diff options
78 files changed, 953 insertions, 569 deletions
diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog index 4aa9c6a1e..be63eea0f 100644 --- a/app-doc/root-docs/ChangeLog +++ b/app-doc/root-docs/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*root-docs-5.34.09 (29 Jun 2013) + + 29 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.08.ebuild, + +root-docs-5.34.09.ebuild: + Version bump. + *root-docs-5.34.08 (08 Jun 2013) 08 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.07.ebuild, diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest index 9f96491bc..a011e5602 100644 --- a/app-doc/root-docs/Manifest +++ b/app-doc/root-docs/Manifest @@ -1 +1 @@ -DIST root_v5.34.08.source.tar.gz 66508773 SHA256 79228cbe5fdfce0ab861b3cba48263d841f0ed04aaf721fb82e246aa567e4011 SHA512 2731b282f45d7a6462ec011ff773224df60fb55140c60f7685afbcd86eec2debbc76fac631fa5e87b3b7893417d8e51a3794c3e017b76dac8206188fb1e0b33f WHIRLPOOL 889ecc8cf5f27e9887c28367645fde8e621a2045a646b4308d132b6a63ca9e138e0718207f265696a146c9e47122384afbcf690bd02e59ba5880b69267502c21 +DIST root_v5.34.09.source.tar.gz 66507220 SHA256 a99cd7f34bf25a52e63228f3f7c245afa9e55420bfb4ce7e78d20c6475a4ea86 SHA512 6a87bc07c157d81649cc02feb3c2a5ab9ddfd0bef7c11893d5d65890b3855d14e6a6db6d2a76d91fcce3fe893091e76b4f477ac05d788aa759dbd34362895a7c WHIRLPOOL 671c7578455aaa5114292496d2cadd0d3ff33bc1dcfb7f590c1febd78db5c67175d35e3c4dc26f64ba1a5b1ca057b4b2b874bbb203e44093ed54ef0bfbd43060 diff --git a/app-doc/root-docs/root-docs-5.34.08.ebuild b/app-doc/root-docs/root-docs-5.34.09.ebuild index 4971cafdb..acf75e759 100644 --- a/app-doc/root-docs/root-docs-5.34.08.ebuild +++ b/app-doc/root-docs/root-docs-5.34.09.ebuild @@ -25,7 +25,7 @@ SLOT="0" LICENSE="LGPL-2.1" IUSE="" -S="${WORKDIR}/${ROOT_PN}-v5-34-00-patches" +S="${WORKDIR}/${ROOT_PN}" VIRTUALX_REQUIRED="always" DEPEND=" diff --git a/dev-java/fits/ChangeLog b/dev-java/fits/ChangeLog index 3c3438523..f3920cf39 100644 --- a/dev-java/fits/ChangeLog +++ b/dev-java/fits/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-java/fits -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*fits-1.11.0 (25 Jun 2013) + + 25 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +fits-1.11.0.ebuild, + -fits-1.08.1.ebuild: + dev-java/fits: Version bump + 14 May 2012; Sébastien Fabbro <bicatali@gentoo.org> fits-1.08.1.ebuild: quotes @@ -15,4 +21,3 @@ +fits-1.08.1.ebuild, +files/02-Update-ArrayFuncsTest.java-to-JUnit-4.patch, +files/README.Gentoo, +files/build.xml, +metadata.xml: Version bump and import to the science overlay - diff --git a/dev-java/fits/Manifest b/dev-java/fits/Manifest index 0cd3df08f..d1f3fe4e1 100644 --- a/dev-java/fits/Manifest +++ b/dev-java/fits/Manifest @@ -1 +1 @@ -DIST fits-1.08.1-src.jar 180266 SHA256 c27671397bddffd5e0b9c4333bbe58ccbdf4aa5f108a4046a159662715895772 SHA512 1cca4a11a92bf9a0253d9f3bf68f448e27ad7f116f4bf35181a775a97a6fb43e9b09800f45e8bb710d817cf09adfd0ff7b4a6855f2b9838994d5c17c05592c5e WHIRLPOOL 415960b39f05b79b2da4cef9e3d37683350c74d39e2648b012578f035c0fb64f62923d013e24837a16c070b09ef28cd03328e5b129cef07233ef03a837e23bf8 +DIST fits-1.11.0-src.jar 247303 SHA256 d4e8a8957d797c06d030d2122dd73c55b72c2e54dfbd709143e51d490fb7713c SHA512 e4ecebe139dfcd9f475c9e588c4d625472a6b147b67b9ce2eb3f08e5e43b278e9df03d86d597881c9f9a7fffbc3a4dbede75b3a76543742ceb705f136d8a9b27 WHIRLPOOL b18c1d902340ac3b542c9ab6cb4e2e5f699e105d2c42f58017a96e650d168355bbb464d21052a994e4927327493956c963a2a17c5e4fd9a4d7d95969c4730309 diff --git a/dev-java/fits/fits-1.08.1.ebuild b/dev-java/fits/fits-1.11.0.ebuild index aac88fcda..a4ab801b3 100644 --- a/dev-java/fits/fits-1.08.1.ebuild +++ b/dev-java/fits/fits-1.11.0.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 JAVA_PKG_IUSE="doc source test" inherit eutils java-pkg-2 java-ant-2 @@ -12,7 +12,7 @@ SRC_URI="http://heasarc.gsfc.nasa.gov/docs/heasarc/${PN}/java/v1.0/v${PV}/${PN}_ LICENSE="public-domain" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" CDEPEND="dev-java/junit:4" diff --git a/metadata/layout.conf b/metadata/layout.conf index 081a32668..493a5feec 100644 --- a/metadata/layout.conf +++ b/metadata/layout.conf @@ -19,3 +19,9 @@ sign-commits = true # Make egencache generate newer (more reliable) # md5-dict cache format (see bug #409445). cache-formats = md5-dict + +# indicate that ebuilds with the specified EAPIs are banned +#eapis-banned = 0 1 2 3 4 + +# indicate that ebuilds with the specified EAPIs are deprecated +eapis-deprecated = 1 2 3 4 diff --git a/sci-chemistry/ambertools/ChangeLog b/sci-chemistry/ambertools/ChangeLog index f4d3a9da3..c46b0af1f 100644 --- a/sci-chemistry/ambertools/ChangeLog +++ b/sci-chemistry/ambertools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ambertools/ChangeLog,v 1.2 2011/08/02 14:42:37 alexxy Exp $ + 28 Jun 2013; Christoph Junghans <ottxor@gentoo.org> ambertools-12.ebuild: + fixed deps + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> ambertools-1.5-r4.ebuild: Add missing multilib.eclass @@ -69,4 +72,3 @@ 28 Jul 2011; Alexey Shvetsov <alexxy@gentoo.org> +ambertools-1.5-r1.ebuild, +files/ambertools-1.5-gentoo.patch, +metadata.xml: Initial import to tree - diff --git a/sci-chemistry/ambertools/ambertools-12.ebuild b/sci-chemistry/ambertools/ambertools-12.ebuild index 70ea7f3c3..83242962d 100644 --- a/sci-chemistry/ambertools/ambertools-12.ebuild +++ b/sci-chemistry/ambertools/ambertools-12.ebuild @@ -26,7 +26,7 @@ RDEPEND=" sci-libs/cifparse-obj sci-chemistry/mopac7 sci-libs/netcdf - sci-libs/fftw:3.0 + >=sci-libs/fftw-3.3:3.0 sci-chemistry/reduce" DEPEND="${RDEPEND} app-shells/tcsh diff --git a/sci-chemistry/gnome-chemistry-utils/ChangeLog b/sci-chemistry/gnome-chemistry-utils/ChangeLog index b71a1a2f3..f45e5bf6a 100644 --- a/sci-chemistry/gnome-chemistry-utils/ChangeLog +++ b/sci-chemistry/gnome-chemistry-utils/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2013; Justin Lecher <jlec@gentoo.org> + gnome-chemistry-utils-0.14.2.ebuild, metadata.xml: + Fix min version of openbabel + 06 Apr 2013; Karl Linden (lilrc) <lilrc@users.sourceforge.net> gnome-chemistry-utils-0.14.2.ebuild: Migrate to gnome2 eclass. diff --git a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild index cbaeea866..e0d8c6a23 100644 --- a/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild +++ b/sci-chemistry/gnome-chemistry-utils/gnome-chemistry-utils-0.14.2.ebuild @@ -23,7 +23,7 @@ RDEPEND=" >=gnome-extra/libgsf-1.14.9 >=sci-chemistry/bodr-5 >=sci-chemistry/chemical-mime-data-0.1.94 - >=sci-chemistry/openbabel-2.1.0 + >=sci-chemistry/openbabel-2.3.0 >=x11-libs/cairo-1.6.0 >=x11-libs/gdk-pixbuf-2.22.0 >=x11-libs/goffice-0.10.0 diff --git a/sci-chemistry/gnome-chemistry-utils/metadata.xml b/sci-chemistry/gnome-chemistry-utils/metadata.xml index 5a8da44f4..94e01b4a7 100644 --- a/sci-chemistry/gnome-chemistry-utils/metadata.xml +++ b/sci-chemistry/gnome-chemistry-utils/metadata.xml @@ -1,11 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> + <longdescription lang="en"> The Gnome Chemistry Utils provide some programs and library containing GTK widgets and some C++ classes related to chemistry. </longdescription> - <use> - <flag name="gnumeric">Build pluging for gnumeric</flag> - </use> + <use> + <flag name="gnumeric">Build pluging for gnumeric</flag> + </use> </pkgmetadata> diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog index 2817f00e5..cedd72b92 100644 --- a/sci-chemistry/modeller/ChangeLog +++ b/sci-chemistry/modeller/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12-r1.ebuild, + +modeller-9.12-r2.ebuild: + Fix lib position, #474696 + *modeller-9.12-r1 (18 Jun 2013) 18 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.12.ebuild, diff --git a/sci-chemistry/modeller/modeller-9.12-r1.ebuild b/sci-chemistry/modeller/modeller-9.12-r2.ebuild index a25aa7fae..9cfd2e3d3 100644 --- a/sci-chemistry/modeller/modeller-9.12-r1.ebuild +++ b/sci-chemistry/modeller/modeller-9.12-r2.ebuild @@ -7,7 +7,7 @@ EAPI=5 PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils-r1 eutils versionator +inherit distutils-r1 eutils multilib versionator DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" HOMEPAGE="http://salilab.org/modeller/" @@ -83,6 +83,7 @@ python_install_all(){ exeinto ${INPATH}/lib/${EXECTYPE}/ doexe lib/${EXECTYPE}/lib* dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so + dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8 use doc && HTML_DOCS=( doc/. ) distutils-r1_python_install_all diff --git a/sci-chemistry/pymol-plugins-ezviz/ChangeLog b/sci-chemistry/pymol-plugins-ezviz/ChangeLog index 86dd9cb13..750b872ab 100644 --- a/sci-chemistry/pymol-plugins-ezviz/ChangeLog +++ b/sci-chemistry/pymol-plugins-ezviz/ChangeLog @@ -2,6 +2,11 