diff options
| author |   Chris Kerr <cjk34@cam.ac.uk> | 2013-06-27 00:12:56 +0100 |
|---|---|---|
| committer | Chris Kerr <cjk34@cam.ac.uk> | 2013-06-27 00:12:56 +0100 |
| commit | abcaad94ebb25bca3f799fce8be60a9174fbff43 (patch) | |
| tree | c04058b6580292bd2c10e5fa80563ad029156706 | |
| parent | condor_config.local is no longer installed in /var/lib/condor (or fowners fai... (diff) | |
| parent | Beautify (diff) | |
| download | sci-abcaad94ebb25bca3f799fce8be60a9174fbff43.tar.gz sci-abcaad94ebb25bca3f799fce8be60a9174fbff43.tar.bz2 sci-abcaad94ebb25bca3f799fce8be60a9174fbff43.zip | |
Merge branch 'master' of https://github.com/gentoo-science/sci into HTCondor
342 files changed, 4115 insertions, 2755 deletions
diff --git a/app-admin/eselect/ChangeLog b/app-admin/eselect/ChangeLog index d7f25de0e..22ea2d48e 100644 --- a/app-admin/eselect/ChangeLog +++ b/app-admin/eselect/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/app-admin/eselect/ChangeLog,v 1.179 2011/01/22 21:38:52 ulm Exp $ +*eselect-1.3.5-r100 (24 Jun 2013) + + 24 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> + +eselect-1.3.5-r100.ebuild, -eselect-1.3.4-r100.ebuild: + app-admin/eselect: Version bump + 24 Jan 2013; Sébastien Fabbro <bicatali@gentoo.org> -eselect-1.3.2-r100.ebuild, -eselect-1.3.3-r100.ebuild, -files/eselect-1.3.2-eroot.patch, metadata.xml: diff --git a/app-admin/eselect/Manifest b/app-admin/eselect/Manifest index b457898c5..e73c757af 100644 --- a/app-admin/eselect/Manifest +++ b/app-admin/eselect/Manifest @@ -1 +1 @@ -DIST eselect-1.3.4.tar.xz 165376 SHA256 9a2fc94d806ca04c20bd60034d3a1acc38caea49fbc66a027a0e9ef531991d33 SHA512 88c35ebee726fa75abe706a547f8ce9239e4bef04620368ae2ea66d7600bff2f17391e145f08e74284668f47a710bdfc427b958023c4f4c4df58bb058ba27a6a WHIRLPOOL b7e8d61218921b89d8cdfb9e42dc6b5401a86a191fe4e792c30fde3d54894e01d0e6c6d702f06a3b88bc7bf6a10d36a95917145b27bc4bcdc9a8968ed9035b45 +DIST eselect-1.3.5.tar.xz 165780 SHA256 aa27fa55863630f81c74486cdca4d3b206d8d8ee71fe3d57fb5c5c5d0117ab9a SHA512 f95400b638ca1a11d7779a80dd742e5b02c68f090beff68090e323d970a18bb35b197bf3c79aea6d12b7c31654b77d57bb01c8d728eff12702ab9854ced0d29d WHIRLPOOL ff45c5dcc061a112f536f271b8b547af1d593f79899c28d6843cb979ecc19a9948ea8123dd64198af0215bfa8f1f2cb0c9a6cf4a627d19f40e2d74f9360026a0 diff --git a/app-admin/eselect/eselect-1.3.4-r100.ebuild b/app-admin/eselect/eselect-1.3.5-r100.ebuild index 02d4c4308..02d4c4308 100644 --- a/app-admin/eselect/eselect-1.3.4-r100.ebuild +++ b/app-admin/eselect/eselect-1.3.5-r100.ebuild diff --git a/app-text/dgs/metadata.xml b/app-text/dgs/metadata.xml index efb490d78..b229aec85 100644 --- a/app-text/dgs/metadata.xml +++ b/app-text/dgs/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/app-text/jabref/ChangeLog b/app-text/jabref/ChangeLog index 220d66d29..cae018a26 100644 --- a/app-text/jabref/ChangeLog +++ b/app-text/jabref/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.10_beta.ebuild: + Fixed bug in jabref ebuild. + +*jabref-2.10_beta (17 Jun 2013) + + 17 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> +jabref-2.10_beta.ebuild, + -jabref-2.10b.ebuild: + Renamed ebuild to conform with Gentoo Ebuild Naming Convention (TM). + http://devmanual.gentoo.org/ebuild-writing/file-format/ + 08 Apr 2013; Nicolas Bock <nicolasbock@gmail.com> jabref-2.10b.ebuild: Jabref-2.10b does not build anymore with Java 6. Bumping java requirement to java 7. diff --git a/app-text/jabref/jabref-2.10b.ebuild b/app-text/jabref/jabref-2.10_beta.ebuild index 3c60f1b5e..0c13e73d7 100644 --- a/app-text/jabref/jabref-2.10b.ebuild +++ b/app-text/jabref/jabref-2.10_beta.ebuild @@ -7,9 +7,11 @@ EAPI=5 EANT_DOC_TARGET=javadocs inherit java-pkg-2 java-ant-2 +SFVERSION="2.10b" + DESCRIPTION="Java GUI for managing BibTeX and other bibliographies" HOMEPAGE="http://jabref.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/JabRef-${PV}-src.tar.bz2" +SRC_URI="mirror://sourceforge/${PN}/JabRef-${SFVERSION}-src.tar.bz2" LICENSE="GPL-2" SLOT="0" @@ -21,8 +23,10 @@ EANT_BUILD_TARGET="jars" DEPEND=">=virtual/jdk-1.7" RDEPEND=">=virtual/jre-1.7" +S="${WORKDIR}/${PN}-${SFVERSION}" + src_install() { - java-pkg_newjar build/lib/JabRef-${PV}.jar + java-pkg_newjar build/lib/JabRef-${SFVERSION}.jar use doc && java-pkg_dojavadoc build/docs/API dodoc src/txt/README java-pkg_dolauncher ${PN} --main net.sf.jabref.JabRef diff --git a/app-vim/freefem++-syntax/metadata.xml b/app-vim/freefem++-syntax/metadata.xml index 76b8e9e22..e831386d6 100644 --- a/app-vim/freefem++-syntax/metadata.xml +++ b/app-vim/freefem++-syntax/metadata.xml @@ -1,8 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> - VIM syntax plugin which provides syntax highlighting for the freefem++ - script files. +<herd>sci</herd> +<longdescription lang="en"> + VIM syntax plugin which provides syntax highlighting for the freefem++ + script files. </longdescription> </pkgmetadata> diff --git a/app-vim/vim-gromacs/metadata.xml b/app-vim/vim-gromacs/metadata.xml index 02f0be7fb..9a7156930 100644 --- a/app-vim/vim-gromacs/metadata.xml +++ b/app-vim/vim-gromacs/metadata.xml @@ -1,7 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <longdescription lang="en"> - VIM syntax plugin which provides syntax highlighting for the gromacs files. +<herd>sci-chemistry</herd> +<longdescription lang="en"> + VIM syntax plugin which provides syntax highlighting for the gromacs files. </longdescription> </pkgmetadata> diff --git a/dev-db/cppdb/metadata.xml b/dev-db/cppdb/metadata.xml index 247592e77..1d2ef4be0 100644 --- a/dev-db/cppdb/metadata.xml +++ b/dev-db/cppdb/metadata.xml @@ -1,13 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>maintainer-wanted@gentoo.org</email> - </maintainer> - <use> - <flag name="mysql_internal">Don't build a separate mysql loadable module but rather build it into the cppdb library itself</flag> - <flag name="odbc_internal">Don't build a separate postgresql loadable module but rather build it into the cppdb library itself</flag> - <flag name="postgres_internal">Don't build a separate odbc loadable module but rather build it into the cppdb library itself</flag> - <flag name="sqlite_internal">Don't build a separate sqlite3 loadable module but rather build it into the cppdb library itself</flag> - </use> +<herd>sci-chemistry</herd> +<maintainer> + <email>maintainer-wanted@gentoo.org</email> +</maintainer> +<use> + <flag name="mysql_internal">Don't build a separate mysql loadable module but rather build it into the cppdb library itself</flag> + <flag name="odbc_internal">Don't build a separate postgresql loadable module but rather build it into the cppdb library itself</flag> + <flag name="postgres_internal">Don't build a separate odbc loadable module but rather build it into the cppdb library itself</flag> + <flag name="sqlite_internal">Don't build a separate sqlite3 loadable module but rather build it into the cppdb library itself</flag> +</use> </pkgmetadata> 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/dev-java/jhealpix/ChangeLog b/dev-java/jhealpix/ChangeLog new file mode 100644 index 000000000..b0d2ba520 --- /dev/null +++ b/dev-java/jhealpix/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-java/jhealpix +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*jhealpix-3.11 (16 Jun 2013) + + 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +jhealpix-3.11.ebuild, + +metadata.xml: + dev-java/jhealpix: Initial import diff --git a/dev-java/jhealpix/Manifest b/dev-java/jhealpix/Manifest new file mode 100644 index 000000000..983581ad4 --- /dev/null +++ b/dev-java/jhealpix/Manifest @@ -0,0 +1 @@ +DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299 diff --git a/dev-java/jhealpix/jhealpix-3.11.ebuild b/dev-java/jhealpix/jhealpix-3.11.ebuild new file mode 100644 index 000000000..e35ff7be6 --- /dev/null +++ b/dev-java/jhealpix/jhealpix-3.11.