sci-biology/mira: Drop old; punt base.eclass

Package-Manager: portage-2.2.8

8 files changed, 9 insertions, 338 deletions

diff --git a/sci-biology/mira/ChangeLog b/sci-biology/mira/ChangeLog
index 56cb51d4c..4dd3e5b50 100644
--- a/sci-biology/mira/ChangeLog
+++ b/sci-biology/mira/ChangeLog
@@ -1,7 +1,12 @@
 # ChangeLog for sci-biology/mira
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  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
+
   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:
diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index 3fb13f0d8..e5b31cc8e 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,8 +1,2 @@
-DIST mira-3.4.0.1.tar.bz2 10262667 SHA256 cafe45601b3c143ac142c022e1fc0a21544e880bb226897824de5dbf6d516d7e SHA512 b42924d75042c9953e084fb2512518fa8ca0b3bc11e67550c53bc4b15422e8a78fc0c8a993a84683b07bcc6e65b45f6956dd5d3c1fbfaf060d6b888f8227df05 WHIRLPOOL 3421299f091c92a34aae2e230ac24f117b1a29cd3557bf0a32f1b78a266dba405d00853a0625dd9526e8b31d80d451ff72ea1c6120608370553b5f2b05e45c83
-DIST mira-3.4.1.1.tar.gz 11665587 SHA256 d523a75ea499886564c2f698397c21d49e970e3d4f773b7fd13098f8f20ccce8 SHA512 f7ecf942b168f0a7b32505dfbc625c6fbded00084ae7511e59d0b236ca8b76deba712ea09239d12aeb3190daf6faecce714cd6bceb02edcbc5df44d021bf36f3 WHIRLPOOL 44bc92e5b02536cbdd09fb08566e7d885cab75a6841d8826450ef1a7e7dcf797a4c77e482c3fadedc8422e93292ea7781705a16a6bc3d848675b717ca60e722f
-DIST mira-3.9.15.tar.bz2 10356048 SHA256 b52adf2884900f5228f2dc8540ba3cf7b85d9db3d4abbb325491696648a60a97 SHA512 4dfa3d03dbfbe97b490aeae2cdb32df7468f97dfa38bd738ca5930826c962f7444f676febb266b841e3cfc993062f793c0d9d8c6a7676d30c2df36a7f5ee017c WHIRLPOOL df6132174aedabf8ff376447277e383dff0cf263c6812a80881733664b71edb4079f9a9e7e5285a16dbf46ed721cfb3dd6e599a6caf130a6205d6a54dc67afbb
-DIST mira-3.9.9.tar.bz2 10356020 SHA256 d80929a9e7807bd0c160301c26d12b94fffd6439f8fea178b550c189da28848b SHA512 da2de917e99ac3825ac45ace7ae72b85d352eb75195db9f87679b45b3fe1a284aa6d53f5c6f3d45e1caa95e0dba20cf7a979bd97df67b65239f0aeb6e8af80d8 WHIRLPOOL 9d3a7b4e78e26b0eeb0f2e3cec804c0a99b9dbe260796f783214cf0c6b71da40fb5fd5480a4ec730e3bd3b0566b53f6e61ae1badee63460bfb4ceef006ac461c
-DIST mira-4.0rc2.tar.bz2 10389866 SHA256 7994d208898c9fb4a8779ec0ce27e6b8fd7235cf684557b07967041c710f26dd SHA512 72fb587e071a03a315b80dc8e9171f8d8d62bcc625ffc5c58264bda0135d914902c3387528c9e2405c42f61d9d367697272099a9bd41481ef9843a676232c390 WHIRLPOOL 70c5778974123cca6cd0b1515f206aa3f92ebd39f13020a2ebf3c4653ba9094afb688d827ee6d6c5c003c5ac56721eee583dc5b27f1f56d7633e79a1d98e0791
 DIST mira-4.0rc4.tar.bz2 10418692 SHA256 5149e25462625be98a18945921e17bb3c9bef110d820af295c7473a44acf09b4 SHA512 9ada6abaf36993e8738cd8fbe7ec710e0672335afc83902fd962fe9c0c430dae80df64f272bfbb1b4d132cb080e93ed791eaf8a7652b22e5e6e816466fe3eb5b WHIRLPOOL f2d605f2ad7985f60038ed93d4c1d45b6b60c97552588ac1daae449f8ee503691c0ef79d52df75bd9241cdc888a107df2801d31c9e6c9b8e3c6f3c561910c09f
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
-DIST mira_3rdparty_09-09-2011.tar.bz2 31285 SHA256 0e00cd0efff5601d559ee8d40d29b8d3b87db3f4cd5b7bfa5970501ea43f840b SHA512 de000592c0ffcf834dc31d33603107bac4ab8ed29cdb4db8e6e8e73d024214a641718c2a917bd7c73b50c4047201d629fc1f82c1618487e62589d0b276f7462f WHIRLPOOL 94c2723218dd6378352b365d36cd488269abeadf09dd544f1fc40c3af31de5b6149a32f97c7365f1df8b947e7a6738fef0448f39a5d74b398e98c1a14f3ef4f3
diff --git a/sci-biology/mira/mira-3.4.0.1.ebuild b/sci-biology/mira/mira-3.4.0.1.ebuild
deleted file mode 100644
index 88d150ac0..000000000
--- a/sci-biology/mira/mira-3.4.0.1.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="09-09-2011"
-
-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="
-	mirror://sourceforge/mira-assembler/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-LICENSE="GPL-2"
-SLOT="0"
-IUSE=""
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-
-CDEPEND="
-	>=dev-libs/boost-1.41.0-r3
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	dev-libs/expat"