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/www/viewcvs.gentoo.org/raw_cvs/gentoo-x86/sci-chemistry/pymol-plugins-ezviz/ChangeLog,v 1.2 2010/04/08 18:47:57 jlec dead $ + 02 Jul 2013; Justin Lecher <jlec@gentoo.org> + -pymol-plugins-ezviz-1.0.2005.ebuild, + +pymol-plugins-ezviz-1.0.2005-r1.ebuild: + Fix path fixation + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-ezviz-1.0.2005.ebuild: Bump to EAPI=5 and bump to python-r1.eclass diff --git a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild b/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005-r1.ebuild index 5f044c6e3..fca4adf0e 100644 --- a/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild +++ b/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005-r1.ebuild @@ -40,6 +40,7 @@ src_prepare() { src_install() { installation() { + cd "${BUILD_DIR}" || die python_moduleinto pmg_tk/startup/ python_domodule *.py python_moduleinto pmg_tk/startup/ez-viz/ diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog index f5e0f9b41..80bd47e8c 100644 --- a/sci-chemistry/pymol/ChangeLog +++ b/sci-chemistry/pymol/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild: + Update repo uri + 25 Mar 2013; Justin Lecher <jlec@gentoo.org> pymol-9999.ebuild, metadata.xml: Sync with tree diff --git a/sci-chemistry/pymol/pymol-9999.ebuild b/sci-chemistry/pymol/pymol-9999.ebuild index 564732c2f..57b5715bd 100644 --- a/sci-chemistry/pymol/pymol-9999.ebuild +++ b/sci-chemistry/pymol/pymol-9999.ebuild @@ -12,7 +12,7 @@ inherit distutils-r1 fdo-mime subversion versionator DESCRIPTION="A Python-extensible molecular graphics system" HOMEPAGE="http://pymol.sourceforge.net/" SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz" -ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol" +ESVN_REPO_URI="svn://svn.code.sf.net/p/pymol/code/trunk/pymol" LICENSE="PSF-2.2" SLOT="0" diff --git a/sci-chemistry/ucsf-tools/ChangeLog b/sci-chemistry/ucsf-tools/ChangeLog index 758f3fd1d..397511d37 100644 --- a/sci-chemistry/ucsf-tools/ChangeLog +++ b/sci-chemistry/ucsf-tools/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Justin Lecher <jlec@gentoo.org> ucsf-tools-9999.ebuild: + Fix compilation with latest gcc + 23 Apr 2013; Justin Lecher <jlec@gentoo.org> ucsf-tools-9999.ebuild, metadata.xml: Fix metadata, #466774; bump EAPI; set restricter license diff --git a/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild b/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild index bacdbce91..127745d4b 100644 --- a/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild +++ b/sci-chemistry/ucsf-tools/ucsf-tools-9999.ebuild @@ -6,7 +6,7 @@ EAPI=5 AUTOTOOLS_AUTORECONF=y -inherit autotools-utils +inherit autotools-utils flag-o-matic DESCRIPTION="The USF program suite" HOMEPAGE="http://xray.bmc.uu.se/usf/" @@ -30,3 +30,14 @@ src_unpack() { cd "${S}" unpack mark-20110912.tgz } + +src_prepare() { + local src + append-fflags -ffixed-line-length-132 + for src in \ + ave coma comap comdem dataman essens imp lsqman mama mapfix \ + mapman mave ncs6d o2d prof solex spancsi; do + mv ${src}/${src}.{f,F} || die + done + autotools-utils_src_prepare +} diff --git a/sci-libs/bigdft-abi/ChangeLog b/sci-libs/bigdft-abi/ChangeLog index 8b17f1fa5..b1fc75cb5 100644 --- a/sci-libs/bigdft-abi/ChangeLog +++ b/sci-libs/bigdft-abi/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*bigdft-abi-1.0.4-r1 (27 Jun 2013) + + 27 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-abi-1.0.4.ebuild, +bigdft-abi-1.0.4-r1.ebuild, + +files/bigdft-abi-1.0.4-CUDA_gethostname.patch: + Added #include <unistd.h> to S_GPU/src/class_utils.h and + src/CUDA/check_cuda.h to know gethostname. + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> bigdft-abi-1.0.4.ebuild: Filter LDFLAGS for cuda use not to break nvcc. diff --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild index 51f1e48c6..f466e9078 100644 --- a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4-r1.ebuild @@ -76,6 +76,9 @@ pkg_setup() { } src_prepare() { + epatch \ + "${FILESDIR}"/"${P}"-CUDA_gethostname.patch + tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/ eautoreconf } diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch new file mode 100644 index 000000000..04c45b4d7 --- /dev/null +++ b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-CUDA_gethostname.patch @@ -0,0 +1,22 @@ +diff -Naurp bigdft-abi-1.0.4-orig/S_GPU/src/class_utils.h bigdft-abi-1.0.4/S_GPU/src/class_utils.h +--- bigdft-abi-1.0.4-orig/S_GPU/src/class_utils.h 2012-07-09 14:43:33.000000000 +0000 ++++ bigdft-abi-1.0.4/S_GPU/src/class_utils.h 2013-06-27 09:52:17.000000000 +0000 +@@ -32,6 +32,7 @@ + #include <config.h> + #endif + ++#include <unistd.h> + #include <sstream> + + class deleter +diff -Naurp bigdft-abi-1.0.4-orig/src/CUDA/check_cuda.h bigdft-abi-1.0.4/src/CUDA/check_cuda.h +--- bigdft-abi-1.0.4-orig/src/CUDA/check_cuda.h 2012-07-09 14:43:33.000000000 +0000 ++++ bigdft-abi-1.0.4/src/CUDA/check_cuda.h 2013-06-27 09:51:50.000000000 +0000 +@@ -1,6 +1,7 @@ + #ifndef __checkcuda__ + #define __checkcuda__ + ++#include <unistd.h> + #include <string> + #include <sstream> + diff --git a/sci-libs/lwpr/ChangeLog b/sci-libs/lwpr/ChangeLog index a0cb73731..bc8987cf1 100644 --- a/sci-libs/lwpr/ChangeLog +++ b/sci-libs/lwpr/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-libs/lwpr -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*lwpr-1.2.5 (25 Jun 2013) + + 25 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +lwpr-1.2.5.ebuild, + -files/lwpr-1.2.2-setup.py.patch, -lwpr-1.2.2.ebuild, metadata.xml: + sci-libs/lwpr: Version bump. Removed python flag, should be a split package + 29 Jun 2010; Justin Lecher <jlec@gentoo.org> lwpr-1.2.2.ebuild: Python ABI fixes @@ -11,4 +17,3 @@ +files/lwpr-1.2.2-setup.py.patch, +metadata.xml: Initial import, ebuild based on bug #288032, initially submitted by Florent Teichteil - diff --git a/sci-libs/lwpr/Manifest b/sci-libs/lwpr/Manifest index 0be84d001..e26c53d4f 100644 --- a/sci-libs/lwpr/Manifest +++ b/sci-libs/lwpr/Manifest @@ -1 +1 @@ -DIST lwpr-1.2.2.tar.gz 723920 SHA256 a55d0ca8b66d4b62d07767ade714f545cf24d933b37d58613d8a79882afcf918 +DIST lwpr-1.2.5.tar.gz 773926 SHA256 02a5b8354551bde8999ad492bc3fece7e5372dd249393d23d1e579544c8ba2c9 SHA512 c0df6d6b8b535aa82b4a575959b00667d59763a9c2291e815bb216bc91dbee8d73dd04cc20c03848967e98bfa1f27f3ae763bf771a9420a44c175c2156ac9ea3 WHIRLPOOL eb4625ee0a4014e2968d326ce57e36a5df67991e2cadb8c5800dd80cc3f42f29060642ca2b53878de531302dcb68280be4a923347f099fa4bf88077abf00af94 diff --git a/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch b/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch deleted file mode 100644 index d560d164f..000000000 --- a/sci-libs/lwpr/files/lwpr-1.2.2-setup.py.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- python/setup.py.orig 2009-10-09 21:53:17.000000000 +0100 -+++ python/setup.py 2009-10-09 21:53:54.000000000 +0100 -@@ -5,7 +5,8 @@ - module = Extension('lwpr', - include_dirs = ['../include', - os.path.join(get_python_lib(),'numpy','core','include')], -- libraries = ['lwpr'], -+ libraries = ['lwpr'], -+ library_dirs=['../src/.libs'], - sources = ['lwprmodule.c']) - - setup (name = 'LWPR Module', diff --git a/sci-libs/lwpr/lwpr-1.2.2.ebuild b/sci-libs/lwpr/lwpr-1.2.2.ebuild deleted file mode 100644 index ba4014b16..000000000 --- a/sci-libs/lwpr/lwpr-1.2.2.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -PYTHON_DEPEND="python? 2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" - -inherit distutils eutils - -DESCRIPTION="The Locally Weighted Projection Regression Library" -HOMEPAGE="http://www.ipab.inf.ed.ac.uk/slmc/software/lwpr/" -SRC_URI="http://www.ipab.inf.ed.ac.uk/slmc/software/${PN}/${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples octave python" - -RDEPEND="octave? ( >=sci-mathematics/octave-3 ) - python? ( dev-python/numpy )" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -src_prepare() { - if use python; then - epatch "${FILESDIR}"/${P}-setup.py.patch - use python && distutils_src_prepare - fi -} - -src_configure() { - econf $(use_with octave octave "$(octave-config -p PREFIX)") - # threads buggy - # $(use_enable threads threads X) \ -} - -src_compile() { - emake || die "emake failed" - if use doc; then - doxygen Doxyfile || die "doxygen failed" - fi - if use python; then - cd python - distutils_src_compile - fi -} - -src_test() { - emake check || die "emake test failed" - if use python; then - cd python - LD_LIBRARY_PATH=../src/.libs \ - PYTHONPATH=$(dir -d build/lib*) \ - "$(PYTHON)" test.py || die "python test failed" - fi -} - -src_install() { - emake DESTDIR="${D}" \ - mexflags="-DMATLAB -I../include -L./.libs -llwproctave" \ - install || die "emake install failed" - dodoc README.TXT || die - if use doc; then - insinto /usr/share/doc/${PF} - doins doc/lwpr_doc.pdf - dohtml html/* || die - fi - if use examples ; then - insinto /usr/share/doc/${PF}/examples - doins example_c/cross.c example_cpp/cross.cc || die - fi - if use octave; then - insinto /usr/share/octave/packages/${P} - doins matlab/*.m || die - fi - if use python; then - cd python - distutils_src_install - fi -} diff --git a/sci-libs/lwpr/lwpr-1.2.5.ebuild b/sci-libs/lwpr/lwpr-1.2.5.ebuild new file mode 100644 index 000000000..29f2ec676 --- /dev/null +++ b/sci-libs/lwpr/lwpr-1.2.5.