() { + use cuda && cuda_src_prepare + + cmake-utils_src_prepare +} + +src_configure() { + local mycmakeargs=( + $(cmake-utils_use_enable mpi MPI) + $(cmake-utils_use_enable doc DOXYGEN) + $(cmake-utils_use_enable cuda CUDA) + $(cmake-utils_use_enable zlib ZLIB) + $(cmake-utils_use_build test BUILD_TESTING) + -DPYTHON_EXECUTABLE="${PYTHON}" + -DPYTHON_SITEDIR=$(python_get_sitedir) + ) + cmake-utils_src_configure +} + +src_install() { + use doc && HTML_DOCS=( "${BUILD_DIR}"/doc/hoomd-*doc* ) + cmake-utils_src_install +} diff --git a/sci-physics/hoomd-blue/metadata.xml b/sci-physics/hoomd-blue/metadata.xml new file mode 100644 index 000000000..8dd7ec69a --- /dev/null +++ b/sci-physics/hoomd-blue/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> + <use> + <flag name="cuda">Enable cuda non-bonded kernels</flag> + </use> +</pkgmetadata> diff --git a/sci-physics/looptools/ChangeLog b/sci-physics/looptools/ChangeLog index 6e5903308..407587aa5 100644 --- a/sci-physics/looptools/ChangeLog +++ b/sci-physics/looptools/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-physics/looptools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*looptools-2.12 (07 Jun 2015) + + 07 Jun 2015; Jauhien Piatlicki <jauhien@gentoo.org> +looptools-2.12.ebuild: + version bump + *looptools-2.11 (31 Aug 2014) *looptools-2.10 (31 Aug 2014) *looptools-2.9 (31 Aug 2014) diff --git a/sci-physics/looptools/Manifest b/sci-physics/looptools/Manifest index 3c4607565..f4810e3a2 100644 --- a/sci-physics/looptools/Manifest +++ b/sci-physics/looptools/Manifest @@ -1,4 +1,5 @@ DIST LoopTools-2.10.tar.gz 550654 SHA256 141ab2153006ca3f1cc01e66e1552c02bf8164b9216304ff1829370b7b5c77bb SHA512 1fc9ef5a9ced8ea08ddc5f494338fb27b55bacdd23a968ca4379e5ca63f8d74ea947fb0bb98a80dfd6dddc0db1e80d2d454433abdcfeac323b51c27432046954 WHIRLPOOL b118d3f5f13b6e23920f7680b4b1a0b1d2c4079ac78c0763e73d30e9750d14ae57cd00f889e5b7392bc2ef53f88122be4d7f52de96f999676aa4e1e603353eae DIST LoopTools-2.11.tar.gz 546351 SHA256 efe14e774fcd66bdd46bbeb8065138793e3c1f5c73594c84c116edbab74c842d SHA512 fbe6c43b857561d0e7f35acdea32c34f2430c2faf23172790ad4426c469e39cd0df413d2c3cdc080ce9c4dcfb95773b7dc70b13738341c9d0438f4445cdbf6ab WHIRLPOOL 74b30ebe59998f2217b7e5cfb6e90671193159e5e3adfb2c26fee9c6f7b4021932ea8158e191f2e538e2e6d037fc86382659a697f638dc22ea3d068dfb92340c +DIST LoopTools-2.12.tar.gz 545153 SHA256 df04d944de15ec73665edaf76f655d1db797cbc02b54baa7664ac761ecfa2f70 SHA512 70726493bd138fb80b85a46955fbe28b7f1432d9b67a100fe3ff74c2fa22232a07e461a6742745b0ead81793bb64b81cc4265d09b91fa048e7bdd32cf6956b27 WHIRLPOOL af3abaf31a4a868e0f65bdb0b21405c413c470063e4c8130e31b2a9e05a4f0e65e9999323e3cdf0b4277e48e84d767288852e984d486468abab3aaa664f66879 DIST LoopTools-2.8.tar.gz 546810 SHA256 2395518d0eac9b0883a2c249b9a5ba80df443929c520c45e60f5a4284166eb42 SHA512 32211669fd092d2d5bb38e26a6471a95df0647d9e7ea0cc4e99ff4fd7c3e3fee107f6432ed9075e3102224f0041fac6f7075b1f0a91f7744ec3890b4b36d276e WHIRLPOOL c8dff8030d7ea1bfc6b65bef3370c5acfec69fa73f223a63b7424163b81a3bdf788eb3ffecd07e9bf61a31a63138b1fd126b6442a298c8fad1f4b04b69663a47 DIST LoopTools-2.9.tar.gz 548404 SHA256 e3cdc10fdbc9fe68e56402d34c6d3abd1ec6d727db8914b0cec0119273f7aa4d SHA512 3a46c94a5ff72079c930d7ec2076b0f5278e897130383fdd656173218840f04e03ebb9fdef362af36a207a71a87c038fec6e008a231ef259120073760aa05534 WHIRLPOOL 50591b6aa4e7e624282ad2102c78060cd421c6f5b7abd293bb18b2ca6844857bdcdbafab8e33c86ff4bd464f1245ba0cd13978800ac4786411a658ffd947cc38 diff --git a/sci-physics/looptools/looptools-2.12.ebuild b/sci-physics/looptools/looptools-2.12.ebuild new file mode 100644 index 000000000..66a959c4a --- /dev/null +++ b/sci-physics/looptools/looptools-2.12.ebuild @@ -0,0 +1,39 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils fortran-2 multilib + +MYP=LoopTools-${PV} + +DESCRIPTION="Tools for evaluation of scalar and tensor one-loop integrals" +HOMEPAGE="http://www.feynarts.de/looptools" +SRC_URI="http://www.feynarts.de/looptools/${MYP}.tar.gz" + +LICENSE="LGPL-3" + +SLOT="0/${PV}" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc static-libs" + +DEPEND="virtual/fortran" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MYP}" + +src_prepare() { + epatch "${FILESDIR}"/${PN}-2.10-makefile.patch + export VER="${PV}" + # necessary fix for prefix + sed -i "s/lib\$(LIBDIRSUFFIX)/$(get_libdir)/" makefile.in || die +} + +src_install() { + default + # another one of these package building archive with pic + # no: ooptools is not a typo + use static-libs || rm "${ED}"/usr/$(get_libdir)/libooptools.a + use doc && dodoc manual/*.pdf +} diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog index 4ef278cf6..14a233ad0 100644 --- a/sci-physics/root/ChangeLog +++ b/sci-physics/root/ChangeLog @@ -2,6 +2,71 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.96 2012/03/29 18:21:49 bicatali Exp $ + 12 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-6.02.05-r2.ebuild, + -files/root-6.00.01-prop-flags.patch, -files/root-6.02.05-dictpch.patch, + -files/root-6.02.05-xrootd4.patch: + root-6.02.05-r2 is in the portage tree now + + 12 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> root-6.02.05-r2.ebuild: + Fix "pg_config: command not found" QA warning if postgres is not + installed. + +*root-6.02.05-r2 (12 Apr 2015) + + 12 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-6.02.05-r1.ebuild, + +root-6.02.05-r2.ebuild, +files/root-6.02.05-dictpch.patch: + Regenerate PCH headers for Gentoo include files layout and remove + extra $PORTAGE_TMPDIR from /etc (github issue #238). + +*root-6.02.05-r1 (11 Apr 2015) + + 11 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-6.02.05.ebuild, + +root-6.02.05-r1.ebuild: + Fix clang buildtime vs runtime mismatch. + + 11 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> root-6.02.05.ebuild: + Drop minimal USE flag, as it is useless with current ROOT and + recently added USE flags. + +*root-6.02.05 (08 Apr 2015) + + 08 Apr 2015; Andrew Savchenko <bircoph@gentoo.org> -root-6.00.02.ebuild, + +root-6.02.05.ebuild, -files/root-6.00.01-tutorials-path.patch, + -files/root-6.00.02-tm_zone.patch, +files/root-6.02.05-xrootd4.patch, + metadata.xml: + Version bump for testing and evaluation, add new flags. + Remove old. + + 03 Mar 2015; Andrew Savchenko <bircoph@gentoo.org> -root-5.34.26.ebuild, + -files/root-5.32.00-dotfont.patch, -files/root-5.34.05-nobyte-compile.patch, + metadata.xml: + 5.34.26 is moved to the portage tree + + 02 Mar 2015; Andrew Savchenko <bircoph@gentoo.org> metadata.xml: + Indentation fixes (in order to conform to portage version) + + 02 Mar 2015; Andrew Savchenko <bircoph@gentoo.org> root-5.34.26.ebuild, + files/root-5.32.00-chklib64.patch, -files/root-5.34.26-prop-flags.patch: + Add configurable LDFLAGS the same way as upstream did for + configurable CFLAGS/CXXFLAGS. Optimize configure variables. + + 24 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> root-5.34.26.ebuild: + Remove full path from local images, otherwise html header + background is missing. + + 23 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> -root-5.34.18-r2.ebuild, + -root-6.00.01-r1.ebuild, -files/root-5.32.00-prop-flags.patch, + -files/root-5.34.18-tutorials-path.patch, -files/root-6.00.01-cling.patch, + metadata.xml: + Remove old versions and unused patches. + +*root-5.34.26 (23 Feb 2015) + + 23 Feb 2015; Andrew Savchenko <bircoph@gentoo.org> +root-5.34.26.ebuild, + +files/root-5.34.26-prop-flags.patch, metadata.xml: + Version bump. Add http support. Add c++14 support. Rework compilers + handling. + 01 Jan 2015; Andrew Savchenko <bircoph@gentoo.org> root-5.34.18-r2.ebuild, root-6.00.01-r1.ebuild, root-6.00.02.ebuild, root-9999.ebuild: Rename virtual/postgresql to dev-db/postgresql diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest deleted file mode 100644 index 9b2800970..000000000 --- a/sci-physics/root/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST root_v5.34.18.source.tar.gz 74218396 SHA256 9196dce7d76b31e5bcabd985bd31bc4d9b7c8c4d0c7ce84f730efa4ef82a3567 SHA512 7c659d1a92e6ad1b901956cf0a04aacc391c936eb2881528d105f61373128e5fd4caad6e76988050a8a8bc69a8ba0b53055974b4c618800345127ae2e6dd7a14 WHIRLPOOL 15221bbdabd5abd50dc87e3cc8fa3de24c5888e3ac0a75535983c8ec0718433c84c2400da59d27f3b83b687c7c5f5d60bf769c8a1eefce45dd7d39cbc002a6b7 -DIST root_v6.00.01.source.tar.gz 97783289 SHA256 245c75fd6b53b84cae6251f950e259311439da678b2cdebb9578d51561a6b61f SHA512 e5f56750a0637aa884ea2d9d2ebf7b677cd1fac1819042948ba3530a25366cb7d853dba6fa7127764e3ae7cec23f89ed60d8913c0ff10ce2664bcc87df1620cf WHIRLPOOL 92f34c13ee0161d556b54b1bdd971774b2637c5cd57916ee75f0572a30713df820df3bb07f276d16ca31d11fda7e762de673c943b8bffda9db501d2ee8848654 -DIST root_v6.00.02.source.tar.gz 97811067 SHA256 db92818781f842c33b8b583f1f9be02b51cedbf5f2943df986cbbd0c0006a06f SHA512 bd72eb43d2a4ace27738ba2dc509f6d81ec3555e59454426d28c2c5522b4b19d2678ed515b84efaf953146c1f50c65e304532456d76076d03598bda67c69e8a5 WHIRLPOOL 12b87e9b1612ea3625f7ea0970b733887051b5173b728b5f13a032eb103eeda22de8a4c18417e02a92fe02f29b9acd9114fa1420fac42bea31bde07c7a0ce697 diff --git a/sci-physics/root/files/root-5.32.00-chklib64.patch b/sci-physics/root/files/root-5.32.00-chklib64.patch index a5c052cdd..979220f02 100644 --- a/sci-physics/root/files/root-5.32.00-chklib64.patch +++ b/sci-physics/root/files/root-5.32.00-chklib64.patch @@ -1,3 +1,4 @@ +bug fix for #406817 --- configure.orig 2012-02-29 19:46:41.000000000 +0400 +++ configure 2012-03-22 03:28:43.458968696 +0400 @@ -441,14 +441,13 @@ diff --git a/sci-physics/root/files/root-5.32.00-dotfont.patch b/sci-physics/root/files/root-5.32.00-dotfont.patch deleted file mode 100644 index 85d6dea76..000000000 --- a/sci-physics/root/files/root-5.32.00-dotfont.patch +++ /dev/null @@ -1,58 +0,0 @@ ---- root/html/src/TClassDocOutput.cxx.orig 2012-05-25 16:18:10.000000000 +0400 -+++ root/html/src/TClassDocOutput.cxx 2012-05-29 21:36:53.813593012 +0400 -@@ -625,7 +625,7 @@ - << "size=\"8,10\";" << endl - << "ratio=auto;" << endl - << "margin=0;" << endl -- << "node [shape=plaintext,fontsize=40,width=4,height=0.75];" << endl -+ << "node [shape=plaintext,fontsize=40,width=4,height=0.75,fontname=\"DejaVu Serif\"];" << endl - << "\"" << fCurrentClass->GetName() << "\" [shape=ellipse];" << endl; - - std::stringstream ssDep; -@@ -704,7 +704,7 @@ - outdot << ";" << endl; - } else if (writeAndMoreFor) { - outdot << " \"...andmore" << writeAndMoreFor->GetName() -- << "\" [label=\"...and more\",fontname=\"Times-Italic\",fillcolor=lightgrey,style=filled];" << endl; -+ << "\" [label=\"...and more\",fontname=\"DejaVu Serif Italic\",fillcolor=lightgrey,style=filled];" << endl; - } - } - if (!levelExists) break; -@@ -733,7 +733,7 @@ - << "ranksep=0.1;" << endl - << "nodesep=0;" << endl - << "margin=0;" << endl; -- outdot << " node [style=filled,width=0.7,height=0.15,fixedsize=true,shape=plaintext,fontsize=10];" << endl; -+ outdot << " node [style=filled,width=0.7,height=0.15,fixedsize=true,shape=plaintext,fontsize=10,fontname=\"DejaVu Serif\"];" << endl; - - std::stringstream ssDep; - const int numColumns = 3; -@@ -939,7 +939,7 @@ - << "ranksep=0;" << endl - << "nodesep=0;" << endl - << "size=\"8,10\";" << endl -- << "node [fontsize=20,shape=plaintext];" << endl; -+ << "node [fontsize=20,shape=plaintext,fontname=\"DejaVu Serif\"];" << endl; - - for (std::list<std::string>::iterator iFile = listFilesToParse.begin(); - iFile != listFilesToParse.end(); ++iFile) { -@@ -999,7 +999,8 @@ - << "ranksep=0.7;" << endl - << "nodesep=0.3;" << endl - << "size=\"8,8\";" << endl -- << "ratio=compress;" << endl; -+ << "ratio=compress;" << endl -+ << "node [fontname=\"DejaVu Serif\"];" << endl; - - TString libs(fCurrentClass->GetSharedLibs()); - outdot << "\"All Libraries\" [URL=\"LibraryDependencies.html\",shape=box,rank=max,fillcolor=lightgray,style=filled];" << endl; -@@ -1109,7 +1110,8 @@ - - dotout << "digraph G {" << endl - << "ratio=auto;" << endl -- << "rankdir=RL;" << endl; -+ << "rankdir=RL;" << endl -+ << "node [fontname=\"DejaVu Serif\"];" << endl; - - // loop on all classes - TClassDocInfo* cdi = 0; diff --git a/sci-physics/root/files/root-5.32.00-prop-flags.patch b/sci-physics/root/files/root-5.32.00-prop-flags.patch deleted file mode 100644 index 7dfeb1cc3..000000000 --- a/sci-physics/root/files/root-5.32.00-prop-flags.patch +++ /dev/null @@ -1,15 +0,0 @@ ---- root/config/Makefile.in.orig 2013-01-21 22:04:43.011452938 +0400 -+++ root/config/Makefile.in 2013-01-21 22:04:18.027352209 +0400 -@@ -25,9 +25,9 @@ - USECONFIG := @useconfig@ - MKLIBOPTIONS := @mkliboption@ - --EXTRA_CFLAGS := -Iinclude @cflags@ --EXTRA_CXXFLAGS := -Iinclude @cflags@ --EXTRA_LDFLAGS := @ldflags@ -+EXTRA_CFLAGS := -Iinclude @cflags@ $(CFLAGS) -+EXTRA_CXXFLAGS := -Iinclude @cflags@ $(CXXFLAGS) -+EXTRA_LDFLAGS := @ldflags@ $(LDFLAGS) - WINRTDEBUG := @winrtdebug@ - - GLBPATCHFLAGS := @glbpatchcflags@ diff --git a/sci-physics/root/files/root-5.34.05-nobyte-compile.patch b/sci-physics/root/files/root-5.34.05-nobyte-compile.patch deleted file mode 100644 index ec67a1588..000000000 --- a/sci-physics/root/files/root-5.34.05-nobyte-compile.patch +++ /dev/null @@ -1,137 +0,0 @@ -diff -Naur root.as-needed/Makefile root/Makefile ---- a/Makefile.orig 2013-02-15 02:27:56.000000000 +0400 -+++ b/Makefile 2013-02-23 02:22:14.556465852 +0400 -@@ -1258,10 +1258,7 @@ - for lib in $(RFLX_GRFLXPY); do \ - rm -f $(DESTDIR)$(LIBDIR)/$${lib#lib/}; \ - done; \ -- for lib in $(RFLX_GRFLXPYC); do \ -- rm -f $(DESTDIR)$(LIBDIR)/$${lib#lib/}; \ -- done; \ -- if test "x$(RFLX_GRFLXPY)$(RFLX_GRFLXPYC)" != "x"; then \ -+ if test "x$(RFLX_GRFLXPY)" != "x"; then \ - dir=$(subst lib/,,$(RFLX_GRFLXDD)); \ - while test "x$${dir}" != "x" && \ - test -d $(DESTDIR)$(LIBDIR)/$${dir} && \ -diff -Naur root.as-needed/bindings/pyroot/Module.mk root/bindings/pyroot/Module.mk ---- root.as-needed/bindings/pyroot/Module.mk 2011-07-10 10:42:48.991561304 +0400 -+++ root/bindings/pyroot/Module.mk 2011-07-10 10:43:21.493339703 +0400 -@@ -48,8 +48,6 @@ - ROOTPY := $(subst $(MODDIR),$(LPATH),$(ROOTPYS)) - $(LPATH)/%.py: $(MODDIR)/%.py; cp $< $@ - endif --ROOTPYC := $(ROOTPY:.py=.pyc) --ROOTPYO := $(ROOTPY:.py=.pyo) - - # used in the main Makefile - ALLHDRS += $(patsubst $(MODDIRI)/%.h,include/%.h,$(PYROOTH)) -@@ -68,10 +66,8 @@ - include/%.h: $(PYROOTDIRI)/%.h - cp $< $@ - --%.pyc: %.py; python -c 'import py_compile; py_compile.compile( "$<" )' --%.pyo: %.py; python -O -c 'import py_compile; py_compile.compile( "$<" )' - --$(PYROOTLIB): $(PYROOTO) $(PYROOTDO) $(ROOTPY) $(ROOTPYC) $(ROOTPYO) \ -+$(PYROOTLIB): $(PYROOTO) $(PYROOTDO) $(ROOTPY) \ - $(ROOTLIBSDEP) $(PYTHONLIBDEP) - @$(MAKELIB) $(PLATFORM) $(LD) "$(LDFLAGS)" \ - "$(SOFLAGS)" libPyROOT.$(SOEXT) $@ \ -@@ -113,7 +109,7 @@ - - distclean-$(MODNAME): clean-$(MODNAME) - @rm -f $(PYROOTDEP) $(PYROOTDS) $(PYROOTDH) $(PYROOTLIB) \ -- $(ROOTPY) $(ROOTPYC) $(ROOTPYO) $(PYROOTMAP) \ -+ $(ROOTPY) $(PYROOTMAP) \ - $(PYROOTPYD) $(PYTHON64DEP) $(PYTHON64) - - distclean:: distclean-$(MODNAME) -diff -Naur root.as-needed/build/package/debian/rules root/build/package/debian/rules ---- root.as-needed/build/package/debian/rules 2011-07-10 10:42:49.241549346 +0400 -+++ root/build/package/debian/rules 2011-07-10 10:48:06.989670589 +0400 -@@ -691,10 +691,6 @@ - -X$(SYSCONFDIR)/root/system.rootauthrc \ - -X$(SYSCONFDIR)/root/system.rootdaemonrc \ - -X$(PREFIX)/lib/root/$(SOVERS)/libAfterImage.a \ -- -X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyc \ -- -X$(PREFIX)/lib/root/$(SOVERS)/PyCintex.pyo \ -- -X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyc \ -- -X$(PREFIX)/lib/root/$(SOVERS)/ROOT.pyo \ - -X$(PREFIX)/lib/root/$(SOVERS)/cint7 \ - -X$(PREFIX)/include/root/Minuit2 - # $(foreach i, \ -diff -Naur root.as-needed/cint/cintex/Module.mk root/cint/cintex/Module.mk ---- root.as-needed/cint/cintex/Module.mk 2011-07-10 10:42:49.104889217 +0400 -+++ root/cint/cintex/Module.mk 2011-07-10 10:43:21.496672876 +0400 -@@ -31,10 +31,6 @@ - CINTEXPY := $(subst $(MODDIR)/python,$(LPATH),$(CINTEXPYS)) - $(LPATH)/%.py: $(MODDIR)/python/%.py; cp $< $@ - endif --ifneq ($(BUILDPYTHON),no) --CINTEXPYC := $(CINTEXPY:.py=.pyc) --CINTEXPYO := $(CINTEXPY:.py=.pyo) --endif - - # used in the main Makefile - ALLHDRS += $(patsubst $(MODDIRI)/Cintex/%.h,include/Cintex/%.h,$(CINTEXH)) -@@ -86,8 +82,6 @@ - fi) - cp $< $@ - --%.pyc: %.py; python -c 'import py_compile; py_compile.compile( "$<" )' --%.pyo: %.py; python -O -c 'import py_compile; py_compile.compile( "$<" )' - - $(CINTEXLIB): $(CINTEXO) $(CINTEXPY) $(CINTEXPYC) $(CINTEXPYO) \ - $(ORDER_) $(subst $(CINTEXLIB),,$(MAINLIBS)) $(CINTEXLIBDEP) -diff -Naur root.as-needed/cint/reflex/Module.mk root/cint/reflex/Module.mk ---- root.as-needed/cint/reflex/Module.mk 2011-07-10 10:42:49.074890651 +0400 -+++ root/cint/reflex/Module.mk 2011-07-10 10:43:21.496672876 +0400 -@@ -48,9 +48,6 @@ - RFLX_GRFLXS := $(wildcard $(RFLX_GRFLXSD)/*.py) - RFLX_GRFLXPY := $(patsubst $(RFLX_GRFLXSD)/%.py,$(RFLX_GRFLXDD)/%.py,$(RFLX_GRFLXS)) - RFLX_GRFLXPY += $(RFLX_GCCXMLPATHPY) --ifneq ($(BUILDPYTHON),no) --RFLX_GRFLXPYC := $(subst .py,.pyc,$(RFLX_GRFLXPY)) --endif - - RFLX_LIBDIR = $(LIBDIR) - -@@ -92,7 +89,7 @@ - - ALLEXECS += $(RFLX_GENMAPX) - --POSTBIN += $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY) -+POSTBIN += $(RFLX_GRFLXPY) - - ##### local rules ##### - .PHONY: all-$(MODNAME) clean-$(MODNAME) distclean-$(MODNAME) \ -@@ -122,8 +119,6 @@ - mkdir -p lib/python/genreflex; fi ) - cp $< $@ - --$(RFLX_GRFLXDD)/%.pyc: $(RFLX_GRFLXDD)/%.py -- @python -c 'import py_compile; py_compile.compile( "$<" )' - - $(RFLX_GENMAPO) : CXXFLAGS += -I$(REFLEXDIRS)/genmap - -@@ -149,7 +144,7 @@ - $(RLIBMAP) -o $@ -l $(REFLEXDICTLIB) \ - -d $(REFLEXDICTLIBDEPM) -c $(REFLEXL) - --all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPYC) $(RFLX_GRFLXPY) -+all-$(MODNAME): $(REFLEXLIB) $(REFLEXDICTLIB) $(REFLEXDICTMAP) $(RFLX_GRFLXPY) - - clean-genreflex: - @rm -rf lib/python/genreflex -diff -Naur root.as-needed/cint/reflex/python/CMakeLists.txt root/cint/reflex/python/CMakeLists.txt ---- root.as-needed/cint/reflex/python/CMakeLists.txt 2011-07-10 10:42:49.074890651 +0400 -+++ root/cint/reflex/python/CMakeLists.txt 2011-07-10 10:43:21.496672876 +0400 -@@ -15,7 +15,7 @@ - ##################### sources #################### - - FILE(GLOB_RECURSE GENREFLEX_SRCS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} genreflex/*.py) --SET(GENREFLEX_SCRIPT ${CMAKE_CURRENT_BINARY_DIR}/genreflex/genreflex.pyc PARENT_SCOPE) -+SET(GENREFLEX_SCRIPT PARENT_SCOPE) - - ##################### gccxmlpath #################### - diff --git a/sci-physics/root/files/root-5.34.18-tutorials-path.patch b/sci-physics/root/files/root-5.34.18-tutorials-path.patch deleted file mode 100644 index 8bf88594d..000000000 --- a/sci-physics/root/files/root-5.34.18-tutorials-path.patch +++ /dev/null @@ -1,94 +0,0 @@ -diff --git a/config/RConfigure.in b/config/RConfigure.in -index 5950401..e4fbfbf 100644 ---- a/config/RConfigure.in -+++ b/config/RConfigure.in -@@ -11,6 +11,7 @@ - #define ROOTDATADIR "@datadir@" - #define ROOTDOCDIR "@docdir@" - #define ROOTMACRODIR "@macrodir@" -+#define ROOTTUTDIR "@tutdir@" - #define ROOTSRCDIR "@srcdir@" - #define ROOTICONPATH "@iconpath@" - #define EXTRAICONPATH "@extraiconpath@" -diff --git a/configure b/configure -index 131df92..2c8ea95 100755 ---- a/configure -+++ b/configure -@@ -7537,6 +7537,7 @@ sed \ - -e "s|@prefix@|$prefix|" \ - -e "s|@srcdir@|$srcdir|" \ - -e "s|@ttffontdir@|$fontdir|" \ -+ -e "s|@tutdir@|$tutdir|" \ - -e "s|@setresuid@|$setresuid|" \ - -e "s|@hasmathmore@|$hasmathmore|" \ - -e "s|@haspthread@|$haspthread|" \ -diff --git a/core/base/src/TApplication.cxx b/core/base/src/TApplication.cxx -index 95fb1e5..3830955 100644 ---- a/core/base/src/TApplication.cxx -+++ b/core/base/src/TApplication.cxx -@@ -794,6 +794,22 @@ Long_t TApplication::ProcessRemote(const char *line, Int_t *) - return 1; - } - -+namespace { -+ static int PrintFile(const char* filename) { -+ TString sFileName(filename); -+ gSystem->ExpandPathName(sFileName); -+ if (gSystem->AccessPathName(sFileName)) { -+ Error("ProcessLine()", "Cannot find file %s", filename); -+ return 1; -+ } -+ std::ifstream instr(sFileName); -+ TString content; -+ content.ReadFile(instr); -+ Printf("%s", content.Data()); -+ return 0; -+ } -+} -+ - //______________________________________________________________________________ - Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err) - { -@@ -827,11 +843,41 @@ Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err) - return 0; - } - -- if (!strncmp(line, "?", 1)) { -+ if (!strncmp(line, "?", 1) || !strncmp(line, ".help", 5)) { - Help(line); - return 1; - } - -+ if (!strncmp(line, ".demo", 5)) { -+ if (gROOT->IsBatch()) { -+ Error("ProcessLine", "Cannot show demos in batch mode!"); -+ return 1; -+ } -+#ifdef ROOTTUTDIR -+ ProcessLine(".x " ROOTTUTDIR "/demos.C"); -+#else -+ ProcessLine(".x $(ROOTSYS)/tutorials/demos.C"); -+#endif -+ return 0; -+ } -+ -+ if (!strncmp(line, ".license", 8)) { -+#ifdef ROOTDOCDIR -+ return PrintFile(ROOTDOCDIR "/LICENSE"); -+#else -+ return PrintFile("$(ROOTSYS)/LICENSE"); -+#endif -+ } -+ -+ if (!strncmp(line, ".credits", 8)) { -+#ifdef ROOTDOCDIR -+ return PrintFile(ROOTDOCDIR "/CREDITS"); -+#else -+ return PrintFile("$(ROOTSYS)/README/CREDITS"); -+#endif -+ -+ } -+ - if (!strncmp(line, ".pwd", 4)) { - if (gDirectory) - Printf("Current directory: %s", gDirectory->GetPath()); diff --git a/sci-physics/root/files/root-6.00.01-cling.patch b/sci-physics/root/files/root-6.00.01-cling.patch deleted file mode 100644 index 146e89fde..000000000 --- a/sci-physics/root/files/root-6.00.01-cling.patch +++ /dev/null @@ -1,19 +0,0 @@ -commit eea9517c17bd86beda895a5a8b3ffe59af18596f -Author: Axel Naumann <Axel.Naumann@cern.ch> -Date: Tue Jul 1 17:45:20 2014 +0200 - - From Pere: go via TSystem to use prefix if defined (ROOT-6410). - -diff --git a/core/meta/src/TCling.cxx b/core/meta/src/TCling.cxx -index baec571..4976d4e 100644 ---- a/core/meta/src/TCling.cxx -+++ b/core/meta/src/TCling.cxx -@@ -4703,7 +4703,7 @@ void* TCling::LazyFunctionCreatorAutoload(const std::string& mangled_name) { - TString lib; - Ssiz_t posLib = 0; - while (libs.Tokenize(lib, posLib)) { -- if (Load(lib, kFALSE /*system*/) < 0) { -+ if (gSystem->Load(lib, "", kFALSE /*system*/) < 0) { - // The library load failed, all done. - //fprintf(stderr, "load failed: %s\n", errmsg.c_str()); - return 0; diff --git a/sci-physics/root/files/root-6.00.01-prop-flags.patch b/sci-physics/root/files/root-6.00.01-prop-flags.patch deleted file mode 100644 index 3a1002478..000000000 --- a/sci-physics/root/files/root-6.00.01-prop-flags.patch +++ /dev/null @@ -1,17 +0,0 @@ -diff --git a/config/Makefile.in b/config/Makefile.in -index dd89044..4fc7de3 100644 ---- a/config/Makefile.in -+++ b/config/Makefile.in -@@ -64,9 +64,9 @@ HOST := @host@ - USECONFIG := @useconfig@ - MKLIBOPTIONS := @mkliboption@ - --EXTRA_CFLAGS := -Iinclude @cflags@ --EXTRA_CXXFLAGS := -Iinclude @cflags@ --EXTRA_LDFLAGS := @ldflags@ -+EXTRA_CFLAGS := -Iinclude @cflags@ $(CFLAGS) -+EXTRA_CXXFLAGS := -Iinclude @cflags@ $(CXXFLAGS) -+EXTRA_LDFLAGS := @ldflags@ $(LDFLAGS) - WERROR := @werror@ - WINRTDEBUG := @winrtdebug@ - CTORSINITARRAY := @ctorsinitarray@ diff --git a/sci-physics/root/files/root-6.00.01-tutorials-path.patch b/sci-physics/root/files/root-6.00.01-tutorials-path.patch deleted file mode 100644 index cb6861554..000000000 --- a/sci-physics/root/files/root-6.00.01-tutorials-path.