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +JAVA_PKG_IUSE="doc" +inherit java-pkg-2 java-ant-2 + +MYP="Healpix_${PV}" +MYPP="2013Apr24" + +DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - Java" +HOMEPAGE="http://healpix.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="doc test" + +DEPEND=">=virtual/jdk-1.5 + test? ( dev-java/junit:4 )" +RDEPEND=">=virtual/jre-1.5" + +S="${WORKDIR}/${MYP}/src/java" + +EANT_BUILD_TARGET="distonly distsrc newcompile" +EANT_DOC_TARGET="docs newdocs" + +src_test() { + EANT_TEST_TARGET="test newtest" + EANT_TEST_GENTOO_CLASSPATH="junit-4" + java-pkg-2_src_test +} + +src_install() { + java-pkg_dojar dist/*.jar + dodoc README CHANGES SuggestedIdeas.txt + dodoc ../../READ_Copyrights_Licenses.txt + use doc && java-pkg_dojavadoc healpixdoc +} diff --git a/dev-java/jhealpix/metadata.xml b/dev-java/jhealpix/metadata.xml new file mode 100644 index 000000000..9bb9481d8 --- /dev/null +++ b/dev-java/jhealpix/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-astronomy</herd> +<longdescription lang="en"> + HEALPix is an acronym for Hierarchical Equal Area isoLatitude + Pixelization of a sphere. As suggested in the name, this pixelization produces a + subdivision of a spherical surface in which each pixel covers the same + surface area as every other pixel. This package contains the Java framework. +</longdescription> +</pkgmetadata> diff --git a/dev-lang/ispc/ChangeLog b/dev-lang/ispc/ChangeLog index dddbc8a4d..e7634ed18 100644 --- a/dev-lang/ispc/ChangeLog +++ b/dev-lang/ispc/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Christoph Junghans <ottxor@gentoo.org> ispc-9999.ebuild: + sync with gx86 + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> ispc-9999.ebuild: Drop KEYWORDS of live ebuilds diff --git a/dev-lang/ispc/ispc-9999.ebuild b/dev-lang/ispc/ispc-9999.ebuild index 3b6eac0d8..fa19e5576 100644 --- a/dev-lang/ispc/ispc-9999.ebuild +++ b/dev-lang/ispc/ispc-9999.ebuild @@ -14,13 +14,14 @@ HOMEPAGE="http://ispc.github.com/" if [[ ${PV} = *9999 ]]; then inherit git-2 EGIT_REPO_URI="git://github.com/ispc/ispc.git" + KEYWORDS="" else SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" fi LICENSE="BSD BSD-2 UoI-NCSA" SLOT="0" -KEYWORDS="" IUSE="examples" RDEPEND=" diff --git a/dev-libs/simclist/metadata.xml b/dev-libs/simclist/metadata.xml index 49fb6b89c..1da3891dc 100644 --- a/dev-libs/simclist/metadata.xml +++ b/dev-libs/simclist/metadata.xml @@ -1,14 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - SimCList is a high quality C (C++ embeddable) library for handling - lists. It exploits several advanced techniques for improving - performance, including freelists, sentinels, automatic sort algorithm - selection, sort randomization, mid pointer and optional multithreading. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> +<longdescription> + SimCList is a high quality C (C++ embeddable) library for handling + lists. It exploits several advanced techniques for improving + performance, including freelists, sentinels, automatic sort algorithm + selection, sort randomization, mid pointer and optional multithreading. +</longdescription> </pkgmetadata> diff --git a/dev-ml/mlgmpidl/metadata.xml b/dev-ml/mlgmpidl/metadata.xml index c6107f8e5..a3fac8132 100644 --- a/dev-ml/mlgmpidl/metadata.xml +++ b/dev-ml/mlgmpidl/metadata.xml @@ -1,17 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - MLGMPIDL is a package offering an interface to the GMP and MPFR - libraries for OCaml version 3.07 or higher. The interface offers access - to almost all the functions of the library, and is decomposed into 7 - submodules. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="mpfr">add support for mpfr, the library for multiple-precision floating-point computations with exact rounding</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + MLGMPIDL is a package offering an interface to the GMP and MPFR + libraries for OCaml version 3.07 or higher. The interface offers access + to almost all the functions of the library, and is decomposed into 7 + submodules. +</longdescription> +<use> + <flag name="mpfr">Add support for <pkg>dev-libs/mpfr</pkg></flag> +</use> </pkgmetadata> diff --git a/dev-ml/ocamlgraph/metadata.xml b/dev-ml/ocamlgraph/metadata.xml index 763c1cd36..87fc10d58 100644 --- a/dev-ml/ocamlgraph/metadata.xml +++ b/dev-ml/ocamlgraph/metadata.xml @@ -1,32 +1,23 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - It provides an easy-to-use graph data structure together with several - operations and algorithms over graphs, in Graph.Pack. It is a reasonably - efficient imperative data structure for directed graphs with vertices - and edges labeled with integers. Several other graph implementations - are proposed for those not satisfied with the one above. Some are - persistent (imutable) and other imperative (mutable). Some are directed - and other are not. Some have labels for vertices, or labels for edges, - or both. Some have abstract types for vertices. etc. These - implementations are written as functors: you give the types of vertices - labels, edge labels, etc. and you get the data structure as a result. - it also provides several classic operations and algorithms over graphs. - They are also written as functors i.e. independently of the data - structure for graphs. One consequence is that you can define your own - data structure for graphs and yet re-use all the algorithms from this - library: you only need to provide a few operations such as iterating - over all vertices, over the successors of a vertex, etc. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="doc">?doc?</flag> - <flag name="examples">?examples?</flag> - <flag name="gtk">?gtk?</flag> - <flag name="ocamlopt">?ocamlopt?</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + It provides an easy-to-use graph data structure together with several + operations and algorithms over graphs, in Graph.Pack. It is a reasonably + efficient imperative data structure for directed graphs with vertices + and edges labeled with integers. Several other graph implementations + are proposed for those not satisfied with the one above. Some are + persistent (imutable) and other imperative (mutable). Some are directed + and other are not. Some have labels for vertices, or labels for edges, + or both. Some have abstract types for vertices. etc. These + implementations are written as functors: you give the types of vertices + labels, edge labels, etc. and you get the data structure as a result. + it also provides several classic operations and algorithms over graphs. + They are also written as functors i.e. independently of the data + structure for graphs. One consequence is that you can define your own + data structure for graphs and yet re-use all the algorithms from this + library: you only need to provide a few operations such as iterating + over all vertices, over the successors of a vertex, etc. +</longdescription> </pkgmetadata> diff --git a/dev-ml/zarith/metadata.xml b/dev-ml/zarith/metadata.xml index e75004328..1ff321877 100644 --- a/dev-ml/zarith/metadata.xml +++ b/dev-ml/zarith/metadata.xml @@ -1,17 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - The Zarith library implements arithmetic and logical operations over - arbitrary-precision integers. It uses GMP to efficiently implement - arithmetic over big integers. Small integers are represented as Caml - unboxed integers, for speed and space economy. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="ocamlopt">?ocamlopt?