-RDEPEND="${CDEPEND}
-	sci-biology/smalt-bin
-	sci-biology/ssaha2-bin"
-
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	# http://sourceforge.net/apps/trac/mira-assembler/ticket/47
-	epatch \
-		"${FILESDIR}"/mira_left_clip.readpool.C.patch \
-		"${FILESDIR}"/libtool.m4.patch
-	AT_M4DIR="config/m4" eautoreconf
-	#epatch "${FILESDIR}"/libtool.patch
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}"/usr/$(get_libdir) \
-		--with-boost-libdir="${EPREFIX}"/usr/$(get_libdir) \
-		--with-boost-thread=boost_thread-mt
-}
-
-src_compile() {
-	default
-	# TODO: resolve docbook incompatibility for building docs
-	if use doc; then
-		emake -C doc clean docs || die "This will probably die because upstream did not improve re-generation of the docs yet."
-	fi
-}
-
-src_install() {
-	default
-	dodoc AUTHORS GETTING_STARTED NEWS README* HELP_WANTED THANKS INSTALL
-	find doc/docs/man -type f | xargs doman
-	find doc/docs/texinfo -type f | xargs doinfo
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
diff --git a/sci-biology/mira/mira-3.4.1.1.ebuild b/sci-biology/mira/mira-3.4.1.1.ebuild
deleted file mode 100644
index 5260ee14a..000000000
--- a/sci-biology/mira/mira-3.4.1.1.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-inherit autotools base 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/${P}.tar.gz
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE=""
-
-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 )
-
-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
-	AT_M4DIR="config/m4" 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() {
-	base_src_install
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
-
-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-3.9.15.ebuild b/sci-biology/mira/mira-3.9.15.ebuild
deleted file mode 100644
index 8dbb921b4..000000000
--- a/sci-biology/mira/mira-3.9.15.ebuild
+++ /dev/null
@@ -1,64 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-inherit autotools base 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/development/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-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
-	AT_M4DIR="config/m4" 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() {
-	base_src_install
-	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-3.9.9.ebuild b/sci-biology/mira/mira-3.9.9.ebuild
deleted file mode 100644
index 0deeb871d..000000000
--- a/sci-biology/mira/mira-3.9.9.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.4.0.2.ebuild,v 1.1 2012/11/07 22:29:56 jlec Exp $
-
-EAPI=4
-
-MIRA_3RDPARTY_PV="06-07-2012"
-
-inherit autotools base 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/development/${P}.tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE=""
-
-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 )
-
-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
-	AT_M4DIR="config/m4" 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() {
-	base_src_install
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-}
-
-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_rc2.ebuild b/sci-biology/mira/mira-4.0_rc2.ebuild
deleted file mode 100644
index 2c26f0a89..000000000
--- a/sci-biology/mira/mira-4.0_rc2.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $
-
-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}"/${PN}-3.4.0.2-boost-1.50.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	sed \
-		-e 's:m4:config/m4:g' \
-		-i Makefile.am configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${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_rc4.ebuild b/sci-biology/mira/mira-4.0_rc4.ebuild
index 813eee057..682bf2369 100644
--- a/sci-biology/mira/mira-4.0_rc4.ebuild
+++ b/sci-biology/mira/mira-4.0_rc4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: /var/cvsroot/gentoo-x86/sci-biology/mira/mira-3.9.18.ebuild,v 1.1 2013/07/07 19:41:05 jlec Exp $
 
@@ -7,12 +7,12 @@ 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
+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"