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff --git a/config/RConfigure.in b/config/RConfigure.in -index 5950401..e4fbfbf 100644 ---- a/config/RConfigure.in -+++ b/config/RConfigure.in -@@ -11,6 +11,7 @@ - #define ROOTDATADIR "@datadir@" - #define ROOTDOCDIR "@docdir@" - #define ROOTMACRODIR "@macrodir@" -+#define ROOTTUTDIR "@tutdir@" - #define ROOTSRCDIR "@srcdir@" - #define ROOTICONPATH "@iconpath@" - #define EXTRAICONPATH "@extraiconpath@" -diff --git a/configure b/configure -index 131df92..2c8ea95 100755 ---- a/configure -+++ b/configure -@@ -7537,6 +7537,7 @@ sed \ - -e "s|@prefix@|$prefix|" \ - -e "s|@srcdir@|$srcdir|" \ - -e "s|@ttffontdir@|$fontdir|" \ -+ -e "s|@tutdir@|$tutdir|" \ - -e "s|@setresuid@|$setresuid|" \ - -e "s|@hasmathmore@|$hasmathmore|" \ - -e "s|@haspthread@|$haspthread|" \ -diff --git a/core/base/src/TApplication.cxx b/core/base/src/TApplication.cxx -index 1c1809a..7d7ed37 100644 ---- a/core/base/src/TApplication.cxx -+++ b/core/base/src/TApplication.cxx -@@ -866,8 +866,8 @@ Long_t TApplication::ProcessLine(const char *line, Bool_t sync, Int_t *err) - Error("ProcessLine", "Cannot show demos in batch mode!"); - return 1; - } --#ifdef ROOTDOCDIR -- ProcessLine(".x " ROOTDOCDIR "/tutorials/demos.C"); -+#ifdef ROOTTUTDIR -+ ProcessLine(".x " ROOTTUTDIR "/demos.C"); - #else - ProcessLine(".x $(ROOTSYS)/tutorials/demos.C"); - #endif diff --git a/sci-physics/root/files/root-6.00.02-tm_zone.patch b/sci-physics/root/files/root-6.00.02-tm_zone.patch deleted file mode 100644 index cdd1b13e4..000000000 --- a/sci-physics/root/files/root-6.00.02-tm_zone.patch +++ /dev/null @@ -1,22 +0,0 @@ -From 08b08412bafc24fa635b0fdb832097a3aa2fa1d2 Mon Sep 17 00:00:00 2001 -From: Pere Mato <pere.mato@cern.ch> -Date: Sun, 21 Sep 2014 19:27:30 +0200 -Subject: [PATCH] Fix for ROOT-6728 - Compilation error in TTimeStamp - ---- - core/base/src/TTimeStamp.cxx | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/core/base/src/TTimeStamp.cxx b/core/base/src/TTimeStamp.cxx -index 8709220..f0ff12d 100644 ---- a/core/base/src/TTimeStamp.cxx -+++ b/core/base/src/TTimeStamp.cxx -@@ -813,7 +813,7 @@ void TTimeStamp::DumpTMStruct(const tm_t &tmstruct) - tmstruct.tm_isdst); - #if (defined(linux) && !defined(R__WINGCC)) || defined(R__MACOSX) - printf(",\n tm_gmtoff %6ld, tm_zone \"%s\"", --#if defined(__USE_BSD) || defined(R__MACOSX) -+#if defined(__USE_BSD) || defined(R__MACOSX) || defined(__USE_MISC) - tmstruct.tm_gmtoff, tmstruct.tm_zone); - #else - tmstruct.__tm_gmtoff, tmstruct.__tm_zone); diff --git a/sci-physics/root/metadata.xml b/sci-physics/root/metadata.xml index 26e546cf2..7e1dbd5bc 100644 --- a/sci-physics/root/metadata.xml +++ b/sci-physics/root/metadata.xml @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>bircoph@gentoo.org</email> - <name>Andrew Savchenko</name> - </maintainer> - <herd>sci-physics</herd> - <longdescription lang="en"> +<maintainer> + <email>bircoph@gentoo.org</email> + <name>Andrew Savchenko</name> +</maintainer> +<herd>sci-physics</herd> +<longdescription lang="en"> ROOT Object Oriented Technologies is an object oriented data analysis framework written in C++ by the CERN. Widely used in high energy physics, but also in other data analysis applications. It @@ -14,15 +14,13 @@ statistics, serialization, optimization, linear algebra, graphics, GUI toolkit, and a complete visualization framework. </longdescription> - <use> - <flag name="c++0x"> Build ROOT using the C++11 standard. Not supported, requires <pkg>sys-devel/gcc</pkg>>=4.7.0</flag> - <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag> - <flag name="geocad">Enable ROOT-CAD interface using <pkg>sci-libs/opencascade</pkg></flag> - <flag name="http">Enable http server support including but not limited to fastcgi support</flag> - <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag> - <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag> - <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag> - <flag name="reflex">Build the reflection database for the C++ interpreter</flag> - <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag> - </use> +<use> + <flag name="fits">Support for images and data from FITS files with <pkg>sci-libs/cfitsio</pkg></flag> + <flag name="geocad">Enable ROOT-CAD interface using <pkg>sci-libs/opencascade</pkg></flag> + <flag name="http">Enable http server support including but not limited to fastcgi support</flag> + <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag> + <flag name="pythia6">Build the interface for <pkg>sci-physics/pythia</pkg> version 6.x </flag> + <flag name="pythia8">Build the interface for <pkg>sci-physics/pythia</pkg> version 8.x </flag> + <flag name="xrootd">Build the interface for <pkg>net-libs/xrootd</pkg> </flag> +</use> </pkgmetadata> diff --git a/sci-physics/root/root-5.34.18-r2.ebuild b/sci-physics/root/root-5.34.18-r2.ebuild deleted file mode 100644 index 7108ae3bc..000000000 --- a/sci-physics/root/root-5.34.18-r2.ebuild +++ /dev/null @@ -1,389 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $ - -EAPI=5 - -if [[ ${PV} == "9999" ]] ; then - inherit git-r3 - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -PYTHON_COMPAT=( python2_{6,7} ) - -inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \ - toolchain-funcs user versionator - -DESCRIPTION="C++ data analysis framework and interpreter from CERN" -HOMEPAGE="http://root.cern.ch/" -DOC_URI="ftp://root.cern.ch/${PN}/doc" - -SLOT="0/$(get_version_component_range 1-3 ${PV})" -LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA" -IUSE="+X afs avahi c++0x doc emacs examples fits fftw graphviz - kerberos ldap +math minimal mpi mysql odbc +opengl openmp - oracle postgres prefix pythia6 pythia8 python qt4 +reflex - ruby sqlite ssl xinetd xml xrootd" - -REQUIRED_USE=" - !X? ( !opengl !qt4 ) - mpi? ( math !openmp ) - openmp? ( math !mpi ) - python? ( ${PYTHON_REQUIRED_USE} )" - -CDEPEND=" - app-arch/xz-utils:0= - >=dev-lang/cfortran-4.4-r2 - dev-libs/libpcre:3= - media-fonts/dejavu - media-libs/freetype:2= - media-libs/giflib:0= - media-libs/libpng:0= - media-libs/tiff:0= - sys-libs/zlib:0= - virtual/jpeg:0 - virtual/shadow - X? ( - media-libs/ftgl:0= - media-libs/glew:0= - x11-libs/libX11:0= - x11-libs/libXext:0= - x11-libs/libXpm:0= - !minimal? ( - || ( - media-libs/libafterimage:0=[gif,jpeg,png,tiff] - >=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff] - ) - opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= ) - qt4? ( - dev-qt/qtgui:4= - dev-qt/qtopengl:4= - dev-qt/qt3support:4= - dev-qt/qtsvg:4= - dev-qt/qtwebkit:4= - dev-qt/qtxmlpatterns:4= - ) - x11-libs/libXft:0= - ) - ) - !minimal? ( - afs? ( net-fs/openafs ) - avahi? ( net-dns/avahi:0= ) - emacs? ( virtual/emacs ) - fits? ( sci-libs/cfitsio:0= ) - fftw? ( sci-libs/fftw:3.0= ) - graphviz? ( media-gfx/graphviz:0= ) - kerberos? ( virtual/krb5 ) - ldap? ( net-nds/openldap:0= ) - math? ( - sci-libs/gsl:0= - sci-mathematics/unuran:0= - mpi? ( virtual/mpi ) - ) - mysql? ( virtual/mysql ) - odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) ) - oracle? ( dev-db/oracle-instantclient-basic:0= ) - postgres? ( dev-db/postgresql:= ) - pythia6? ( sci-physics/pythia:6= ) - pythia8? ( >=sci-physics/pythia-8.1.80:8= ) - python? ( ${PYTHON_DEPS} ) - ruby? ( - dev-lang/ruby - dev-ruby/rubygems - ) - sqlite? ( dev-db/sqlite:3= ) - ssl? ( dev-libs/openssl:0= ) - xml? ( dev-libs/libxml2:2= ) - xrootd? ( >=net-libs/xrootd-3.3.5:0= ) - )" - -DEPEND="${CDEPEND} - virtual/pkgconfig" - -RDEPEND="${CDEPEND} - reflex? ( dev-cpp/gccxml ) - xinetd? ( sys-apps/xinetd )" - -PDEPEND="doc? ( ~app-doc/root-docs-${PV}[math=] )" - -S="${WORKDIR}/${PN}" - -# install stuff in ${P} and not ${PF} for easier tracking in root-docs -DOC_DIR="/usr/share/doc/${P}" - -pkg_setup() { - fortran-2_pkg_setup - use python && python-single-r1_pkg_setup - echo - elog "There are extra options on packages not yet in Gentoo:" - elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite," - elog "HDFS, Monalisa, MaxDB/SapDB, SRP." - elog "You can use the env variable EXTRA_ECONF variable for this." - elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\"" - echo - - enewgroup rootd - enewuser rootd -1 -1 /var/spool/rootd rootd - - use minimal && return - - if use math; then - if use openmp; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "You are using a g++ without OpenMP capabilities" - die "Need an OpenMP capable compiler" - else - export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 - fi - elif use mpi; then - export USE_MPI=1 USE_PARALLEL_MINUIT2=1 - fi - fi - if use c++0x && [[ $(tc-getCXX) == *g++* ]] && \ - ! version_is_at_least "4.7" "$(gcc-version)"; then - eerror "You are using a g++ without C++0x capabilities" - die "Need an C++0x capable compiler" - fi -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \ - "${FILESDIR}"/${PN}-5.32.00-prop-flags.patch \ - "${FILESDIR}"/${PN}-5.32.00-afs.patch \ - "${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \ - "${FILESDIR}"/${PN}-5.32.00-chklib64.patch \ - "${FILESDIR}"/${PN}-5.32.00-dotfont.patch \ - "${FILESDIR}"/${PN}-5.34.05-nobyte-compile.patch \ - "${FILESDIR}"/${PN}-5.34.13-unuran.patch \ - "${FILESDIR}"/${PN}-5.34.13-desktop.patch \ - "${FILESDIR}"/${PN}-5.34.18-tutorials-path.patch - - # make sure we use system libs and headers - rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die - rm -r graf2d/asimage/src/libAfterImage || die - rm -r graf3d/ftgl/{inc,src} || die - rm -r graf2d/freetype/src || die - rm -r graf3d/glew/{inc,src} || die - rm -r core/pcre/src || die - rm -r math/unuran/src/unuran-*.tar.gz || die - LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \ - xargs -0 rm || die - rm -r core/lzma/src/*.tar.gz || die - rm graf3d/gl/{inc,src}/gl2ps.* || die - sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \ - graf3d/gl/Module.mk || die - - # In Gentoo, libPythia6 is called libpythia6 - # iodbc is in /usr/include/iodbc - # pg_config.h is checked instead of libpq-fe.h - sed -i \ - -e 's:libPythia6:libpythia6:g' \ - -e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \ - -e 's:libpq-fe.h:pg_config.h:' \ - configure || die "adjusting configure for Gentoo failed" - - # prefixify the configure script - sed -i \ - -e 's:/usr:${EPREFIX}/usr:g' \ - configure || die "prefixify configure failed" - - # fix reflex path (bug #497280) - sed -i -e 's|${ROOTSYS}/lib|@libdir@|' config/genreflex.in || die - - # QTDIR only used for qt3 in gentoo, and configure looks for it. - unset QTDIR -} - -src_configure() { - - # the configure script is not the standard autotools - local myconf=( - --prefix="${EPREFIX}/usr" - --etcdir="${EPREFIX}/etc/root" - --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" - --docdir="${EPREFIX}${DOC_DIR}" - --tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials" - --testdir="${EPREFIX}${DOC_DIR}/examples/tests" - --with-cc="$(tc-getCC)" - --with-cxx="$(tc-getCXX)" - --with-f77="$(tc-getFC)" - --with-ld="$(tc-getCXX)" - --nohowto - ) - - if use minimal; then - myconf+=( $(usex X --gminimal --minimal) ) - else - myconf+=( - --with-afs-shared=yes - --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" - --disable-builtin-afterimage - --disable-builtin-ftgl - --disable-builtin-freetype - --disable-builtin-glew - --disable-builtin-pcre - --disable-builtin-zlib - --disable-builtin-lzma - --disable-cling - --enable-astiff - --enable-explicitlink - --enable-gdml - --enable-memstat - --enable-shadowpw - --enable-shared - --enable-soversion - --enable-table - --fail-on-missing - $(use_enable X x11) - $(use_enable X asimage) - $(use_enable X xft) - $(use_enable afs) - $(use_enable avahi bonjour) - $(use_enable c++0x cxx11) - $(use_enable fits fitsio) - $(use_enable fftw fftw3) - $(use_enable graphviz gviz) - $(use_enable kerberos krb5) - $(use_enable ldap) - $(use_enable math gsl-shared) - $(use_enable math genvector) - $(use_enable math mathmore) - $(use_enable math minuit2) - $(use_enable math roofit) - $(use_enable math tmva) - $(use_enable math unuran) - $(use_enable mysql) - $(usex mysql \ - "--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "") - $(use_enable odbc) - $(use_enable opengl) - $(use_enable oracle) - $(use_enable postgres pgsql) - $(usex postgres \ - "--with-pgsql-incdir=$(pg_config --includedir)" "") - $(use_enable prefix rpath) - $(use_enable pythia6) - $(use_enable pythia8) - $(use_enable python) - $(use_enable qt4 qt) - $(use_enable qt4 qtgsi) - $(use_enable reflex cintex) - $(use_enable reflex) - $(use_enable ruby) - $(use_enable sqlite) - $(use_enable ssl) - $(use_enable xml) - $(use_enable xrootd) - ${EXTRA_ECONF} - ) - fi - - ./configure ${myconf[@]} || die "configure failed" -} - -src_compile() { - emake \ - OPT="${CXXFLAGS}" \ - F77OPT="${FFLAGS}" \ - ROOTSYS="${S}" \ - LD_LIBRARY_PATH="${S}/lib" - use emacs && ! use minimal && elisp-compile build/misc/*.el -} - -daemon_install() { - local daemons="rootd proofd" - dodir /var/spool/rootd - fowners rootd:rootd /var/spool/rootd - dodir /var/spool/rootd/{pub,tmp} - fperms 1777 /var/spool/rootd/{pub,tmp} - - for i in ${daemons}; do - newinitd "${FILESDIR}"/${i}.initd ${i} - newconfd "${FILESDIR}"/${i}.confd ${i} - done - if use xinetd; then - insinto /etc/xinetd - doins "${S}"/etc/daemons/{rootd,proofd}.xinetd - fi -} - -desktop_install() { - cd "${S}" - echo "Icon=root-system-bin" >> etc/root.desktop - domenu etc/root.desktop - doicon build/package/debian/root-system-bin.png - - insinto /usr/share/icons/hicolor/48x48/mimetypes - doins build/package/debian/application-x-root.png - - insinto /usr/share/icons/hicolor/48x48/apps - doicon build/package/debian/root-system-bin.xpm -} - -cleanup_install() { - # Cleanup of files either already distributed or unused on Gentoo - pushd "${ED}" > /dev/null - rm usr/share/root/fonts/LICENSE || die - rm etc/root/proof/*.sample || die - rm -r etc/root/daemons || die - # these should be in PATH - mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die - rm ${DOC_DIR#/}/{INSTALL,LICENSE,COPYING.CINT} || die - use examples || rm -r ${DOC_DIR#/}/examples || die - cd usr/$(get_libdir)/root/cint/cint - rm lib/posix/mktypes lib/dll_stl/setup lib/G__* || die - rm lib/dll_stl/G__* lib/dll_stl/rootcint_* lib/posix/exten.o || die - rm include/makehpib || die - popd > /dev/null -} - -src_install() { - emake DESTDIR="${D}" install - - echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root - - if ! use minimal; then - use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root - if use python; then - echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root - python_optimize "${D}/usr/$(get_libdir)/root" - fi - use ruby && \ - echo "RUBYLIB=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root - use emacs && elisp-install ${PN} build/misc/*.{el,elc} - if use examples; then - # these should really be taken care of by the root make install - insinto ${DOC_DIR}/examples/tutorials/tmva - doins -r tmva/test - fi - fi - doenvd 99root - - # The build system installs Emacs support unconditionally in the wrong - # directory. Remove it and call elisp-install in case of USE=emacs. - rm -r "${ED}"/usr/share/emacs || die - - daemon_install - desktop_install - cleanup_install - - # do not copress files used by ROOT's CLI (.credit, .demo, .license) - docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials} - # needed for .license command to work - dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE" -} - -pkg_postinst() { - fdo-mime_desktop_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update -} diff --git a/sci-physics/root/root-6.00.01-r1.ebuild b/sci-physics/root/root-6.00.01-r1.ebuild deleted file mode 100644 index fae938eff..000000000 --- a/sci-physics/root/root-6.00.01-r1.ebuild +++ /dev/null @@ -1,442 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $ - -EAPI=5 - -if [[ ${PV} == "9999" ]] ; then - inherit git-r3 - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - S="${WORKDIR}/${PN}" -fi - -PYTHON_COMPAT=( python2_{6,7} ) - -inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \ - toolchain-funcs user versionator - -DESCRIPTION="C++ data analysis framework and interpreter from CERN" -HOMEPAGE="http://root.cern.ch/" -DOC_URI="ftp://root.cern.ch/${PN}/doc" - -SLOT="0/$(get_version_component_range 1-3 ${PV})" -LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA" -IUSE="+X afs avahi doc emacs examples fits fftw geocad graphviz - http kerberos ldap +math minimal mpi mysql odbc +opengl openmp - oracle postgres prefix pythia6 pythia8 python qt4 sqlite ssl - xinetd xml xrootd" - -# TODO: add support for: davix -# TODO: ROOT-6 supports x32 ABI, but half of its dependencies doesn't -# TODO: unbundle: cling, vdt - -REQUIRED_USE=" - mpi? ( math !openmp ) - opengl? ( X ) - openmp? ( math !mpi ) - python? ( ${PYTHON_REQUIRED_USE} ) - qt4? ( X ) -" - -CDEPEND=" - app-arch/xz-utils:0= - >=dev-lang/cfortran-4.4-r2 - dev-libs/libpcre:3= - media-fonts/dejavu - media-libs/freetype:2= - media-libs/giflib:0= - media-libs/libpng:0= - media-libs/tiff:0= - >=sys-devel/clang-3.4 - sys-libs/zlib:0= - virtual/jpeg:0 - virtual/shadow - X? ( - media-libs/ftgl:0= - media-libs/glew:0= - x11-libs/libX11:0= - x11-libs/libXext:0= - x11-libs/libXpm:0= - !minimal? ( - opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= ) - qt4? ( - dev-qt/qtgui:4= - dev-qt/qtopengl:4= - dev-qt/qt3support:4= - dev-qt/qtsvg:4= - dev-qt/qtwebkit:4= - dev-qt/qtxmlpatterns:4= - ) - x11-libs/libXft:0= - ) - ) - !minimal? ( - afs? ( net-fs/openafs ) - avahi? ( net-dns/avahi:0= ) - emacs? ( virtual/emacs ) - fits? ( sci-libs/cfitsio:0= ) - fftw? ( sci-libs/fftw:3.0= ) - geocad? ( sci-libs/opencascade:= ) - graphviz? ( media-gfx/graphviz:0= ) - http? ( dev-libs/fcgi:0= ) - kerberos? ( virtual/krb5 ) - ldap? ( net-nds/openldap:0= ) - math? ( - sci-libs/gsl:0= - sci-mathematics/unuran:0= - mpi? ( virtual/mpi ) - ) - mysql? ( virtual/mysql ) - odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) ) - oracle? ( dev-db/oracle-instantclient-basic:0= ) - postgres? ( dev-db/postgresql:= ) - pythia6? ( sci-physics/pythia:6= ) - pythia8? ( >=sci-physics/pythia-8.1.80:8= ) - python? ( ${PYTHON_DEPS} ) - sqlite? ( dev-db/sqlite:3= ) - ssl? ( dev-libs/openssl:0= ) - xml? ( dev-libs/libxml2:2= ) - xrootd? ( >=net-libs/xrootd-3.3.5:0= ) - )" - -# TODO: ruby is not yet ported to ROOT-6, reenable when (if?) ready -# ruby? ( -# dev-lang/ruby -# dev-ruby/rubygems -# ) -# -# TODO: root-6.00.01 crashes with system libafterimage -# || ( -# media-libs/libafterimage:0=[gif,jpeg,png,tiff] -# >=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff] -# ) -# --disable-builtin-afterimage - -DEPEND="${CDEPEND} - virtual/pkgconfig" - -RDEPEND="${CDEPEND} - xinetd? ( sys-apps/xinetd )" - -PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )" - -# install stuff in ${P} and not ${PF} for easier tracking in root-docs -DOC_DIR="/usr/share/doc/${P}" - -die_compiler() { - die "Need one of the following C++11 capable compilers:" - die " >=sys-devel/gcc[cxx]-4.8" - die " >=sys-devel/clang-3.4" - die " >=dev-lang/icc-13" -} - -pkg_setup() { - fortran-2_pkg_setup - use python && python-single-r1_pkg_setup - echo - elog "There are extra options on packages not yet in Gentoo:" - elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite," - elog "HDFS, Monalisa, MaxDB/SapDB, SRP." - elog "You can use the env variable EXTRA_ECONF variable for this." - elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\"" - echo - - enewgroup rootd - enewuser rootd -1 -1 /var/spool/rootd rootd - - use minimal && return - - if use math; then - if use openmp; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "You are using a g++ without OpenMP capabilities" - die "Need an OpenMP capable compiler" - else - export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 - fi - elif use mpi; then - export USE_MPI=1 USE_PARALLEL_MINUIT2=1 - fi - fi - - # check for supported compilers - case $(tc-getCXX) in - *g++*) - if ! version_is_at_least "4.8" "$(gcc-version)"; then - eerror "You are using a g++ without C++11 capabilities" - die_compiler - fi - ;; - *clang++*) - # >=clang-3.4 is already in DEPEND - ;; - *icc*|*icpc*) - if ! version_is_at_least "13" "$(has_version dev-lang/icc)"; then - eerror "You are using an icc without C++11 capabilities" - die_compiler - fi - ;; - *) - ewarn "You are using an unsupported compiler." - ewarn "Please report any issues upstream." - ;; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \ - "${FILESDIR}"/${PN}-5.32.00-afs.patch \ - "${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \ - "${FILESDIR}"/${PN}-5.32.00-chklib64.patch \ - "${FILESDIR}"/${PN}-5.34.13-unuran.patch \ - "${FILESDIR}"/${PN}-5.34.13-desktop.patch \ - "${FILESDIR}"/${PN}-6.00.01-dotfont.patch \ - "${FILESDIR}"/${PN}-6.00.01-nobyte-compile.patch \ - "${FILESDIR}"/${PN}-6.00.01-prop-flags.patch \ - "${FILESDIR}"/${PN}-6.00.01-llvm.patch \ - "${FILESDIR}"/${PN}-6.00.01-geocad.patch \ - "${FILESDIR}"/${PN}-6.00.01-cling.patch \ - "${FILESDIR}"/${PN}-6.00.01-tutorials-path.patch - - # make sure we use system libs and headers - rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die - #rm -r graf2d/asimage/src/libAfterImage || die - rm -r graf3d/ftgl/{inc,src} || die - rm -r graf2d/freetype/src || die - rm -r graf3d/glew/{inc,src} || die - rm -r core/pcre/src || die - rm -r math/unuran/src/unuran-*.tar.gz || die - LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \ - xargs -0 rm || die - rm -r core/lzma/src/*.tar.gz || die - rm graf3d/gl/{inc,src}/gl2ps.* || die - sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \ - graf3d/gl/Module.mk || die - - # In Gentoo, libPythia6 is called libpythia6 - # iodbc is in /usr/include/iodbc - # pg_config.h is checked instead of libpq-fe.h - sed -i \ - -e 's:libPythia6:libpythia6:g' \ - -e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \ - -e 's:libpq-fe.h:pg_config.h:' \ - configure || die "adjusting configure for Gentoo failed" - - # prefixify the configure script - sed -i \ - -e 's:/usr:${EPREFIX}/usr:g' \ - configure || die "prefixify configure failed" - - # CSS should use local images - sed -i -e 's,http://.