</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + The Zarith library implements arithmetic and logical operations over + arbitrary-precision integers. It uses GMP to efficiently implement + arithmetic over big integers. Small integers are represented as Caml + unboxed integers, for speed and space economy. +</longdescription> </pkgmetadata> diff --git a/dev-perl/opal-client/metadata.xml b/dev-perl/opal-client/metadata.xml index efb490d78..b229aec85 100644 --- a/dev-perl/opal-client/metadata.xml +++ b/dev-perl/opal-client/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/dev-python/healpy/ChangeLog b/dev-python/healpy/ChangeLog new file mode 100644 index 000000000..aec23ab26 --- /dev/null +++ b/dev-python/healpy/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for dev-python/healpy +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*healpy-1.6.2 (17 Jun 2013) + + 17 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +healpy-1.6.2.ebuild, + +metadata.xml: + dev-python/healpy: Initial import diff --git a/dev-python/healpy/Manifest b/dev-python/healpy/Manifest new file mode 100644 index 000000000..cf81bf69d --- /dev/null +++ b/dev-python/healpy/Manifest @@ -0,0 +1 @@ +DIST healpy-1.6.2.tar.gz 7238630 SHA256 76f13969898c29823fba3540b5690fb3ff22d3b8dfcdb6fc9d7f888d0ddbdda1 SHA512 75afd814d5636f69bbeb5012deb5e32a64271711d1bde3f3bed3e8f553515f4c656b62bd113e57178bb9c75328843e016f7c0e785848593e389f88c6090fde55 WHIRLPOOL c5afe980a5f7ef328f7d8aa66e248c9815a13261c1ac4e932e7464a5ef44d55df96d4c312e537c4e1babea96c4ec4e8ce5c2bbddde2174a504c0d45447dcf75c diff --git a/dev-python/healpy/healpy-1.6.2.ebuild b/dev-python/healpy/healpy-1.6.2.ebuild new file mode 100644 index 000000000..485c1b820 --- /dev/null +++ b/dev-python/healpy/healpy-1.6.2.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 + +DESCRIPTION="Python wrapper for healpix" +HOMEPAGE="https://github.com/healpy" +SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyfits[${PYTHON_USEDEP}] + sci-astronomy/healpix_cxx + sci-libs/cfitsio" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +python_test() { + cd "${BUILD_DIR}"/lib* + echo "backend: Agg" > matplotlibrc + MPLCONFIGDIR=. PYTHONPATH=. nosetests-"${EPYTHON}" || die + rm matplotlibrc +} diff --git a/dev-python/healpy/metadata.xml b/dev-python/healpy/metadata.xml new file mode 100644 index 000000000..044ede51b --- /dev/null +++ b/dev-python/healpy/metadata.xml @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-astronomy</herd> +<longdescription lang='en'> + Healpy provides a python package to manipulate healpix maps. It is + based on the standard numeric and visualisation tools for Python, + Numpy and matplotlib. +</longdescription> +</pkgmetadata> diff --git a/dev-python/opal-client/ChangeLog b/dev-python/opal-client/ChangeLog index ac3fec3a2..d9bb7eb3e 100644 --- a/dev-python/opal-client/ChangeLog +++ b/dev-python/opal-client/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for dev-python/opal-client -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*opal-client-2.4.1 (15 Jun 2013) + + 15 Jun 2013; Justin Lecher <jlec@gentoo.org> -opal-client-2.2-r1.ebuild, + +opal-client-2.4.1.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and python-r1.eclass + *opal-client-2.2-r1 (02 Dec 2010) 02 Dec 2010; Justin Lecher <jlec@gentoo.org> -opal-client-2.2.ebuild, diff --git a/dev-python/opal-client/Manifest b/dev-python/opal-client/Manifest index 45e1445b1..adef77f5c 100644 --- a/dev-python/opal-client/Manifest +++ b/dev-python/opal-client/Manifest @@ -1 +1 @@ -DIST opal-py-2.2.tar.gz 1012870 SHA256 d11588ed29dac2812b4293204e0f0d75ba3b765f31af095e0e6333365afe0b47 +DIST opal-py-2.4.1.tar.gz 1089581 SHA256 78d82dbdab607a3acb40e0462a0418b856f3ef8c83cb302f55c4549d672e7085 SHA512 8b8563507d5905a2bc2d36552b52a9ce4da555910496242cfed207ea573da973ac78678fff158066db91154a6f38b5dc8701b8484781143ebd4134b440d01292 WHIRLPOOL 3ebd0992c2ff85974fc369820d42f44a866a1a5fcbbdca80839b14e66b27cb4f1cf2a70a9375078700b117316493934ef8e82965045f4d5602a6d669b6d38587 diff --git a/dev-python/opal-client/metadata.xml b/dev-python/opal-client/metadata.xml index efb490d78..34294c65c 100644 --- a/dev-python/opal-client/metadata.xml +++ b/dev-python/opal-client/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> +<herd>sci-biology</herd> </pkgmetadata> diff --git a/dev-python/opal-client/opal-client-2.2-r1.ebuild b/dev-python/opal-client/opal-client-2.2-r1.ebuild deleted file mode 100644 index 69f0ed7e4..000000000 --- a/dev-python/opal-client/opal-client-2.2-r1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2010 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.*" - -inherit python - -MY_PN="${PN/client/py}" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Python Opal Web Service Client" -HOMEPAGE="http://nbcr.net/software/opal/" -SRC_URI="mirror://sourceforge/opaltoolkit/${MY_P}.tar.gz" - -LICENSE="opal" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - >=dev-python/zsi-2.1_alpha1 - !=sci-chemistry/apbs-1.1.0" -DEPEND="${RDEPEND}" - -S="${WORKDIR}"/${MY_P} - -src_prepare() { - python_copy_sources -} - -src_install() { - "${EPREFIX}"/usr/bin/wsdl2py wsdl/opal.wsdl || die - - installation() { - insinto $(python_get_sitedir)/AppService - doins AppService_*.py || die - } - python_execute_function -s installation - - dodoc README CHANGELOG etc/* *Client.py || die - dohtml docs/* || die -} - -pkg_postinst() { - python_mod_optimize AppService -} - -pkg_postrm() { - python_mod_cleanup AppService -} diff --git a/dev-python/opal-client/opal-client-2.4.1.ebuild b/dev-python/opal-client/opal-client-2.4.1.ebuild new file mode 100644 index 000000000..0eefd41b6 --- /dev/null +++ b/dev-python/opal-client/opal-client-2.4.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit python-r1 versionator + +MY_PN="${PN/client/py}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Python Opal Web Service Client" +HOMEPAGE="http://www.nbcr.net/data/docs/opal/documentation.html" +SRC_URI="mirror://sourceforge/opaltoolkit/opal-python/$(get_version_component_range 1-2)/${MY_P}.tar.gz" + +LICENSE="opal" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + >=dev-python/zsi-2.1_alpha1[${PYTHON_USEDEP}] + !=sci-chemistry/apbs-1.1.0" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/${MY_P} + +src_install() { + "${EPREFIX}"/usr/bin/wsdl2py wsdl/opal.wsdl || die + + installation() { + python_moduleinto AppService + python_domodule AppService_*.py + python_optimize "${ED}"/$(python_get_sitedir) + } + python_parallel_foreach_impl installation + + dodoc README CHANGELOG etc/* *Client.py + dohtml docs/* +} diff --git a/dev-tcltk/img_rotate/metadata.xml b/dev-tcltk/img_rotate/metadata.xml index 4bf6dbc6b..b229aec85 100644 --- a/dev-tcltk/img_rotate/metadata.xml +++ b/dev-tcltk/img_rotate/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/dev-tcltk/togl/metadata.xml b/dev-tcltk/togl/metadata.xml index efb490d78..b229aec85 100644 --- a/dev-tcltk/togl/metadata.xml +++ b/dev-tcltk/togl/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/licenses/GRL b/licenses/GRL new file mode 100644 index 000000000..8a897b7c9 --- /dev/null +++ b/licenses/GRL @@ -0,0 +1,15 @@ +This software has been created by Genome Research Limited (GRL). +GRL hereby grants permission to use, copy, modify and distribute +this software and its documentation for non-commercial purposes +without fee at the user's own risk on the basis set out below. +GRL neither undertakes nor accepts any duty whether contractual or +otherwise in connection with the software, its use or the use of +any derivative, and makes no representations or warranties, express +or implied, concerning the software, its suitability, fitness for +a particular purpose or non-infringement. +In no event shall the authors of the software or GRL be +responsible or liable for any loss or damage whatsoever arising in +any way directly or indirectly out of the use of this software or + its derivatives, even if advised of the possibility of such damage. +Our software can be freely distributed under the conditions set +out above, and must contain this copyright notice.