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_IN_SOURCE_BUILD=1 +inherit autotools-utils + +DESCRIPTION="The Locally Weighted Projection Regression Library" +HOMEPAGE="http://www.ipab.inf.ed.ac.uk/slmc/software/lwpr/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="doc examples octave static-libs" + +RDEPEND=" + octave? ( >=sci-mathematics/octave-3 )" +DEPEND="${RDEPEND} + doc? ( app-doc/doxygen )" + +src_configure() { + local myeconfargs=( + --enable-threads=3 + $(use_with octave octave "$(octave-config -p PREFIX)") + ) + autotools-utils_src_configure +} + +src_compile() { + autotools-utils_src_compile + if use doc; then + doxygen Doxyfile || die "doxygen failed" + fi +} + +src_install() { + autotools-utils_src_install \ + mexflags="-DMATLAB -I../include -L./.libs -llwproctave" + use doc && dodoc doc/lwpr_doc.pdf && dohtml html/* + if use examples ; then + insinto /usr/share/doc/${PF}/examples + doins example_c/cross.c example_cpp/cross.cc + fi + if use octave; then + insinto /usr/share/octave/packages/${P} + doins matlab/*.m + fi +} diff --git a/sci-libs/lwpr/metadata.xml b/sci-libs/lwpr/metadata.xml index dbae229f0..b9d1fd6a7 100644 --- a/sci-libs/lwpr/metadata.xml +++ b/sci-libs/lwpr/metadata.xml @@ -1,15 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<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 - locally linear models, spanned by a small number of univariate regressions in - selected directions in input space. A locally weighted variant of - Partial Least Squares (PLS) is employed for doing the dimensionality - reduction. + locally linear models, spanned by a small number of univariate + regressions in selected directions in input space. A locally + 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> diff --git a/sci-libs/msms/ChangeLog b/sci-libs/msms/ChangeLog index 1622441f4..1246097c8 100644 --- a/sci-libs/msms/ChangeLog +++ b/sci-libs/msms/ChangeLog @@ -1,7 +1,15 @@ # ChangeLog for sci-libs/msms -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 30 Jun 2013; Justin Lecher <jlec@gentoo.org> -msms-1.5.4-r1.ebuild, + -msms-1.5.6_rc2.ebuild, +msms-1.5.6.ebuild, metadata.xml: + Version BUmp; Bump to new distutil-r1.eclass + + 30 Jun 2013; Justin Lecher <jlec@gentoo.org> -msms-1.5.4-r1.ebuild, + -msms-1.5.6_rc2.ebuild, +msms-1.5.6.ebuild, metadata.xml: + Version BUmp; Bump to new distutil-r1.eclass + 27 Apr 2012; Justin Lecher <jlec@gentoo.org> msms-1.5.4-r1.ebuild, msms-1.5.6_rc2.ebuild: RESTRICT pypy diff --git a/sci-libs/msms/Manifest b/sci-libs/msms/Manifest index 70b53d4f3..9d502556c 100644 --- a/sci-libs/msms/Manifest +++ b/sci-libs/msms/Manifest @@ -1,2 +1 @@ -DIST mgltools_source_1.5.4.tar.gz 25503517 SHA256 1ea3da342b4d49d7a92dcb5d6da1d805e71652fd70ba7a5653335990629c80f0 SHA512 e3372776674f5cf31d61627a52be938b6309392137e55250d4ba57f7d6112874ab4647faeb3c90db3b567590c67aa54e452e0f09fc1da547b1a4baccbe1e83d0 WHIRLPOOL c4a80d5b80eac042b533ff5dd815353e868233ea385a74374bc57709e89150227234a2f2af6c477d0efa1a3e1c17cedfd5a15eb6a950e49f09ef960613d15726 -DIST mgltools_source_1.5.6rc2.tar.gz 40248519 SHA256 a783ca8ed4a44c6fcc6e31f8f54c91dd87f39a0521368717b49a354958ef0d49 SHA512 c1df3d87d218a2a10e376136ad545f8e578b05fc5c617844be713242714d6dd85c094d03928e1b7cfee5e59f47dc996a199d4aee16bede5c83bd5c204e9af315 WHIRLPOOL 62e0448a13d87694d45756ddc5443034e3287938f4f0c4c42036583f92505a52d5add89d13f2855fc087c00705c8bf239cfdbdefbeac709d3ebd535009074ab8 +DIST mgltools_source_1.5.6.tar.gz 40275811 SHA256 60123b11d4a0b65d09781fe61f6d42b5d731c04d86de09364f59a245f193842d SHA512 4ed956197f08b7c3779f0bb39393b40cdaff3461071b48815200c6ad0dce2de87375cda96fe20d3ace4ab81ba6b8cdb50b58d82f5e5b54fe2c7751201ff2f63e WHIRLPOOL 0f0454f4a773c9dce0f3b7bebbf8e089b2ccdeb827b38a3fd7dfa0bcb5bc92f4355cac44720498ac2b7b37546390e809938d5846002b335667c1dbd807f23350 diff --git a/sci-libs/msms/metadata.xml b/sci-libs/msms/metadata.xml index 9ac9ffdb3..51fdedab1 100644 --- a/sci-libs/msms/metadata.xml +++ b/sci-libs/msms/metadata.xml @@ -1,5 +1,5 @@ <?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> </pkgmetadata> diff --git a/sci-libs/msms/msms-1.5.4-r1.ebuild b/sci-libs/msms/msms-1.5.4-r1.ebuild deleted file mode 100644 index ccbf5d931..000000000 --- a/sci-libs/msms/msms-1.5.4-r1.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="3" - -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.* 2.7-pypy-*" - -inherit distutils eutils - -MY_PN="mslib" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="MSMS library python extension module" -HOMEPAGE="http://mgltools.scripps.edu/downloads#msms" -#SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" -SRC_URI="http://dev.gentooexperimental.org/~jlec/distfiles/mgltools_source_${PV}.tar.gz" - -LICENSE="MGLTOOLS" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="" -DEPEND="${RDEPEND} - dev-lang/swig" - -RESTRICT_PYTHON_ABIS="3.*" -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 -} - -src_prepare() { - epatch "${FILESDIR}"/build-with-linux-3.0.patch - pushd "${S}"/lib >/dev/null - # Set up symlinks for 3.x kernels - for x in *inux2; do - ln -s ${x} ${x%2}3 - done - popd >/dev/null -} - -pkg_postinst() { - python_mod_optimize ${MY_PN} -} - -pkg_postrm() { - python_mod_cleanup ${MY_PN} -} diff --git a/sci-libs/msms/msms-1.5.6_rc2.ebuild b/sci-libs/msms/msms-1.5.6.ebuild index a6e6a6dc0..4ccd4a49c 100644 --- a/sci-libs/msms/msms-1.5.6_rc2.ebuild +++ b/sci-libs/msms/msms-1.5.6.ebuild @@ -1,22 +1,19 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI="3" +EAPI=5 -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.* 2.7-pypy-*" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils eutils +inherit distutils-r1 MY_PN="mslib" MY_P="${MY_PN}-${PV/_rc2/}" DESCRIPTION="MSMS library python extension module" HOMEPAGE="http://mgltools.scripps.edu/downloads#msms" -#SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" -SRC_URI="http://dev.gentoo.org/~jlec/distfiles/mgltools_source_${PV/_/}.tar.gz" +SRC_URI="http://mgltools.scripps.edu/downloads/tars/releases/REL${PV}/mgltools_source_${PV}.tar.gz" LICENSE="MGLTOOLS" SLOT="0" @@ -29,13 +26,15 @@ DEPEND="${RDEPEND} S="${WORKDIR}"/${MY_P} +PATCHES=( "${FILESDIR}"/build-with-linux-3.0.patch ) + src_unpack() { tar xzpf "${DISTDIR}"/${A} mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz tar xzpf mgltools_source_${PV/_/}/MGLPACKS/${MY_P}.tar.gz } -src_prepare() { - epatch "${FILESDIR}"/build-with-linux-3.0.patch +python_prepare_all() { + distutils-r1_python_prepare_all pushd "${S}"/lib >/dev/null # Set up symlinks for 3.x kernels for x in *inux2; do diff --git a/sci-mathematics/ufc/ChangeLog b/sci-mathematics/ufc/ChangeLog index e65857704..cbba8f5a0 100644 --- a/sci-mathematics/ufc/ChangeLog +++ b/sci-mathematics/ufc/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-mathematics/ufc -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Jul 2013; Christoph Junghans <ottxor@gentoo.org> ufc-1.4.2.ebuild: + bumped to EAPI=5 + *ufc-1.4.2 (13 Dec 2010) 13 December 2010; Nico Schlömer <nico.schloemer@gmail.com> diff --git a/sci-mathematics/ufc/ufc-1.4.2.ebuild b/sci-mathematics/ufc/ufc-1.4.2.ebuild index 560c678d6..47a9f8249 100644 --- a/sci-mathematics/ufc/ufc-1.4.2.ebuild +++ b/sci-mathematics/ufc/ufc-1.4.2.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=5 + inherit cmake-utils DESCRIPTION="Unified framework for finite element assembly" diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog deleted file mode 100644 index 7734e6588..000000000 --- a/sci-physics/lammps/ChangeLog +++ /dev/null @@ -1,58 +0,0 @@ -# ChangeLog for sci-physics/lammps -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 26 Jun 2013; Christoph Junghans <ottxor@gentoo.org> lammps-20130526.ebuild: - clean up - - 28 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130526.ebuild: - Moved html documentation one folder up. - -*lammps-20130526 (28 May 2013) - - 28 May 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130526.ebuild: - Version bump. - - 28 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130514.ebuild: - Added html documentation. - - 16 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130514.ebuild: - Fixed spelling in doc install. - -*lammps-20130514 (16 May 2013) - - 16 May 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130514.ebuild: - Version bump to 14 May 2013. - - 15 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild - -files/Makefile.gentoo-serial.patch: - Added mpi use flag. This ebuild builds either the serial version (without the - mpi use flag), or the parallel version. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild: - Moved a variable definition. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild, - metadata.xml: - Added more use flags to control the build process. It seems, at least on my - system, that the LAMMPS_MEMALIGN option is a guarantee for a segfault. I made - the use of this macro optional. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild: - Cleaned up the make command line arguments. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild: - The meam package doesn't like to be built in parallel. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130512.ebuild, - metadata.xml: - lammps: Added use flags for some optional packages. - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> metadata.xml: - Added maintainer (myself) to metadata.xml for lammps. - -*lammps-20130512 (10 May 2013) - - 10 May 2013; Nicolas Bock <nicolasbock@gmail.com> - +files/Makefile.gentoo-serial.patch, +lammps-20130512.ebuild, +metadata.xml: - Added first draft version of lammps. For now this is only the serial version. diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest deleted file mode 100644 index 2bff44d2a..000000000 --- a/sci-physics/lammps/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST lammps-12May13.tar.gz 46932918 SHA256 d2ac793bda61edb17d128320a778b2cb2fcfae78082b8a5ad2703ccb099521c4 SHA512 85c20e0ae951e63eccc40d64541b2f628cd5fcc9928d66ecf1da99dee6b5b0633fa69a64076ecea98e3eda39857e43a5f13d6469a94f0b85da8902eb49482487 WHIRLPOOL f2f8e592c590dbf57b22b64fbe213f037669b64ad30dab59d7ddfd385e5223d1cf93bf1ff6b8527bdfc08cf06069a66d53f8e4eae22f6e2ed27d4a2bce97959a -DIST lammps-14May13.tar.gz 46940072 SHA256 d8e2efb2599422889a5a2fdd57a665e993c0420400e0a7f7df6757ac50e4e68d SHA512 d7404aeb78a2878607821b673c74ba115006262197c2058b0272742e53edc59adf70691a8e1f1c57efc89712e6ed37ee72e1dad6a817c9552abf4411ae92de7a WHIRLPOOL 3955e808752c94e85101e38f496109b6e704cc2963493bd883e0f3a3cf0d9b75563fdb654d90eb10c21faec5d83d378b61b003921e3018bc9062719a1f1acb22 -DIST lammps-26May13.tar.gz 46937785 SHA256 c3568846ac818857e9cb131f16a7298becd4bc26237a8c4423fb403fbf54d6c0 SHA512 71424d8a422424105a95c63bcdbdafca68f97beb0f7e4a4d8ac4df927191ea3003a73c94c19047953d278151bc6d59120cae49fa11b81e2ab23c719dbc26ca01 WHIRLPOOL b150311fef0d55ea4c046d9138512344ba4add646a712cf86ec1569302e7d96d1d166f67b2b6f452d4a0573b501bd3f25d1f4fb175d2daa261530a843da19d05 diff --git a/sci-physics/lammps/lammps-20130512.ebuild b/sci-physics/lammps/lammps-20130512.ebuild deleted file mode 100644 index dcb882e98..000000000 --- a/sci-physics/lammps/lammps-20130512.ebuild +++ /dev/null @@ -1,72 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -LAMMPSDATE="12May13" - -DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" -HOMEPAGE="http://lammps.sandia.gov/" -SRC_URI="http://lammps.sandia.gov/tars/lammps-${LAMMPSDATE}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}-${LAMMPSDATE}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS= - use gzip && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_GZIP" - use lammps-memalign && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_MEMALIGN" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(use mpi && echo mpic++ || echo $(tc-getCXX)) \ - F90=$(use mpi && echo mpif90 || echo $(tc-getFC)) \ - LINK=$(use mpi && echo mpic++ || echo $(tc-getCXX)) \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(use mpi || echo -I../STUBS) \ - MPI_PATH=$(use mpi || echo -L../STUBS) \ - MPI_LIB=$(use mpi || echo -lmpi_stubs) \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "$S/src/lmp_serial" "lmp" - if use examples; then - insinto "/usr/share/doc/${PF}" - doins -r examples - fi - dodoc README - use doc && dohtml -r docs/*.html -} diff --git a/sci-physics/lammps/lammps-20130514.ebuild b/sci-physics/lammps/lammps-20130514.ebuild deleted file mode 100644 index 61c2e12d3..000000000 --- a/sci-physics/lammps/lammps-20130514.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -LAMMPSDATE="14May13" - -DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" -HOMEPAGE="http://lammps.sandia.gov/" -SRC_URI="http://lammps.sandia.gov/tars/lammps-${LAMMPSDATE}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}-${LAMMPSDATE}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS= - use gzip && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_GZIP" - use lammps-memalign && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_MEMALIGN" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(use mpi && echo mpic++ || echo $(tc-getCXX)) \ - F90=$(use mpi && echo mpif90 || echo $(tc-getFC)) \ - LINK=$(use mpi && echo mpic++ || echo $(tc-getCXX)) \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(use mpi || echo -I../STUBS) \ - MPI_PATH=$(use mpi || echo -L../STUBS) \ - MPI_LIB=$(use mpi || echo -lmpi_stubs) \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - if use examples; then - insinto "/usr/share/doc/${PF}" - doins -r examples - fi - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc - fi -} diff --git a/sci-physics/lammps/lammps-20130526.ebuild b/sci-physics/lammps/lammps-20130526.ebuild deleted file mode 100644 index af4830cdd..000000000 --- a/sci-physics/lammps/lammps-20130526.ebuild +++ /dev/null @@ -1,74 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -MY_P="${PN}-$(date -d "${PV}" +"%d%b%y")" - -DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" -HOMEPAGE="http://lammps.sandia.gov/" -SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - if use examples; then - insinto "/usr/share/doc/${PF}" - doins -r examples - fi - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/metadata.xml b/sci-physics/lammps/metadata.xml deleted file mode 100644 index b5e2ddd5d..000000000 --- a/sci-physics/lammps/metadata.xml +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <longdescription lang="en"> - LAMMPS is a classical molecular dynamics code, and an acronym for - Large-scale Atomic/Molecular Massively Parallel Simulator. - - LAMMPS has potentials for soft materials (biomolecules, polymers) and - solid-state materials (metals, semiconductors) and coarse-grained or - mesoscopic systems. It can be used to model atoms or, more generically, - as a parallel particle simulator at the atomic, meso, or continuum - scale. - - LAMMPS runs on single processors or in parallel using message-passing - techniques and a spatial-decomposition of the simulation domain. The - code is designed to be easy to modify or extend with new functionality. - </longdescription> - <use> - <flag name="lammps-memalign">Enables the use of the posix_memalign() - call instead of malloc() when large chunks or memory are allocated - by LAMMPS</flag> - <flag name="package-meam">modified EAM potential</flag> - <flag name="package-dipole">point dipole particles</flag> - <flag name="package-rigid">rigid bodies</flag> - </use> - <maintainer> - <email>nicolasbock@gmail.com</email> - </maintainer> -</pkgmetadata> - diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog index 34d215b16..4bbc58b3a 100644 --- a/sci-physics/root/ChangeLog +++ b/sci-physics/root/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 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 $ +*root-5.34.09 (29 Jun 2013) + + 29 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-5.34.08.ebuild, + +root-5.34.09.ebuild: + Version bump. + *root-5.34.08 (08 Jun 2013) 08 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-5.34.07.ebuild, diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest index 34616469e..5dd7d5b7b 100644 --- a/sci-physics/root/Manifest +++ b/sci-physics/root/Manifest @@ -1,8 +1,9 @@ -DIST ROOTUsersGuide-5.34.08.pdf 11179787 SHA256 1e153329297a6ec44c13f4dd38b64ae687df6ba4594023adb9c5e644437b608b SHA512 dce9621d162fb34262e6156de5440e6fa4853ff75d6c4139ce688126b5dd417f6db4cde25da6949a5aff40c9d727411ac4edea61f4b6c49b893cf9f231912bc9 WHIRLPOOL 4fde24b2a52389e9706f81a75adfa62e15ef37031453ee42689f277b392ebc66c88c6e3afa628acc73cfad9ef09e234598ce0c268302dc4313de4ab1487de272 DIST ROOTUsersGuide.pdf 9124822 SHA256 70a96c4a2573dc0d320142f86993ecfda24caa755e910340a3014120f2997c8b SHA512 c3b4c18ef2e13968afdf67c6003249d4cfe6ea661fa32ce25127361bae7e3376a25cd3b11591292f3975bcd8105291aca52f2f6214c9fe45f4bd6e7e44d54b25 WHIRLPOOL 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the new cling interactive interpreter based on <pkg>sys-devel/llvm</pkg></flag> <flag name="math">Build all math related libraries plugins, needs <pkg>sci-libs/gsl</pkg> </flag> + <flag name="metric">Default to A4 paper size and metric measurement</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> diff --git a/sci-physics/root/root-5.34.08.ebuild b/sci-physics/root/root-5.34.09.ebuild index 42e4cbd9c..24465e0fe 100644 --- a/sci-physics/root/root-5.34.08.ebuild +++ b/sci-physics/root/root-5.34.09.