*/images/,,' etc/html/ROOT.css || die "html sed failed" -} - -# NB: ROOT uses bundled LLVM, because it is patched and API-incompatible with -# system LLVM. -# NB: As of 6.00.0.1 cmake is not ready as it can't fully replace configure, -# e.g. for afs and geocad. - -src_configure() { - local -a myconf - # Some compilers need special care - case $(tc-getCXX) in - *clang++*) - myconf=( - --with-clang - --with-f77="$(tc-getFC)" - ) - ;; - *icc*|*icpc*) - # For icc we need to provide architecture manually - # and not to tamper with tc-get* - use x86 && myconf=( linuxicc ) - use amd64 && myconf=( linuxx8664icc ) - ;; - *) # gcc goes here too - myconf=( - --with-cc="$(tc-getCC)" - --with-cxx="$(tc-getCXX)" - --with-f77="$(tc-getFC)" - --with-ld="$(tc-getCXX)" - ) - ;; - esac - - # the configure script is not the standard autotools - myconf+=( - --prefix="${EPREFIX}/usr" - --etcdir="${EPREFIX}/etc/root" - --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" - --docdir="${EPREFIX}${DOC_DIR}" - --tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials" - --testdir="${EPREFIX}${DOC_DIR}/examples/tests" - --disable-werror - --nohowto - ) - - if use minimal; then - myconf+=( $(usex X --gminimal --minimal) ) - else - myconf+=( - --with-afs-shared=yes - --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" - --disable-builtin-ftgl - --disable-builtin-freetype - --disable-builtin-glew - --disable-builtin-pcre - --disable-builtin-zlib - --disable-builtin-lzma - --enable-astiff - --enable-explicitlink - --enable-gdml - --enable-memstat - --enable-shadowpw - --enable-shared - --enable-soversion - --enable-table - --fail-on-missing - $(use_enable X x11) - $(use_enable X asimage) - $(use_enable X xft) - $(use_enable afs) - $(use_enable avahi bonjour) - $(use_enable fits fitsio) - $(use_enable fftw fftw3) - $(use_enable geocad) - $(use_enable graphviz gviz) - $(use_enable kerberos krb5) - $(use_enable ldap) - $(use_enable math genvector) - $(use_enable math gsl-shared) - $(use_enable math mathmore) - $(use_enable math minuit2) - $(use_enable math roofit) - $(use_enable math tmva) - $(use_enable math vc) - $(use_enable math vdt) - $(use_enable math unuran) - $(use_enable mysql) - $(usex mysql \ - "--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "") - $(use_enable odbc) - $(use_enable opengl) - $(use_enable oracle) - $(use_enable postgres pgsql) - $(usex postgres \ - "--with-pgsql-incdir=$(pg_config --includedir)" "") - $(use_enable prefix rpath) - $(use_enable pythia6) - $(use_enable pythia8) - $(use_enable python) - $(use_enable qt4 qt) - $(use_enable qt4 qtgsi) - $(use_enable sqlite) - $(use_enable ssl) - $(use_enable xml) - $(use_enable xrootd) - ${EXTRA_ECONF} - ) - fi - - ./configure ${myconf[@]} || die "configure failed" -} - -src_compile() { - emake \ - OPT="${CXXFLAGS}" \ - F77OPT="${FFLAGS}" \ - ROOTSYS="${S}" \ - LD_LIBRARY_PATH="${S}/lib" - use emacs && ! use minimal && elisp-compile build/misc/*.el -} - -daemon_install() { - local daemons="rootd proofd" - dodir /var/spool/rootd - fowners rootd:rootd /var/spool/rootd - dodir /var/spool/rootd/{pub,tmp} - fperms 1777 /var/spool/rootd/{pub,tmp} - - for i in ${daemons}; do - newinitd "${FILESDIR}"/${i}.initd ${i} - newconfd "${FILESDIR}"/${i}.confd ${i} - done - if use xinetd; then - insinto /etc/xinetd - doins "${S}"/etc/daemons/{rootd,proofd}.xinetd - fi -} - -desktop_install() { - cd "${S}" - echo "Icon=root-system-bin" >> etc/root.desktop - domenu etc/root.desktop - doicon build/package/debian/root-system-bin.png - - insinto /usr/share/icons/hicolor/48x48/mimetypes - doins build/package/debian/application-x-root.png - - insinto /usr/share/icons/hicolor/48x48/apps - doicon build/package/debian/root-system-bin.xpm -} - -cleanup_install() { - # Cleanup of files either already distributed or unused on Gentoo - pushd "${ED}" > /dev/null - rm usr/share/root/fonts/LICENSE || die - rm etc/root/proof/*.sample || die - rm -r etc/root/daemons || die - # these should be in PATH - mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die - rm ${DOC_DIR#/}/{INSTALL,LICENSE} || die - use examples || rm -r ${DOC_DIR#/}/examples || die -} - -src_install() { - emake DESTDIR="${D}" install - dodoc README.md - - echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root - - if ! use minimal; then - use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root - if use python; then - echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root - python_optimize "${D}/usr/$(get_libdir)/root" - fi - use emacs && elisp-install ${PN} build/misc/*.{el,elc} - if use examples; then - # these should really be taken care of by the root make install - insinto ${DOC_DIR}/examples/tutorials/tmva - doins -r tmva/test - fi - fi - doenvd 99root - - # The build system installs Emacs support unconditionally in the wrong - # directory. Remove it and call elisp-install in case of USE=emacs. - rm -r "${ED}"/usr/share/emacs || die - - daemon_install - desktop_install - cleanup_install - - # do not copress files used by ROOT's CLI (.credit, .demo, .license) - docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials} - # needed for .license command to work - dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE" -} - -pkg_postinst() { - fdo-mime_desktop_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update -} diff --git a/sci-physics/root/root-6.00.02.ebuild b/sci-physics/root/root-6.00.02.ebuild deleted file mode 100644 index 271117044..000000000 --- a/sci-physics/root/root-6.00.02.ebuild +++ /dev/null @@ -1,442 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $ - -EAPI=5 - -if [[ ${PV} == "9999" ]] ; then - inherit git-r3 - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - S="${WORKDIR}/${PN}" -fi - -PYTHON_COMPAT=( python2_{6,7} ) - -inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \ - toolchain-funcs user versionator - -DESCRIPTION="C++ data analysis framework and interpreter from CERN" -HOMEPAGE="http://root.cern.ch/" -DOC_URI="ftp://root.cern.ch/${PN}/doc" - -SLOT="0/$(get_version_component_range 1-3 ${PV})" -LICENSE="LGPL-2.1 freedist MSttfEULA LGPL-3 libpng UoI-NCSA" -IUSE="+X afs avahi doc emacs examples fits fftw geocad graphviz - http kerberos ldap +math minimal mpi mysql odbc +opengl openmp - oracle postgres prefix pythia6 pythia8 python qt4 sqlite ssl - xinetd xml xrootd" - -# TODO: add support for: davix -# TODO: ROOT-6 supports x32 ABI, but half of its dependencies doesn't -# TODO: unbundle: cling, vdt - -REQUIRED_USE=" - mpi? ( math !openmp ) - opengl? ( X ) - openmp? ( math !mpi ) - python? ( ${PYTHON_REQUIRED_USE} ) - qt4? ( X ) -" - -CDEPEND=" - app-arch/xz-utils:0= - >=dev-lang/cfortran-4.4-r2 - dev-libs/libpcre:3= - media-fonts/dejavu - media-libs/freetype:2= - media-libs/giflib:0= - media-libs/libpng:0= - media-libs/tiff:0= - >=sys-devel/clang-3.4 - sys-libs/zlib:0= - virtual/jpeg:0 - virtual/shadow - X? ( - media-libs/ftgl:0= - media-libs/glew:0= - x11-libs/libX11:0= - x11-libs/libXext:0= - x11-libs/libXpm:0= - !minimal? ( - opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps:0= ) - qt4? ( - dev-qt/qtgui:4= - dev-qt/qtopengl:4= - dev-qt/qt3support:4= - dev-qt/qtsvg:4= - dev-qt/qtwebkit:4= - dev-qt/qtxmlpatterns:4= - ) - x11-libs/libXft:0= - ) - ) - !minimal? ( - afs? ( net-fs/openafs ) - avahi? ( net-dns/avahi:0= ) - emacs? ( virtual/emacs ) - fits? ( sci-libs/cfitsio:0= ) - fftw? ( sci-libs/fftw:3.0= ) - geocad? ( sci-libs/opencascade:= ) - graphviz? ( media-gfx/graphviz:0= ) - http? ( dev-libs/fcgi:0= ) - kerberos? ( virtual/krb5 ) - ldap? ( net-nds/openldap:0= ) - math? ( - sci-libs/gsl:0= - sci-mathematics/unuran:0= - mpi? ( virtual/mpi ) - ) - mysql? ( virtual/mysql ) - odbc? ( || ( dev-db/libiodbc:0= dev-db/unixODBC:0= ) ) - oracle? ( dev-db/oracle-instantclient-basic:0= ) - postgres? ( dev-db/postgresql:= ) - pythia6? ( sci-physics/pythia:6= ) - pythia8? ( >=sci-physics/pythia-8.1.80:8= ) - python? ( ${PYTHON_DEPS} ) - sqlite? ( dev-db/sqlite:3= ) - ssl? ( dev-libs/openssl:0= ) - xml? ( dev-libs/libxml2:2= ) - xrootd? ( >=net-libs/xrootd-3.3.5:0= ) - )" - -# TODO: ruby is not yet ported to ROOT-6, reenable when (if?) ready -# ruby? ( -# dev-lang/ruby -# dev-ruby/rubygems -# ) -# -# TODO: root-6.00.01 crashes with system libafterimage -# || ( -# media-libs/libafterimage:0=[gif,jpeg,png,tiff] -# >=x11-wm/afterstep-2.2.11:0=[gif,jpeg,png,tiff] -# ) -# --disable-builtin-afterimage - -DEPEND="${CDEPEND} - virtual/pkgconfig" - -RDEPEND="${CDEPEND} - xinetd? ( sys-apps/xinetd )" - -PDEPEND="doc? ( ~app-doc/root-docs-${PV}[http=,math=] )" - -# install stuff in ${P} and not ${PF} for easier tracking in root-docs -DOC_DIR="/usr/share/doc/${P}" - -die_compiler() { - die "Need one of the following C++11 capable compilers:"\ - " >=sys-devel/gcc[cxx]-4.8"\ - " >=sys-devel/clang-3.4"\ - " >=dev-lang/icc-13" -} - -pkg_setup() { - fortran-2_pkg_setup - use python && python-single-r1_pkg_setup - echo - elog "There are extra options on packages not yet in Gentoo:" - elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite," - elog "HDFS, Monalisa, MaxDB/SapDB, SRP." - elog "You can use the env variable EXTRA_ECONF variable for this." - elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\"" - echo - - enewgroup rootd - enewuser rootd -1 -1 /var/spool/rootd rootd - - use minimal && return - - if use math; then - if use openmp; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "You are using a g++ without OpenMP capabilities" - die "Need an OpenMP capable compiler" - else - export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 - fi - elif use mpi; then - export USE_MPI=1 USE_PARALLEL_MINUIT2=1 - fi - fi - - # check for supported compilers - case $(tc-getCXX) in - *g++*) - if ! version_is_at_least "4.8" "$(gcc-version)"; then - eerror "You are using a g++ without C++11 capabilities" - die_compiler - fi - ;; - *clang++*) - # >=clang-3.4 is already in DEPEND - ;; - *icc*|*icpc*) - if ! version_is_at_least "13" "$(has_version dev-lang/icc)"; then - eerror "You are using an icc without C++11 capabilities" - die_compiler - fi - ;; - *) - ewarn "You are using an unsupported compiler." - ewarn "Please report any issues upstream." - ;; - esac -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-5.28.00b-glibc212.patch \ - "${FILESDIR}"/${PN}-5.32.00-afs.patch \ - "${FILESDIR}"/${PN}-5.32.00-cfitsio.patch \ - "${FILESDIR}"/${PN}-5.32.00-chklib64.patch \ - "${FILESDIR}"/${PN}-5.34.13-unuran.patch \ - "${FILESDIR}"/${PN}-5.34.13-desktop.patch \ - "${FILESDIR}"/${PN}-6.00.01-dotfont.patch \ - "${FILESDIR}"/${PN}-6.00.01-nobyte-compile.patch \ - "${FILESDIR}"/${PN}-6.00.01-prop-flags.patch \ - "${FILESDIR}"/${PN}-6.00.01-llvm.patch \ - "${FILESDIR}"/${PN}-6.00.01-geocad.patch \ - "${FILESDIR}"/${PN}-6.00.01-tutorials-path.patch \ - "${FILESDIR}"/${PN}-6.00.02-tm_zone.patch - - # make sure we use system libs and headers - rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die - #rm -r graf2d/asimage/src/libAfterImage || die - rm -r graf3d/ftgl/{inc,src} || die - rm -r graf2d/freetype/src || die - rm -r graf3d/glew/{inc,src} || die - rm -r core/pcre/src || die - rm -r math/unuran/src/unuran-*.tar.gz || die - LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | \ - xargs -0 rm || die - rm -r core/lzma/src/*.tar.gz || die - rm graf3d/gl/{inc,src}/gl2ps.* || die - sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' \ - graf3d/gl/Module.mk || die - - # In Gentoo, libPythia6 is called libpythia6 - # iodbc is in /usr/include/iodbc - # pg_config.h is checked instead of libpq-fe.h - sed -i \ - -e 's:libPythia6:libpythia6:g' \ - -e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \ - -e 's:libpq-fe.h:pg_config.h:' \ - configure || die "adjusting configure for Gentoo failed" - - # prefixify the configure script - sed -i \ - -e 's:/usr:${EPREFIX}/usr:g' \ - configure || die "prefixify configure failed" - - # CSS should use local images - sed -i -e 's,http://.*/images/,,' etc/html/ROOT.css || die "html sed failed" -} - -# NB: ROOT uses bundled LLVM, because it is patched and API-incompatible with -# system LLVM. -# NB: As of 6.00.0.1 cmake is not ready as it can't fully replace configure, -# e.g. for afs and geocad. - -src_configure() { - local -a myconf - # Some compilers need special care - case $(tc-getCXX) in - *clang++*) - myconf=( - --with-clang - --with-f77="$(tc-getFC)" - ) - ;; - *icc*|*icpc*) - # For icc we need to provide architecture manually - # and not to tamper with tc-get* - use x86 && myconf=( linuxicc ) - use amd64 && myconf=( linuxx8664icc ) - ;; - *) # gcc goes here too - myconf=( - --with-cc="$(tc-getCC)" - --with-cxx="$(tc-getCXX)" - --with-f77="$(tc-getFC)" - --with-ld="$(tc-getCXX)" - ) - ;; - esac - - # the configure script is not the standard autotools - myconf+=( - --prefix="${EPREFIX}/usr" - --etcdir="${EPREFIX}/etc/root" - --libdir="${EPREFIX}/usr/$(get_libdir)/${PN}" - --docdir="${EPREFIX}${DOC_DIR}" - --tutdir="${EPREFIX}${DOC_DIR}/examples/tutorials" - --testdir="${EPREFIX}${DOC_DIR}/examples/tests" - --disable-werror - --nohowto - ) - - if use minimal; then - myconf+=( $(usex X --gminimal --minimal) ) - else - myconf+=( - --with-afs-shared=yes - --with-sys-iconpath="${EPREFIX}/usr/share/pixmaps" - --disable-builtin-ftgl - --disable-builtin-freetype - --disable-builtin-glew - --disable-builtin-pcre - --disable-builtin-zlib - --disable-builtin-lzma - --enable-astiff - --enable-explicitlink - --enable-gdml - --enable-memstat - --enable-shadowpw - --enable-shared - --enable-soversion - --enable-table - --fail-on-missing - $(use_enable X x11) - $(use_enable X asimage) - $(use_enable X xft) - $(use_enable afs) - $(use_enable avahi bonjour) - $(use_enable fits fitsio) - $(use_enable fftw fftw3) - $(use_enable geocad) - $(use_enable graphviz gviz) - $(use_enable kerberos krb5) - $(use_enable ldap) - $(use_enable math genvector) - $(use_enable math gsl-shared) - $(use_enable math mathmore) - $(use_enable math minuit2) - $(use_enable math roofit) - $(use_enable math tmva) - $(use_enable math vc) - $(use_enable math vdt) - $(use_enable math unuran) - $(use_enable mysql) - $(usex mysql \ - "--with-mysql-incdir=${EPREFIX}/usr/include/mysql" "") - $(use_enable odbc) - $(use_enable opengl) - $(use_enable oracle) - $(use_enable postgres pgsql) - $(usex postgres \ - "--with-pgsql-incdir=$(pg_config --includedir)" "") - $(use_enable prefix rpath) - $(use_enable pythia6) - $(use_enable pythia8) - $(use_enable python) - $(use_enable qt4 qt) - $(use_enable qt4 qtgsi) - $(use_enable sqlite) - $(use_enable ssl) - $(use_enable xml) - $(use_enable xrootd) - ${EXTRA_ECONF} - ) - fi - - ./configure ${myconf[@]} || die "configure failed" -} - -src_compile() { - emake \ - OPT="${CXXFLAGS}" \ - F77OPT="${FFLAGS}" \ - ROOTSYS="${S}" \ - LD_LIBRARY_PATH="${S}/lib" - use emacs && ! use minimal && elisp-compile build/misc/*.el -} - -daemon_install() { - local daemons="rootd proofd" - dodir /var/spool/rootd - fowners rootd:rootd /var/spool/rootd - dodir /var/spool/rootd/{pub,tmp} - fperms 1777 /var/spool/rootd/{pub,tmp} - - for i in ${daemons}; do - newinitd "${FILESDIR}"/${i}.initd ${i} - newconfd "${FILESDIR}"/${i}.confd ${i} - done - if use xinetd; then - insinto /etc/xinetd - doins "${S}"/etc/daemons/{rootd,proofd}.xinetd - fi -} - -desktop_install() { - cd "${S}" - echo "Icon=root-system-bin" >> etc/root.desktop - domenu etc/root.desktop - doicon build/package/debian/root-system-bin.png - - insinto /usr/share/icons/hicolor/48x48/mimetypes - doins build/package/debian/application-x-root.png - - insinto /usr/share/icons/hicolor/48x48/apps - doicon build/package/debian/root-system-bin.xpm -} - -cleanup_install() { - # Cleanup of files either already distributed or unused on Gentoo - pushd "${ED}" > /dev/null - rm usr/share/root/fonts/LICENSE || die - rm etc/root/proof/*.sample || die - rm -r etc/root/daemons || die - # these should be in PATH - mv etc/root/proof/utils/pq2/pq2* usr/bin/ || die - rm ${DOC_DIR#/}/{INSTALL,LICENSE} || die - use examples || rm -r ${DOC_DIR#/}/examples || die -} - -src_install() { - emake DESTDIR="${D}" install - dodoc README.md - - echo "LDPATH=${EPREFIX%/}/usr/$(get_libdir)/root" > 99root - - if ! use minimal; then - use pythia8 && echo "PYTHIA8=${EPREFIX%/}/usr" >> 99root - if use python; then - echo "PYTHONPATH=${EPREFIX%/}/usr/$(get_libdir)/root" >> 99root - python_optimize "${D}/usr/$(get_libdir)/root" - fi - use emacs && elisp-install ${PN} build/misc/*.{el,elc} - if use examples; then - # these should really be taken care of by the root make install - insinto ${DOC_DIR}/examples/tutorials/tmva - doins -r tmva/test - fi - fi - doenvd 99root - - # The build system installs Emacs support unconditionally in the wrong - # directory. Remove it and call elisp-install in case of USE=emacs. - rm -r "${ED}"/usr/share/emacs || die - - daemon_install - desktop_install - cleanup_install - - # do not copress files used by ROOT's CLI (.credit, .demo, .license) - docompress -x "${DOC_DIR}"/{CREDITS,LICENSE,examples/tutorials} - # needed for .license command to work - dosym "${ED}"usr/portage/licenses/LGPL-2.1 "${DOC_DIR}/LICENSE" -} - -pkg_postinst() { - fdo-mime_desktop_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update -} diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild index ac10320ec..bd946b81a 100644 --- a/sci-physics/root/root-9999.ebuild +++ b/sci-physics/root/root-9999.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.18-r1.ebuild,v 1.3 2014/03/27 18:51:54 bicatali Exp $ +# $Header: $ EAPI=5 @@ -14,7 +14,7 @@ else S="${WORKDIR}/${PN}" fi -PYTHON_COMPAT=( python2_{6,7} ) +PYTHON_COMPAT=( python2_7 ) inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 \ toolchain-funcs user versionator diff --git a/sci-visualization/gnuplot/ChangeLog b/sci-visualization/gnuplot/ChangeLog index 224469137..70dc9bcbd 100644 --- a/sci-visualization/gnuplot/ChangeLog +++ b/sci-visualization/gnuplot/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-visualization/gnuplot -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 25 May 2015; Christoph Junghans <ottxor@gentoo.org> -gnuplot-4.6.9999.ebuild, + metadata.xml: + remove old + + 25 May 2015; Christoph Junghans <ottxor@gentoo.org> gnuplot-5.0.9999.ebuild, + gnuplot-5.1.9999.ebuild, metadata.xml: + added compat use flag (bug #550370) + *gnuplot-5.1.9999 (08 Nov 2014) 08 Nov 2014; Christoph Junghans <ottxor@gentoo.org> +gnuplot-5.1.9999.ebuild, diff --git a/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild b/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild deleted file mode 100644 index 9330bbacd..000000000 --- a/sci-visualization/gnuplot/gnuplot-4.6.9999.ebuild +++ /dev/null @@ -1,194 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils flag-o-matic multilib readme.gentoo toolchain-funcs wxwidgets - -DESCRIPTION="Command-line driven interactive plotting program" -HOMEPAGE="http://www.gnuplot.info/" - -if [[ -z ${PV%%*9999} ]]; then - inherit autotools cvs - ECVS_SERVER="gnuplot.cvs.sourceforge.net:/cvsroot/gnuplot" - ECVS_MODULE="gnuplot" - ECVS_BRANCH="branch-4-6-stable" - ECVS_USER="anonymous" - ECVS_CVS_OPTIONS="-dP" - MY_P="${PN}" - SRC_URI="" -else - MY_P="${P/_/.}" - SRC_URI="mirror://sourceforge/gnuplot/${MY_P}.tar.gz - mirror://gentoo/${PN}.info-4.6.2.tar.xz" -fi - -LICENSE="gnuplot bitmap? ( free-noncomm )" -SLOT="0" -KEYWORDS="" -IUSE="aqua bitmap cairo doc examples +gd ggi latex lua plotutils qt4 readline svga thin-splines wxwidgets X" - -RDEPEND=" - cairo? ( - x11-libs/cairo - x11-libs/pango ) - gd? ( >=media-libs/gd-2.0.35-r3[png] ) - ggi? ( media-libs/libggi ) - latex? ( - virtual/latex-base - lua? ( - dev-tex/pgf - >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) - lua? ( dev-lang/lua ) - plotutils? ( media-libs/plotutils ) - qt4? ( >=dev-qt/qtcore-4.5:4 - >=dev-qt/qtgui-4.5:4 - >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) - svga? ( media-libs/svgalib ) - wxwidgets? ( - x11-libs/wxGTK:2.8[X] - x11-libs/cairo - x11-libs/pango - x11-libs/gtk+:2 ) - X? ( x11-libs/libXaw )" -DEPEND="${RDEPEND} - virtual/pkgconfig - doc? ( - virtual/latex-base - dev-texlive/texlive-latexextra - app-text/ghostscript-gpl )" - -S="${WORKDIR}/${MY_P}" - -GP_VERSION="${PV%.*}" -E_SITEFILE="lisp/50${PN}-gentoo.el" -TEXMF="${EPREFIX}/usr/share/texmf-site" - -src_prepare() { - if [[ -n ${PV%%*9999} ]]; then - epatch "${FILESDIR}/${PN}-4.6.1-eldoc.patch" - epatch "${FILESDIR}/${PN}-4.6.2-gdversion.patch" #462996 - else - local dir - for dir in config demo m4 term tutorial; do - emake -C "$dir" -f Makefile.am.in Makefile.am - done - eautoreconf - fi - - # Add special version identification as required by provision 2 - # of the gnuplot license - sed -i -e "1s/.*/& (Gentoo revision ${PR})/" PATCHLEVEL || die - - # hacky workaround - # Please hack the buildsystem if you like - if use prefix && use qt4; then - append-ldflags -Wl,-rpath,"${EPREFIX}"/usr/$(get_libdir)/qt4 - fi - - DOC_CONTENTS='Gnuplot no longer links against pdflib, see the ChangeLog - for details. You can use the "pdfcairo" terminal for PDF output.' - use cairo || DOC_CONTENTS+=' It is available with USE="cairo".' - use svga && DOC_CONTENTS+='\n\nIn order to enable ordinary users to use - SVGA console graphics, gnuplot needs to be set up as setuid root. - Please note that this is usually considered to be a security hazard. - As root, manually "chmod u+s /usr/bin/gnuplot".' - use gd && DOC_CONTENTS+='\n\nFor font support in png/jpeg/gif output, - you may have to set the GDFONTPATH and GNUPLOT_DEFAULT_GDFONT - environment variables. See the FAQ file in /usr/share/doc/${PF}/ - for more information.' -} - -src_configure() { - if ! use latex; then - sed -i -e '/SUBDIRS/s/LaTeX//' share/Makefile.in || die - fi - - if use wxwidgets; then - WX_GTK_VER="2.8" - need-wxwidgets unicode - fi - - tc-export CC CXX #453174 - - econf \ - --without-pdf \ - --with-texdir="${TEXMF}/tex/latex/${PN}" \ - --with-readline=$(usex readline gnu builtin) \ - --without-lisp-files \ - $(use_with bitmap bitmap-terminals) \ - $(use_with cairo) \ - $(use_with doc tutorial) \ - $(use_with gd) \ - "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ - "$(use_with ggi xmi "${EPREFIX}/usr/$(get_libdir)")" \ - $(use_with lua) \ - "$(use_with plotutils plot "${EPREFIX}/usr/$(get_libdir)")" \ - $(use_with svga linux-vga) \ - $(use_with X x) \ - --enable-stats \ - $(use_enable qt4 qt) \ - $(use_enable thin-splines) \ - $(use_enable wxwidgets) \ - DIST_CONTACT="http://bugs.gentoo.org/" \ - EMACS=no -} - -src_compile() { - # Prevent access violations, see bug 201871 - VARTEXFONTS="${T}/fonts" - - # We believe that the following line is no longer needed. - # In case of problems file a bug report at bugs.gentoo.org. - #addwrite /dev/svga:/dev/mouse:/dev/tts/0 - - emake all - - if use doc; then - # Avoid sandbox violation in epstopdf/ghostscript - addpredict /var/cache/fontconfig - emake -C docs pdf - emake -C tutorial pdf - fi -} - -src_install () { - emake DESTDIR="${D}" install - - dodoc BUGS ChangeLog NEWS PGPKEYS PORTING README* - newdoc term/PostScript/README README-ps - newdoc term/js/README README-js - use lua && newdoc term/lua/README README-lua - readme.gentoo_create_doc - - if use examples; then - # Demo files - insinto /usr/share/${PN}/${GP_VERSION} - doins -r demo - rm -f "${ED}"/usr/share/${PN}/${GP_VERSION}/demo/Makefile* - rm -f "${ED}"/usr/share/${PN}/${GP_VERSION}/demo/binary* - fi - - if use doc; then - # Manual, tutorial, FAQ - dodoc docs/gnuplot.pdf tutorial/{tutorial.dvi,tutorial.pdf} FAQ.pdf - # Documentation for making PostScript files - docinto psdoc - dodoc docs/psdoc/{*.doc,*.tex,*.ps,*.gpi,README} - fi -} - -src_test() { - GNUTERM="unknown" default_src_test -} - -pkg_postinst() { - use latex && texmf-update - readme.gentoo_print_elog -} - -pkg_postrm() { - use latex && texmf-update -} diff --git a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild index ba3a990ef..fbc18cfe7 100644 --- a/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-5.0.