\ No newline at end of file diff --git a/licenses/Tablet b/licenses/Tablet index 984a28b72..d81931aad 100644 --- a/licenses/Tablet +++ b/licenses/Tablet @@ -6,7 +6,7 @@ The licence and copyright for Tablet is as follows: - Copyright © 2009-2010, Plant Bioinformatics Group, SCRI + Copyright © 2009-2013, Information & Computational Sciences, JHI. All rights reserved. Redistribution and use in binary form, without modification, is @@ -15,9 +15,9 @@ - Redistributions must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. - - Neither the name of SCRI nor the names of its contributors may be - used to endorse or promote products derived from this software without - specific prior written permission. + - Neither the name of The James Hutton Institute nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED diff --git a/media-gfx/librecad/ChangeLog b/media-gfx/librecad/ChangeLog index 136cdde70..be52d5aad 100644 --- a/media-gfx/librecad/ChangeLog +++ b/media-gfx/librecad/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header$ + 17 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> + -files/1.0.0_rc2-gcc4.6.patch, -files/librecad-1.0.0_rc2-version.patch, + -librecad-1.0.2.ebuild, -librecad-2.0.0_beta5.ebuild, + librecad-2.0.0_rc1.ebuild, metadata.xml: + media-gfx/librecad: Cleanup and apply patch from bug #473388 + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> librecad-9999.ebuild: Drop KEYWORDS of live ebuilds diff --git a/media-gfx/librecad/Manifest b/media-gfx/librecad/Manifest index b9ea34fe7..d74adebb1 100644 --- a/media-gfx/librecad/Manifest +++ b/media-gfx/librecad/Manifest @@ -1,4 +1,2 @@ -DIST librecad-1.0.2.tar.gz 4577097 SHA256 f04ad98b6c9bc0e8f748ef99a7052794155f246c36663e09508810d9acebadad SHA512 4cb8732b047ba01e7d796c51bbc1300e4ee3b674a4ca65c6ff3f18acd0107d3d0e83610f45af86dc164cbf22241558dddc2fb77e31bd2fb33425cb6d7b582889 WHIRLPOOL 73099244f56eb3953fb0a7b80aa5ea3a20adcbaa19a40ca51c14501316e7ebec2a44e30bb669e6ed6797a74c42b0640f959e648c3cee8c7865a9a5f3427b1591 DIST librecad-1.0.3.tar.gz 4578450 SHA256 8c2f5a7e55a4ae41a9bd47e2e7981577c740edd526e1f305cd6cbf581d053f30 SHA512 5a8e6e612bc954f3af0dfc26d1fc19938c80e216ac252fb65a38a13651c6e2313d593a3ee834ecc98bbd72a4dfd28ef1c39dd9ed6a6f9140d28b765edb59bee9 WHIRLPOOL d8157af2021bba2cee626d023125045455a2fe5f453ae065c9660be61f4c0d687a1c72957d1af1aa640cfde3815625bb7d0899dc5541fcb82bfe0eea4cfad6c6 -DIST librecad-2.0.0_beta5.tar.gz 15196079 SHA256 8d21a2b887d65ea28ac7fde1d0dea373f8267767e33ae26c0207ec1f6d42656f SHA512 22ec041a0a36bd9f59d2bf22aa343824b54c83febeb8b6fd836e4e3a821617ae80f2e5b7c38250b5791b946f8494561b49d9a880b49383c52395a04f0cb57547 WHIRLPOOL 20805394d0576c380b491fe7c02af3adfcbf09850ff84dee3155206746746e5f39b9cc2556836e74bd9c9449e7c50757b9f3ff3fcab6083abd140d0a3934ed06 -DIST librecad-2.0.0_rc1.tar.gz 15196079 SHA256 8d21a2b887d65ea28ac7fde1d0dea373f8267767e33ae26c0207ec1f6d42656f SHA512 22ec041a0a36bd9f59d2bf22aa343824b54c83febeb8b6fd836e4e3a821617ae80f2e5b7c38250b5791b946f8494561b49d9a880b49383c52395a04f0cb57547 WHIRLPOOL 20805394d0576c380b491fe7c02af3adfcbf09850ff84dee3155206746746e5f39b9cc2556836e74bd9c9449e7c50757b9f3ff3fcab6083abd140d0a3934ed06 +DIST librecad-2.0.0_rc1.zip 16210997 SHA256 9a5345463c19b64cf5f4e4f308460988a60ce4c8c8d311b08d16805fbec68f90 SHA512 b97eaf81050cfe06a7910ac3a7c64d7906dec3159ac3e5f24f92bd74e60d86c67b661b65fd6c258996043e8c4ae09b1d8d5cb92aea28b313eca10e54149abde1 WHIRLPOOL 768244e63bf34bfff259712fd1c5e9aee872eda496106bc8e33ab5f4c3f1c8c0131167984d55bf5d6e82d9af0e2cdb5e01a5d125f19749369679dfbf7bd60f5f diff --git a/media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch b/media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch deleted file mode 100644 index b912801d6..000000000 --- a/media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch +++ /dev/null @@ -1,38 +0,0 @@ - fparser/fparser.cc | 4 ++-- - src/lib/engine/rs_ellipse.cpp | 1 + - 2 files changed, 3 insertions(+), 2 deletions(-) - -diff --git a/fparser/fparser.cc b/fparser/fparser.cc -index 49e6ae0..0e65dbb 100644 ---- a/fparser/fparser.cc -+++ b/fparser/fparser.cc -@@ -899,7 +899,7 @@ namespace - byte -= n; - if(byte > (unsigned char)('9'-n)) return false; - unsigned long shifted = 1UL << byte; -- const unsigned long mask = LiteralMask<Value_t, n>::mask; -+ const unsigned long mask = LiteralMask<Value_t, static_cast<unsigned int>(n)>::mask; - return (mask & shifted) != 0; - } - -@@ -956,7 +956,7 @@ U+000B \v - if(byte <= (unsigned char)(' '-n)) - { - unsigned long shifted = 1UL << byte; -- const unsigned long mask = SimpleSpaceMask<n>::mask; -+ const unsigned long mask = SimpleSpaceMask<static_cast<unsigned int>(n)>::mask; - if(mask & shifted) - { ++function; continue; } // \r, \n, \t, \v and space - break; -diff --git a/src/lib/engine/rs_ellipse.cpp b/src/lib/engine/rs_ellipse.cpp -index 452de0a..7ccc807 100644 ---- a/src/lib/engine/rs_ellipse.cpp -+++ b/src/lib/engine/rs_ellipse.cpp -@@ -24,6 +24,7 @@ - ** - **********************************************************************/ - -+#include <algorithm> - - #include "rs_ellipse.h" - diff --git a/media-gfx/librecad/files/librecad-1.0.0_rc2-version.patch b/media-gfx/librecad/files/librecad-1.0.0_rc2-version.patch deleted file mode 100644 index da103c51b..000000000 --- a/media-gfx/librecad/files/librecad-1.0.0_rc2-version.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- LibreCAD-LibreCAD-460bd78/librecad.pro 2011-08-26 22:26:35.201935340 -0400 -+++ LibreCAD-LibreCAD-460bd78/librecad.pro 2011-08-26 22:26:59.138898865 -0400 -@@ -24,7 +24,7 @@ - # Get SVN revision number - # SVNREVISION = $$system(svn info -R | grep -o \"Revision: [0-9]*\" | sed -e \"s/Revision: //\" | head -n1) - # Temporary disabled getting SCM version -- SCMREVISION=$$system(git describe --tags) -+ SCMREVISION=1.0.0_rc2 - DEFINES += QC_SCMREVISION=\"$$SCMREVISION\" - macx { - CONFIG += x86 x86_64 diff --git a/media-gfx/librecad/librecad-1.0.2.ebuild b/media-gfx/librecad/librecad-1.0.2.ebuild deleted file mode 100644 index c9f90681f..000000000 --- a/media-gfx/librecad/librecad-1.0.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit qt4-r2 eutils - -DESCRIPTION="An generic 2D CAD program" -HOMEPAGE="http://www.librecad.org/" -SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/v1.0.2.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc" - -RDEPEND=" - dev-qt/qtgui[qt3support] - dev-qt/qthelp:4 - dev-qt/qt3support:4 - dev-cpp/muParser - " - -DEPEND="${RDEPEND}" - -src_unpack() { - unpack ${A} - mv * ${P} -} - -src_prepare() { -sed -i -e "s:\\\$\+system(git describe --tags):1.0.2:" "${PN}.pro" -} - -src_install() { - dobin unix/librecad || die - insinto /usr/share/"${PN}" - doins -r unix/resources/* || die - if use doc ; then - dohtml -r support/doc/* - fi - doicon res/main/"${PN}".png - make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics -} diff --git a/media-gfx/librecad/librecad-2.0.0_beta5.ebuild b/media-gfx/librecad/librecad-2.0.0_beta5.ebuild deleted file mode 100644 index a16e4c8f6..000000000 --- a/media-gfx/librecad/librecad-2.0.0_beta5.