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.07.ebuild,v 1.1 2013/05/23 23:52:31 bicatali Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.08.ebuild,v 1.2 2013/06/11 16:29:51 bicatali Exp $ EAPI=5 @@ -26,10 +26,12 @@ PATCH_PV3=5.34.05 DESCRIPTION="C++ data analysis framework and interpreter from CERN" HOMEPAGE="http://root.cern.ch/" SRC_URI="${SRC_URI} - doc? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideA4.pdf -> ROOTUsersGuide-${PV}.pdf + doc? ( math? ( ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf ) + metric? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideA4.pdf -> ROOTUsersGuideA4-${PV}.pdf ) + !metric? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideLetter.pdf -> ROOTUsersGuideLetter-${PV}.pdf ) htmldoc? ( http://root.cern.ch/drupal/sites/default/files/rootdrawing-logo.png http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/root-banner.png @@ -38,8 +40,8 @@ SRC_URI="${SRC_URI} SLOT="0" LICENSE="LGPL-2.1" IUSE="+X afs avahi -c++0x doc emacs examples fits fftw graphviz htmldoc - kerberos ldap +math mpi mysql odbc +opengl openmp oracle postgres prefix - pythia6 pythia8 python qt4 +reflex ruby ssl xinetd xml xrootd" + kerberos ldap +math +metric mpi mysql odbc +opengl openmp oracle postgres + prefix pythia6 pythia8 python qt4 +reflex ruby ssl xinetd xml xrootd" REQUIRED_USE=" !X? ( !opengl !qt4 ) @@ -112,7 +114,7 @@ RDEPEND="${CDEPEND} PDEPEND="htmldoc? ( ~app-doc/root-docs-${PV} )" -S="${WORKDIR}/${PN}-v5-34-00-patches" +S="${WORKDIR}/${PN}" pkg_setup() { fortran-2_pkg_setup @@ -289,7 +291,8 @@ doc_install() { cd "${S}" if use doc; then einfo "Installing user's guides" - dodoc "${DISTDIR}"/ROOTUsersGuide-${PV}.pdf + use metric && dodoc "${DISTDIR}"/ROOTUsersGuideA4-${PV}.pdf || \ + dodoc "${DISTDIR}"/ROOTUsersGuideLetter-${PV}.pdf use math && dodoc \ "${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \ "${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog index c7d282511..4d51c0e33 100644 --- a/sys-cluster/charm/ChangeLog +++ b/sys-cluster/charm/ChangeLog @@ -2,34 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ - 26 Jun 2013; Christoph Junghans <ottxor@gentoo.org> charm-6.5.0.ebuild: - make use of usex + 02 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> + +files/charm-6.5.0-charmc-gentoo.patch, charm-6.5.1.ebuild: + Added missing patch. - 24 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - sys-cluster/charm-6.5.0: Reorganized DEPENDs. +*charm-6.5.1 (02 Jul 2013) - 24 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - sys-cluster/charm-6.5.0: Added mpi use flag. - - 31 May 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - Added die to test. - - 31 May 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - Added src_test(). - - 31 May 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - The "-DALLOCA_H" compiler flag appears to be unnecessary... - - 30 May 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild, - metadata.xml: - More cleanup. Beautify! - - 30 May 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: - Added examples use flag. - -*charm-6.5.0 (30 May 2013) - - 30 May 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.5.0.ebuild, - +files/charm-6.5.0-charmc-gentoo.patch, +metadata.xml: - Version bump to sys-cluster/charm-6.5.0. This ebuild fixes bugs - 471740 and 432834. + 02 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +charm-6.5.1.ebuild, + +metadata.xml: + Version bump to sys-cluster/charm-6.5.1 diff --git a/sys-cluster/charm/Manifest b/sys-cluster/charm/Manifest index c5a8d5b5e..0a0377625 100644 --- a/sys-cluster/charm/Manifest +++ b/sys-cluster/charm/Manifest @@ -1 +1 @@ -DIST charm-6.5.0.tar.gz 19215019 SHA256 2f9b8a92a532924f056a398b46779d58a7f9cd58380ba32d22823a63065c8719 SHA512 5826cb83e7cf377c463d51c6206a48ad2d416f7d17cbfe5289980ee20005b3e20ad617f726114294e796a393abbdc60066ca5e2cd63c0f24f26c05b9a5dacce7 WHIRLPOOL 8f0ab920202acb48f1e5a4cc5ab1902c1f58c7cc61627c6637012743f011d12f131369b598071598afaf33ce53a407d167d06778a9de9c52f22877a4b1d4f25e +DIST charm-6.5.1.tar.gz 19265741 SHA256 68aa43e2a6e476e116a7e80e385c25c6ac6497807348025505ba8bfa256ed34a SHA512 1a25c76f3699e30d0614e85f39ea0f594896cbc299b0e670c52fcea176171e8834ea7f9ba3ba0c1957598b0f1cbfa6a4ed9279ae0c030fa32faa6acca879b694 WHIRLPOOL 0def514af09c137b951842250fe112c68e573e8eff7d5911a71ccbe55cc38b319f1d9c4587e706777f748b0c1ef69b63c4161bbf663b05984a566ff325fa49c3 diff --git a/sys-cluster/charm/charm-6.5.0.ebuild b/sys-cluster/charm/charm-6.5.1.ebuild index a6a654594..74ba894be 100644 --- a/sys-cluster/charm/charm-6.5.0.ebuild +++ b/sys-cluster/charm/charm-6.5.1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: $ +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/charm/charm-6.5.0.ebuild,v 1.1 2013/06/26 23:58:38 ottxor Exp $ EAPI=5 @@ -13,7 +13,7 @@ SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}.tar.gz" LICENSE="charm" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="charmdebug cmkopt doc examples mpi smp static-libs tcp" +IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mpi smp static-libs tcp" RDEPEND="mpi? ( virtual/mpi )" DEPEND=" @@ -24,14 +24,26 @@ DEPEND=" virtual/tex-base )" -REQUIRED_USE="charmdebug? ( !cmkopt )" +REQUIRED_USE=" + cmkopt? ( !charmdebug !charmtracing ) + charmproduction? ( !charmdebug !charmtracing )" FORTRAN_STANDARD="90" src_prepare() { # Build shared libraries by default. CHARM_OPTS="--build-shared" - CHARM_OPTS+=" --with-$(usex charmdebug charmdebug production)" + if use charmproduction; then + CHARM_OPTS+=" --with-production" + else + if use charmdebug; then + CHARM_OPTS+=" --with-charmdebug" + fi + + if use charmtracing; then + CHARM_OPTS+=" --with-tracing --with-tracing-commthread" + fi + fi # TCP instead of default UDP for socket comunication # protocol @@ -49,7 +61,7 @@ src_prepare() { -e "/CMK_CC/s:gcc:$(usex mpi "mpicc" "$(tc-getCC)"):g" \ -e '/CMK_F90_MODINC/s:-p:-I:g' \ -e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \ - -i src/arch/$(usex mpi && "mpi" "net")-linux*/*sh || die + -i src/arch/$(usex mpi "mpi" "net")-linux*/*sh || die sed \ -e "s:-o conv-cpm:${LDFLAGS} &:g" \ @@ -63,6 +75,9 @@ src_prepare() { src/scripts/Makefile \ src/arch/net/charmrun/Makefile || die + # Fix QA notice. + append-cflags -DALLOCA_H + einfo "charm opts: ${CHARM_OPTS}" } diff --git a/sys-cluster/charm/metadata.xml b/sys-cluster/charm/metadata.xml index 37dbe451e..ea5896e21 100644 --- a/sys-cluster/charm/metadata.xml +++ b/sys-cluster/charm/metadata.xml @@ -2,8 +2,13 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> + <maintainer> + <email>nicolasbock@gmail.com</email> + </maintainer> <use> <flag name="charmdebug">Enable the charm debugger</flag> + <flag name="charmproduction">Optimize performance of Charm++ runtime</flag> + <flag name="charmtracing">Enable tracing support in Charm++</flag> <flag name="cmkopt">Enable CMK optimisation</flag> <flag name="tcp">Use TCP (instead of UPD) for socket communication</flag> </use> diff --git a/sys-cluster/charmdebug/ChangeLog b/sys-cluster/charmdebug/ChangeLog index 916d97d60..f6f5e32e9 100644 --- a/sys-cluster/charmdebug/ChangeLog +++ b/sys-cluster/charmdebug/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 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, diff --git a/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild b/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild index 50e9505be..bd227a653 100644 --- a/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild +++ b/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild @@ -18,7 +18,9 @@ KEYWORDS="~amd64 ~x86" IUSE="" DEPEND="" -RDEPEND=">=virtual/jre-1.6" +RDEPEND=" + >=virtual/jre-1.6 + sys-cluster/charm[charmdebug]" src_install() { java-pkg_newjar ${PN}.jar diff --git a/sys-cluster/empi/ChangeLog b/sys-cluster/empi/ChangeLog index b69a7dfb4..067558d85 100644 --- a/sys-cluster/empi/ChangeLog +++ b/sys-cluster/empi/ChangeLog @@ -2,6 +2,20 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Jul 2013; Justin Lecher <jlec@gentoo.org> empi-0.9.ebuild, + -files/ChangeLog-0.8, -files/eselect.mpi-0.8, +files/ChangeLog-0.9, + +files/eselect.mpi-0.9: + Fix version Bump + + 02 Jul 2013; Justin Lecher <jlec@gentoo.org> empi-0.9.ebuild, metadata.xml: + Bump EAPI, fix DESCRIPTION + +*empi-0.9 (02 Jul 2013) + + 02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> -empi-0.8.ebuild, + +empi-0.9.ebuild, -files/empi-0.8, +files/empi-0.9: + bump + *empi-0.8 (22 Feb 2013) 22 Feb 2013; Justin Bronder <jsbronder@gentoo.org> -files/ChangeLog-0.7, diff --git a/sys-cluster/empi/empi-0.8.ebuild b/sys-cluster/empi/empi-0.9.ebuild index bb3daffe0..a78565a9e 100644 --- a/sys-cluster/empi/empi-0.8.ebuild +++ b/sys-cluster/empi/empi-0.9.ebuild @@ -2,9 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=5 + inherit eutils -DESCRIPTION="empi" +DESCRIPTION="Handling Multiple MPI Implementations" HOMEPAGE="http://dev.gentoo.org/~jsbronder/empi.xml" SRC_URI="" @@ -15,13 +17,15 @@ IUSE="" DEPEND="app-admin/eselect" RDEPEND="${DEPEND}" +S="${WORKDIR}" + src_install() { - newbin "${FILESDIR}"/${P} ${PN} || die - dodoc "${FILESDIR}"/README.txt || die - dodoc "${FILESDIR}"/ChangeLog-${PV} || die + newbin "${FILESDIR}"/${P} ${PN} + dodoc "${FILESDIR}"/README.txt + dodoc "${FILESDIR}"/ChangeLog-${PV} insinto /usr/share/eselect/modules - newins "${FILESDIR}"/eselect.mpi-${PV} mpi.eselect || die + newins "${FILESDIR}"/eselect.mpi-${PV} mpi.eselect exeinto /etc/profile.d doexe "${FILESDIR}"/mpi.sh doexe "${FILESDIR}"/mpi.csh diff --git a/sys-cluster/empi/files/ChangeLog-0.8 b/sys-cluster/empi/files/ChangeLog-0.9 index 15652b092..15652b092 100644 --- a/sys-cluster/empi/files/ChangeLog-0.8 +++ b/sys-cluster/empi/files/ChangeLog-0.9 diff --git a/sys-cluster/empi/files/empi-0.8 b/sys-cluster/empi/files/empi-0.9 index a1e6009b6..8a9523c58 100755 --- a/sys-cluster/empi/files/empi-0.8 +++ b/sys-cluster/empi/files/empi-0.9 @@ -1,5 +1,5 @@ #!/bin/bash -VERSION=0.8 +VERSION=0.9 source /etc/init.d/functions.sh @@ -356,7 +356,7 @@ add_packages(){ fi # I don't know about this, but do you have a better idea? - deps="$(emerge --color=n --onlydeps -p --quiet ${TARGETS[i]})" + deps="$(emerge --color=n --onlydeps -p --quiet ${TARGETS[i]} | grep '^\[')" if [[ $? -ne 0 ]]; then emerge --onlydeps -p ${TARGETS[i]} die "Unable to calculate deps for ${TARGETS[i]}" diff --git a/sys-cluster/empi/files/eselect.mpi-0.8 b/sys-cluster/empi/files/eselect.mpi-0.9 index e1f0902a9..e1f0902a9 100644 --- a/sys-cluster/empi/files/eselect.mpi-0.8 +++ b/sys-cluster/empi/files/eselect.mpi-0.9 diff --git a/sys-cluster/empi/metadata.xml b/sys-cluster/empi/metadata.xml index 3d994f9db..16a601fe0 100644 --- a/sys-cluster/empi/metadata.xml +++ b/sys-cluster/empi/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>cluster</herd> - <maintainer> - <email>jsbronder@gentoo.org</email> - </maintainer> + <herd>cluster</herd> + <maintainer> + <email>jsbronder@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sys-cluster/hpl/ChangeLog b/sys-cluster/hpl/ChangeLog index b061ae1b1..9a1784a3b 100644 --- a/sys-cluster/hpl/ChangeLog +++ b/sys-cluster/hpl/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*hpl-2.1 (29 Jun 2013) + + 29 Jun 2013; Andrew Savchenko <bircoph@gmail.com> +hpl-2.1.ebuild: + Version bump. + Fix bug 452984 (use system CFLAGS). + Install HPL.dat properly. + Import ebuild improvements from portage. + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> hpl-2.0-r1.ebuild: Sort *DEPEND correctly diff --git a/sys-cluster/hpl/Manifest b/sys-cluster/hpl/Manifest index 21c146598..86c4ee494 100644 --- a/sys-cluster/hpl/Manifest +++ b/sys-cluster/hpl/Manifest @@ -1 +1,2 @@ -DIST hpl-2.0.tar.gz 591087 SHA256 d8d118c310d34a5a2acf5a689270a9f7bea60245552d24af8641599651909bec +DIST hpl-2.0.tar.gz 591087 SHA256 d8d118c310d34a5a2acf5a689270a9f7bea60245552d24af8641599651909bec SHA512 3aa76144526b01ec40d940cae50d47e480e2760a36d1e95bc6e431b216407db190946fc3d99a6a7caf7b61bcc76d805d28da3ef0b141ff467854e1cdf10bb274 WHIRLPOOL 79da0950089d8e7d6128a2af7a44de704c2666aeb74de08e9e0a06fc23f8c4d17da2ab5107b5f6a82ca073800ec2af4f003c7792ae84e1ec032d9572e78bc0b2 +DIST hpl-2.1.tar.gz 527433 SHA256 dd437dd34a098c51092319983addff1d8076fc8dd692d19c488252477363af15 SHA512 ed39e407341d1cfe2d4d7e50f029e3ca62c7e87e82c3b09a89fd231c5cb4f1c95857f050a940bfd60b724eaa9fdab8631a0693a14b6e9dac82c05897bff557a4 WHIRLPOOL 7e0ff3132590869cff9366c3e34d1abcbfc2be6fceccd336785ce680412981bde658fb67a3663235e15b432c7e0b7e95b79296029d051dbccec239c0c960ae20 diff --git a/sys-cluster/hpl/hpl-2.1.ebuild b/sys-cluster/hpl/hpl-2.1.ebuild new file mode 100644 index 000000000..ac066244b --- /dev/null +++ b/sys-cluster/hpl/hpl-2.1.ebuild @@ -0,0 +1,71 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sys-cluster/hpl/hpl-2.0-r2.ebuild,v 1.1 2013/02/27 15:57:37 jlec Exp $ + +EAPI=5 + +inherit eutils mpi multilib + +DESCRIPTION="A Portable Implementation of the High-Performance Linpack Benchmark for Distributed-Memory Computers" +HOMEPAGE="http://www.netlib.org/benchmark/hpl/" +SRC_URI="http://www.netlib.org/benchmark/hpl/hpl-${PV}.tar.gz" + +SLOT="0" +LICENSE="HPL" +KEYWORDS="~x86 ~amd64" +IUSE="doc" + +RDEPEND=" + $(mpi_pkg_deplist) + virtual/blas + virtual/lapack" +DEPEND="${DEPEND} + virtual/pkgconfig" + +src_prepare() { + local mpicc_path="$(mpi_pkg_cc)" + local a="" + local locallib="${EPREFIX}/usr/$(get_libdir)/lib" + local localblas="$(for i in $($(tc-getPKG_CONFIG) --libs-only-l blas lapack);do a="${a} ${i/-l/${locallib}}.so "; done; echo ${a})" + + cp setup/Make.Linux_PII_FBLAS Make.gentoo_hpl_fblas_x86 || die + sed -i \ + -e "/^TOPdir/s,= .*,= ${S}," \ + -e '/^HPL_OPTS\>/s,=,= -DHPL_DETAILED_TIMING -DHPL_COPY_L,' \ + -e '/^ARCH\>/s,= .*,= gentoo_hpl_fblas_x86,' \ + -e '/^MPdir\>/s,= .*,=,' \ + -e '/^MPlib\>/s,= .*,=,' \ + -e "/^LAlib\>/s,= .*,= ${localblas}," \ + -e "/^LINKER\>/s,= .*,= ${mpicc_path}," \ + -e "/^CC\>/s,= .*,= ${mpicc_path}," \ + -e "/^CCFLAGS\>/s|= .*|= \$(HPL_DEFS) ${CFLAGS}|" \ + -e "/^LINKFLAGS\>/s|= .*|= ${LDFLAGS}|" \ + Make.gentoo_hpl_fblas_x86 || die +} + +src_compile() { + mpi_pkg_set_env + # parallel make failure bug #321539 + HOME=${WORKDIR} emake -j1 arch=gentoo_hpl_fblas_x86 + mpi_pkg_restore_env +} + +src_install() { + mpi_dobin bin/gentoo_hpl_fblas_x86/xhpl + mpi_dolib.a lib/gentoo_hpl_fblas_x86/libhpl.a + mpi_dodoc INSTALL BUGS COPYRIGHT HISTORY README TUNING + mpi_doman man/man3/*.3 + if use doc; then + mpi_dohtml -r www/* + fi + insinto $(mpi_root)usr/share/hpl + mpi_doins bin/gentoo_hpl_fblas_x86/HPL.dat +} + +pkg_postinst() { + local d=$(mpi_root) + einfo "Remember to copy $(mpi_root)usr/share/hpl/HPL.dat to your working directory" + einfo "before running xhpl. Typically one may run hpl by executing:" + einfo "\"mpiexec -np 4 /usr/bin/xhpl\"" + einfo "where -np specifies the number of processes." +} diff --git a/sys-cluster/modules/ChangeLog b/sys-cluster/modules/ChangeLog index b41003680..2c395a5fe 100644 --- a/sys-cluster/modules/ChangeLog +++ b/sys-cluster/modules/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*modules-3.2.10-r1 (26 Jun 2013) + + 26 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +files/createmodule.py, + +files/createmodule.sh, +files/modules-3.2.10-avail.patch, + +files/modules-3.2.10-bindir.patch, +files/modules-3.2.10-clear.patch, + +files/modules-3.2.10-versioning.patch, +files/modules.sh.in, + +modules-3.2.10-r1.ebuild, metadata.xml: + sys-cluster/modules: Prefix keyworded. Added tests. FHS fixes. Add bunch of + fedora patches + *modules-3.2.10 (06 Jun 2013) 06 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> +modules-3.2.10.ebuild: diff --git a/sys-cluster/modules/files/createmodule.py b/sys-cluster/modules/files/createmodule.py new file mode 100755 index 000000000..60c6ba7fa --- /dev/null +++ b/sys-cluster/modules/files/createmodule.py @@ -0,0 +1,186 @@ +#!