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -22,13 +22,13 @@ if [[ -z ${PV%%*9999} ]]; then else MY_P="${P/_/.}" SRC_URI="mirror://sourceforge/gnuplot/${MY_P}.tar.gz" - KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" + KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~s390 ~sparc ~x86 ~ppc-aix ~x86-fbsd ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~x64-solaris ~x86-solaris" inherit autotools fi LICENSE="gnuplot bitmap? ( free-noncomm )" SLOT="0" -IUSE="aqua bitmap cairo doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" +IUSE="aqua bitmap cairo compat doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" RDEPEND=" cairo? ( @@ -42,11 +42,11 @@ RDEPEND=" dev-tex/pgf >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) libcaca? ( media-libs/libcaca ) - lua? ( dev-lang/lua ) + lua? ( dev-lang/lua:0 ) qt4? ( >=dev-qt/qtcore-4.5:4 >=dev-qt/qtgui-4.5:4 >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) + readline? ( sys-libs/readline:0 ) libcerf? ( sci-libs/libcerf ) svga? ( media-libs/svgalib ) wxwidgets? ( @@ -75,9 +75,6 @@ src_prepare() { emake -C "$dir" -f Makefile.am.in Makefile.am done eautoreconf - else - epatch "${FILESDIR}/${PN}-5.0_rc1-libcerf.patch" - eautoreconf fi # Add special version identification as required by provision 2 @@ -121,6 +118,7 @@ src_configure() { --with-readline=$(usex readline gnu builtin) \ $(use_with bitmap bitmap-terminals) \ $(use_with cairo) \ + $(use_enable compat backwards-compatibility) \ $(use_with doc tutorial) \ $(use_with gd) \ "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ diff --git a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild index 05eabe319..f8f88c274 100644 --- a/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-5.1.9999.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2014 Gentoo Foundation +# Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -28,7 +28,7 @@ fi LICENSE="gnuplot bitmap? ( free-noncomm )" SLOT="0" -IUSE="aqua bitmap cairo doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" +IUSE="aqua bitmap cairo compat doc examples +gd ggi latex libcaca libcerf lua qt4 readline svga wxwidgets X" RDEPEND=" cairo? ( @@ -42,11 +42,11 @@ RDEPEND=" dev-tex/pgf >=dev-texlive/texlive-latexrecommended-2008-r2 ) ) libcaca? ( media-libs/libcaca ) - lua? ( dev-lang/lua ) + lua? ( dev-lang/lua:0 ) qt4? ( >=dev-qt/qtcore-4.5:4 >=dev-qt/qtgui-4.5:4 >=dev-qt/qtsvg-4.5:4 ) - readline? ( sys-libs/readline ) + readline? ( sys-libs/readline:0 ) libcerf? ( sci-libs/libcerf ) svga? ( media-libs/svgalib ) wxwidgets? ( @@ -121,6 +121,7 @@ src_configure() { --with-readline=$(usex readline gnu builtin) \ $(use_with bitmap bitmap-terminals) \ $(use_with cairo) \ + $(use_enable compat backwards-compatibility) \ $(use_with doc tutorial) \ $(use_with gd) \ "$(use_with ggi ggi "${EPREFIX}/usr/$(get_libdir)")" \ diff --git a/sci-visualization/gnuplot/metadata.xml b/sci-visualization/gnuplot/metadata.xml index 1a66c9402..cccec8e78 100644 --- a/sci-visualization/gnuplot/metadata.xml +++ b/sci-visualization/gnuplot/metadata.xml @@ -16,11 +16,11 @@ three-dimensional plots in many different formats. It is designed primarily for the visual display of scientific data. </longdescription> - <use> +<use> + <flag name="compat">Enable backwards compatibility with version 4 syntax</flag> <flag name="gd">Add support for <pkg>media-libs/gd</pkg>. Needed for GIF, JPEG, and PNG image output.</flag> <flag name="libcerf">Enable special functions from <pkg>sci-libs/libcerf</pkg></flag> - <flag name="thin-splines">Enable thin plate splines</flag> <flag name="bitmap">Enable dot-matrix printers and pbm terminal</flag> </use> <upstream> diff --git a/sci-visualization/labplot/ChangeLog b/sci-visualization/labplot/ChangeLog deleted file mode 100644 index e046a74a8..000000000 --- a/sci-visualization/labplot/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-visualization/labplot -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 06 Jan 2014; Justin Lecher <jlec@gentoo.org> labplot-9999.ebuild, - metadata.xml: - Bump EAPI - diff --git a/sci-visualization/labplot/files/labplot-9999-liborigin2.patch b/sci-visualization/labplot/files/labplot-9999-liborigin2.patch deleted file mode 100644 index 1af610b65..000000000 --- a/sci-visualization/labplot/files/labplot-9999-liborigin2.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ruN labplot.orig/CMakeLists.txt labplot/CMakeLists.txt ---- labplot.orig/CMakeLists.txt 2012-01-21 15:09:43.792562578 +0100 -+++ labplot/CMakeLists.txt 2012-01-21 15:13:07.421573963 +0100 -@@ -105,7 +105,7 @@ - - ### OPJ ##################################### - FIND_LIBRARY(OPJ_LIBRARY -- NAMES origin -+ NAMES origin origin2 - ) - IF(OPJ_LIBRARY) - MESSAGE ("-- Found liborigin library: ${OPJ_LIBRARY}") diff --git a/sci-visualization/labplot/labplot-9999.ebuild b/sci-visualization/labplot/labplot-9999.ebuild deleted file mode 100644 index fbf5b0f11..000000000 --- a/sci-visualization/labplot/labplot-9999.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit subversion kde4-base - -MY_PN=LabPlot -MY_P=${MY_PN}-${PV} - -DESCRIPTION="KDE data analysis and visualisation program" -HOMEPAGE="http://labplot.sourceforge.net/" - -# SRC_URI="http://prdownloads.sourceforge.net/${PN}/${MY_P}.tar.gz" -ESVN_REPO_URI="https://labplot.svn.sourceforge.net/svnroot/labplot/2.0/" - -LICENSE="GPL-2" -SLOT="4" -KEYWORDS="" -IUSE="" - -DEPEND=" - sci-libs/cdf - sci-libs/gsl - sci-libs/hdf5 - sci-libs/liborigin - sci-libs/netcdf -" -RDEPEND="$DEPEND" - -S=${WORKDIR}/${PN} - -PATCHES=( "${FILESDIR}/${P}-liborigin2.patch" ) - -# this is partly hardwired in the build system :( -CMAKE_BUILD_DIR=${S}/build diff --git a/sci-visualization/mantid/ChangeLog b/sci-visualization/mantid/ChangeLog index 642a8f282..dc58dbba4 100644 --- a/sci-visualization/mantid/ChangeLog +++ b/sci-visualization/mantid/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 08 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-visualization/mantid: Updating remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mantid-3.3.0.ebuild, metadata.xml: sci-visualization/mantid: fix SLOT operators; fix whitespaces diff --git a/sci-visualization/mantid/metadata.xml b/sci-visualization/mantid/metadata.xml index 52e887f3c..6a018c74f 100644 --- a/sci-visualization/mantid/metadata.xml +++ b/sci-visualization/mantid/metadata.xml @@ -20,4 +20,7 @@ <flag name="paraview">Enable the Visualisation and Analysis Toolkit ExtensionS (VATES)</flag> <flag name="tcmalloc">Use thread-caching malloc</flag> </use> + <upstream> + <remote-id type="sourceforge">mantid</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/mayavi/ChangeLog b/sci-visualization/mayavi/ChangeLog index f0c228bda..588ac41ad 100644 --- a/sci-visualization/mayavi/ChangeLog +++ b/sci-visualization/mayavi/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: Exp $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sci-visualization/mayavi: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> mayavi-4.4.0.ebuild, metadata.xml: sci-visualization/mayavi: fix SLOT operators diff --git a/sci-visualization/mayavi/mayavi-4.4.0.ebuild b/sci-visualization/mayavi/mayavi-4.4.0.ebuild index 2b00d1a39..c144a8dda 100644 --- a/sci-visualization/mayavi/mayavi-4.4.0.ebuild +++ b/sci-visualization/mayavi/mayavi-4.4.0.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: Exp $ +# $Header: $ EAPI=5 diff --git a/sci-visualization/mayavi/metadata.xml b/sci-visualization/mayavi/metadata.xml index a76fa19f9..023851c52 100644 --- a/sci-visualization/mayavi/metadata.xml +++ b/sci-visualization/mayavi/metadata.xml @@ -21,4 +21,7 @@ used as an Envisage plug-in which allows it to be embedded in other Envisage based applications natively. </longdescription> + <upstream> + <remote-id type="github">enthought/mayavi</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/visit/Manifest b/sci-visualization/visit/Manifest deleted file mode 100644 index 04355989e..000000000 --- a/sci-visualization/visit/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST visit2.7.1.tar.gz 82430276 SHA256 3d538a92b75c9166eee8f48a9e0c9f76c27f9bec63ecd2d2e4761f0a9451e369 SHA512 1ac151722275dab57ebf6825268e6cdcec5638e9ba4a7fa34eb50007510f7de08da8da5986943b8fc317882cdb7fb07fd363c6e6677ef4d9d82a7f08ee625407 WHIRLPOOL 0187fb7653f4b440bd9f09a8e90ad06a46af39a70430787689ff0a8bda9f83a6fc62b34b8b49ab3eb660e9e66803ed7c7f98814dd2ad7f91ebdbfb0851a78b88 -DIST visit2.7.2.tar.gz 82434931 SHA256 e5d1e3faee7bb2eaa67669354bd261658cbdfa86745df78f664abb05cbd0bcf2 SHA512 4a4c32d5104a5f076836fae1d135b04d82e87595a95348c723d9ac534fe095fe58bd6a95086a0fe04a974f46fdae0a2931828de2c60b8b06652c539140f7300d WHIRLPOOL 74c6c92c296a8731b957d80021e59636a9845bcfb8db471064217f0ede3bfc85f12d6286fbd62e8dddb98093793f9311b98ff118f3ab0d20c3cc9256c9c4156f -DIST visit2.7.3.tar.gz 82475238 SHA256 e4ed7b20c4c0fb5aac49181f8ddeae3d2d5a73b1662756ddcaa9d08776a7c39f SHA512 5eea2667482a9b70cf4794446da69595c1145839dfae0afdf961589a09b0f3ad41c44b607f96dbb3e4a3c1ba77161d77a1e0342d6a4e2df8bc73040110c7e8f1 WHIRLPOOL a1157d2424d93037e1ffd8dd10ebc47ae9f3d074a63a811bcadf6db5349dea348432e63d414d4a62a156c9423a1d5fdb240f34b2ec4262e8647def40d999759a diff --git a/sci-visualization/visit/files/visit-2.7.1-dont_symlink_visit_dir.patch b/sci-visualization/visit/files/visit-2.7.1-dont_symlink_visit_dir.patch deleted file mode 100644 index 0953e5b9e..000000000 --- a/sci-visualization/visit/files/visit-2.7.1-dont_symlink_visit_dir.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff -ru visit2.7.1.old2/src/CMakeLists.txt visit2.7.1/src/CMakeLists.txt ---- visit2.7.1.old2/src/CMakeLists.txt 2014-01-27 22:10:06.520297262 +0100 -+++ visit2.7.1/src/CMakeLists.txt 2014-01-27 22:11:30.520298002 +0100 -@@ -807,14 +807,6 @@ - \"${VISIT_VERSION}\" - \"${CMAKE_INSTALL_PREFIX}/beta\") - ") -- ELSE(VISIT_INSTALL_AS_BETA) -- INSTALL(CODE " -- MESSAGE(\"Symlinking current to ${VISIT_VERSION}\") -- EXECUTE_PROCESS(WORKING_DIRECTORY \${CMAKE_INSTALL_PREFIX} -- COMMAND \${CMAKE_COMMAND} -E create_symlink -- \"${VISIT_VERSION}\" -- \"${CMAKE_INSTALL_PREFIX}/current\") -- ") - ENDIF(VISIT_INSTALL_AS_BETA) - ENDIF(WIN32) - MARK_AS_ADVANCED( diff --git a/sci-visualization/visit/files/visit-2.7.1-findpython.patch b/sci-visualization/visit/files/visit-2.7.1-findpython.patch deleted file mode 100644 index 180ffbf37..000000000 --- a/sci-visualization/visit/files/visit-2.7.1-findpython.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItPython.cmake visit2.7.1.new/src/CMake/FindVisItPython.cmake ---- visit2.7.1.old/src/CMake/FindVisItPython.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItPython.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -141,11 +141,12 @@ - FIND_LIBRARY(PYTHON_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION} - PATHS -- ${PYTHON_DIR}/lib -- ${PYTHON_DIR}/libs -- [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs -+ ${PYTHON_DIR}/lib -+ ${PYTHON_DIR}/lib64 -+ ${PYTHON_DIR}/libs -+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs - NO_DEFAULT_PATH - NO_CMAKE_ENVIRONMENT_PATH - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - diff --git a/sci-visualization/visit/files/visit-2.7.1-findsilo.patch b/sci-visualization/visit/files/visit-2.7.1-findsilo.patch deleted file mode 100644 index 04d73c37f..000000000 --- a/sci-visualization/visit/files/visit-2.7.1-findsilo.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru visit2.7.1-old/src/CMake/FindSilo.cmake visit2.7.1-new/src/CMake/FindSilo.cmake ---- visit2.7.1-old/src/CMake/FindSilo.cmake 2013-11-20 20:30:44.000000000 +0100 -+++ visit2.7.1-new/src/CMake/FindSilo.cmake 2014-02-01 02:22:29.410541850 +0100 -@@ -90,7 +90,7 @@ - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - IF(SILOH5_LIBRARY_EXISTS) -- SET_UP_THIRD_PARTY(SILO lib include siloh5) -+ SET_UP_THIRD_PARTY(SILO lib include siloh5 hdf5 z) - ELSE(SILOH5_LIBRARY_EXISTS) - SET_UP_THIRD_PARTY(SILO lib include silo) - ENDIF(SILOH5_LIBRARY_EXISTS) diff --git a/sci-visualization/visit/files/visit-2.7.1-findvtk.patch b/sci-visualization/visit/files/visit-2.7.1-findvtk.patch deleted file mode 100644 index c241e139e..000000000 --- a/sci-visualization/visit/files/visit-2.7.1-findvtk.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItVTK.cmake visit2.7.1.new/src/CMake/FindVisItVTK.cmake ---- visit2.7.1.old/src/CMake/FindVisItVTK.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItVTK.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -234,11 +234,17 @@ - - # check for python wrappers - IF (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VTK_LIBRARY_DIRS}/python*/) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VTK_LIBRARY_DIRS}/python*/) - ELSE (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VISIT_VTK_DIR}/lib) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VISIT_VTK_DIR}/lib) - ENDIF (NOT WIN32) --MESSAGE(STATUS " VTK_PY_WRAPPERS_DIR=${VTK_PY_WRAPPERS_DIR}") -+MESSAGE(STATUS " VTK_PY_WRAPPERS_DIRECTORIES=${VTK_PY_WRAPPERS_DIRECTORIES}") -+ -+FOREACH(X ${VTK_PY_WRAPPERS_DIRECTORIES}) -+ IF(EXISTS "${X}/site-packages/vtk") -+ SET(VTK_PY_WRAPPERS_DIR "${X}") -+ ENDIF() -+ENDFOREACH(X) - - IF(EXISTS ${VTK_PY_WRAPPERS_DIR}/site-packages/vtk) - MESSAGE(STATUS "Found VTK Python Wrappers - ${VTK_PY_WRAPPERS_DIR}") diff --git a/sci-visualization/visit/files/visit-2.7.1-vtklibs.patch b/sci-visualization/visit/files/visit-2.7.1-vtklibs.patch deleted file mode 100644 index 9f2416dba..000000000 --- a/sci-visualization/visit/files/visit-2.7.1-vtklibs.patch +++ /dev/null @@ -1,142 +0,0 @@ -diff -ru visit2.7.1.old/src/engine/main/CMakeLists.txt visit2.7.1.new/src/engine/main/CMakeLists.txt ---- visit2.7.1.old/src/engine/main/CMakeLists.txt 2013-09-13 21:13:13.000000000 +0200 -+++ visit2.7.1.new/src/engine/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -184,8 +184,8 @@ - ${engine_ser_exe_EPlot_ser} - engine_ser - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -@@ -268,8 +268,8 @@ - ${engine_par_exe_EPlot_par} - engine_par - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/mdserver/main/CMakeLists.txt visit2.7.1.new/src/mdserver/main/CMakeLists.txt ---- visit2.7.1.old/src/mdserver/main/CMakeLists.txt 2013-09-13 21:07:04.000000000 +0200 -+++ visit2.7.1.new/src/mdserver/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -118,10 +118,10 @@ - visit_verdict - vtkCommonCore - vtkIOCore -- vtktiff -+ tiff - ${VTKZLIB_LIB} -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${ZLIB_LIB} - ${CMAKE_THREAD_LIBS} - ${DL_LIB} -diff -ru visit2.7.1.old/src/svn_bin/static_simV2.py visit2.7.1.new/src/svn_bin/static_simV2.py ---- visit2.7.1.old/src/svn_bin/static_simV2.py 2013-09-13 21:12:52.000000000 +0200 -+++ visit2.7.1.new/src/svn_bin/static_simV2.py 2014-01-25 20:30:06.948654123 +0100 -@@ -176,7 +176,7 @@ - # - # Print the link lines that we'd have to use to get the -l's - # --vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -lvtkjpeg -lvtktiff -lvtkpng -lvtkexpat -lvtklibxml2 -lvtkzlib " -+vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -ljpeg -ltiff -lpng -lexpat -lvtklibxml2 -lz " - frameworks = "-lGL " - if sys.platform == "darwin": - frameworks = "-framework OpenGL -framework AGL -framework SystemConfiguration -framework IOKit -framework Cocoa " -diff -ru visit2.7.1.old/src/tools/convert/CMakeLists.txt visit2.7.1.new/src/tools/convert/CMakeLists.txt ---- visit2.7.1.old/src/tools/convert/CMakeLists.txt 2013-10-09 22:15:21.000000000 +0200 -+++ visit2.7.1.new/src/tools/convert/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,8 +104,8 @@ - ) - - SET(VTK_EXTRA_LIBS --vtkjpeg --vtkpng -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/dataserver/CMakeLists.txt visit2.7.1.new/src/tools/dataserver/CMakeLists.txt ---- visit2.7.1.old/src/tools/dataserver/CMakeLists.txt 2013-09-13 21:08:25.000000000 +0200 -+++ visit2.7.1.new/src/tools/dataserver/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -69,9 +69,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt ---- visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt 2013-09-13 21:08:15.000000000 +0200 -+++ visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,9 +104,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/protocol/CMakeLists.txt visit2.7.1.new/src/tools/protocol/CMakeLists.txt ---- visit2.7.1.old/src/tools/protocol/CMakeLists.txt 2013-09-13 21:08:16.000000000 +0200 -+++ visit2.7.1.new/src/tools/protocol/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -75,9 +75,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/viewer/main/CMakeLists.txt visit2.7.1.new/src/viewer/main/CMakeLists.txt ---- visit2.7.1.old/src/viewer/main/CMakeLists.txt 2013-09-13 21:08:36.000000000 +0200 -+++ visit2.7.1.new/src/viewer/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -272,8 +272,8 @@ - ${viewer_exe_IPlot} - ${viewer_exe_VPlot} - viewer -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt ---- visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt 2013-09-13 21:07:03.000000000 +0200 -+++ visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -122,7 +122,7 @@ - LINK_DIRECTORIES(${LIBRARY_OUTPUT_DIRECTORY} ${VTK_LIBRARY_DIRS}) - - ADD_LIBRARY(visit_vtk ${VISIT_VTK_SOURCES}) --TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle vtktiff) -+TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle tiff) - # Add vtk definitions - ADD_TARGET_DEFINITIONS(visit_vtk "${VTK_DEFINITIONS}") - diff --git a/sci-visualization/visit/files/visit-2.7.2-dont_symlink_visit_dir.patch b/sci-visualization/visit/files/visit-2.7.2-dont_symlink_visit_dir.patch deleted file mode 100644 index 0953e5b9e..000000000 --- a/sci-visualization/visit/files/visit-2.7.2-dont_symlink_visit_dir.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff -ru visit2.7.1.old2/src/CMakeLists.txt visit2.7.1/src/CMakeLists.txt ---- visit2.7.1.old2/src/CMakeLists.txt 2014-01-27 22:10:06.520297262 +0100 -+++ visit2.7.1/src/CMakeLists.txt 2014-01-27 22:11:30.520298002 +0100 -@@ -807,14 +807,6 @@ - \"${VISIT_VERSION}\" - \"${CMAKE_INSTALL_PREFIX}/beta\") - ") -- ELSE(VISIT_INSTALL_AS_BETA) -- INSTALL(CODE " -- MESSAGE(\"Symlinking current to ${VISIT_VERSION}\") -- EXECUTE_PROCESS(WORKING_DIRECTORY \${CMAKE_INSTALL_PREFIX} -- COMMAND \${CMAKE_COMMAND} -E create_symlink -- \"${VISIT_VERSION}\" -- \"${CMAKE_INSTALL_PREFIX}/current\") -- ") - ENDIF(VISIT_INSTALL_AS_BETA) - ENDIF(WIN32) - MARK_AS_ADVANCED( diff --git a/sci-visualization/visit/files/visit-2.7.2-findpython.patch b/sci-visualization/visit/files/visit-2.7.2-findpython.patch deleted file mode 100644 index 180ffbf37..000000000 --- a/sci-visualization/visit/files/visit-2.7.2-findpython.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItPython.cmake visit2.7.1.new/src/CMake/FindVisItPython.cmake ---- visit2.7.1.old/src/CMake/FindVisItPython.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItPython.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -141,11 +141,12 @@ - FIND_LIBRARY(PYTHON_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION} - PATHS -- ${PYTHON_DIR}/lib -- ${PYTHON_DIR}/libs -- [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs -+ ${PYTHON_DIR}/lib -+ ${PYTHON_DIR}/lib64 -+ ${PYTHON_DIR}/libs -+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs - NO_DEFAULT_PATH - NO_CMAKE_ENVIRONMENT_PATH - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - diff --git a/sci-visualization/visit/files/visit-2.7.2-findsilo.patch b/sci-visualization/visit/files/visit-2.7.2-findsilo.patch deleted file mode 100644 index 04d73c37f..000000000 --- a/sci-visualization/visit/files/visit-2.7.2-findsilo.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru visit2.7.1-old/src/CMake/FindSilo.cmake visit2.7.1-new/src/CMake/FindSilo.cmake ---- visit2.7.1-old/src/CMake/FindSilo.cmake 2013-11-20 20:30:44.000000000 +0100 -+++ visit2.7.1-new/src/CMake/FindSilo.cmake 2014-02-01 02:22:29.410541850 +0100 -@@ -90,7 +90,7 @@ - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - IF(SILOH5_LIBRARY_EXISTS) -- SET_UP_THIRD_PARTY(SILO lib include siloh5) -+ SET_UP_THIRD_PARTY(SILO lib include siloh5 hdf5 z) - ELSE(SILOH5_LIBRARY_EXISTS) - SET_UP_THIRD_PARTY(SILO lib include silo) - ENDIF(SILOH5_LIBRARY_EXISTS) diff --git a/sci-visualization/visit/files/visit-2.7.2-findvtk.patch b/sci-visualization/visit/files/visit-2.7.2-findvtk.patch deleted file mode 100644 index c241e139e..000000000 --- a/sci-visualization/visit/files/visit-2.7.2-findvtk.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItVTK.cmake visit2.7.1.new/src/CMake/FindVisItVTK.cmake ---- visit2.7.1.old/src/CMake/FindVisItVTK.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItVTK.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -234,11 +234,17 @@ - - # check for python wrappers - IF (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VTK_LIBRARY_DIRS}/python*/) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VTK_LIBRARY_DIRS}/python*/) - ELSE (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VISIT_VTK_DIR}/lib) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VISIT_VTK_DIR}/lib) - ENDIF (NOT WIN32) --MESSAGE(STATUS " VTK_PY_WRAPPERS_DIR=${VTK_PY_WRAPPERS_DIR}") -+MESSAGE(STATUS " VTK_PY_WRAPPERS_DIRECTORIES=${VTK_PY_WRAPPERS_DIRECTORIES}") -+ -+FOREACH(X ${VTK_PY_WRAPPERS_DIRECTORIES}) -+ IF(EXISTS "${X}/site-packages/vtk") -+ SET(VTK_PY_WRAPPERS_DIR "${X}") -+ ENDIF() -+ENDFOREACH(X) - - IF(EXISTS ${VTK_PY_WRAPPERS_DIR}/site-packages/vtk) - MESSAGE(STATUS "Found VTK Python Wrappers - ${VTK_PY_WRAPPERS_DIR}") diff --git a/sci-visualization/visit/files/visit-2.7.2-vtklibs.patch b/sci-visualization/visit/files/visit-2.7.2-vtklibs.patch deleted file mode 100644 index 9f2416dba..000000000 --- a/sci-visualization/visit/files/visit-2.7.2-vtklibs.patch +++ /dev/null @@ -1,142 +0,0 @@ -diff -ru visit2.7.1.old/src/engine/main/CMakeLists.txt visit2.7.1.new/src/engine/main/CMakeLists.txt ---- visit2.7.1.old/src/engine/main/CMakeLists.txt 2013-09-13 21:13:13.000000000 +0200 -+++ visit2.7.1.new/src/engine/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -184,8 +184,8 @@ - ${engine_ser_exe_EPlot_ser} - engine_ser - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -@@ -268,8 +268,8 @@ - ${engine_par_exe_EPlot_par} - engine_par - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/mdserver/main/CMakeLists.txt visit2.7.1.new/src/mdserver/main/CMakeLists.txt ---- visit2.7.1.old/src/mdserver/main/CMakeLists.txt 2013-09-13 21:07:04.000000000 +0200 -+++ visit2.7.1.new/src/mdserver/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -118,10 +118,10 @@ - visit_verdict - vtkCommonCore - vtkIOCore -- vtktiff -+ tiff - ${VTKZLIB_LIB} -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${ZLIB_LIB} - ${CMAKE_THREAD_LIBS} - ${DL_LIB} -diff -ru visit2.7.1.old/src/svn_bin/static_simV2.py visit2.7.1.new/src/svn_bin/static_simV2.py ---- visit2.7.1.old/src/svn_bin/static_simV2.py 2013-09-13 21:12:52.000000000 +0200 -+++ visit2.7.1.new/src/svn_bin/static_simV2.py 2014-01-25 20:30:06.948654123 +0100 -@@ -176,7 +176,7 @@ - # - # Print the link lines that we'd have to use to get the -l's - # --vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -lvtkjpeg -lvtktiff -lvtkpng -lvtkexpat -lvtklibxml2 -lvtkzlib " -+vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -ljpeg -ltiff -lpng -lexpat -lvtklibxml2 -lz " - frameworks = "-lGL " - if sys.platform == "darwin": - frameworks = "-framework OpenGL -framework AGL -framework SystemConfiguration -framework IOKit -framework Cocoa " -diff -ru visit2.7.1.old/src/tools/convert/CMakeLists.txt visit2.7.1.new/src/tools/convert/CMakeLists.txt ---- visit2.7.1.old/src/tools/convert/CMakeLists.txt 2013-10-09 22:15:21.000000000 +0200 -+++ visit2.7.1.new/src/tools/convert/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,8 +104,8 @@ - ) - - SET(VTK_EXTRA_LIBS --vtkjpeg --vtkpng -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/dataserver/CMakeLists.txt visit2.7.1.new/src/tools/dataserver/CMakeLists.txt ---- visit2.7.1.old/src/tools/dataserver/CMakeLists.txt 2013-09-13 21:08:25.000000000 +0200 -+++ visit2.7.1.new/src/tools/dataserver/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -69,9 +69,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt ---- visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt 2013-09-13 21:08:15.000000000 +0200 -+++ visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,9 +104,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/protocol/CMakeLists.txt visit2.7.1.new/src/tools/protocol/CMakeLists.txt ---- visit2.7.1.old/src/tools/protocol/CMakeLists.txt 2013-09-13 21:08:16.000000000 +0200 -+++ visit2.7.1.new/src/tools/protocol/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -75,9 +75,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/viewer/main/CMakeLists.txt visit2.7.1.new/src/viewer/main/CMakeLists.txt ---- visit2.7.1.old/src/viewer/main/CMakeLists.txt 2013-09-13 21:08:36.000000000 +0200 -+++ visit2.7.1.new/src/viewer/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -272,8 +272,8 @@ - ${viewer_exe_IPlot} - ${viewer_exe_VPlot} - viewer -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt ---- visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt 2013-09-13 21:07:03.000000000 +0200 -+++ visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -122,7 +122,7 @@ - LINK_DIRECTORIES(${LIBRARY_OUTPUT_DIRECTORY} ${VTK_LIBRARY_DIRS}) - - ADD_LIBRARY(visit_vtk ${VISIT_VTK_SOURCES}) --TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle vtktiff) -+TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle tiff) - # Add vtk definitions - ADD_TARGET_DEFINITIONS(visit_vtk "${VTK_DEFINITIONS}") - diff --git a/sci-visualization/visit/files/visit-2.7.3-dont_symlink_visit_dir.patch b/sci-visualization/visit/files/visit-2.7.3-dont_symlink_visit_dir.patch deleted file mode 100644 index 0953e5b9e..000000000 --- a/sci-visualization/visit/files/visit-2.7.3-dont_symlink_visit_dir.patch +++ /dev/null @@ -1,18 +0,0 @@ -diff -ru visit2.7.1.old2/src/CMakeLists.txt visit2.7.1/src/CMakeLists.txt ---- visit2.7.1.old2/src/CMakeLists.txt 2014-01-27 22:10:06.520297262 +0100 -+++ visit2.7.1/src/CMakeLists.txt 2014-01-27 22:11:30.520298002 +0100 -@@ -807,14 +807,6 @@ - \"${VISIT_VERSION}\" - \"${CMAKE_INSTALL_PREFIX}/beta\") - ") -- ELSE(VISIT_INSTALL_AS_BETA) -- INSTALL(CODE " -- MESSAGE(\"Symlinking current to ${VISIT_VERSION}\") -- EXECUTE_PROCESS(WORKING_DIRECTORY \${CMAKE_INSTALL_PREFIX} -- COMMAND \${CMAKE_COMMAND} -E create_symlink -- \"${VISIT_VERSION}\" -- \"${CMAKE_INSTALL_PREFIX}/current\") -- ") - ENDIF(VISIT_INSTALL_AS_BETA) - ENDIF(WIN32) - MARK_AS_ADVANCED( diff --git a/sci-visualization/visit/files/visit-2.7.3-findpython.patch b/sci-visualization/visit/files/visit-2.7.3-findpython.patch deleted file mode 100644 index 180ffbf37..000000000 --- a/sci-visualization/visit/files/visit-2.7.3-findpython.patch +++ /dev/null @@ -1,19 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItPython.cmake visit2.7.1.new/src/CMake/FindVisItPython.cmake ---- visit2.7.1.old/src/CMake/FindVisItPython.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItPython.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -141,11 +141,12 @@ - FIND_LIBRARY(PYTHON_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION} - PATHS -- ${PYTHON_DIR}/lib -- ${PYTHON_DIR}/libs -- [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs -+ ${PYTHON_DIR}/lib -+ ${PYTHON_DIR}/lib64 -+ ${PYTHON_DIR}/libs -+ [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs - NO_DEFAULT_PATH - NO_CMAKE_ENVIRONMENT_PATH - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - diff --git a/sci-visualization/visit/files/visit-2.7.3-findsilo.patch b/sci-visualization/visit/files/visit-2.7.3-findsilo.patch deleted file mode 100644 index 04d73c37f..000000000 --- a/sci-visualization/visit/files/visit-2.7.3-findsilo.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru visit2.7.1-old/src/CMake/FindSilo.cmake visit2.7.1-new/src/CMake/FindSilo.cmake ---- visit2.7.1-old/src/CMake/FindSilo.cmake 2013-11-20 20:30:44.000000000 +0100 -+++ visit2.7.1-new/src/CMake/FindSilo.cmake 2014-02-01 02:22:29.410541850 +0100 -@@ -90,7 +90,7 @@ - NO_CMAKE_PATH - NO_SYSTEM_ENVIRONMENT_PATH) - IF(SILOH5_LIBRARY_EXISTS) -- SET_UP_THIRD_PARTY(SILO lib include siloh5) -+ SET_UP_THIRD_PARTY(SILO lib include siloh5 hdf5 z) - ELSE(SILOH5_LIBRARY_EXISTS) - SET_UP_THIRD_PARTY(SILO lib include silo) - ENDIF(SILOH5_LIBRARY_EXISTS) diff --git a/sci-visualization/visit/files/visit-2.7.3-findvtk.patch b/sci-visualization/visit/files/visit-2.7.3-findvtk.patch deleted file mode 100644 index c241e139e..000000000 --- a/sci-visualization/visit/files/visit-2.7.3-findvtk.patch +++ /dev/null @@ -1,24 +0,0 @@ -diff -ru visit2.7.1.old/src/CMake/FindVisItVTK.cmake visit2.7.1.new/src/CMake/FindVisItVTK.cmake ---- visit2.7.1.old/src/CMake/FindVisItVTK.cmake 2013-09-13 21:06:57.000000000 +0200 -+++ visit2.7.1.new/src/CMake/FindVisItVTK.cmake 2014-01-25 20:30:06.948654123 +0100 -@@ -234,11 +234,17 @@ - - # check for python wrappers - IF (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VTK_LIBRARY_DIRS}/python*/) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VTK_LIBRARY_DIRS}/python*/) - ELSE (NOT WIN32) -- FILE(GLOB VTK_PY_WRAPPERS_DIR ${VISIT_VTK_DIR}/lib) -+ FILE(GLOB VTK_PY_WRAPPERS_DIRECTORIES ${VISIT_VTK_DIR}/lib) - ENDIF (NOT WIN32) --MESSAGE(STATUS " VTK_PY_WRAPPERS_DIR=${VTK_PY_WRAPPERS_DIR}") -+MESSAGE(STATUS " VTK_PY_WRAPPERS_DIRECTORIES=${VTK_PY_WRAPPERS_DIRECTORIES}") -+ -+FOREACH(X ${VTK_PY_WRAPPERS_DIRECTORIES}) -+ IF(EXISTS "${X}/site-packages/vtk") -+ SET(VTK_PY_WRAPPERS_DIR "${X}") -+ ENDIF() -+ENDFOREACH(X) - - IF(EXISTS ${VTK_PY_WRAPPERS_DIR}/site-packages/vtk) - MESSAGE(STATUS "Found VTK Python Wrappers - ${VTK_PY_WRAPPERS_DIR}") diff --git a/sci-visualization/visit/files/visit-2.7.3-vtklibs.patch b/sci-visualization/visit/files/visit-2.7.3-vtklibs.patch deleted file mode 100644 index 9f2416dba..000000000 --- a/sci-visualization/visit/files/visit-2.7.3-vtklibs.patch +++ /dev/null @@ -1,142 +0,0 @@ -diff -ru visit2.7.1.old/src/engine/main/CMakeLists.txt visit2.7.1.new/src/engine/main/CMakeLists.txt ---- visit2.7.1.old/src/engine/main/CMakeLists.txt 2013-09-13 21:13:13.000000000 +0200 -+++ visit2.7.1.new/src/engine/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -184,8 +184,8 @@ - ${engine_ser_exe_EPlot_ser} - engine_ser - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -@@ -268,8 +268,8 @@ - ${engine_par_exe_EPlot_par} - engine_par - visit_verdict -- vtkjpeg -- vtkpng -+ jpeg -+ png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/mdserver/main/CMakeLists.txt visit2.7.1.new/src/mdserver/main/CMakeLists.txt ---- visit2.7.1.old/src/mdserver/main/CMakeLists.txt 2013-09-13 21:07:04.000000000 +0200 -+++ visit2.7.1.new/src/mdserver/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -118,10 +118,10 @@ - visit_verdict - vtkCommonCore - vtkIOCore -- vtktiff -+ tiff - ${VTKZLIB_LIB} -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${ZLIB_LIB} - ${CMAKE_THREAD_LIBS} - ${DL_LIB} -diff -ru visit2.7.1.old/src/svn_bin/static_simV2.py visit2.7.1.new/src/svn_bin/static_simV2.py ---- visit2.7.1.old/src/svn_bin/static_simV2.py 2013-09-13 21:12:52.000000000 +0200 -+++ visit2.7.1.new/src/svn_bin/static_simV2.py 2014-01-25 20:30:06.948654123 +0100 -@@ -176,7 +176,7 @@ - # - # Print the link lines that we'd have to use to get the -l's - # --vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -lvtkjpeg -lvtktiff -lvtkpng -lvtkexpat -lvtklibxml2 -lvtkzlib " -+vtk_libs="-lvtkCommon -lvtkGraphics -lvtkHybrid -lvtkRendering -lvtkImaging -lvtkGenericFiltering -lvtkFiltering -lvtkIO -lvtksys -lvtkfreetype -lvtkftgl -ljpeg -ltiff -lpng -lexpat -lvtklibxml2 -lz " - frameworks = "-lGL " - if sys.platform == "darwin": - frameworks = "-framework OpenGL -framework AGL -framework SystemConfiguration -framework IOKit -framework Cocoa " -diff -ru visit2.7.1.old/src/tools/convert/CMakeLists.txt visit2.7.1.new/src/tools/convert/CMakeLists.txt ---- visit2.7.1.old/src/tools/convert/CMakeLists.txt 2013-10-09 22:15:21.000000000 +0200 -+++ visit2.7.1.new/src/tools/convert/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,8 +104,8 @@ - ) - - SET(VTK_EXTRA_LIBS --vtkjpeg --vtkpng -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/dataserver/CMakeLists.txt visit2.7.1.new/src/tools/dataserver/CMakeLists.txt ---- visit2.7.1.old/src/tools/dataserver/CMakeLists.txt 2013-09-13 21:08:25.000000000 +0200 -+++ visit2.7.1.new/src/tools/dataserver/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -69,9 +69,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt ---- visit2.7.1.old/src/tools/mcurvit/CMakeLists.txt 2013-09-13 21:08:15.000000000 +0200 -+++ visit2.7.1.new/src/tools/mcurvit/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -104,9 +104,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/tools/protocol/CMakeLists.txt visit2.7.1.new/src/tools/protocol/CMakeLists.txt ---- visit2.7.1.old/src/tools/protocol/CMakeLists.txt 2013-09-13 21:08:16.000000000 +0200 -+++ visit2.7.1.new/src/tools/protocol/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -75,9 +75,9 @@ - ) - - SET(VTK_EXTRA_LIBS --vtktiff --vtkjpeg --vtkpng -+tiff -+jpeg -+png - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/viewer/main/CMakeLists.txt visit2.7.1.new/src/viewer/main/CMakeLists.txt ---- visit2.7.1.old/src/viewer/main/CMakeLists.txt 2013-09-13 21:08:36.000000000 +0200 -+++ visit2.7.1.new/src/viewer/main/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -272,8 +272,8 @@ - ${viewer_exe_IPlot} - ${viewer_exe_VPlot} - viewer -- vtkpng -- vtkjpeg -+ png -+ jpeg - ${VTKZLIB_LIB} - ${VTK_FREETYPE_LIBRARIES} - vtkftgl -diff -ru visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt ---- visit2.7.1.old/src/visit_vtk/full/CMakeLists.txt 2013-09-13 21:07:03.000000000 +0200 -+++ visit2.7.1.new/src/visit_vtk/full/CMakeLists.txt 2014-01-25 20:30:06.948654123 +0100 -@@ -122,7 +122,7 @@ - LINK_DIRECTORIES(${LIBRARY_OUTPUT_DIRECTORY} ${VTK_LIBRARY_DIRS}) - - ADD_LIBRARY(visit_vtk ${VISIT_VTK_SOURCES}) --TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle vtktiff) -+TARGET_LINK_LIBRARIES(visit_vtk lightweight_visit_vtk vtkFiltersExtraction vtkFiltersFlowPaths vtkImagingHybrid vtkRenderingOpenGL vtkRenderingFreeType vtkRenderingFreeTypeOpenGL vtkInteractionStyle tiff) - # Add vtk definitions - ADD_TARGET_DEFINITIONS(visit_vtk "${VTK_DEFINITIONS}") - diff --git a/sci-visualization/visit/metadata.xml b/sci-visualization/visit/metadata.xml deleted file mode 100644 index 65f194d1a..000000000 --- a/sci-visualization/visit/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>cluster</herd> - <longdescription> - VisIt is a free, open source, platform independent, distributed, - parallel, visualization tool for visualizing data defined on two- - and three-dimensional structured and unstructured meshes. - </longdescription> - <maintainer> - <email>gentryx@gmx.de</email> - </maintainer> - <use> - <flag name="cgns"> - Builds the reader for the CFD General Notation System file format. - </flag> - <flag name="silo"> - Adds support for reading .silo files. - </flag> - </use> -</pkgmetadata> diff --git a/sci-visualization/visit/visit-2.7.1.ebuild b/sci-visualization/visit/visit-2.7.1.ebuild deleted file mode 100644 index 198e35055..000000000 --- a/sci-visualization/visit/visit-2.7.1.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 - -DESCRIPTION="A software that delivers parallel interactive visualizations" -HOMEPAGE="https://wci.llnl.gov/codes/visit/home.html" -SRC_URI="http://portal.nersc.gov/svn/visit/trunk/releases/${PV}/visit${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="debug hdf5 tcmalloc cgns silo netcdf threads" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - hdf5? ( sci-libs/hdf5 ) - tcmalloc? ( dev-util/google-perftools ) - cgns? ( sci-libs/cgnslib ) - silo? ( sci-libs/silo ) - netcdf? ( sci-libs/netcdf ) - >=sci-libs/vtk-6.0.0[imaging,python,rendering,${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}${PV}/src" -PATCHES=( - "${FILESDIR}/${P}-findpython.patch" - "${FILESDIR}/${P}-findsilo.patch" - "${FILESDIR}/${P}-findvtk.patch" - "${FILESDIR}/${P}-vtklibs.patch" - "${FILESDIR}/${P}-dont_symlink_visit_dir.patch" -) - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX=/opt/visit - -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" - -DPYTHON_DIR="${EPREFIX}/usr" - -DVISIT_PYTHON_SKIP_INSTALL=true - -DVISIT_VTK_SKIP_INSTALL=true - -DQT_BIN="${EPREFIX}/usr/bin" - -DVISIT_ZLIB_DIR="${EPREFIX}/usr" - $(cmake-utils_use threads VISIT_THREAD) - ) - if use hdf5; then - mycmakeargs+=( -DHDF5_DIR="${EPREFIX}/usr" ) - fi - if use tcmalloc; then - mycmakeargs+=( -DTCMALLOC_DIR="${EPREFIX}/usr" ) - fi - if use cgns; then - mycmakeargs+=( -DCGNS_DIR="${EPREFIX}/usr" ) - fi - if use silo; then - mycmakeargs+=( -DSILO_DIR="${EPREFIX}/usr" ) - fi - if use netcdf; then - mycmakeargs+=( -DNETCDF_DIR="${EPREFIX}/usr" ) - fi - - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - cat > "${T}"/99visit <<- EOF - PATH=${EPREFIX}/opt/visit/bin - EOF - doenvd "${T}"/99visit -} diff --git a/sci-visualization/visit/visit-2.7.2.ebuild b/sci-visualization/visit/visit-2.7.2.ebuild deleted file mode 100644 index 593318c78..000000000 --- a/sci-visualization/visit/visit-2.7.2.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 - -DESCRIPTION="A software that delivers parallel interactive visualizations" -HOMEPAGE="https://wci.llnl.gov/codes/visit/home.html" -SRC_URI="http://portal.nersc.gov/svn/visit/trunk/releases/${PV}/visit${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="debug hdf5 tcmalloc cgns silo netcdf threads" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - hdf5? ( sci-libs/hdf5 ) - tcmalloc? ( dev-util/google-perftools ) - cgns? ( sci-libs/cgnslib ) - silo? ( sci-libs/silo ) - netcdf? ( sci-libs/netcdf ) - >=sci-libs/vtk-6.0.0[imaging,python,rendering,${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}${PV}/src" -PATCHES=( - "${FILESDIR}/${P}-findpython.patch" - "${FILESDIR}/${P}-findsilo.patch" - "${FILESDIR}/${P}-findvtk.patch" - "${FILESDIR}/${P}-vtklibs.patch" - "${FILESDIR}/${P}-dont_symlink_visit_dir.patch" -) - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX=/opt/visit - -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" - -DPYTHON_DIR="${EPREFIX}/usr" - -DVISIT_PYTHON_SKIP_INSTALL=true - -DVISIT_VTK_SKIP_INSTALL=true - -DQT_BIN="${EPREFIX}/usr/bin" - -DVISIT_ZLIB_DIR="${EPREFIX}/usr" - $(cmake-utils_use threads VISIT_THREAD) - ) - if use hdf5; then - mycmakeargs+=( -DHDF5_DIR="${EPREFIX}/usr" ) - fi - if use tcmalloc; then - mycmakeargs+=( -DTCMALLOC_DIR="${EPREFIX}/usr" ) - fi - if use cgns; then - mycmakeargs+=( -DCGNS_DIR="${EPREFIX}/usr" ) - fi - if use silo; then - mycmakeargs+=( -DSILO_DIR="${EPREFIX}/usr" ) - fi - if use netcdf; then - mycmakeargs+=( -DNETCDF_DIR="${EPREFIX}/usr" ) - fi - - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - PACKAGES_DIR="/opt/visit/${PV}/linux-$(arch)/lib/site-packages" - cd "${ED}${PACKAGES_DIR}" - for i in *; do - dosym "${PACKAGES_DIR}/${i}" "$(python_get_sitedir)/$i" - done - - cat > "${T}"/99visit <<- EOF - PATH=${EPREFIX}/opt/visit/bin - EOF - doenvd "${T}"/99visit -} diff --git a/sci-visualization/visit/visit-2.7.3.ebuild b/sci-visualization/visit/visit-2.7.3.ebuild deleted file mode 100644 index 67442edcd..000000000 --- a/sci-visualization/visit/visit-2.7.3.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 -PYTHON_COMPAT=( python2_7 ) - -inherit cmake-utils python-single-r1 - -DESCRIPTION="A software that delivers parallel interactive visualizations" -HOMEPAGE="https://wci.llnl.gov/codes/visit/home.html" -SRC_URI="http://portal.nersc.gov/svn/visit/trunk/releases/${PV}/visit${PV}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64" -IUSE="debug hdf5 tcmalloc cgns silo netcdf threads" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - ${PYTHON_DEPS} - hdf5? ( sci-libs/hdf5 ) - tcmalloc? ( dev-util/google-perftools ) - cgns? ( sci-libs/cgnslib ) - silo? ( sci-libs/silo ) - netcdf? ( sci-libs/netcdf ) - >=sci-libs/vtk-6.0.0[imaging,python,rendering,${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}${PV}/src" -PATCHES=( - "${FILESDIR}/${P}-findpython.patch" - "${FILESDIR}/${P}-findsilo.patch" - "${FILESDIR}/${P}-findvtk.patch" - "${FILESDIR}/${P}-vtklibs.patch" - "${FILESDIR}/${P}-dont_symlink_visit_dir.patch" -) - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_PREFIX=/opt/visit - -DPYTHON_INCLUDE_DIR="$(python_get_includedir)" - -DPYTHON_DIR="${EPREFIX}/usr" - -DVISIT_PYTHON_SKIP_INSTALL=true - -DVISIT_VTK_SKIP_INSTALL=true - -DQT_BIN="${EPREFIX}/usr/bin" - -DVISIT_ZLIB_DIR="${EPREFIX}/usr" - $(cmake-utils_use threads VISIT_THREAD) - ) - if use hdf5; then - mycmakeargs+=( -DHDF5_DIR="${EPREFIX}/usr" ) - fi - if use tcmalloc; then - mycmakeargs+=( -DTCMALLOC_DIR="${EPREFIX}/usr" ) - fi - if use cgns; then - mycmakeargs+=( -DCGNS_DIR="${EPREFIX}/usr" ) - fi - if use silo; then - mycmakeargs+=( -DSILO_DIR="${EPREFIX}/usr" ) - fi - if use netcdf; then - mycmakeargs+=( -DNETCDF_DIR="${EPREFIX}/usr" ) - fi - - cmake-utils_src_configure -} - -src_install() { - cmake-utils_src_install - - PACKAGES_DIR="/opt/visit/${PV}/linux-$(arch)/lib/site-packages" - cd "${ED}${PACKAGES_DIR}" - for i in *; do - dosym "${PACKAGES_DIR}/${i}" "$(python_get_sitedir)/$i" - done - - cat > "${T}"/99visit <<- EOF - PATH=${EPREFIX}/opt/visit/bin - LDPATH=${EPREFIX}/opt/visit/${PV}/linux-$(arch)/lib/ - EOF - doenvd "${T}"/99visit -} diff --git a/sci-visualization/yt/metadata.xml b/sci-visualization/yt/metadata.xml index fc0769f7f..ebd98f7b5 100644 --- a/sci-visualization/yt/metadata.xml +++ b/sci-visualization/yt/metadata.xml @@ -1,15 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>xarthisius@gentoo.org</email> - <name>Kacper Kowalik</name> - </maintainer> - <longdescription>yt is an analysis and visualization system written in Python, + <herd>sci</herd> + <maintainer> + <email>xarthisius@gentoo.org</email> + <name>Kacper Kowalik</name> + </maintainer> + <longdescription>yt is an analysis and visualization system written in Python, designed for use with Astrophysical Simulation codes. yt can process data in a myriad of ways and make a variety of visualizations. It is designed to be portable across simulation codes, and it is developed by developers from a variety of institutions and backgrounds. </longdescription> + <upstream> + <remote-id type="pypi">yt</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-apps/hwloc/ChangeLog b/sys-apps/hwloc/ChangeLog deleted file mode 100644 index 48256ef85..000000000 --- a/sys-apps/hwloc/ChangeLog +++ /dev/null @@ -1,240 +0,0 @@ -# ChangeLog for sys-apps/hwloc -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sys-apps/hwloc/ChangeLog,v 1.49 2015/01/05 17:56:52 aballier Exp $ - - 19 Feb 2015; Justin Lecher <jlec@gentoo.org> hwloc-1.10.1.ebuild: - sys-apps/hwloc: Set minimum support cuda toolkit version - - 18 Feb 2015; Christoph Junghans <ottxor@gentoo.org> hwloc-1.10.1.ebuild: - fixed cuda build - - 18 Feb 2015; Justin Lecher <jlec@gentoo.org> hwloc-1.10.1.ebuild, - metadata.xml: - sys-apps/hwloc: fix SLOT operators - -*hwloc-1.10.1 (17 Feb 2015) - - 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +hwloc-1.10.1.ebuild, - -hwloc-1.10.0-r2.ebuild: - version bump - - 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> hwloc-1.10.0-r2.ebuild: - filter -ftracer - - 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> hwloc-1.10.0-r2.ebuild: - use multilib nvidia-cuda-toolkit - - 05 Jan 2015; Alexis Ballier <aballier@gentoo.org> hwloc-1.10.0-r1.ebuild: - keyword ~arm - -*hwloc-1.10.0-r1 (06 Nov 2014) - - 06 Nov 2014; Mike Frysinger <vapier@gentoo.org> +hwloc-1.10.0-r1.ebuild: - Depend on libltdl rather than libtool #528294 by Pacho Ramos. - -*hwloc-1.10.0 (16 Oct 2014) - - 16 Oct 2014; Justin Bronder <jsbronder@gentoo.org> +hwloc-1.10.0.ebuild: - bump, working with mpich2-1.5 and openmpi-1.8.3. - -*hwloc-1.9 (08 Apr 2014) - - 08 Apr 2014; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.9.ebuild, - -hwloc-1.4.2.ebuild, -hwloc-1.5.ebuild: - [sys-apps/hwloc] Version bump - - 17 Mar 2014; Kacper Kowalik <xarthisius@gentoo.org> metadata.xml: - Remove myself from metadata.xml - - 28 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> - +files/hwloc-1.8.1-gl.patch, hwloc-1.8.1.ebuild: - Fixed underlinking for gl flag, thanks Andrew Savchenko bug #502956 - -*hwloc-1.8.1 (16 Feb 2014) - - 16 Feb 2014; Sébastien Fabbro <bicatali@gentoo.org> +hwloc-1.8.1.ebuild, - metadata.xml: - Version bump. Fixes bug #499618 by <teidakankan@gmail.com> - - 19 Jan 2014; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for alpha, wrt bug #484320 - - 12 Jan 2014; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for ia64, wrt bug #484320 - - 05 Jan 2014; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for sparc, wrt bug #484320 - - 16 Nov 2013; Kacper Kowalik <xarthisius@gentoo.org> hwloc-1.7.2.ebuild: - whitespace - -*hwloc-1.7.2 (16 Nov 2013) - - 16 Nov 2013; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.7.2.ebuild, - -hwloc-1.7.1.ebuild: - Version bump, drop old. Fixes #480642 by Juergen Rose <rose@rz.uni- - potsdam.de>. Thanks to LE GARREC Vincent <legarrec.vincent@gmail.com> and - Charlie Gehlin <charlie@gehlin.com> for their help. - -*hwloc-1.7.1 (09 Aug 2013) - - 09 Aug 2013; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.7.1.ebuild, - metadata.xml: - Version bump wrt #469708 by Mario Kicherer <dev@kicherer.org> - -*hwloc-1.6.2 (21 Mar 2013) - - 21 Mar 2013; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.6.2.ebuild: - Version bump for 1.6 series - - 28 Feb 2013; Jeroen Roovers <jer@gentoo.org> hwloc-1.6.1.ebuild: - Stable for HPPA (bug #458206). - - 23 Feb 2013; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for ppc64, wrt bug #458206 - - 22 Feb 2013; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for ppc, wrt bug #458206 - - 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for x86, wrt bug #458206 - - 20 Feb 2013; Agostino Sarubbo <ago@gentoo.org> hwloc-1.6.1.ebuild: - Stable for amd64, wrt bug #458206 - -*hwloc-1.4.2 (18 Feb 2013) - - 18 Feb 2013; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.4.2.ebuild: - Restore last available version from 1.4 branch as it is required for sys- - cluster/mpich2-1.4.1_p1. Thanks to Michael Sterrett <mr_bones_@gentoo.org> for - cathing this - -*hwloc-1.6.1 (18 Jan 2013) - - 18 Jan 2013; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.6.1.ebuild, - -hwloc-1.3.1.ebuild, -hwloc-1.3.2.ebuild, -hwloc-1.4.1.ebuild, - -hwloc-1.4.2.ebuild, -hwloc-1.6.ebuild: - Version bump, drop old - -*hwloc-1.6 (06 Dec 2012) - - 06 Dec 2012; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.6.ebuild, - metadata.xml: - Version bump - -*hwloc-1.5 (07 Oct 2012) - - 07 Oct 2012; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.5.ebuild: - [sys-apps/hwloc] Version bump - - 30 May 2012; Alexis Ballier <aballier@gentoo.org> hwloc-1.4.2.ebuild: - keyword ~amd64-fbsd - -*hwloc-1.4.2 (11 May 2012) - - 11 May 2012; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.4.2.ebuild, - -hwloc-1.4.ebuild: - Version bump, drop old - - 04 May 2012; Jeff Horelick <jdhore@gentoo.org> hwloc-1.3.1.ebuild, - hwloc-1.3.2.ebuild, hwloc-1.4.ebuild, hwloc-1.4.1.ebuild: - dev-util/pkgconfig -> virtual/pkgconfig - -*hwloc-1.3.2 (05 Mar 2012) -*hwloc-1.4.1 (05 Mar 2012) - - 05 Mar 2012; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.3.2.ebuild, - +hwloc-1.4.1.ebuild: - Version bump - - 10 Feb 2012; Kacper Kowalik <xarthisius@gentoo.org> hwloc-1.4.ebuild: - Add actual use_enable for numa - -*hwloc-1.4 (26 Jan 2012) - - 26 Jan 2012; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.4.ebuild: - Version bump - - 13 Jan 2012; Mike Frysinger <vapier@gentoo.org> hwloc-1.3.1.ebuild: - Use common tc-getPKG_CONFIG helper. - -*hwloc-1.3.1 (21 Dec 2011) - - 21 Dec 2011; Kacper Kowalik <xarthisius@gentoo.org> -hwloc-1.2.1.ebuild, - -hwloc-1.3.ebuild, +hwloc-1.3.1.ebuild: - Version bump, drop old - - 07 Dec 2011; Nathan Phillip Brink <binki@gentoo.org> hwloc-1.2.1.ebuild, - hwloc-1.3.ebuild: - Force hwloc's ./configure to respect PKG_CONFIG, fixes bug #393467 and some - portage-multilib compat. - -*hwloc-1.3 (20 Nov 2011) - - 20 Nov 2011; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.3.ebuild, - -hwloc-1.1.1-r1.ebuild, -hwloc-1.2-r1.ebuild, -hwloc-1.2.ebuild, metadata.xml: - Version bump, drop old - - 01 Sep 2011; Jeroen Roovers <jer@gentoo.org> hwloc-1.2-r1.ebuild, - hwloc-1.2.1.ebuild: - Marked ~hppa (bug #381313). - -*hwloc-1.2.1 (31 Aug 2011) - - 31 Aug 2011; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.2.1.ebuild: - version bump - - 31 Aug 2011; Alexey Shvetsov <alexxy@gentoo.org> hwloc-1.2-r1.ebuild: - drop hppa keyword as requested by rej - -*hwloc-1.2-r1 (31 Aug 2011) - - 31 Aug 2011; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.2-r1.ebuild: - Update deps - - 02 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> hwloc-1.2.ebuild: - Fix sandbox violation wrt bug 377375 by Vasileios Lourdas - <bugzilla@lourdas.name> - -*hwloc-1.2 (02 Aug 2011) - - 02 Aug 2011; Kacper Kowalik <xarthisius@gentoo.org> -hwloc-1.0.3.ebuild, - -hwloc-1.1.1.ebuild, +hwloc-1.2.ebuild: - Version bump, drop old - - 10 Jul 2011; Alexis Ballier <aballier@gentoo.org> hwloc-1.1.1-r1.ebuild: - keyword ~x86-fbsd, bug #372885 - -*hwloc-1.1.1-r1 (02 Jul 2011) - - 02 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +hwloc-1.1.1-r1.ebuild: - Enable prefix support for ~amd64-linux =D - -*hwloc-1.1.1 (26 Jan 2011) - - 26 Jan 2011; Justin Bronder <jsbronder@gentoo.org> +hwloc-1.1.1.ebuild: - Version bump, fix tests, push docs to correct directory - - 24 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> hwloc-1.0.3.ebuild: - Mark ~ppc64 wrt #345231 - - 18 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> -hwloc-1.0.2.ebuild: - Drop old. - -*hwloc-1.0.3 (16 Dec 2010) - - 16 Dec 2010; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.0.3.ebuild: - Version bump, add USE static-libs, migrate to autotools-utils.eclass - - 27 Nov 2010; Raúl Porcel <armin76@gentoo.org> hwloc-1.0.2.ebuild: - Add ~alpha/~ia64/~sparc wrt #345231 - - 13 Nov 2010; Jeroen Roovers <jer@gentoo.org> hwloc-1.0.2.ebuild: - Marked ~hppa ~ppc (bug #345231). - -*hwloc-1.0.2 (11 Sep 2010) - - 11 Sep 2010; Kacper Kowalik <xarthisius@gentoo.org> +hwloc-1.0.2.ebuild, - +metadata.xml: - Initial import wrt bug 299818. Ebuild written by Ruggero Morsucci - <mors_1tflops@yahoo.it> diff --git a/sys-apps/hwloc/Manifest b/sys-apps/hwloc/Manifest deleted file mode 100644 index 36bc2418a..000000000 --- a/sys-apps/hwloc/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST hwloc-1.10.1.tar.bz2 3771665 SHA256 35ce13a9a0737d2de1c6facb5c3c0438f7c83b45d6ce652e05ba000f6f2e514a SHA512 47cc1f084730021996ae0c18996e13dde5b991004fe9160bc1e118b6cb0288fe5d65d149450f05bd7b9e13bd6f16dfe82181d1e731dd1b0e46a43fd4435850cc WHIRLPOOL b7e089c1de3f967295768dc2dbc6acec80fa99f66d9340cedf3b02c1d2e869a339fa9fdd71a5f8ef77554ec8622a246abae6ca5f41354790bf09bf2d0d8236d7 diff --git a/sys-apps/hwloc/files/hwloc-1.8.1-gl.patch b/sys-apps/hwloc/files/hwloc-1.8.1-gl.patch deleted file mode 100644 index 47daa9593..000000000 --- a/sys-apps/hwloc/files/hwloc-1.8.1-gl.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- hwloc-1.8.1/config/hwloc.m4.orig 2014-01-30 17:46:58.000000000 +0400 -+++ hwloc-1.8.1/config/hwloc.m4 2014-02-27 13:46:28.587238873 +0400 -@@ -948,7 +948,7 @@ - hwloc_gl_happy=no]) - - AC_CHECK_HEADERS([NVCtrl/NVCtrl.h], [ -- AC_CHECK_LIB([XNVCtrl], [XNVCTRLQueryTargetAttribute], [:], [hwloc_gl_happy=no], [-lXext]) -+ AC_CHECK_LIB([XNVCtrl], [XNVCTRLQueryTargetAttribute], [:], [hwloc_gl_happy=no], [-lXext -lX11]) - ], [hwloc_gl_happy=no]) - - if test "x$hwloc_gl_happy" = "xyes"; then diff --git a/sys-apps/hwloc/hwloc-1.10.1.ebuild b/sys-apps/hwloc/hwloc-1.10.1.ebuild deleted file mode 100644 index e6f9c90d4..000000000 --- a/sys-apps/hwloc/hwloc-1.10.1.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-apps/hwloc/hwloc-1.10.0-r1.ebuild,v 1.2 2015/01/05 17:56:52 aballier Exp $ - -EAPI=5 - -inherit flag-o-matic cuda autotools-multilib multilib versionator - -MY_PV=v$(get_version_component_range 1-2) - -DESCRIPTION="displays the hardware topology in convenient formats" -HOMEPAGE="http://www.open-mpi.org/projects/hwloc/" -SRC_URI="http://www.open-mpi.org/software/${PN}/${MY_PV}/downloads/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0/5" -KEYWORDS="~alpha ~amd64 ~arm ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux ~x86-linux" -IUSE="cairo cuda debug gl +numa opencl +pci plugins svg static-libs xml X" - -# TODO opencl only works with AMD so no virtual -# dev-util/nvidia-cuda-toolkit is always multilib - -RDEPEND=">=sys-libs/ncurses-5.9-r3[${MULTILIB_USEDEP}] - cairo? ( >=x11-libs/cairo-1.12.14-r4[X?,svg?,${MULTILIB_USEDEP}] ) - cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 ) - gl? ( media-video/nvidia-settings ) - opencl? ( x11-drivers/ati-drivers:* ) - pci? ( - >=sys-apps/pciutils-3.3.0-r2[${MULTILIB_USEDEP}] - >=x11-libs/libpciaccess-0.13.1-r1[${MULTILIB_USEDEP}] - ) - plugins? ( dev-libs/libltdl:0[${MULTILIB_USEDEP}] ) - numa? ( >=sys-process/numactl-2.0.10-r1[${MULTILIB_USEDEP}] ) - xml? ( >=dev-libs/libxml2-2.9.1-r4[${MULTILIB_USEDEP}] )" -DEPEND="${RDEPEND} - >=virtual/pkgconfig-0-r1[${MULTILIB_USEDEP}]" - -DOCS=( AUTHORS NEWS README VERSION ) - -PATCHES=( "${FILESDIR}/${PN}-1.8.1-gl.patch" ) -AUTOTOOLS_AUTORECONF=1 - -src_prepare() { - if use cuda ; then - append-cflags -I/opt/cuda/include - append-cppflags -I/opt/cuda/include - fi - autotools-utils_src_prepare -} - -multilib_src_configure() { - export HWLOC_PKG_CONFIG=$(tc-getPKG_CONFIG) #393467 - use cuda && local LDFLAGS="${LDFLAGS} -L/opt/cuda/$(get_libdir)" - local myeconfargs=( - --disable-silent-rules - --docdir="${EPREFIX}"/usr/share/doc/${PF} - $(use_enable cairo) - $(use_enable cuda) - $(use_enable debug) - $(multilib_native_use_enable gl) - $(multilib_native_use_enable opencl) - $(use_enable pci) - $(use_enable plugins) - $(use_enable numa libnuma) - $(use_enable xml libxml2) - $(use_with X x) - ) - autotools-utils_src_configure -} diff --git a/sys-apps/hwloc/metadata.xml b/sys-apps/hwloc/metadata.xml deleted file mode 100644 index 22128ee6b..000000000 --- a/sys-apps/hwloc/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>cluster</herd> - <longdescription> - The Portable Hardware Locality (hwloc) software package provides a portable abstraction - (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, - including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. - It also gathers various system attributes such as cache and memory information. - It primarily aims at helping applications with gathering information about modern computing - hardware so as to exploit it accordingly and efficiently. -</longdescription> - <use> - <flag name="cuda">Enable CUDA device discovery</flag> - <flag name="gl">Enable GL display device discovery (NVCtrl)</flag> - <flag name="numa">Add support for numa memory allocation</flag> - <flag name="opencl">Enable OpenCL device discovery (AMD only)</flag> - <flag name="pci">Enable PCI device discovery using libpci</flag> - <flag name="plugins">Build hwloc components as plugins so that the hwloc core library does not directly depend on their dependencies (for instance the libpci library)</flag> - </use> -</pkgmetadata> diff --git a/sys-apps/likwid/Manifest b/sys-apps/likwid/Manifest deleted file mode 100644 index 4e163abcf..000000000 --- a/sys-apps/likwid/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST likwid-3.0.0.tar.gz 458629 SHA256 968ea55497af9971b20295b5290f355e9b4054bcbcfac91bfeaca8c1f5f1b72e SHA512 4227a91822f7e452b5172b2a203d4e9c04327d7d6139ccdf1e7f2f0dcb372dd7e98c9ac2f9b55c768fc1c9e59973d5afbfd038757247b462b9a02038c78b5ab2 WHIRLPOOL 4e270a931b923e44ff2dad94891f4668ee89d95aed3635e81a3a644c40821bf41fec2c6d1d9199eff7a319b9b7d9fb4f88d2f559b797f808bc830a1ffc67bac1 -DIST likwid-3.1.1.tar.gz 477223 SHA256 03c9696cce9f8845ccbc82d254877121322a6429ba766ddc5aefc100cb1118d3 SHA512 119778e5f12b00524e89711008c43338f5554cd5d135eacf75ad82fd4de4f4de2c059953191ff39548be10d54c387848c6f6cf4f4349723dcf6f9bad5775d0f4 WHIRLPOOL 4db98222ac03dfef349b98bc16725ee3aa8e7982bbfb827df69ca50a132c8c2c32b39ed616f4184b987e2f807106ea6ae2e12fd4c5c31b8c30a5397866b974b5 diff --git a/sys-apps/likwid/files/likwid-3.0-paths.patch b/sys-apps/likwid/files/likwid-3.0-paths.patch deleted file mode 100644 index 01ee6a2b6..000000000 --- a/sys-apps/likwid/files/likwid-3.0-paths.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff -ur likwid-3.0/config.mk likwid-3.0-nju/config.mk ---- likwid-3.0/config.mk 2012-11-29 18:16:13.000000000 +0100 -+++ likwid-3.0-nju/config.mk 2013-01-30 15:32:47.896140004 +0100 -@@ -10,12 +10,12 @@ - - # Path were to install likwid - PREFIX = /usr/local#NO SPACE --MANPREFIX = $(PREFIX)/man#NO SPACE -+MANPREFIX = $(PREFIX)/share/man#NO SPACE - - # For the daemon based secure msr/pci access configure - # the absolute path to the msr daemon executable. - # $(PREFIX)/bin/likwid-accessD --ACCESSDAEMON = $(PREFIX)/bin/likwid-accessD#NO SPACE -+ACCESSDAEMON = /usr/bin/likwid-accessD#NO SPACE - # Path to the msrd-socket in system daemon mode. - SYSDAEMONSOCKETPATH = /var/run/likwid-msrd.sock#NO SPACE - -@@ -31,7 +31,7 @@ - ENABLE_SNB_UNCORE = false#NO SPACE - - # Change to YES to a build shared library instead of a static one --SHARED_LIBRARY = false#NO SPACE -+SHARED_LIBRARY = true#NO SPACE - - # Instrument likwid-bench for use with likwid-perfctr - INSTRUMENT_BENCH = false#NO SPACE diff --git a/sys-apps/likwid/files/likwid-3.1.1-paths.patch b/sys-apps/likwid/files/likwid-3.1.1-paths.patch deleted file mode 100644 index 79fa0ca72..000000000 --- a/sys-apps/likwid/files/likwid-3.1.1-paths.patch +++ /dev/null @@ -1,22 +0,0 @@ -diff -ru likwid-3.1.1/config.mk likwid-3.1.1-nju/config.mk ---- likwid-3.1.1/config.mk 2014-02-12 17:14:16.000000000 +0100 -+++ likwid-3.1.1-nju/config.mk 2014-02-19 00:22:02.530917183 +0100 -@@ -10,8 +10,8 @@ - - # Path were to install likwid - PREFIX = /usr/local#NO SPACE --MANPREFIX = $(PREFIX)/man#NO SPACE -+MANPREFIX = $(PREFIX)/share/man#NO SPACE - - # For the daemon based secure msr/pci access configure - # the absolute path to the msr daemon executable. - # $(PREFIX)/bin/likwid-accessD -@@ -26,7 +26,7 @@ - ACCESSMODE = accessdaemon#NO SPACE - - # Change to true to a build shared library instead of a static one --SHARED_LIBRARY = false#NO SPACE -+SHARED_LIBRARY = true#NO SPACE - - # Build Fortran90 module interface for marker API. Adopt Fortran compiler - # in ./make/include_<COMPILER>.mk if necessary. Default: ifort . diff --git a/sys-apps/likwid/files/likwid-3.1.1-shared_lib.patch b/sys-apps/likwid/files/likwid-3.1.1-shared_lib.patch deleted file mode 100644 index 6499fa221..000000000 --- a/sys-apps/likwid/files/likwid-3.1.1-shared_lib.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ru likwid-3.1.1-nju/Makefile likwid-3.1.1-njv/Makefile ---- likwid-3.1.1-nju/Makefile 2014-02-19 00:20:55.620918453 +0100 -+++ likwid-3.1.1-njv/Makefile 2014-02-19 00:47:28.250888224 +0100 -@@ -184,7 +184,7 @@ - - $(APPS): $(addprefix $(SRC_DIR)/applications/,$(addsuffix .c,$(APPS))) $(BUILD_DIR) $(GENGROUPLOCK) $(OBJ) $(OBJ_BENCH) - @echo "===> LINKING $@" -- $(Q)${CC} $(CFLAGS) $(ANSI_CFLAGS) $(CPPFLAGS) ${LFLAGS} -o $@ $(addprefix $(SRC_DIR)/applications/,$(addsuffix .c,$@)) $(OBJ_BENCH) $(STATIC_TARGET_LIB) $(LIBS) -+ $(Q)${CC} $(CFLAGS) $(ANSI_CFLAGS) $(CPPFLAGS) ${LFLAGS} -o $@ $(addprefix $(SRC_DIR)/applications/,$(addsuffix .c,$@)) $(OBJ_BENCH) $(STATIC_TARGET_LIB) $(DYNAMIC_TARGET_LIB) $(LIBS) - - $(STATIC_TARGET_LIB): $(OBJ) - @echo "===> CREATE STATIC LIB $(STATIC_TARGET_LIB)" diff --git a/sys-apps/likwid/files/use_access_daemon.patch b/sys-apps/likwid/files/use_access_daemon.patch deleted file mode 100644 index d0724bb6d..000000000 --- a/sys-apps/likwid/files/use_access_daemon.patch +++ /dev/null @@ -1,27 +0,0 @@ -diff -ur likwid-3.0/config.mk likwid-3.0-new/config.mk ---- likwid-3.0/config.mk 2012-11-29 18:16:13.000000000 +0100 -+++ likwid-3.0-new/config.mk 2013-01-29 09:05:08.406319092 +0100 -@@ -20,12 +20,12 @@ - SYSDAEMONSOCKETPATH = /var/run/likwid-msrd.sock#NO SPACE - - # Build the accessDaemon. Have a look in the WIKI for details. --BUILDDAEMON = false#NO SPACE -+BUILDDAEMON = true#NO SPACE - - # Set the default mode for MSR access. - # This can usually be overriden on the commandline. - # Valid values are: direct, accessdaemon, sysdaemon --ACCESSMODE = direct#NO SPACE -+ACCESSMODE = accessdaemon#NO SPACE - - # Set to true to enable SandyBridge Uncore support - ENABLE_SNB_UNCORE = false#NO SPACE -Nur in likwid-3.0-new: liblikwid.a. -Nur in likwid-3.0-new: liblikwidpin.so. -Nur in likwid-3.0-new: likwid-accessD. -Nur in likwid-3.0-new: likwid-features. -Nur in likwid-3.0-new: likwid-memsweeper. -Nur in likwid-3.0-new: likwid-perfctr. -Nur in likwid-3.0-new: likwid-pin. -Nur in likwid-3.0-new: likwid-powermeter. -Nur in likwid-3.0-new: likwid-topology. diff --git a/sys-apps/likwid/files/use_uncore.patch b/sys-apps/likwid/files/use_uncore.patch deleted file mode 100644 index 06724106f..000000000 --- a/sys-apps/likwid/files/use_uncore.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -ur likwid-3.0.old/config.mk likwid-3.0/config.mk ---- likwid-3.0.old/config.mk 2013-02-19 16:06:21.867704619 +0100 -+++ likwid-3.0/config.mk 2013-02-19 16:06:08.277704352 +0100 -@@ -28,7 +28,7 @@ - ACCESSMODE = direct#NO SPACE - - # Set to true to enable SandyBridge Uncore support --ENABLE_SNB_UNCORE = false#NO SPACE -+ENABLE_SNB_UNCORE = true#NO SPACE - - # Change to YES to a build shared library instead of a static one - SHARED_LIBRARY = true#NO SPACE diff --git a/sys-apps/likwid/likwid-3.0.ebuild b/sys-apps/likwid/likwid-3.0.ebuild deleted file mode 100644 index 82fde9a06..000000000 --- a/sys-apps/likwid/likwid-3.0.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="Command line tools for developing high performance multi threaded programs" -HOMEPAGE="http://code.google.com/p/likwid/" -SRC_URI="http://likwid.googlecode.com/files/${P}.0.tar.gz" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64" -IUSE="+access-daemon uncore" - -src_prepare() { - epatch "${FILESDIR}/${P}-paths.patch" - use access-daemon && epatch "${FILESDIR}/use_access_daemon.patch" - use uncore && epatch "${FILESDIR}/use_uncore.patch" - sed -i -e "s:/usr/local:${D}/usr:" config.mk || die "Couldn't set prefix!" -} - -src_compile() { - default - emake likwid-bench -} - -src_install() { - default - use access-daemon && fperms 4755 /usr/bin/likwid-accessD -} diff --git a/sys-apps/likwid/likwid-3.1.1.ebuild b/sys-apps/likwid/likwid-3.1.1.ebuild deleted file mode 100644 index 5ce618e51..000000000 --- a/sys-apps/likwid/likwid-3.1.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils - -DESCRIPTION="Command line tools for developing high performance multi threaded programs" -HOMEPAGE="http://code.google.com/p/likwid/" -SRC_URI="http://gentryx.de/~gentryx/${P}.tar.gz" - -SLOT="0" -LICENSE="GPL-3" -KEYWORDS="~amd64" -IUSE="" - -src_prepare() { - epatch "${FILESDIR}/${P}-paths.patch" - epatch "${FILESDIR}/${P}-shared_lib.patch" - sed -i -e "s:/usr/local:${ED}/usr:" config.mk || die "Couldn't set directories!" -} - -src_compile() { - emake PREFIX="${EPREFIX}/usr" - emake likwid-bench -} - -src_install() { - default - fperms 4755 /usr/bin/likwid-accessD -} diff --git a/sys-apps/likwid/metadata.xml b/sys-apps/likwid/metadata.xml deleted file mode 100644 index c8cd82659..000000000 --- a/sys-apps/likwid/metadata.xml +++ /dev/null @@ -1,22 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>cluster</herd> - <longdescription> - Likwid stands for Like I knew what I am doing. This project - contributes easy to use command line tools for Linux to support - programmers in developing high performance multi threaded - programs. - </longdescription> - <maintainer> - <email>gentryx@gmx.de</email> - </maintainer> - <use> - <flag name="access-daemon"> - Build access-daemon for secure access to /dev/cpu/*/msr. - </flag> - <flag name="uncore"> - Yield access to uncore events. - </flag> - </use> -</pkgmetadata> diff --git a/sys-cluster/charmdebug/ChangeLog b/sys-cluster/charmdebug/ChangeLog deleted file mode 100644 index 9a078d90a..000000000 --- a/sys-cluster/charmdebug/ChangeLog +++ /dev/null @@ -1,27 +0,0 @@ -# ChangeLog for sys-cluster/charmdebug -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*charmdebug-6.2.0-r1 (13 Aug 2013) - - 13 Aug 2013; Nicolas Bock <nicolasbock@gmail.com> +charmdebug-6.2.0-r1.ebuild, - -charmdebug-6.2.0.ebuild: - sys-cluster/charmdebug: Updated manifest. The Charm++ developers replaced the - tar file on their webpage with a bug fix release with the same filename and - version as before (6.2.0). I updated the manifest and bumped the ebuild so - that users will get the benefit of this new version. Since the old tar file is - not available anymore from the charm download page, I renamed the ebuild - instead of copying it. - - 31 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> charmdebug-6.2.0.ebuild: - sys-cluster/charmdebug: Added USE flag conditional. charmdebug does not work - for SMP compiled charm. - - 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charmdebug-6.2.0.ebuild: - Beautify - -*charmdebug-6.2.0 (21 Jun 2013) - - 21 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> +charmdebug-6.2.0.ebuild, - +metadata.xml: - Added new package: charmdebug. diff --git a/sys-cluster/charmdebug/Manifest b/sys-cluster/charmdebug/Manifest deleted file mode 100644 index 5683eb276..000000000 --- a/sys-cluster/charmdebug/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST charmdebug_6.2.0.tar.gz 269703 SHA256 858074b59f8eff1870a75f3b52b194122c1c31d06b65bf3b1209592cf73b6d96 SHA512 03f894c36d4231381cac22c05bc08b6673c3df23259f44539b8bea5c8e812ce53124e832f0df789c45aa15cfbfb3edb69bc4634c1839cef3b42340b19094f5e2 WHIRLPOOL c6705d7c5532d9ffdb959af1fd980998b47642feb06784a058439b69e605821cbd59c167579af932cc1deb355c3de42aca44409f9ab0382acbd72aa5cbef48c0 diff --git a/sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild b/sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild deleted file mode 100644 index 4ee18b9b7..000000000 --- a/sys-cluster/charmdebug/charmdebug-6.2.0-r1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 - -DESCRIPTION="A debugger for Charm++ applications" -HOMEPAGE="http://charm.cs.uiuc.edu/" -SRC_URI="http://charm.cs.illinois.edu/distrib/binaries/charmdebug/charmdebug_${PV}.tar.gz" - -S="${WORKDIR}/${PN}" - -LICENSE="charm" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - >=virtual/jre-1.6 - sys-cluster/charm[charmdebug,-smp]" - -src_install() { - java-pkg_newjar ${PN}.jar - java-pkg_dolauncher ${PN} \ - --main charm/debug/ParDebug \ - --jar ${PN}.jar \ - --java_args -ms100000000 -mx512000000 -} diff --git a/sys-cluster/charmdebug/metadata.xml b/sys-cluster/charmdebug/metadata.xml deleted file mode 100644 index d369d068f..000000000 --- a/sys-cluster/charmdebug/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> -</pkgmetadata> diff --git a/sys-cluster/gasnet/ChangeLog b/sys-cluster/gasnet/ChangeLog new file mode 100644 index 000000000..9739af22e --- /dev/null +++ b/sys-cluster/gasnet/ChangeLog @@ -0,0 +1,14 @@ +# ChangeLog for sys-cluster/gasnet +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*gasnet-9999 (04 Mar 2015) + + 04 Mar 2015; Christoph Junghans <ottxor@gentoo.org> +gasnet-9999.ebuild: + added live version + +*gasnet-1.24.0 (01 Mar 2015) + + 01 Mar 2015; Christoph Junghans <ottxor@gentoo.org> +gasnet-1.24.0.ebuild, + +metadata.xml: + initial commit diff --git a/sys-cluster/gasnet/Manifest b/sys-cluster/gasnet/Manifest new file mode 100644 index 000000000..9f2638920 --- /dev/null +++ b/sys-cluster/gasnet/Manifest @@ -0,0 +1 @@ +DIST GASNet-1.24.0.tar.gz 2471271 SHA256 76b4d897d5e2261ef83d0885c192e8ac039e32cb2464f11eb64eb3f9f2df38c0 SHA512 90457b1aa25a5e4c0220fb0f0ecfef7cb1518ecbcb825744cbc320e9cbbcbcf47d7b1e5ec98b42e0e47ddbf8217b20e2bd430fc470ae8cf97ddfc1ab543d6383 WHIRLPOOL faf84253b04840bfbbe579cfe5f24895a8fdb9cd0fbe153c3e57603f727fe248e8cb5f8941c57272022f491b8c2d77bf9e01ae28614b8d2e0ac0b35b0ffa95ba diff --git a/sys-cluster/gasnet/gasnet-1.24.0.ebuild b/sys-cluster/gasnet/gasnet-1.24.0.ebuild new file mode 100644 index 000000000..15e6cef02 --- /dev/null +++ b/sys-cluster/gasnet/gasnet-1.24.0.