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit qt4-r2 eutils flag-o-matic - -DESCRIPTION="An generic 2D CAD program" -HOMEPAGE="http://www.librecad.org/" -SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/2.0.0beta5.tar.gz -> -${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc" - -DEPEND=" - dev-qt/qthelp:4 - dev-qt/qtgui:4 - dev-qt/qtsvg:4 - dev-libs/boost - dev-cpp/muParser - media-libs/freetype - " - -RDEPEND="${DEPEND}" - -src_unpack() { - unpack ${A} - mv * ${P} -} - -src_prepare() { - sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro -} - -src_install() { - dobin unix/librecad - insinto /usr/share/"${PN}" - doins -r unix/resources/* - if use doc ; then - dohtml -r support/doc/* - fi - doicon librecad/res/main/"${PN}".png - make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics -} diff --git a/media-gfx/librecad/librecad-2.0.0_rc1.ebuild b/media-gfx/librecad/librecad-2.0.0_rc1.ebuild index a16e4c8f6..7017bccb8 100644 --- a/media-gfx/librecad/librecad-2.0.0_rc1.ebuild +++ b/media-gfx/librecad/librecad-2.0.0_rc1.ebuild @@ -2,29 +2,27 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit qt4-r2 eutils flag-o-matic -DESCRIPTION="An generic 2D CAD program" +DESCRIPTION="Generic 2D CAD program" HOMEPAGE="http://www.librecad.org/" -SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/2.0.0beta5.tar.gz -> -${P}.tar.gz" +SRC_URI="https://github.com/LibreCAD/LibreCAD/archive/${PV/_/}.zip -> ${P}.zip" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug doc 3d" DEPEND=" - dev-qt/qthelp:4 dev-qt/qtgui:4 + dev-qt/qthelp:4 dev-qt/qtsvg:4 dev-libs/boost dev-cpp/muParser media-libs/freetype " - RDEPEND="${DEPEND}" src_unpack() { @@ -33,16 +31,15 @@ src_unpack() { } src_prepare() { - sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro + # currently RS_VECTOR3D causes an internal compiler error on GCC-4.8 + use 3d || sed -i -e '/RS_VECTOR2D/ s/^#//' librecad/src/src.pro } src_install() { dobin unix/librecad - insinto /usr/share/"${PN}" + insinto /usr/share/${PN} doins -r unix/resources/* - if use doc ; then - dohtml -r support/doc/* - fi - doicon librecad/res/main/"${PN}".png - make_desktop_entry "${PN}" LibreCAD "${PN}.png" Graphics + use doc && dohtml -r support/doc/* + doicon librecad/res/main/${PN}.png + make_desktop_entry ${PN} LibreCAD ${PN} Graphics } diff --git a/media-gfx/librecad/metadata.xml b/media-gfx/librecad/metadata.xml index c79d2dfcf..19375c344 100644 --- a/media-gfx/librecad/metadata.xml +++ b/media-gfx/librecad/metadata.xml @@ -1,15 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>Package maintainer and upstream developer</description> - </maintainer> - <longdescription> -LibreCAD is a 2D CAD drawing tool based on the community edition of QCad -(www.qcad.org). LibreCAD has been re-structured and ported to qt4 and -works natively cross platform. +<herd>sci</herd> +<maintainer> + <email>dongxuli2011@gmail.com</email> + <name>Dongxu Li</name> + <description>Package maintainer and upstream developer</description> +</maintainer> +<longdescription> + LibreCAD is a 2D CAD drawing tool based on the community edition of QCad + (www.qcad.org). LibreCAD has been re-structured and ported to qt4 and + works natively cross platform. </longdescription> +<use> + <flag name="3d">Use 3D vectors</flag> +</use> </pkgmetadata> diff --git a/media-libs/OpenMOIV/metadata.xml b/media-libs/OpenMOIV/metadata.xml index efb490d78..b229aec85 100644 --- a/media-libs/OpenMOIV/metadata.xml +++ b/media-libs/OpenMOIV/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml index efb490d78..b229aec85 100644 --- a/media-libs/libgfx/metadata.xml +++ b/media-libs/libgfx/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/profiles/package.mask b/profiles/package.mask index 05296c8e8..f354cdf57 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -32,6 +32,11 @@ # Live ebuilds go here # keep this on top +>=media-gfx/brlcad-9999 +>=dev-lang/path64-9999 +>=dev-lang/julia-9999 +>=dev-lang/ispc-9999 +>=app-benchmarks/btl-9999 >=sci-chemistry/freeon-9999 >=sci-astronomy/eye-9999 >=sci-astronomy/missfits-9999 @@ -63,6 +68,12 @@ >=sci-chemistry/coot-9999 >=sci-chemistry/pymol-9999 +# Honza Macháček <Hloupy.Honza@centrum.cz> (17 June 2013) +# bigdft moved from sci-libs to sci-physics +# sci-physics/abinit now uses sci-libs/bigdft-abi instead +# sci-libs/bigdft should be deleted in 30 days +sci-libs/bigdft + # Justin Lecher <jlec@gentoo.org> (03 March 2013) # Missing deps sci-biology/gbrowse diff --git a/sci-astronomy/astrometry/ChangeLog b/sci-astronomy/astrometry/ChangeLog index 506805eec..afb42de9e 100644 --- a/sci-astronomy/astrometry/ChangeLog +++ b/sci-astronomy/astrometry/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 14 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> metadata.xml: + sci-astronomy/astrometry: Added extra use flag to plot + + 14 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> astrometry-0.43.ebuild, + files/0.43-system-libs.patch, metadata.xml: + sci-astronomy/astrometry: Added python bindings. Fixed more gsl bundling + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> astrometry-0.43.ebuild, metadata.xml: Fix unquoted variable diff --git a/sci-astronomy/astrometry/astrometry-0.43.ebuild b/sci-astronomy/astrometry/astrometry-0.43.ebuild index 4f197d7dd..96a303520 100644 --- a/sci-astronomy/astrometry/astrometry-0.43.ebuild +++ b/sci-astronomy/astrometry/astrometry-0.43.ebuild @@ -16,20 +16,22 @@ LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="examples" +IUSE="examples extra python" RDEPEND=" dev-python/numpy - media-libs/libpng - media-libs/netpbm sci-astronomy/wcslib sci-libs/cfitsio sci-libs/gsl sys-libs/zlib - virtual/jpeg virtual/pyfits - x11-libs/cairo" + extra? ( + media-libs/libpng + media-libs/netpbm + virtual/jpeg + x11-libs/cairo )" DEPEND="${RDEPEND} + dev-lang/swig virtual/pkgconfig" S="${WORKDIR}/${MYP}" @@ -45,17 +47,31 @@ src_compile() { emake \ CC=$(tc-getCC) \ RANLIB=$(tc-getRANLIB) \ - AR=$(tc-getAR) - emake \ - CC=$(tc-getCC) \ - RANLIB=$(tc-getRANLIB) \ AR=$(tc-getAR) \ - extra + all report.txt + if use extra; then + emake \ + CC=$(tc-getCC) \ + RANLIB=$(tc-getRANLIB) \ + AR=$(tc-getAR) \ + extra + fi + # TODO: work it out for multiple python abi + if use python; then + emake \ + CC=$(tc-getCC) \ + RANLIB=$(tc-getRANLIB) \ + AR=$(tc-getAR) \ + py + fi } src_install() { + # TODO: install in standard directories to respect FHS export INSTALL_DIR="${ED}"/usr/astrometry - emake install + emake install-core + use extra && emake -C blind install-extras + # remove cfitsio duplicates rm ${INSTALL_DIR}/bin/{fitscopy,imcopy,listhead} || die @@ -66,6 +82,6 @@ src_install() { if use examples; then mv ${INSTALL_DIR}/examples "${ED}"/usr/share/doc/${PF} || die else - rm -r ${INSTALL_DIR}/examples + rm -r ${INSTALL_DIR}/examples || die fi } diff --git a/sci-astronomy/astrometry/files/0.43-system-libs.patch b/sci-astronomy/astrometry/files/0.43-system-libs.patch index 7027e0954..dd106b95d 100644 --- a/sci-astronomy/astrometry/files/0.43-system-libs.patch +++ b/sci-astronomy/astrometry/files/0.43-system-libs.patch @@ -1,10 +1,6 @@ -effort to link with gsl installed from system -to be applied after the as-needed patch -bicatali@gentoo.org - 06/2013 - diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind/Makefile ---- astrometry.net-0.43.as-needed/blind/Makefile 2013-06-13 15:54:15.915430597 -0700 -+++ astrometry.net-0.43/blind/Makefile 2013-06-13 17:09:54.247653801 -0700 +--- astrometry.net-0.43.as-needed/blind/Makefile 2013-06-14 10:25:20.789175016 -0700 ++++ astrometry.net-0.43/blind/Makefile 2013-06-14 10:25:58.643379797 -0700 @@ -56,7 +56,7 @@ LDFLAGS += -fPIC @@ -19,7 +15,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind quadcenters startree2rdls -ANLIBS := $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ANLIBS := $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ANLIBS := $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) BACKEND_LIB := libbackend.a @@ -30,7 +26,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind -$(BACKEND_SO): $(BACKEND_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(LIBKD_LIB) \ - $(QFITS_LIB) $(GSL_LIB) - $(CC) $(SHAREDLIBFLAGS) $^ -o $@ -+$(BACKEND_SO): $(BACKEND_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) \ ++$(BACKEND_SO): $(BACKEND_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) \ + $(QFITS_LIB) + $(CC) $(LDFLAGS) $(SHAREDLIBFLAGS) $^ $(GSL_LIB) -o $@ @@ -68,19 +64,19 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind #../util/cutest.o \ -test_2mass: 2mass.o 2mass-fits.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_2mass: 2mass.o 2mass-fits.