/usr/bin/python +# +# createmodule.py - Takes the name of a environment init script and +# produces a modulefile that duplicates the changes made by the init script +# +# Copyright (C) 2012 by Orion E. Poplawski <orion@cora.nwra.com> +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 2 of the License, or +# (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +from optparse import OptionParser +import os,sys +from subprocess import * + +# Handle options +usage = "Usage: %prog [-p prefix] <initscript> [args]" +parser = OptionParser() +parser.set_usage(usage) +parser.add_option('-p', '--prefix', dest='prefix', help='Specify path prefix') +(options, args) = parser.parse_args() + +# Need a script name +if not args: + parser.print_usage() + exit(1) + +# Return environment after a command +def getenv(cmd = ':'): + env = {} + p = Popen(cmd + ";env", shell=True, stdout=PIPE, stderr=PIPE) + (stdout, stderr) = p.communicate() + if p.returncode != 0: + print "EROR: Could not execute initscript:" + print "%s returned exit code %d" % (cmd, p.returncode) + print stderr + exit(1) + if stderr != '': + print "WARNING: initscript sent the following to stderr:" + print stderr + # Parse the output key=value pairs + for line in stdout.splitlines(): + try: + (var,value) = line.split('=',1) + except ValueError: + print "ERROR: Could not parse output:" + print stdout + exit(1) + env[var] = value + return env + +#Record initial environment +env1=getenv() + +#Record environment after sourcing the initscript +env2=getenv(". " + " ".join(args)) + +# Initialize our variables for storing modifications +chdir = None +appendpath = {} +prependpath = {} +setenv = {} +unsetenv = [] +pathnames = [] + +# Function to nomalize all paths in a list of paths and remove duplicate items +def normpaths(paths): + newpaths = [] + for path in paths: + normpath = os.path.normpath(path) + if normpath not in newpaths: + newpaths.append(os.path.normpath(path)) + return newpaths + +# Start with existing keys and look for changes +for key in env1.keys(): + # Test for delete + if key not in env2: + unsetenv.append(key) + continue + # No change + if env1[key] == env2[key]: + del env2[key] + continue + #Working directory change + if key == 'PWD': + chdir=os.path.normpath(env2[key]) + pathnames.append(chdir) + del env2[key] + continue + # Determine modifcations to beginning and end of the string + (prepend,append) = env2[key].split(env1[key]) + if prepend: + prependpaths = prepend.strip(':').split(':') + # LICENSE variables often include paths outside install directory + if 'LICENSE' not in key: + pathnames += prependpaths + prependpath[key] = ':'.join(normpaths(prependpaths)) + if append: + appendpaths = append.strip(':').split(':') + # LICENSE variables often include paths outside install directory + if 'LICENSE' not in key: + pathnames += appendpaths + appendpath[key] = ':'.join(normpaths(appendpaths)) + del env2[key] + +# We're left with new keys in env2 +for key in env2.keys(): + # Use prepend-path for new paths + if ('PATH' in key) or (':' in env2[key]): + prependpaths = env2[key].strip(':').split(':') + # MANPATH can have system defaults added it it wasn't previously set + # LICENSE variables often include paths outside install directory + if key != 'MANPATH' and 'LICENSE' not in key: + pathnames += prependpaths + prependpath[key] = ':'.join(normpaths(prependpaths)) + continue + # Set new variables + setenv[key] = os.path.normpath(env2[key]) + if 'LICENSE' not in key: + pathnames.append(setenv[key]) + +# Determine a prefix +prefix = None +if options.prefix: + prefix = options.prefix +else: + prefix = os.path.commonprefix(pathnames).rstrip('/') + if prefix == '': + prefix = None + +# Print out the modulefile +print "#%Module 1.0" + +# Prefix +if prefix is not None: + print "\nset prefix " + prefix + "\n" + +# Chdir +if chdir is not None: + print "chdir\t" + chdir + +# Function to format output line with tabs and substituting prefix +def formatline(item, key, value=None): + print item, + print "\t"*(2-(len(item)+1)/8), + print key, + if value is not None: + print "\t"*(3-(len(key)+1)/8), + if prefix is not None: + print value.replace(prefix,'$prefix') + else: + print value + +# Paths first, grouped by variable name +pathkeys = appendpath.keys() + prependpath.keys() +pathkeys.sort() +for key in pathkeys: + if key in prependpath: + formatline("prepend-path",key,prependpath[key]) + if key in appendpath: + formatline("append-path",key,appendpath[key]) + +# Setenv +setenvkeys = setenv.keys() +setenvkeys.sort() +if setenvkeys: + print +for key in setenvkeys: + formatline("setenv",key,setenv[key]) + +# Unsetenv +unsetenv.sort() +if unsetenv: + print +for key in unsetenv: + formatline("unsetenv",key) diff --git a/sys-cluster/modules/files/createmodule.sh b/sys-cluster/modules/files/createmodule.sh new file mode 100755 index 000000000..b44cf0512 --- /dev/null +++ b/sys-cluster/modules/files/createmodule.sh @@ -0,0 +1,166 @@ +#!/bin/bash +# +# createmodule.sh - Takes the name of a environment init script and +# produces a modulefile that duplicates the changes made by the init script +# +# Copyright (C) 2010-2012 by Orion E. Poplawski <orion@cora.nwra.com> +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 2 of the License, or +# (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. + +# You should have received a copy of the GNU General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +usage="Usage: $0 [-p prefix] <initscript> [args]" + +usage() { + echo $usage 1>&2 + exit 1 +} + +while getopts "p:" opt +do + case $opt in + p) prefix=$OPTARG; shift 2;; + *) usage;; + esac +done + +# Need a script name +[ -z "$1" ] && usage + +# Need to be a readable script +if [ ! -r "$1" ] +then + echo "ERROR: Cannot read $1" 1>&2 + exit 1 +fi + +#Will print out array assignment list +printenvarray () { + env | while read x + do + key=${x%%=*} + value=${x#*=} + echo [$key]="'$value'" + done +} + +#Apparently we need to declare the associative arrays +declare -A env1 env2 + +#Record starting environment +eval env1=(`printenvarray`) + +#Source the environment script +. "$@" + +#Record ending environment +eval env2=(`printenvarray`) + +#Print out the modulefile +echo "#%Module 1.0" + +#Prefix +[ -n "$prefix" ] && echo -e "\nset prefix $prefix\n" + +#Subshell so we can sort the output +( +dedup() { + list=`mktemp` + echo $1 | sed -r -e 's,[^/]+/\.\./,,g' -e 's,[^/]+/\.\./,,g' -e 's/:/\n/g' | + while read x + do + grep -Fx ${x} $list && continue + if [ -n "$prefix" ] + then + echo $x | sed -e s,$prefix,\$prefix, + else + echo $x + fi + echo $x >> $list + done | tr '\n' : | sed -e 's/:$//' + rm $list +} + +#Keys that changed +for key in "${!env1[@]}" +do + if [ "${env1[$key]}" != "${env2[$key]}" ] + then + #Working directory change + if [ "$key" = PWD ] + then + if [ -n "$prefix" ] + then + echo -e "chdir\t\t${env2[PWD]}" | sed -e s,$prefix,\$prefix,g + else + echo -e "chdir\t\t${env2[PWD]}" + fi + #Test for delete + elif [ -z "${env2[$key]}" ] + then + echo -e "unsetenv\t${key}\t${env2[$key]}" + #Test for prepend + elif [ "${env2[$key]%${env1[$key]}}" != "${env2[$key]}" ] + then + added=$(dedup ${env2[$key]%:${env1[$key]}}) + echo -e "prepend-path\t$key\t${added}" + #Test for prepend plus : added at end (MANPATH) + elif [ "${env2[$key]%${env1[$key]}:}" != "${env2[$key]}" ] + then + added=$(dedup ${env2[$key]%${env1[$key]}:}) + echo -e "prepend-path\t$key\t${added}" + #Test for append + elif [ "${env2[$key]#${env1[$key]}}" != "${env2[$key]}" ] + then + added=$(dedup ${env2[$key]#:${env1[$key]}}) + echo -e "append-path\t$key\t${added}" + #Test for prepend plus append + elif [ "${env2[$key]%${env1[$key]}:*}" != "${env2[$key]}" ] + then + added=$(dedup ${env2[$key]%:${env1[$key]}*}) + echo -e "prepend-path\t$key\t${added}" + added=$(dedup ${env2[$key]#*${env1[$key]}:}) + echo -e "append-path\t$key\t${added}" + else + #Unhandled + echo "Unhandled change of $key" 1>&2 + echo "Before <${env1[$key]}>" 1>&2 + echo "After <${env2[$key]}>" 1>&2 + fi + fi + #Delete keys we've handled + unset env1[$key] + unset env2[$key] +done + +#New keys +for key in "${!env2[@]}" +do + if [ "$key" = OLDPWD ] + then + continue + fi + #Use prepend-path for new paths + if [ "${key/PATH/}" != "$key" ] + then + # TODO - Need to handle stripping of default MANPATH + echo -e "prepend-path\t${key}\t"$(dedup ${env2[$key]}) + else + if [ -n "$prefix" ] + then + echo -e "setenv\t\t${key}\t${env2[$key]}" | sed -e s,$prefix,\$prefix,g + else + echo -e "setenv\t\t${key}\t${env2[$key]}" + fi + fi +done +) | sort diff --git a/sys-cluster/modules/files/modules-3.2.10-avail.patch b/sys-cluster/modules/files/modules-3.2.10-avail.patch new file mode 100644 index 000000000..8d6f52b92 --- /dev/null +++ b/sys-cluster/modules/files/modules-3.2.10-avail.patch @@ -0,0 +1,12 @@ +diff -up modules-3.2.10/init/bash_completion.in.avail modules-3.2.10/init/bash_completion.in +--- modules-3.2.10/init/bash_completion.in.avail 2012-10-25 13:33:34.000000000 -0600 ++++ modules-3.2.10/init/bash_completion.in 2013-01-15 12:05:37.247309733 -0700 +@@ -56,7 +56,7 @@ _module() { + unuse) COMPREPLY=( $(IFS=: compgen -W "${MODULEPATH}" -- "$cur") );; + use|*-a*) ;; # let readline handle the completion + -u|--userlvl) COMPREPLY=( $(compgen -W "novice expert advanced" -- "$cur") );; +- display|help|show|whatis) ++ av*|disp*|help|show|whatis) + COMPREPLY=( $(compgen -W "$(_module_avail)" -- "$cur") );; + *) if test $COMP_CWORD -gt 2 + then diff --git a/sys-cluster/modules/files/modules-3.2.10-bindir.patch b/sys-cluster/modules/files/modules-3.2.10-bindir.patch new file mode 100644 index 000000000..2066d7f13 --- /dev/null +++ b/sys-cluster/modules/files/modules-3.2.10-bindir.patch @@ -0,0 +1,11 @@ +--- modules-3.2.10.orig/init/Makefile.in 2009-09-22 12:13:52.000000000 -0600 ++++ modules-3.2.10/init/Makefile.in 2009-09-23 12:19:50.797470155 -0600 +@@ -404,7 +404,7 @@ + sed -e "/@$(if $(subst 0,,$(WANTS_VERSIONING)),NOT,)VERSIONING\@/d; \ + s,@$(if $(subst 0,,$(WANTS_VERSIONING)),,NOT)VERSIONING\@,,g; \ + s,@prefix\@,${prefix},g; \ +- s,@bindir\@,${exec_prefix}/bin,g; \ ++ s,@bindir\@,${bindir},g; \ + s,@VERSION\@,@VERSION@,g; \ + s,@BASEPREFIX\@,@BASEPREFIX@,g;" < $< > $@ + diff --git a/sys-cluster/modules/files/modules-3.2.10-clear.patch b/sys-cluster/modules/files/modules-3.2.10-clear.patch new file mode 100644 index 000000000..0817db5c2 --- /dev/null +++ b/sys-cluster/modules/files/modules-3.2.10-clear.patch @@ -0,0 +1,11 @@ +--- modules-3.2.9/utility.c 2011-11-28 22:27:13.000000000 +0100 ++++ modules-3.2.9-new/utility.c 2012-06-13 15:17:41.570629148 +0200 +@@ -727,7 +727,7 @@ int Output_Modulefile_Changes( Tcl_Inter + output_unset_variable( (char*) key); + } else { + val = EMGetEnv(interp, key); +- if(val && *val) ++ if(val) + output_set_variable(interp, (char*) key, val); + null_free((void *)&val); + } diff --git a/sys-cluster/modules/files/modules-3.2.10-versioning.patch b/sys-cluster/modules/files/modules-3.2.10-versioning.patch new file mode 100644 index 000000000..7bda92023 --- /dev/null +++ b/sys-cluster/modules/files/modules-3.2.10-versioning.patch @@ -0,0 +1,10 @@ +diff -up modules-3.2.10/modulefiles/modules.in.versioning modules-3.2.10/modulefiles/modules.in +--- modules-3.2.10/modulefiles/modules.in.versioning 2012-10-25 13:33:34.000000000 -0600 ++++ modules-3.2.10/modulefiles/modules.in 2013-01-15 11:30:22.046031158 -0700 +@@ -26,5 +26,5 @@ setenv MODULESHOME $prefix + prepend-path PATH @bindir@ + prepend-path MANPATH @mandir@ + +-module use @VERSIONPATH@ ++@VERSIONING@module use @VERSIONPATH@ + diff --git a/sys-cluster/modules/files/modules.sh.in b/sys-cluster/modules/files/modules.sh.in new file mode 100644 index 000000000..6ed502e87 --- /dev/null +++ b/sys-cluster/modules/files/modules.sh.in @@ -0,0 +1,7 @@ +shell=$(basename $(ps -p $$ -ocomm=)) +if [ -f @EPREFIX@/usr/share/Modules/init/${shell} ] +then + . @EPREFIX@/usr/share/Modules/init/${shell} +else + . @PREFIX@/usr/share/Modules/init/sh +fi diff --git a/sys-cluster/modules/metadata.xml b/sys-cluster/modules/metadata.xml index 4c7ca47e8..807627455 100644 --- a/sys-cluster/modules/metadata.xml +++ b/sys-cluster/modules/metadata.xml @@ -1,12 +1,16 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> - The Environment Modules package provides for the dynamic modification of a user's environment via modulefiles. - </longdescription> - <herd>cluster</herd> - <maintainer> - <email>nicolasbock@gmail.com</email> - <name>Nicolas Bock</name> - </maintainer> +<herd>cluster</herd> +<maintainer> + <email>nicolasbock@gmail.com</email> + <name>Nicolas Bock</name> +</maintainer> +<longdescription lang="en"> + The environment modules package provides for an easy dynamic + modification of a user's environment via modulefiles. which + typically instruct the module command to alter or set shell + environment variables such as PATH, MANPATH, etc. as well as define + aliases over a variety of shells. +</longdescription> </pkgmetadata> diff --git a/sys-cluster/modules/modules-3.2.10-r1.ebuild b/sys-cluster/modules/modules-3.2.10-r1.ebuild new file mode 100644 index 000000000..fd8fdd804 --- /dev/null +++ b/sys-cluster/modules/modules-3.2.10-r1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit autotools-utils multilib + +DESCRIPTION="Dynamic modification of a user's environment via modulefiles" +HOMEPAGE="http://modules.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="test X" + +RDEPEND=" + dev-lang/tcl + dev-tcltk/tclx + X? ( x11-libs/libX11 )" +DEPEND="${RDEPEND} + test? ( dev-util/dejagnu )" + +S="${WORKDIR}/${P%[a-z]}" + +DOCS=(ChangeLog README NEWS TODO) + +src_prepare() { + has_version ">=dev-lang/tcl-8.6.0" && \ + epatch "${FILESDIR}"/${P}-errorline.patch + epatch \ + "${FILESDIR}"/${P}-bindir.patch \ + "${FILESDIR}"/${P}-versioning.patch \ + "${FILESDIR}"/${P}-clear.patch \ + "${FILESDIR}"/${P}-avail.patch + sed -e "s:@EPREFIX@:${EPREFIX}:g" \ + "${FILESDIR}"/modules.sh.in > modules.sh +} + +src_configure() { + local myeconfargs=( + --disable-versioning + --prefix="${EPREFIX}/usr/share" + --exec-prefix="${EPREFIX}/usr/share/Modules" + --with-module-path="${EPREFIX}/etc/modulefiles" + --with-tcl="${EPREFIX}/usr/$(get_libdir)" + $(use_with X x) + ) + autotools-utils_src_configure +} + +src_install() { + autotools-utils_src_install + insinto /etc/profile.d + doins modules.sh + exeinto /usr/share/Modules/bin + doexe "${FILESDIR}"/createmodule.{sh,py} + dosym /usr/share/Modules/init/csh /etc/profile.d/modules.csh + dodir /etc/modulesfiles +} diff --git a/sys-cluster/openmpi/ChangeLog b/sys-cluster/openmpi/ChangeLog index 695797172..9b844ff43 100644 --- a/sys-cluster/openmpi/ChangeLog +++ b/sys-cluster/openmpi/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> -openmpi-1.6.4.ebuild: + Remove old + +*openmpi-1.6.4-r1 (02 Jul 2013) + + 02 Jul 2013; Justin Bronder <jsbronder@gentoo.org> + +files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch, + +openmpi-1.6.4-r1.ebuild: + Do not override malloc when in a sandbox environment. Resolves #462602. + *openmpi-1.6.4 (09 Apr 2013) 09 Apr 2013; Justin Bronder <jsbronder@gentoo.org> -openmpi-1.6.3.ebuild, @@ -137,4 +147,3 @@ 20 Jan 2009; Alexey Shvetsov <alexxy@gentoo.org> +openmpi-1.3.ebuild: Version bump - diff --git a/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch b/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch new file mode 100644 index 000000000..5683c81b4 --- /dev/null +++ b/sys-cluster/openmpi/files/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch @@ -0,0 +1,42 @@ +From 094de74dc5e518a931c495692143ea3282553674 Mon Sep 17 00:00:00 2001 +From: Justin Bronder <jsbronder@gmail.com> +Date: Mon, 1 Jul 2013 20:37:17 -0400 +Subject: [PATCH] hooks: disable malloc override inside of Gentoo sandbox + +As described in the comments in the source, Gentoo's own version of +fakeroot, sandbox, also runs into hangs when malloc is overridden. +Sandbox environments can easily be detected by looking for SANDBOX_PID +in the environment. When detected, employ the same fix used for +fakeroot. + +See https://bugs.gentoo.org/show_bug.cgi?id=462602 +--- + opal/mca/memory/linux/hooks.c | 11 +++++++++-- + 1 file changed, 9 insertions(+), 2 deletions(-) + +diff --git a/opal/mca/memory/linux/hooks.c b/opal/mca/memory/linux/hooks.c +index 6a1646f..ce91e76 100644 +--- a/opal/mca/memory/linux/hooks.c ++++ b/opal/mca/memory/linux/hooks.c +@@ -747,9 +747,16 @@ static void opal_memory_linux_malloc_init_hook(void) + "fakeroot" build environment that allocates memory during + stat() (see http://bugs.debian.org/531522). It may not be + necessary any more since we're using access(), not stat(). But +- we'll leave the check, anyway. */ ++ we'll leave the check, anyway. ++ ++ This is also an issue when using Gentoo's version of 'fakeroot', ++ sandbox v2.5. Sandbox environments can also be detected fairly ++ easily by looking for SANDBOX_PID. ++ */ ++ + if (getenv("FAKEROOTKEY") != NULL || +- getenv("FAKED_MODE") != NULL) { ++ getenv("FAKED_MODE") != NULL || ++ getenv("SANDBOX_PID") != NULL ) { + return; + } + +-- +1.8.1.5 + diff --git a/sys-cluster/openmpi/openmpi-1.6.4.ebuild b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild index 3625aa196..1016b4209 100644 --- a/sys-cluster/openmpi/openmpi-1.6.4.ebuild +++ b/sys-cluster/openmpi/openmpi-1.6.4-r1.ebuild @@ -95,6 +95,9 @@ src_prepare() { echo 'oob_tcp_listen_mode = listen_thread' \ >> opal/etc/openmpi-mca-params.conf fi + + # 462602 + epatch "${FILESDIR}"/hooks-disable-malloc-override-inside-of-Gentoo-sandb.patch } src_configure() { @@ -155,6 +158,5 @@ src_test() { # Doesn't work with the default src_test as the dry run (-n) fails. # Do not override malloc during build. Works around #462602 - export FAKEROOTKEY=1 emake -j1 check || die "emake check failed" } diff --git a/sys-cluster/projections/ChangeLog b/sys-cluster/projections/ChangeLog new file mode 100644 index 000000000..a6f3e8ee0 --- /dev/null +++ b/sys-cluster/projections/ChangeLog @@ -0,0 +1,13 @@ +# 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 new file mode 100644 index 000000000..fd66e12c7 --- /dev/null +++ b/sys-cluster/projections/Manifest @@ -0,0 +1 @@ +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 new file mode 100644 index 000000000..334411aca --- /dev/null +++ b/sys-cluster/projections/metadata.xml @@ -0,0 +1,7 @@ +<?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 new file mode 100644 index 000000000..01ed546e4 --- /dev/null +++ b/sys-cluster/projections/projections-6.2.1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 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 +} |