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit autotools-utils + +MY_P="${PN^^[gasn]}-${PV}" +DESCRIPTION="networking middleware layer to implementing partitioned global address space (PGAS) language" +HOMEPAGE="http://gasnet.lbl.gov/" +SRC_URI="http://gasnet.lbl.gov/${MY_P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="mpi threads" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +S="${WORKDIR}/${MY_P}" + +src_prepare() { + find . \( -name Makefile.am -or -name "*.mak" \) -exec sed -i '/^docdir/s/^/#/' {} + || die + AUTOTOOLS_AUTORECONF=yes + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable threads pthreads) + $(use_enable mpi) + ) + autotools-utils_src_configure +} diff --git a/sys-cluster/gasnet/gasnet-9999.ebuild b/sys-cluster/gasnet/gasnet-9999.ebuild new file mode 100644 index 000000000..d6cc303b6 --- /dev/null +++ b/sys-cluster/gasnet/gasnet-9999.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit autotools-utils + +MY_P="${PN^^[gasn]}-${PV}" +DESCRIPTION="networking middleware layer to implementing partitioned global address space (PGAS) language" +HOMEPAGE="http://gasnet.lbl.gov/" + +if [[ $PV = 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://bitbucket.org/berkeleylab/${PN}.git" + AUTOTOOLS_AUTORECONF=yes +else + KEYWORDS="~amd64" + SRC_URI="http://gasnet.lbl.gov/${MY_P}.tar.gz" + S="${WORKDIR}/${MY_P}" +fi + +LICENSE="BSD" +SLOT="0" +IUSE="mpi threads" + +DEPEND="mpi? ( virtual/mpi )" +RDEPEND="${DEPEND}" + +pkg_setup() { + echo + elog "GASNet has an overwhelming count of configuration options." + elog "Don't forget the EXTRA_ECONF environment variable can let you" + elog "specify configure options if you find them necessary." + echo +} + +src_configure() { + local myeconfargs=( + $(use_enable threads pthreads) + $(use_enable mpi) + ) + autotools-utils_src_configure +} diff --git a/dev-java/glazedlists/metadata.xml b/sys-cluster/gasnet/metadata.xml index 7303cef96..98defee4b 100644 --- a/dev-java/glazedlists/metadata.xml +++ b/sys-cluster/gasnet/metadata.xml @@ -1,5 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>java</herd> + <herd>cluster</herd> + <maintainer> + <email>ottxor@gentoo.org</email> + <name>Christoph Junghans</name> + </maintainer> </pkgmetadata> diff --git a/sys-cluster/hpx/hpx-9999.ebuild b/sys-cluster/hpx/hpx-9999.ebuild index 9627b8caf..3d7a50ede 100644 --- a/sys-cluster/hpx/hpx-9999.ebuild +++ b/sys-cluster/hpx/hpx-9999.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) if [ ${PV} == "9999" ] ; then inherit git-r3 diff --git a/sys-cluster/htcondor/ChangeLog b/sys-cluster/htcondor/ChangeLog index 7215000f4..959952f85 100644 --- a/sys-cluster/htcondor/ChangeLog +++ b/sys-cluster/htcondor/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + sys-cluster/htcondor: Add github to remote-id in metadata.xml + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> htcondor-8.0.0.ebuild, htcondor-8.3.2.ebuild: sys-cluster/htcondor: fix SLOT operators diff --git a/sys-cluster/htcondor/metadata.xml b/sys-cluster/htcondor/metadata.xml index 6485807ae..7767e2fac 100644 --- a/sys-cluster/htcondor/metadata.xml +++ b/sys-cluster/htcondor/metadata.xml @@ -26,4 +26,7 @@ <flag name="minimal">Don't support standard universe jobs</flag> <flag name="X">Enable the HTCondor Keyboard Daemon to monitor logged in X users for activity</flag> </use> + <upstream> + <remote-id type="github">htcondor/htcondor</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-cluster/libquo/libquo-9999.ebuild b/sys-cluster/libquo/libquo-9999.ebuild index ad2adffd2..f2e00b49f 100644 --- a/sys-cluster/libquo/libquo-9999.ebuild +++ b/sys-cluster/libquo/libquo-9999.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-cluster/libquo/libquo-1.2.2.ebuild,v 1.1 2015/01/06 21:56:20 ottxor Exp $ +# $Header: $ EAPI=5 diff --git a/sys-cluster/mpich/ChangeLog b/sys-cluster/mpich/ChangeLog index 719cc52e1..d3577a56c 100644 --- a/sys-cluster/mpich/ChangeLog +++ b/sys-cluster/mpich/ChangeLog @@ -2,6 +2,25 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*mpich-3.1.4-r1 (20 Apr 2015) + + 20 Apr 2015; Justin Bronder <jsbronder@gentoo.org> +mpich-3.1.4-r1.ebuild: + bump + +*mpich-3.1.3-r99 (20 Apr 2015) + + 20 Apr 2015; Justin Bronder <jsbronder@gentoo.org> +mpich-3.1.3-r99.ebuild, + -mpich-3.1.3-r1.ebuild: + drop keywords from non-empi version Every other version of the various MPI's + supports empi so it was unexpected to have that dropped. However this version + is still useful for porting/testing. + + 21 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mpich-3.1.3-r1.ebuild: + added fortran hack for bug #540508 + + 20 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mpich-3.1.3-r1.ebuild: + disable natvie fortran + *mpich-3.1.3-r1 (17 Feb 2015) 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +mpich-3.1.3-r1.ebuild: diff --git a/sys-cluster/mpich/Manifest b/sys-cluster/mpich/Manifest index 81e54b9d9..f630841da 100644 --- a/sys-cluster/mpich/Manifest +++ b/sys-cluster/mpich/Manifest @@ -1,2 +1,3 @@ DIST mpich-3.0.4.tar.gz 10921075 SHA256 cf638c85660300af48b6f776e5ecd35b5378d5905ec5d34c3da7a27da0acf0b3 SHA512 f9d8b2cf561fe5f85c12512ef4dd7b0cf5ec8b53ddb07bfa0d1db2e3c8ae0382c77e0661f46b82ec96b05d18ea2d25328bb84e9528ac06e5925f30ec8ef030d0 WHIRLPOOL 52c811d1adcba26424bb3f05b7b97faff16ab3762782474fcde5f49e9ca77155fb91d80967120d9277eed2adb116443afe444671eb6315a610587d55ac4ec9ed DIST mpich-3.1.3.tar.gz 11487313 SHA256 afb690aa828467721e9d9ab233fe00c68cae2b7b930d744cb5f7f3eb08c8602c SHA512 3071d75e925808c13ea528aaff81a2ee44a4eb9732c74005a0cedd5a710aeafc691d30c7a035ae0aba14bd2b837c1c788202a7612599d3ffac8e5a9299467c09 WHIRLPOOL ade5a2ab7a98a3ee353a0b41ad8c57b8676ea7e381e625c01237519c88e9e16c5330cf6c569707ded26462022dd8647ba0a24dc2c1559240781b0e4fa1c69511 +DIST mpich-3.1.4.tar.gz 11325036 SHA256 f68b5330e94306c00ca5a1c0e8e275c7f53517d01d6c524d51ce9359d240466b SHA512 55bd4d12a42b9ebc116016bd777eb2b8ed8c51e69f5ea5faf823eba0aeb7eadfe2848c4cca3032aa38841a25a4902c07cec2409811149a057c4aa99a25c6b6da WHIRLPOOL 243ea40dd67b7f8e6fecde58740c21703833ca2857922ad59c5744888145bbf0ee934a69128818cd5bb91f39a3e842c26b2eced20ba23e08c8968b903f1f9992 diff --git a/sys-cluster/mpich/mpich-3.1.3-r2.ebuild b/sys-cluster/mpich/mpich-3.1.3-r2.ebuild new file mode 100644 index 000000000..142d5112d --- /dev/null +++ b/sys-cluster/mpich/mpich-3.1.3-r2.ebuild @@ -0,0 +1,122 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 mpi + +MY_PV=${PV/_/} +DESCRIPTION="A high performance and portable MPI implementation" +HOMEPAGE="http://www.mpich.org/" +SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="mpich" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+cxx doc fortran mpi-threads romio threads" + +COMMON_DEPEND=" + dev-libs/libaio + >=sys-apps/hwloc-1.9 + romio? ( net-fs/nfs-utils ) + $(mpi_imp_deplist)" + +DEPEND="${COMMON_DEPEND} + dev-lang/perl + sys-devel/libtool" + +RDEPEND="${COMMON_DEPEND}" + +S="${WORKDIR}"/${PN}-${MY_PV} + +pkg_setup() { + FORTRAN_STANDARD="77 90" + fortran-2_pkg_setup + MPI_ESELECT_FILE="eselect.mpi.mpich" + + if use mpi-threads && ! use threads; then + ewarn "mpi-threads requires threads, assuming that's what you want" + fi +} + +src_prepare() { + # Using MPICHLIB_LDFLAGS doesn't seem to fully work. + sed -i 's| *@WRAPPER_LDFLAGS@ *||' \ + src/packaging/pkgconfig/mpich.pc.in \ + src/env/*.in \ + || die +} + +src_configure() { + local c="--enable-shared" + + # The configure statements can be somewhat confusing, as they + # don't all show up in the top level configure, however, they + # are picked up in the children directories. + + if use mpi-threads; then + # MPI-THREAD requries threading. + c="${c} --with-thread-package=pthreads" + c="${c} --enable-threads=runtime" + else + if use threads ; then + c="${c} --with-thread-package=pthreads" + else + c="${c} --with-thread-package=none" + fi + c="${c} --enable-threads=single" + fi + + if ! mpi_classed; then + c="${c} --sysconfdir=${EPREFIX}/etc/${PN}" + c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}" + else + c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}" + fi + + export MPICHLIB_CFLAGS=${CFLAGS} + export MPICHLIB_CPPFLAGS=${CPPFLAGS} + export MPICHLIB_CXXFLAGS=${CXXFLAGS} + export MPICHLIB_FFLAGS=${FFLAGS} + export MPICHLIB_FCFLAGS=${FCFLAGS} + export MPICHLIB_LDFLAGS=${LDFLAGS} + unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS + + econf $(mpi_econf_args) ${c} \ + --with-pm=hydra \ + --disable-mpe \ + --disable-fast \ + --enable-smpcoll \ + --enable-versioning \ + --with-hwloc-prefix=/usr \ + $(use_enable romio) \ + $(use_enable cxx) \ + $(use_enable fortran f77) \ + $(use_enable fortran fc) +} + +src_test() { + emake -j1 check +} + +src_install() { + local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g') + + default + + mpi_dodir /usr/share/doc/${PF} + mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES + mpi_newdoc src/pm/hydra/README README.hydra + if use romio; then + mpi_newdoc src/mpi/romio/README README.romio + fi + + if ! use doc; then + rm -rf "${d}"usr/share/doc/${PF}/www* + fi + + mpi_imp_add_eselect +} diff --git a/sys-cluster/mpich/mpich-3.1.3-r1.ebuild b/sys-cluster/mpich/mpich-3.1.3-r99.ebuild index 3aea43762..0d3d9c006 100644 --- a/sys-cluster/mpich/mpich-3.1.3-r1.ebuild +++ b/sys-cluster/mpich/mpich-3.1.3-r99.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-cluster/mpich/mpich-3.1.3.ebuild,v 1.1 2014/10/16 04:50:05 jsbronder Exp $ +# $Header: $ EAPI=5 @@ -15,7 +15,7 @@ SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz" SLOT="0" LICENSE="mpich" -KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +KEYWORDS="" IUSE="+cxx doc fortran mpi-threads romio threads" COMMON_DEPEND=" @@ -36,7 +36,6 @@ S="${WORKDIR}"/${PN}-${MY_PV} MULTILIB_WRAPPED_HEADERS=( /usr/include/mpicxx.h /usr/include/mpi.h - /usr/include/mpif.h /usr/include/opa_config.h ) @@ -97,7 +96,7 @@ multilib_src_configure() { --with-hwloc-prefix=/usr \ $(use_enable romio) \ $(use_enable cxx) \ - $(use_enable fortran fortran all) + $(multilib_native_use_enable fortran fortran all) } multilib_src_test() { @@ -107,13 +106,20 @@ multilib_src_test() { multilib_src_install() { default - #fortran modules are arch-specific, follow OpenMPI and put them in lib - if use fortran; then - mv "${ED}"/usr/include/*.mod "${ED}"/usr/$(get_libdir) || die + # fortran header cannot be wrapped (bug #540508), workaround part 1 + if multilib_is_native_abi && use fortran; then + mkdir "${T}"/fortran || die + mv "${ED}"/usr/include/mpif* "${T}"/fortran || die + mv "${ED}"/usr/include/*.mod "${T}"/fortran || die fi } multilib_src_install_all() { + # fortran header cannot be wrapped (bug #540508), workaround part 2 + if use fortran; then + mv "${T}"/fortran/* "${ED}"/usr/include || die + fi + dodir /usr/share/doc/${PF} dodoc README{,.envvar} CHANGES RELEASE_NOTES newdoc src/pm/hydra/README README.hydra diff --git a/sys-cluster/mpich/mpich-3.1.4-r1.ebuild b/sys-cluster/mpich/mpich-3.1.4-r1.ebuild new file mode 100644 index 000000000..ee89bd1ea --- /dev/null +++ b/sys-cluster/mpich/mpich-3.1.4-r1.ebuild @@ -0,0 +1,122 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit fortran-2 mpi + +MY_PV=${PV/_/} +DESCRIPTION="A high performance and portable MPI implementation" +HOMEPAGE="http://www.mpich.org/" +SRC_URI="http://www.mpich.org/static/downloads/${PV}/${P}.tar.gz" + +SLOT="0" +LICENSE="mpich" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" +IUSE="+cxx doc fortran mpi-threads romio threads" + +COMMON_DEPEND=" + dev-libs/libaio + >=sys-apps/hwloc-1.9 + romio? ( net-fs/nfs-utils ) + $(mpi_imp_deplist)" + +DEPEND="${COMMON_DEPEND} + dev-lang/perl + sys-devel/libtool" + +RDEPEND="${COMMON_DEPEND}" + +S="${WORKDIR}"/${PN}-${MY_PV} + +pkg_setup() { + FORTRAN_STANDARD="77 90" + fortran-2_pkg_setup + MPI_ESELECT_FILE="eselect.mpi.mpich" + + if use mpi-threads && ! use threads; then + ewarn "mpi-threads requires threads, assuming that's what you want" + fi +} + +src_prepare() { + # Using MPICHLIB_LDFLAGS doesn't seem to fully work. + sed -i 's| *@WRAPPER_LDFLAGS@ *||' \ + src/packaging/pkgconfig/mpich.pc.in \ + src/env/*.in \ + || die +} + +src_configure() { + local c="--enable-shared" + local hydra_c="--with-hwloc-prefix=/usr" + + # The configure statements can be somewhat confusing, as they + # don't all show up in the top level configure, however, they + # are picked up in the children directories. Hence the separate + # local vars. + + if use mpi-threads; then + # MPI-THREAD requries threading. + c="${c} --with-thread-package=pthreads" + c="${c} --enable-threads=runtime" + else + if use threads ; then + c="${c} --with-thread-package=pthreads" + else + c="${c} --with-thread-package=none" + fi + c="${c} --enable-threads=single" + fi + + if ! mpi_classed; then + c="${c} --sysconfdir=${EPREFIX}/etc/${PN}" + c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}" + else + c="${c} --docdir=$(mpi_root)/usr/share/doc/${PF}" + fi + + export MPICHLIB_CFLAGS=${CFLAGS} + export MPICHLIB_CPPFLAGS=${CPPFLAGS} + export MPICHLIB_CXXFLAGS=${CXXFLAGS} + export MPICHLIB_FFLAGS=${FFLAGS} + export MPICHLIB_FCFLAGS=${FCFLAGS} + export MPICHLIB_LDFLAGS=${LDFLAGS} + unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS + + econf $(mpi_econf_args) ${c} \ + --with-pm=hydra \ + --disable-fast \ + --enable-versioning \ + ${hydra_c} \ + $(use_enable romio) \ + $(use_enable cxx) \ + $(use_enable fortran f77) \ + $(use_enable fortran fc) +} + +src_test() { + emake -j1 check +} + +src_install() { + local d=$(echo ${ED}/$(mpi_root)/ | sed 's,///*,/,g') + + default + + mpi_dodir /usr/share/doc/${PF} + mpi_dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES + mpi_newdoc src/pm/hydra/README README.hydra + if use romio; then + mpi_newdoc src/mpi/romio/README README.romio + fi + + if ! use doc; then + rm -rf "${d}"usr/share/doc/${PF}/www* + fi + + mpi_imp_add_eselect +} diff --git a/sys-cluster/mpich2/ChangeLog b/sys-cluster/mpich2/ChangeLog index 0d8cea555..d25dbb0af 100644 --- a/sys-cluster/mpich2/ChangeLog +++ b/sys-cluster/mpich2/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Feb 2015; Christoph Junghans <ottxor@gentoo.org> -mpich2-1.5-r1.ebuild: + mpich2 will not be ported to multilib + + 20 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mpich2-1.5-r1.ebuild: + disable natvie fortran + *mpich2-1.5-r1 (17 Feb 2015) 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +mpich2-1.5-r1.ebuild: diff --git a/sys-cluster/mpich2/mpich2-1.5-r1.ebuild b/sys-cluster/mpich2/mpich2-1.5-r1.ebuild deleted file mode 100644 index a1ae784bf..000000000 --- a/sys-cluster/mpich2/mpich2-1.5-r1.ebuild +++ /dev/null @@ -1,125 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-cluster/mpich2/mpich2-1.5.ebuild,v 1.9 2013/07/09 22:26:38 jsbronder Exp $ - -EAPI=5 - -FORTRAN_NEEDED=fortran - -inherit fortran-2 multilib-minimal - -MY_PV=${PV/_/} -DESCRIPTION="A high performance and portable MPI implementation" -HOMEPAGE="http://www.mcs.anl.gov/research/projects/mpich2/index.php" -SRC_URI="http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/${MY_PV}/${PN}-${MY_PV}.tar.gz" - -SLOT="0" -LICENSE="mpich2" -KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux" -IUSE="+cxx doc fortran mpi-threads romio threads" - -COMMON_DEPEND=" - >=dev-libs/libaio-0.3.109-r5[${MULTILIB_USEDEP}] - >=sys-apps/hwloc-1.10.0-r2[${MULTILIB_USEDEP}] - romio? ( net-fs/nfs-utils )" - -DEPEND="${COMMON_DEPEND} - dev-lang/perl - sys-devel/libtool" - -RDEPEND="${COMMON_DEPEND} - !sys-cluster/mpich - !sys-cluster/openmpi" - -S="${WORKDIR}"/${PN}-${MY_PV} - -MULTILIB_WRAPPED_HEADERS=( - /usr/include/mpicxx.h - /usr/include/mpi.h - /usr/include/mpif.h - /usr/include/opa_config.h -) - -pkg_setup() { - FORTRAN_STANDARD="77 90" - fortran-2_pkg_setup - - if use mpi-threads && ! use threads; then - ewarn "mpi-threads requires threads, assuming that's what you want" - fi -} - -src_prepare() { - # Using MPICH2LIB_LDFLAGS doesn't seem to full work. - sed -i 's| *@WRAPPER_LDFLAGS@ *||' \ - src/packaging/pkgconfig/mpich2.pc.in \ - src/env/*.in \ - || die -} - -multilib_src_configure() { - local c="--enable-shared" - - # The configure statements can be somewhat confusing, as they - # don't all show up in the top level configure, however, they - # are picked up in the children directories. - - if use mpi-threads; then - # MPI-THREAD requries threading. - c="${c} --with-thread-package=pthreads" - c="${c} --enable-threads=runtime" - else - if use threads ; then - c="${c} --with-thread-package=pthreads" - else - c="${c} --with-thread-package=none" - fi - c="${c} --enable-threads=single" - fi - - export MPICH2LIB_CFLAGS=${CFLAGS} - export MPICH2LIB_CPPFLAGS=${CPPFLAGS} - export MPICH2LIB_CXXFLAGS=${CXXFLAGS} - export MPICH2LIB_FFLAGS=${FFLAGS} - export MPICH2LIB_FCFLAGS=${FCFLAGS} - export MPICH2LIB_LDFLAGS=${LDFLAGS} - unset CFLAGS CPPFLAGS CXXFLAGS FFLAGS FCFLAGS LDFLAGS - - c="${c} --sysconfdir=${EPREFIX}/etc/${PN}" - c="${c} --docdir=${EPREFIX}/usr/share/doc/${PF}" - ECONF_SOURCE=${S} econf ${c} \ - --with-pm=hydra \ - --disable-mpe \ - --disable-fast \ - --enable-smpcoll \ - --enable-versioning \ - $(use_enable romio) \ - $(use_enable cxx) \ - $(use_enable fortran fortran all) -} - -multilib_src_test() { - emake -j1 check -} - -multilib_src_install() { - default - - #fortran modules are arch-specific, follow OpenMPI and put them in lib - if use fortran; then - mv "${ED}"/usr/include/*.mod "${ED}"/usr/$(get_libdir) || die - fi -} - -multilib_src_install_all() { - dodir /usr/share/doc/${PF} - dodoc COPYRIGHT README{,.envvar} CHANGES RELEASE_NOTES - newdoc src/pm/hydra/README README.hydra - if use romio; then - newdoc src/mpi/romio/README README.romio - fi - - if ! use doc; then - rm -rf "${D}"usr/share/doc/${PF}/www* - fi -} diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 0fa386e78..c0baafcbd 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -2,6 +2,42 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*openmpi-1.8.5 (12 May 2015) + + 12 May 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.8.5.ebuild: + bump + +*openmpi-1.8.4-r4 (20 Apr 2015) + + 20 Apr 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.8.4-r4.ebuild: + sync with upstream + +*openmpi-1.8.4-r99 (20 Apr 2015) + + 20 Apr 2015; Justin Bronder <jsbronder@gentoo.org> +openmpi-1.8.4-r99.ebuild, + -openmpi-1.8.4-r3.ebuild: + drop keywords from non-empi version Every other version of the various MPI's + supports empi so it was unexpected to have that dropped. However this version + is still useful for porting/testing. + + 22 Feb 2015; Christoph Junghans <ottxor@gentoo.org> openmpi-1.8.4-r3.ebuild: + drop some useless slots + + 21 Feb 2015; Christoph Junghans <ottxor@gentoo.org> openmpi-1.8.4-r3.ebuild: + fixed USE=-fortran install + + 20 Feb 2015; Christoph Junghans <ottxor@gentoo.org> openmpi-1.8.4-r3.ebuild: + enabled multilib cuda + + 20 Feb 2015; Christoph Junghans <ottxor@gentoo.org> openmpi-1.8.4-r3.ebuild: + added fortran hack for bug #540508 + +*openmpi-1.8.4-r3 (19 Feb 2015) + + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +openmpi-1.8.4-r3.ebuild, + -openmpi-1.8.4-r2.ebuild, metadata.xml: + added changes from openmpi-1.8.4-r2::gentoo + 18 Feb 2015; Justin Lecher <jlec@gentoo.org> metadata.xml, openmpi-1.6.5.ebuild, openmpi-1.7.3.ebuild, openmpi-1.8.1.ebuild, openmpi-1.8.3.ebuild, openmpi-1.8.4-r2.ebuild: diff --git a/sys-cluster/openmpi/Manifest b/sys-cluster/openmpi/Manifest index 61fa743b4..7316db6f0 100644 --- a/sys-cluster/openmpi/Manifest +++ b/sys-cluster/openmpi/Manifest @@ -3,3 +3,4 @@ DIST openmpi-1.7.3.tar.bz2 12479769 SHA256 438d96c178dbf5a1bc92fa1d238a8225d87b6 DIST openmpi-1.8.1.tar.bz2 13297716 SHA256 171427ebc007943265f33265ec32e15e786763952e2bfa2eac95e3e192c1e18f SHA512 f1b35ace5c62c89dccdab3f2ee774dae8eaf7d7bd9e41136bb5953f9c61207620917d1905be95350215c6dbc03b494ddd18732b6b7520893e51c5b1a8861fb99 WHIRLPOOL 4d429e7c23131f050aebad11f6eb9048b09979af58d1efbbdc5f6d1d349bd5164745fdbc2ec53f326d8ae99b9af2313e2bc2bf1fb675343e8e231b787ff0aa4d DIST openmpi-1.8.3.tar.bz2 13301056 SHA256 2ef02dab61febeb74714ff80d508c00b05defc635b391ed2c8dcc1791fbc88b3 SHA512 dbb8ae576d5272defdf5fd9cc09ddcd488d9076e2f4f6b1bc1a49e7ce6345784e1a637615705873feead7c86b20c3ec204cddda8fdbab58342e76f07752154dc WHIRLPOOL 98ef14928e1f620d89212ae53c2353fc96e801a3da96997bd09572e411e7debd30d49b846af459bfe92f7b79e3efadfe74ed4668a85d82ef0324cfaf4e07ed80 DIST openmpi-1.8.4.tar.bz2 13488749 SHA256 23158d916e92c80e2924016b746a93913ba7fae9fff51bf68d5c2a0ae39a2f8a SHA512 d4c8ce2bd3359cf2e85958b58ba18b52c9cef6676718eb3d948309b164b2f54544f8f8419ef6881c7a51ba268a876cd56e9b2d340a106a16fa25fb9fc3e4eff9 WHIRLPOOL 793f64ad44c2e3451a269bcb53d747d15a01649978d80f13599596e1bdd6a6011b50fdd60222bbe3a4ebe567a4785b2660e3c1eb09bdba77420581a0062480a2 +DIST openmpi-1.8.5.tar.bz2 13241083 SHA256 4cea06a9eddfa718b09b8240d934b14ca71670c2dc6e6251a585ce948a93fbc4 SHA512 a8be6f99d43b52077c15a7aaf869ec38519c16b75fe62a833050cb0fbef74b2e88168eca00cda73b6e520c04f3a5b5829797765ed965e235e3ec3b1f88b72814 WHIRLPOOL c4c932203fdb47a54e57dd2f3ed489befb4ae49048d968044278c2669d9850ae4d4089293d72889bd479e773afa8c273e46d0db513f0c7b3ab3819f50c74dd41 diff --git a/sys-cluster/openmpi/metadata.xml b/sys-cluster/openmpi/metadata.xml index 4dd7acd26..d6e99ae4d 100644 --- a/sys-cluster/openmpi/metadata.xml +++ b/sys-cluster/openmpi/metadata.xml @@ -12,6 +12,7 @@ platform support</flag> <flag name="romio">Build the ROMIO MPI-IO component</flag> <flag name="mpi-threads">Enable MPI_THREAD_MULTIPLE</flag> + <flag name='numa'>Enable numactl to allow binding processes to CPUs</flag> <flag name="vt">Enable bundled VampirTrace support</flag> </use> </pkgmetadata> diff --git a/sys-cluster/openmpi/openmpi-1.8.4-r4.ebuild b/sys-cluster/openmpi/openmpi-1.8.4-r4.ebuild new file mode 100644 index 000000000..acabe9eb6 --- /dev/null +++ b/sys-cluster/openmpi/openmpi-1.8.4-r4.ebuild @@ -0,0 +1,169 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit autotools cuda eutils flag-o-matic fortran-2 multilib mpi toolchain-funcs versionator + +MY_P=${P/-mpi} +S=${WORKDIR}/${MY_P} + +IUSE_OPENMPI_FABRICS=" + openmpi_fabrics_ofed + openmpi_fabrics_knem + openmpi_fabrics_open-mx + openmpi_fabrics_psm" + +IUSE_OPENMPI_RM=" + openmpi_rm_pbs + openmpi_rm_slurm" + +IUSE_OPENMPI_OFED_FEATURES=" + openmpi_ofed_features_control-hdr-padding + openmpi_ofed_features_connectx-xrc + openmpi_ofed_features_udcm + openmpi_ofed_features_rdmacm + openmpi_ofed_features_dynamic-sl + openmpi_ofed_features_failover" + +DESCRIPTION="A high-performance message passing library (MPI)" +HOMEPAGE="http://www.open-mpi.org" +SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2" +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux" +IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads numa romio threads vt + ${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}" + +REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs ) + openmpi_rm_pbs? ( !openmpi_rm_slurm ) + openmpi_fabrics_psm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )" + +MPI_UNCLASSED_DEP_STR=" + vt? ( + !dev-libs/libotf + !app-text/lcdf-typetools + )" + +RDEPEND=" + dev-libs/libevent + dev-libs/libltdl:0 + >=sys-apps/hwloc-1.9.1[numa?] + sys-libs/zlib + cuda? ( dev-util/nvidia-cuda-toolkit ) + elibc_FreeBSD? ( dev-libs/libexecinfo ) + openmpi_fabrics_ofed? ( sys-infiniband/ofed:* ) + openmpi_fabrics_knem? ( sys-cluster/knem ) + openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) + openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm:* ) + openmpi_rm_pbs? ( sys-cluster/torque ) + openmpi_rm_slurm? ( sys-cluster/slurm ) + openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm:* ) + $(mpi_imp_deplist)" +DEPEND="${RDEPEND}" + +pkg_setup() { + fortran-2_pkg_setup + MPI_ESELECT_FILE="eselect.mpi.openmpi" + + if use mpi-threads; then + echo + ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by" + ewarn "default and officially unsupported by upstream." + ewarn "You may stop now and set USE=-mpi-threads" + echo + fi + + echo + elog "OpenMPI has an overwhelming count of configuration options." + elog "Don't forget the EXTRA_ECONF environment variable can let you" + elog "specify configure options if you find them necessary." + echo +} + +src_prepare() { + # Necessary for scalibility, see + # http://www.open-mpi.org/community/lists/users/2008/09/6514.php + if use threads; then + echo 'oob_tcp_listen_mode = listen_thread' \ + >> opal/etc/openmpi-mca-params.conf + fi + + # https://github.com/open-mpi/ompi/issues/163 + epatch "${FILESDIR}"/openmpi-ltdl.patch + + AT_M4DIR=config eautoreconf +} + +src_configure() { + local myconf=( + --sysconfdir="${EPREFIX}/etc/${PN}" + --enable-pretty-print-stacktrace + --enable-orterun-prefix-by-default + --with-hwloc="${EPREFIX}/usr" + --with-libltdl=external + ) + + if use mpi-threads; then + myconf+=(--enable-mpi-threads + --enable-opal-multi-threads) + fi + + if use fortran; then + myconf+=(--enable-mpi-fortran=all) + else + myconf+=(--enable-mpi-fortran=no) + fi + + ! use vt && myconf+=(--enable-contrib-no-build=vt) + + econf $(mpi_econf_args) "${myconf[@]}" \ + $(use_enable cxx mpi-cxx) \ + $(use_with cma) \ + $(use_with cuda cuda "${EPREFIX}"/opt/cuda) \ + $(use_enable romio io-romio) \ + $(use_enable heterogeneous) \ + $(use_enable ipv6) \ + $(use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_open-mx mx "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \ + $(use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \ + $(use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \ + $(use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \ + $(use_enable openmpi_ofed_features_udcm openib-udcm) \ + $(use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \ + $(use_enable openmpi_ofed_features_failover btl-openib-failover) \ + $(use_with openmpi_rm_pbs tm) \ + $(use_with openmpi_rm_slurm slurm) +} + +src_install () { + emake DESTDIR="${D}" install + + # From USE=vt see #359917 + rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null + + # Avoid collisions with libevent + rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null + + # Remove la files, no static libs are installed and we have pkg-config + find "${ED}"/$(mpi_root)/usr/$(get_libdir)/ -type f -name '*.la' -delete + + mpi_dodoc README AUTHORS NEWS VERSION || die + mpi_imp_add_eselect +} + +src_test() { + # Doesn't work with the default src_test as the dry run (-n) fails. + emake -j1 check +} diff --git a/sys-cluster/openmpi/openmpi-1.8.4-r2.ebuild b/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild index 5174cde35..ca95d0346 100644 --- a/sys-cluster/openmpi/openmpi-1.8.4-r2.ebuild +++ b/sys-cluster/openmpi/openmpi-1.8.4-r99.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-cluster/openmpi/openmpi-1.8.4-r1.ebuild,v 1.1 2015/02/04 21:46:32 jsbronder Exp $ +# $Header: $ EAPI=5 @@ -34,8 +34,8 @@ HOMEPAGE="http://www.open-mpi.org" SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2" LICENSE="BSD" SLOT="0" -KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux" -IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads romio threads vt +KEYWORDS="" +IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads numa romio threads vt ${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}" REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs ) @@ -54,35 +54,29 @@ MPI_UNCLASSED_DEP_STR=" !app-text/lcdf-typetools )" +# dev-util/nvidia-cuda-toolkit is always multilib RDEPEND=" !sys-cluster/mpich !sys-cluster/mpich2 !sys-cluster/mpiexec >=dev-libs/libevent-2.0.21[${MULTILIB_USEDEP}] dev-libs/libltdl:0[${MULTILIB_USEDEP}] - >=sys-apps/hwloc-1.10.0-r2[${MULTILIB_USEDEP}] + >=sys-apps/hwloc-1.10.0-r2[${MULTILIB_USEDEP},numa?] >=sys-libs/zlib-1.2.8-r1[${MULTILIB_USEDEP}] - cuda? ( dev-util/nvidia-cuda-toolkit ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.19-r1 ) elibc_FreeBSD? ( dev-libs/libexecinfo ) - openmpi_fabrics_ofed? ( sys-infiniband/ofed:* ) + openmpi_fabrics_ofed? ( sys-infiniband/ofed ) openmpi_fabrics_knem? ( sys-cluster/knem ) openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) - openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm:* ) + openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm ) openmpi_rm_pbs? ( sys-cluster/torque ) openmpi_rm_slurm? ( sys-cluster/slurm ) - openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm:* ) + openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm ) " DEPEND="${RDEPEND}" MULTILIB_WRAPPED_HEADERS=( - /usr/include/mpif-io-handles.h - /usr/include/mpif-constants.h /usr/include/mpi.h - /usr/include/mpif-externals.h - /usr/include/mpif-io-constants.h - /usr/include/mpif-config.h - /usr/include/mpif-sentinels.h - /usr/include/mpif-handles.h ) pkg_setup() { @@ -142,7 +136,7 @@ multilib_src_configure() { ECONF_SOURCE=${S} econf "${myconf[@]}" \ $(use_enable cxx mpi-cxx) \ $(use_with cma) \ - $(multilib_native_use_with cuda cuda "${EPREFIX}"/opt/cuda) \ + $(use_with cuda cuda "${EPREFIX}"/opt/cuda) \ $(use_enable romio io-romio) \ $(use_enable heterogeneous) \ $(use_enable ipv6) \ @@ -165,12 +159,26 @@ multilib_src_install() { # Remove la files, no static libs are installed and we have pkg-config find "${ED}"/usr/$(get_libdir)/ -type f -name '*.la' -delete + + # fortran header cannot be wrapped (bug #540508), workaround part 1 + if multilib_is_native_abi && use fortran; then + mkdir "${T}"/fortran || die + mv "${ED}"/usr/include/mpif* "${T}"/fortran || die + else + #some fortran files get installed unconditionally + rm "${ED}"/usr/include/mpif* "${ED}"/usr/bin/mpif* || die + fi } multilib_src_install_all() { # From USE=vt see #359917 rm "${ED}"/usr/share/libtool &> /dev/null + # fortran header cannot be wrapped (bug #540508), workaround part 2 + if use fortran; then + mv "${T}"/fortran/mpif* "${ED}"/usr/include || die + fi + # Avoid collisions with libevent rm -rf "${ED}"/usr/include/event2 &> /dev/null diff --git a/sys-cluster/openmpi/openmpi-1.8.5.ebuild b/sys-cluster/openmpi/openmpi-1.8.5.ebuild new file mode 100644 index 000000000..fbe39263f --- /dev/null +++ b/sys-cluster/openmpi/openmpi-1.8.5.ebuild @@ -0,0 +1,164 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +FORTRAN_NEEDED=fortran + +inherit cuda eutils flag-o-matic fortran-2 multilib mpi toolchain-funcs versionator + +MY_P=${P/-mpi} +S=${WORKDIR}/${MY_P} + +IUSE_OPENMPI_FABRICS=" + openmpi_fabrics_ofed + openmpi_fabrics_knem + openmpi_fabrics_open-mx + openmpi_fabrics_psm" + +IUSE_OPENMPI_RM=" + openmpi_rm_pbs + openmpi_rm_slurm" + +IUSE_OPENMPI_OFED_FEATURES=" + openmpi_ofed_features_control-hdr-padding + openmpi_ofed_features_connectx-xrc + openmpi_ofed_features_udcm + openmpi_ofed_features_rdmacm + openmpi_ofed_features_dynamic-sl + openmpi_ofed_features_failover" + +DESCRIPTION="A high-performance message passing library (MPI)" +HOMEPAGE="http://www.open-mpi.org" +SRC_URI="http://www.open-mpi.org/software/ompi/v$(get_version_component_range 1-2)/downloads/${MY_P}.tar.bz2" +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-fbsd ~x86-fbsd ~amd64-linux" +IUSE="cma cuda +cxx elibc_FreeBSD fortran heterogeneous ipv6 mpi-threads numa romio threads vt + ${IUSE_OPENMPI_FABRICS} ${IUSE_OPENMPI_RM} ${IUSE_OPENMPI_OFED_FEATURES}" + +REQUIRED_USE="openmpi_rm_slurm? ( !openmpi_rm_pbs ) + openmpi_rm_pbs? ( !openmpi_rm_slurm ) + openmpi_fabrics_psm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_control-hdr-padding? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_connectx-xrc? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_udcm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_rdmacm? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_dynamic-sl? ( openmpi_fabrics_ofed ) + openmpi_ofed_features_failover? ( openmpi_fabrics_ofed )" + +MPI_UNCLASSED_DEP_STR=" + vt? ( + !dev-libs/libotf + !app-text/lcdf-typetools + )" + +RDEPEND=" + dev-libs/libevent + dev-libs/libltdl:0 + >=sys-apps/hwloc-1.9.1[numa?] + sys-libs/zlib + cuda? ( dev-util/nvidia-cuda-toolkit ) + elibc_FreeBSD? ( dev-libs/libexecinfo ) + openmpi_fabrics_ofed? ( sys-infiniband/ofed:* ) + openmpi_fabrics_knem? ( sys-cluster/knem ) + openmpi_fabrics_open-mx? ( sys-cluster/open-mx ) + openmpi_fabrics_psm? ( sys-infiniband/infinipath-psm:* ) + openmpi_rm_pbs? ( sys-cluster/torque ) + openmpi_rm_slurm? ( sys-cluster/slurm ) + openmpi_ofed_features_rdmacm? ( sys-infiniband/librdmacm:* ) + $(mpi_imp_deplist)" +DEPEND="${RDEPEND}" + +pkg_setup() { + fortran-2_pkg_setup + MPI_ESELECT_FILE="eselect.mpi.openmpi" + + if use mpi-threads; then + echo + ewarn "WARNING: use of MPI_THREAD_MULTIPLE is still disabled by" + ewarn "default and officially unsupported by upstream." + ewarn "You may stop now and set USE=-mpi-threads" + echo + fi + + echo + elog "OpenMPI has an overwhelming count of configuration options." + elog "Don't forget the EXTRA_ECONF environment variable can let you" + elog "specify configure options if you find them necessary." + echo +} + +src_prepare() { + # Necessary for scalibility, see + # http://www.open-mpi.org/community/lists/users/2008/09/6514.php + if use threads; then + echo 'oob_tcp_listen_mode = listen_thread' \ + >> opal/etc/openmpi-mca-params.conf + fi +} + +src_configure() { + local myconf=( + --sysconfdir="${EPREFIX}/etc/${PN}" + --enable-pretty-print-stacktrace + --enable-orterun-prefix-by-default + --with-hwloc="${EPREFIX}/usr" + --with-libltdl="${EPREFIX}/usr" + ) + + if use mpi-threads; then + myconf+=(--enable-mpi-threads + --enable-opal-multi-threads) + fi + + if use fortran; then + myconf+=(--enable-mpi-fortran=all) + else + myconf+=(--enable-mpi-fortran=no) + fi + + ! use vt && myconf+=(--enable-contrib-no-build=vt) + + econf $(mpi_econf_args) "${myconf[@]}" \ + $(use_enable cxx mpi-cxx) \ + $(use_with cma) \ + $(use_with cuda cuda "${EPREFIX}"/opt/cuda) \ + $(use_enable romio io-romio) \ + $(use_enable heterogeneous) \ + $(use_enable ipv6) \ + $(use_with openmpi_fabrics_ofed verbs "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_knem knem "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_open-mx mx "${EPREFIX}"/usr) \ + $(use_with openmpi_fabrics_psm psm "${EPREFIX}"/usr) \ + $(use_enable openmpi_ofed_features_control-hdr-padding openib-control-hdr-padding) \ + $(use_enable openmpi_ofed_features_connectx-xrc openib-connectx-xrc) \ + $(use_enable openmpi_ofed_features_rdmacm openib-rdmacm) \ + $(use_enable openmpi_ofed_features_udcm openib-udcm) \ + $(use_enable openmpi_ofed_features_dynamic-sl openib-dynamic-sl) \ + $(use_enable openmpi_ofed_features_failover btl-openib-failover) \ + $(use_with openmpi_rm_pbs tm) \ + $(use_with openmpi_rm_slurm slurm) +} + +src_install () { + emake DESTDIR="${D}" install + + # From USE=vt see #359917 + rm "${ED}"/$(mpi_root)/usr/share/libtool &> /dev/null + + # Avoid collisions with libevent + rm -rf "${ED}"/$(mpi_root)/usr/include/event2 &> /dev/null + + # Remove la files, no static libs are installed and we have pkg-config + find "${ED}"/$(mpi_root)/usr/$(get_libdir)/ -type f -name '*.la' -delete + + mpi_dodoc README AUTHORS NEWS VERSION || die + mpi_imp_add_eselect +} + +src_test() { + # Doesn't work with the default src_test as the dry run (-n) fails. + emake -j1 check +} diff --git a/sys-cluster/projections/ChangeLog b/sys-cluster/projections/ChangeLog deleted file mode 100644 index a6f3e8ee0..000000000 --- a/sys-cluster/projections/ChangeLog +++ /dev/null @@ -1,13 +0,0 @@ -# ChangeLog for sys-cluster/projections -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> projections-6.2.1.ebuild: - Beautify - -*projections-6.2.1 (26 Jun 2013) - - 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> +metadata.xml, - +projections-6.2.1.ebuild: - Added new package: projections A performance analysis framework for Charm++ - applications. diff --git a/sys-cluster/projections/Manifest b/sys-cluster/projections/Manifest deleted file mode 100644 index fd66e12c7..000000000 --- a/sys-cluster/projections/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST projections_6.2.1.tar.gz 3713748 SHA256 8d47164f3765a1d7dae28bf35d2963dc87542f1f08025b6aa01d3952199deaa8 SHA512 2a6e4b787491066dec31de05d777243252c08b4504743577297da7e3ecd9c4c3b96db46c295c55c413a98ebe5e338e6b90c213346925a20d89b47bb0b77eeaf8 WHIRLPOOL 10a8a8ac6ec283d95c7485b02075d69eb37b9445b89db000ebcd4ffeec62dc74773807b564af9f89d2e488ec3965eb58f937fb53b889d54b72bfa5c2abc2dad1 diff --git a/sys-cluster/projections/metadata.xml b/sys-cluster/projections/metadata.xml deleted file mode 100644 index 334411aca..000000000 --- a/sys-cluster/projections/metadata.xml +++ /dev/null @@ -1,7 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci</herd> - <use> - </use> -</pkgmetadata> diff --git a/sys-cluster/projections/projections-6.2.1.ebuild b/sys-cluster/projections/projections-6.2.1.ebuild deleted file mode 100644 index 39e3cb039..000000000 --- a/sys-cluster/projections/projections-6.2.1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2014 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit java-pkg-2 - -DESCRIPTION="Projections Performance Analysis Framework for Charm++ Applications" -HOMEPAGE="http://charm.cs.uiuc.edu/" -SRC_URI="http://charm.cs.illinois.edu/distrib/binaries/projections/projections_${PV}.tar.gz" - -S="${WORKDIR}/${PN}_${PV}" - -LICENSE="charm" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND=" - >=virtual/jre-1.6 - sys-cluster/charm[charmtracing]" - -src_install() { - java-pkg_newjar ${PN}.jar - java-pkg_dolauncher ${PN} \ - --main projections.analysis.ProjMain \ - --jar ${PN}.jar -} diff --git a/sys-cluster/pyslice/metadata.xml b/sys-cluster/pyslice/metadata.xml index 65f154a4c..d2d79a4da 100644 --- a/sys-cluster/pyslice/metadata.xml +++ b/sys-cluster/pyslice/metadata.xml @@ -5,4 +5,7 @@ <longdescription> Templating system for parametric modeling. </longdescription> + <upstream> + <remote-id type="pypi">pyslice</remote-id> + </upstream> </pkgmetadata> diff --git a/sys-cluster/pyslice/pyslice-1.7.ebuild b/sys-cluster/pyslice/pyslice-1.7.ebuild index 96d6d558c..d3a449b1f 100644 --- a/sys-cluster/pyslice/pyslice-1.7.ebuild +++ b/sys-cluster/pyslice/pyslice-1.7.ebuild @@ -4,7 +4,7 @@ EAPI=5 -PYTHON_COMPAT=( python{2_6,2_7} ) +PYTHON_COMPAT=( python2_7 ) inherit distutils-r1 diff --git a/sys-process/numactl/ChangeLog b/sys-process/numactl/ChangeLog deleted file mode 100644 index 8d4eb17da..000000000 --- a/sys-process/numactl/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for sys-process/numactl -# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*numactl-2.0.10-r1 (16 Feb 2015) - - 16 Feb 2015; Christoph Junghans <ottxor@gentoo.org> - +files/numactl-2.0.8-cpuid-pic.patch, +metadata.xml, - +numactl-2.0.10-r1.ebuild: - added as deps for multilib hwloc/mpi diff --git a/sys-process/numactl/Manifest b/sys-process/numactl/Manifest deleted file mode 100644 index 5d6c2efc8..000000000 --- a/sys-process/numactl/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST numactl-2.0.10.tar.gz 98999 SHA256 9d197fefac81c73dc2b2e554f1758b2ec56d4e9b2f04a7f45dff5d6cb14fb9ce SHA512 3a82b28bbc724a2340950ac33396055da852ee06e5b1d3414cd83dd6f9e26fbb648faae35ce4009c76d6a180f3067a8f3fb18e3ffaa6b6db68adfc0877e94975 WHIRLPOOL 59a172c14d96b01b1e13d2913f6f820d4f9bacb2f80e2920d4350273ff01ab57d56ab4a163fde2df3898c4b7cf204bd4a333c99f9feb9d5bcd89fea799a3d2db diff --git a/sys-process/numactl/files/numactl-2.0.8-cpuid-pic.patch b/sys-process/numactl/files/numactl-2.0.8-cpuid-pic.patch deleted file mode 100644 index 02e84b725..000000000 --- a/sys-process/numactl/files/numactl-2.0.8-cpuid-pic.patch +++ /dev/null @@ -1,17 +0,0 @@ -make the code work on x86/PIC. this code is only used in the demo, -and the overhead of always running this is system noise, so don't -bother bracketing with __i386__/__PIC__ defines. - -http://bugs.gentoo.org/456238 - ---- a/clearcache.c -+++ b/clearcache.c -@@ -57,7 +57,7 @@ void clearcache(unsigned char *mem, unsigned size) - #if defined(__i386__) || defined(__x86_64__) - unsigned i, cl, eax, feat; - /* get clflush unit and feature */ -- asm("cpuid" : "=a" (eax), "=b" (cl), "=d" (feat) : "0" (1) : "cx"); -+ asm("xchg %%ebx, %%esi; cpuid; xchg %%esi, %%ebx;" : "=a" (eax), "=S" (cl), "=d" (feat) : "0" (1) : "cx"); - if (!(feat & (1 << 19))) - fallback_clearcache(); - cl = ((cl >> 8) & 0xff) * 8; diff --git a/sys-process/numactl/metadata.xml b/sys-process/numactl/metadata.xml deleted file mode 100644 index bee9f9ae6..000000000 --- a/sys-process/numactl/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>base-system</herd> -</pkgmetadata> diff --git a/sys-process/numactl/numactl-2.0.10-r1.ebuild b/sys-process/numactl/numactl-2.0.10-r1.ebuild deleted file mode 100644 index b73678fa0..000000000 --- a/sys-process/numactl/numactl-2.0.10-r1.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2015 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sys-process/numactl/numactl-2.0.10.ebuild,v 1.2 2014/11/12 14:56:05 jlec Exp $ - -EAPI=5 - -inherit autotools eutils toolchain-funcs multilib-minimal - -DESCRIPTION="Utilities and libraries for NUMA systems" -HOMEPAGE="http://oss.sgi.com/projects/libnuma/" -SRC_URI="ftp://oss.sgi.com/www/projects/libnuma/download/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -# ARM lacks the __NR_migrate_pages syscall. -KEYWORDS="~amd64 -arm ~ia64 ~ppc ~ppc64 ~x86 ~amd64-linux" -IUSE="" - -ECONF_SOURCE=${S} - -src_prepare() { - eautoreconf - epatch "${FILESDIR}"/${PN}-2.0.8-cpuid-pic.patch #456238 -} - -src_test() { - if [ -d /sys/devices/system/node ]; then - einfo "The only generically safe test is regress2." - einfo "The other test cases require 2 NUMA nodes." - emake regress2 - else - ewarn "You do not have baseline NUMA support in your kernel, skipping tests." - fi -} - -multilib_src_compile() { - multilib_is_native_abi && default || emake libnuma.la -} - -multilib_src_install() { - emake DESTDIR="${D}" install$(multilib_is_native_abi || echo "-libLTLIBRARIES install-includeHEADERS") -} - -multilib_src_install_all() { - DOCS=( README TODO CHANGES DESIGN ) - einstalldocs - # delete man pages provided by the man-pages package #238805 - rm -r "${ED}"/usr/share/man/man[25] || die -} diff --git a/virtual/mpi/ChangeLog b/virtual/mpi/ChangeLog index 3187e907b..403d5c1f2 100644 --- a/virtual/mpi/ChangeLog +++ b/virtual/mpi/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mpi-2.0-r4.ebuild: + mpich2 will not be ported to multilib + + 19 Feb 2015; Christoph Junghans <ottxor@gentoo.org> mpi-2.0-r4.ebuild: + dropped keywords like for >=sys-cluster/openmpi-1.8.4-r3 + *mpi-2.0-r4 (17 Feb 2015) 17 Feb 2015; Christoph Junghans <ottxor@gentoo.org> +mpi-2.0-r4.ebuild: diff --git a/virtual/mpi/mpi-2.0-r4.ebuild b/virtual/mpi/mpi-2.0-r4.ebuild index e1c2283b7..dbb4347e7 100644 --- a/virtual/mpi/mpi-2.0-r4.ebuild +++ b/virtual/mpi/mpi-2.0-r4.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2015 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/virtual/mpi/mpi-2.0-r3.ebuild,v 1.1 2013/07/12 00:07:03 jsbronder Exp $ +# $Header: $ EAPI=5 @@ -11,14 +11,14 @@ HOMEPAGE="" SRC_URI="" LICENSE="" SLOT="0" -KEYWORDS="~alpha ~amd64 ~hppa ~ia64 ~ppc ~ppc64 ~sparc ~x86 ~x86-fbsd ~amd64-linux ~x86-linux" +KEYWORDS="~amd64 ~hppa ~ppc ~ppc64 ~x86 ~x86-fbsd ~amd64-linux ~x86-linux" IUSE="cxx fortran romio threads" RDEPEND="|| ( - >=sys-cluster/openmpi-1.8.4-r2[${MULTILIB_USEDEP},cxx?,fortran?,romio?,threads?] + >=sys-cluster/openmpi-1.8.4-r3[${MULTILIB_USEDEP},cxx?,fortran?,romio?,threads?] >=sys-cluster/mpich-3.1.3-r1[${MULTILIB_USEDEP},cxx?,fortran?,romio?,threads?] - >=sys-cluster/mpich2-1.5-r1[${MULTILIB_USEDEP},cxx?,fortran?,romio?,threads?] abi_x86_64? ( !abi_x86_32? ( sys-cluster/mvapich2[fortran?,romio?,threads?] ) ) + x86? ( sys-cluster/mvapich2[fortran?,romio?,threads?] ) prefix? ( sys-cluster/native-mpi ) )" diff --git a/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild b/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild index ae4fda430..a69cc0eec 100644 --- a/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild +++ b/virtual/perl-encoding-warnings/perl-encoding-warnings-0.11.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2014 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/virtual/perl-Time-HiRes/perl-Time-HiRes-1.972.600-r1.ebuild,v 1.1 2014/07/15 18:10:42 dilfridge Exp $ +# $Header: $ EAPI=5 diff --git a/x11-misc/envytools/ChangeLog b/x11-misc/envytools/ChangeLog index 87328eb68..b9a57bd18 100644 --- a/x11-misc/envytools/ChangeLog +++ b/x11-misc/envytools/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for x11-misc/envytools -# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 05 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml: + x11-misc/envytools: Add github to remote-id in metadata.xml + 16 Apr 2014; Wilhelm Erasmus <webmaster@wilhelm.co.za> envytools-9999.ebuild: x11-misc/envytools: Updated github url, Resolves gentoo-science/sci#103 diff --git a/x11-misc/envytools/metadata.xml b/x11-misc/envytools/metadata.xml index 098ac091a..cff6c9ef4 100644 --- a/x11-misc/envytools/metadata.xml +++ b/x11-misc/envytools/metadata.xml @@ -6,4 +6,7 @@ <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> </maintainer> + <upstream> + <remote-id type="github">pathscale/envytools</remote-id> + </upstream> </pkgmetadata> |