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_2mass: 2mass.o 2mass-fits.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += 2mass-fits.o 2mass.o -test_usnob: usnob-fits.o usnob.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_usnob: usnob-fits.o usnob.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_usnob: usnob-fits.o usnob.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += usnob-fits.o usnob.o -test_nomad: nomad-fits.o nomad.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_nomad: nomad-fits.o nomad.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_nomad: nomad-fits.o nomad.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += nomad-fits.o nomad.o -test_matchfile: matchfile.o matchobj.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_matchfile: matchfile.o matchobj.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_matchfile: matchfile.o matchobj.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += matchfile.o matchobj.o -test_blindutils: blindutils.o $(ANUTILS_LIB) $(GSL_LIB) @@ -91,19 +87,19 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind ALL_TEST_EXTRA_OBJS += dcen3x3.o -test_simplexy: $(SIMPLEXY_OBJ) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_simplexy: $(SIMPLEXY_OBJ) $(ANUTILS_LIB) $(QFITS_LIB) ++test_simplexy: $(SIMPLEXY_OBJ) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += $(SIMPLEXY_OBJ) -test_resort-xylist: resort-xylist.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_resort-xylist: resort-xylist.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_resort-xylist: resort-xylist.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += resort-xylist.o -test_tweak: test_tweak.o tweak.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+test_tweak: test_tweak.o tweak.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_tweak: test_tweak.o tweak.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_TEST_EXTRA_OBJS += tweak.o -ALL_TEST_LIBS += $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ALL_TEST_LIBS += $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ALL_TEST_LIBS += $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) include $(COMMON)/makefile.tests @@ -113,7 +109,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind demo_dsmooth: demo_dsmooth.o dsmooth.o \ - $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) -pg $(LDLIBS) -o $@ -+ $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(QFITS_LIB) ++ $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) -pg $(GSL_LIB) $(LDLIBS) -o $@ control-program: control-program.o \ @@ -125,41 +121,41 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind # qfits is only needed for writing debugging images... -image2xy: image2xy-main.o image2xy-files.o $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(CFITS_LIB) $(LDLIBS) -o $@ -+image2xy: image2xy-main.o image2xy-files.o $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANUTILS_LIB) $(QFITS_LIB) ++image2xy: image2xy-main.o image2xy-files.o $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(CFITS_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += image2xy-main.o image2xy-files.o -new-wcs: new-wcs-main.o new-wcs.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+new-wcs: new-wcs-main.o new-wcs.o $(ANUTILS_LIB) $(QFITS_LIB) ++new-wcs: new-wcs-main.o new-wcs.o $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += new-wcs-main.o rdls2hpls: rdls2hpls.o \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) rdlstohealpix: rdlstohealpix.o \ - $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANUTILS_LIB) $(QFITS_LIB) xylist2fits: xylist2fits.o \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) certifiable: certifiable.o matchfile.o matchobj.o solvedfile.o \ - $(UTILS_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTILS_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTILS_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) fits-guess-scale: fits-guess-scale-main.o fits-guess-scale.o \ - $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += fits-guess-scale-main.o get-wcs: get-wcs.o \ - $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANUTILS_LIB) $(QFITS_LIB) ifdef WCSTOOLS_EXISTS @@ -169,14 +165,14 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind wcs-xy2rd: wcs-xy2rd-main.o wcs-xy2rd.o $(UTIL_OBJS) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCS_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCS_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += wcs-xy2rd-main.o wcs-rd2xy: wcs-rd2xy-main.o wcs-rd2xy.o $(UTIL_OBJS) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCS_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCS_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += wcs-rd2xy-main.o @@ -204,93 +200,93 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind nomadtofits: nomadtofits.o nomad-fits.o nomad.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ucac3tofits: ucac3tofits.o ucac3-fits.o ucac3.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) -lbz2 $(LDLIBS) -o $@ -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) -lbz2 $(GSL_LIB) $(LDLIBS) -o $@ read_nomad: read_nomad.o nomad.o -2masstofits: $(2MASSOBJ) $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(ZLIB_LIB) $(LDLIBS) -o $@ -+2masstofits: $(2MASSOBJ) $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++2masstofits: $(2MASSOBJ) $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(ZLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ diffractionFlag_check: diffractionFlag_check.o usnob-fits.o usnob.o \ - $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) project-usnob: project-usnob.o usnob-fits.o usnob.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) usnobtofits: usnobtofits.o usnob-fits.o usnob.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) -hpowned: hpowned.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+hpowned: hpowned.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++hpowned: hpowned.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) build-an-catalog: build-an-catalog.o usnob-fits.o usnob.o \ 2mass-fits.o 2mass.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) cut-an: cut-an.o catalog.o usnob.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) startree: startree.o catalog.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) startree2: startree2-main.o startree2.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += startree2-main.o startree2.o uniformize-catalog: uniformize-catalog-main.o uniformize-catalog.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += uniformize-catalog-main.o uniformize-catalog.o build-index: build-index-main.o build-index.o uniformize-catalog.o startree2.o hpquads.o \ quad-builder.o quad-utils.o codefile.o codetree.o unpermute-stars.o \ unpermute-quads.o merge-index.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += build-index-main.o build-index.o uniformize-catalog.o quad-utils.o hpquads: hpquads-main.o hpquads.o quad-builder.o quad-utils.o codefile.o pnpoly.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += hpquads-main.o quad-builder.o hpquads.o allquads: allquads-main.o allquads.o quad-builder.o quad-utils.o codefile.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) codetree: codetree-main.o codetree.o codefile.o quad-utils.o \ - $(UTIL_OBJS) $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += codetree-main.o unpermute-stars: unpermute-stars-main.o unpermute-stars.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += unpermute-stars-main.o unpermute-quads: unpermute-quads-main.o unpermute-quads.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += unpermute-quads-main.o merge-index: merge-index-main.o merge-index.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += merge-index-main.o local-index: local-index.o build-index.o codetree.o startree2.o codetree.o \ @@ -298,13 +294,13 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind quad-builder.o quad-utils.o codefile.o wcs-xy2rd.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCSLIB_LIB) $(LDLIBS) -o $@ -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCSLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += local-index.o index-to-table: index-to-table.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) threadtest: threadtest.o $(BACKEND_LIB) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) $(GSL_LIB) @@ -332,7 +328,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind dstnthing: dstnthing.o tweak2.o tweak.o matchfile.o matchobj.o verify.o scamp.o $(PLOTSTUFF) \ - $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) $(GSL_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LDLIBS) -o $@ -+ $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) ++ $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += dstnthing.o @@ -343,7 +339,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind scamp.o \ - $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCSLIB_LIB) $(CFITS_LIB) $(LDLIBS) -o $@ -+ $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(SIMPLEXY_OBJ) $(CFITS_DEP) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(WCSLIB_LIB) $(CFITS_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += scamp.o cut-table.o @@ -362,7 +358,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind $(UTIL_OBJS) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) $(GSL_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(LDLIBS) -o $@.tmp -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(GSL_LIB) $(LDLIBS) -o $@.tmp mv $@.tmp $@ @@ -379,7 +375,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind $(PLOTSTUFF) $(COMMON)/cairoutils.o $(CATS_LIB) \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) $(GSL_LIB) - $(CC) $(CFLAGS) $(LDFLAGS) $^ $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LDLIBS) -o $@ -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) $(QFITS_LIB) + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += whynot.o @@ -389,20 +385,20 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind agreeable: agreeable.o matchfile.o matchobj.o solvedfile.o solvedclient.o verify.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(LIBKD_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(LIBKD_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(LIBKD_LIB) $(QFITS_LIB) -rdlsinfo: rdlsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+rdlsinfo: rdlsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++rdlsinfo: rdlsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) -xylsinfo: xylsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+xylsinfo: xylsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++xylsinfo: xylsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) wcsinfo: wcsinfo.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) \ - $(QFITS_LIB) $(GSL_LIB) + $(QFITS_LIB) -index-info: index-info.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+index-info: index-info.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++index-info: index-info.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) subwcs: subwcs.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) \ - $(QFITS_LIB) $(GSL_LIB) @@ -410,27 +406,27 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind ALL_OBJS += subwcs.o -wcs-grab: wcs-grab.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) \ -+wcs-grab: wcs-grab.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) \ ++wcs-grab: wcs-grab.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) \ $(QFITS_LIB) -printsolved: printsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+printsolved: printsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++printsolved: printsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) -setsolved: setsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+setsolved: setsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++setsolved: setsolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) -mergesolved: mergesolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+mergesolved: mergesolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++mergesolved: mergesolved.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) -solvedserver: solvedserver.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) \ -+solvedserver: solvedserver.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) \ ++solvedserver: solvedserver.o solvedfile.o $(UTIL_OBJS) $(ANUTILS_LIB) \ $(QFITS_LIB) - $(CC) $(CFLAGS) $^ $(LDLIBS) -o $@ + $(CC) $(CFLAGS) $(LDFLAGS) $^ $(GSL_LIB) $(LDLIBS) -o $@ plotcat: plotcat.o 2mass-fits.o 2mass.o nomad-fits.o nomad.o catalog.o usnob-fits.o usnob.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(LIBKD_LIB) \ -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) \ ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(LIBKD_LIB) \ $(QFITS_LIB) plotquad.o: plotquad.c @@ -444,13 +440,13 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind plotquad: plotquad.o matchfile.o matchobj.o $(COMMON)/cairoutils.o \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(GSL_LIB) $(LDLIBS) -o $@ plot-xy-and-quad: plot-xy-and-quad.o matchfile.o $(COMMON)/cairoutils.o \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(GSL_LIB) $(LDLIBS) -o $@ plot-constellations.o: plot-constellations.c @@ -459,16 +455,16 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind plot-constellations: plot-constellations.o $(CATS_LIB) $(COMMON)/cairoutils.o \ - $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(LDFLAGS) $^ $(CAIRO_LIB) $(NETPBM_LIB) $(PNG_LIB) $(JPEG_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(LDFLAGS) $^ $(CAIRO_LIB) $(NETPBM_LIB) $(PNG_LIB) $(JPEG_LIB) $(GSL_LIB) $(LDLIBS) -o $@ catalog-dists: catalog-dists.o 2mass-fits.o usnob-fits.o usnob.o \ - $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(LIBKD_LIB) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) -add-text: add-text.o $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $(LDFLAGS) $^ $(CAIRO_LIB) $(NETPBM_LIB) $(PNG_LIB) $(JPEG_LIB) $(LDLIBS) -o $@ -+add-text: add-text.o $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(QFITS_LIB) ++add-text: add-text.o $(COMMON)/cairoutils.o $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $(LDFLAGS) $^ $(CAIRO_LIB) $(NETPBM_LIB) $(PNG_LIB) $(JPEG_LIB) $(GSL_LIB) $(LDLIBS) -o $@ PYTHON_EXECS := plotann.py @@ -479,7 +475,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind -plotstuff: plotstuff-main.o $(PLOTSTUFF) $(CATS_LIB) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LDLIBS) -o $@ -+plotstuff: plotstuff-main.o $(PLOTSTUFF) $(CATS_LIB) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++plotstuff: plotstuff-main.o $(PLOTSTUFF) $(CATS_LIB) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += plotstuff-main.o @@ -489,7 +485,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind _plotstuff_c.so: plotstuff_wrap.c setup.py $(PLOTSTUFF) $(CATS_LIB) \ $(COMMON)/cairoutils.o \ - $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) python setup.py build --force --build-base build --build-platlib build/lib cp build/lib/_plotstuff_c.so $@ @@ -499,13 +495,13 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind plotxy: plotxy-main.o $(PLOTSTUFF) $(CATS_LIB) $(COMMON)/cairoutils.o \ - $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LDLIBS) -o $@ -+ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(GSL_LIB) $(LDLIBS) -o $@ ALL_OBJ += plotxy-main.o -test_plotstuff: test_plotstuff-main.o test_plotstuff.o $(COMMON)/cutest.o $(PLOTSTUFF) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(LDLIBS) -o $@ -+test_plotstuff: test_plotstuff-main.o test_plotstuff.o $(COMMON)/cutest.o $(PLOTSTUFF) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++test_plotstuff: test_plotstuff-main.o test_plotstuff.o $(COMMON)/cutest.o $(PLOTSTUFF) $(COMMON)/cairoutils.o $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(WCSLIB_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(GSL_LIB) $(LDLIBS) -o $@ test_plotstuff-main.c: test_plotstuff.c $(AN_SHELL) $(MAKE_TESTS) $^ > $@ @@ -514,7 +510,7 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind ALL_OBJ += query-starkd.o -quadidx: quadidx.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+quadidx: quadidx.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++quadidx: quadidx.o $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) codeprojections: codeprojections.o $(UTIL_OBJS) $(ANLIBS) @@ -534,46 +530,60 @@ diff -Nur astrometry.net-0.43.as-needed/blind/Makefile astrometry.net-0.43/blind $(QFITS_LIB) -fitsgetext: fitsgetext.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+fitsgetext: fitsgetext.o $(ANUTILS_LIB) $(QFITS_LIB) ++fitsgetext: fitsgetext.o $(ANUTILS_LIB) $(QFITS_LIB) -fits-dedup: fits-dedup.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+fits-dedup: fits-dedup.o $(ANUTILS_LIB) $(QFITS_LIB) ++fits-dedup: fits-dedup.o $(ANUTILS_LIB) $(QFITS_LIB) -subtable: subtable.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+subtable: subtable.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++subtable: subtable.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) -tabsort: tabsort-main.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+tabsort: tabsort-main.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++tabsort: tabsort-main.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += tabsort-main.o -column-merge: column-merge.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+column-merge: column-merge.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++column-merge: column-merge.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) resort-xylist: resort-xylist-main.o resort-xylist.o $(UTIL_OBJS) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ALL_OBJ += resort-xylist-main.o -bgsubtract: bgsubtract.o ctmf.o $(COMMON)/cairoutils.o $(UTIL_OBJS) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) - $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(LDLIBS) -o $@ -+bgsubtract: bgsubtract.o ctmf.o $(COMMON)/cairoutils.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) ++bgsubtract: bgsubtract.o ctmf.o $(COMMON)/cairoutils.o $(UTIL_OBJS) $(ANUTILS_LIB) $(QFITS_LIB) + $(CC) $^ $(LDFLAGS) $(CAIRO_LIB) $(PNG_LIB) $(NETPBM_LIB) $(JPEG_LIB) $(GSL_LIB) $(LDLIBS) -o $@ usnob-scamp-catalog: usnob-scamp-catalog.o usnob-fits.o usnob.o $(UTIL_OBJS) \ - $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) create-scamp-catalog: create-scamp-catalog.o \ - $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) -+ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) ++ $(UTIL_OBJS) $(ANFILES_LIB) $(ANUTILS_LIB) $(QFITS_LIB) DEP_OBJ := $(ALL_OBJ) DEP_PREREQS := $(QFITS_LIB) +diff -Nur astrometry.net-0.43.as-needed/blind/setup.py astrometry.net-0.43/blind/setup.py +--- astrometry.net-0.43.as-needed/blind/setup.py 2013-06-14 10:25:20.786175152 -0700 ++++ astrometry.net-0.43/blind/setup.py 2013-06-14 10:34:33.657232232 -0700 +@@ -68,9 +68,8 @@ + '../libkd/libkd.a', + '../util/libanutils.a', + '../qfits-an/lib/libqfits.a', +- '../gsl-an/libgsl-an.a', + ], +- libraries=reduce(lambda x,y: x+y, [get_libs(x,req) for x,req in [('cairo',True), ('wcslib',False)]]) + ['jpeg'] + extra_link_libs, ++ libraries=reduce(lambda x,y: x+y, [get_libs(x,req) for x,req in [('cairo',True), ('wcslib',False)]]) + ['jpeg'] + ['gsl'] + extra_link_libs, + library_dirs=reduce(lambda x,y: x+y, [get_lib_dirs(x,req) for x,req in [('cairo',True), ('wcslib',False)]]) + extra_link_dirs, + extra_compile_args=compile_args, + extra_link_args=link_args, diff -Nur astrometry.net-0.43.as-needed/Makefile astrometry.net-0.43/Makefile ---- astrometry.net-0.43.as-needed/Makefile 2013-06-13 15:54:15.934430711 -0700 -+++ astrometry.net-0.43/Makefile 2013-06-13 15:56:14.795089358 -0700 +--- astrometry.net-0.43.as-needed/Makefile 2013-06-14 10:25:20.809174220 -0700 ++++ astrometry.net-0.43/Makefile 2013-06-14 10:26:38.497600024 -0700 @@ -67,7 +67,7 @@ $(MAKE) -C qfits-an/src @@ -583,9 +593,25 @@ diff -Nur astrometry.net-0.43.as-needed/Makefile astrometry.net-0.43/Makefile .PHONY: subdirs thirdparty qfits-an gsl-an +@@ -81,7 +81,6 @@ + # Targets that create python bindings (requiring swig) + py: + $(MAKE) -C qfits-an +- $(MAKE) -C gsl-an + $(MAKE) -C catalogs + $(MAKE) -C util pyutil + $(MAKE) -C util cairoutils.o +@@ -91,7 +90,6 @@ + + pyutil: + $(MAKE) -C qfits-an +- $(MAKE) -C gsl-an + $(MAKE) -C util pyutil + + install: all report.txt diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/Makefile ---- astrometry.net-0.43.as-needed/util/Makefile 2013-06-13 17:05:10.551069687 -0700 -+++ astrometry.net-0.43/util/Makefile 2013-06-13 17:10:31.830861262 -0700 +--- astrometry.net-0.43.as-needed/util/Makefile 2013-06-14 10:25:20.813174107 -0700 ++++ astrometry.net-0.43/util/Makefile 2013-06-14 10:30:57.575032667 -0700 @@ -181,7 +181,7 @@ resample: resample-main.o \ @@ -595,7 +621,7 @@ diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/M ALL_OBJ += resampe.o tycho2tofits: tycho2tofits.o \ -@@ -194,18 +194,18 @@ +@@ -194,17 +194,17 @@ _sip.so: sip-utils.o gslutils.o sip.o starutil.o mathutil.o sip_qfits.o \ fitsioutils.o errors.o ioutils.o bl.o os-features.o an-endian.o \ @@ -613,12 +639,10 @@ diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/M _util.so: util_wrap.c setup-util.py \ - $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(GSL_LIB) -- WCSLIB_LIB="$(WCSLIB_LIB)" GSL_LIB="$(GSL_LIB)" \ + $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) -+ WCSLIB_LIB="$(WCSLIB_LIB)" GSL_LIB="" \ + WCSLIB_LIB="$(WCSLIB_LIB)" GSL_LIB="$(GSL_LIB)" \ python setup-util.py build --force --build-base build --build-platlib build/lib cp build/lib/_util.so $@ - @@ -224,23 +224,23 @@ cp build/lib/_index_c.so _index_c.so cp build/lib/_index_util.so _index_util.so @@ -631,13 +655,13 @@ diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/M -wcs-resample: wcs-resample-main.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) - $(CC) $^ $(LDFLAGS) $(WCS_LIB) $(LDLIBS) -o $@ -+wcs-resample: wcs-resample-main.o $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) ++wcs-resample: wcs-resample-main.o $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) + $(CC) $(LDFLAGS) $^ $(GSL_LIB) $(WCS_LIB) $(LDLIBS) -o $@ ALL_OBJ += wcs-resample-main.o -fit-wcs: fit-wcs-main.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) - $(CC) $^ $(LDFLAGS) $(WCS_LIB) $(LDLIBS) -o $@ -+fit-wcs: fit-wcs-main.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) ++fit-wcs: fit-wcs-main.o $(ANFILES_LIB) $(LIBKD_LIB) $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) + $(CC) $^ $(LDFLAGS) $(GSL_LIB) $(WCS_LIB) $(LDLIBS) -o $@ ALL_OBJ += fit-wcs-main.o @@ -647,7 +671,7 @@ diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/M -wcs-to-tan: wcs-to-tan.o $(ANUTILS_LIB) $(GSL_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) - $(CC) $^ $(LDFLAGS) $(WCS_LIB) $(LDLIBS) -o $@ -+wcs-to-tan: wcs-to-tan.o $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) ++wcs-to-tan: wcs-to-tan.o $(ANUTILS_LIB) $(QFITS_LIB) $(WCS_LIB_DEP) + $(CC) $^ $(LDFLAGS) $(GSL_LIB) $(WCS_LIB) $(LDLIBS) -o $@ ALL_OBJ += wcs-to-tan.o @@ -687,8 +711,8 @@ diff -Nur astrometry.net-0.43.as-needed/util/Makefile astrometry.net-0.43/util/M ### /TESTS diff -Nur astrometry.net-0.43.as-needed/util/makefile.gsl astrometry.net-0.43/util/makefile.gsl ---- astrometry.net-0.43.as-needed/util/makefile.gsl 2013-06-13 15:54:15.937430729 -0700 -+++ astrometry.net-0.43/util/makefile.gsl 2013-06-13 15:54:33.183525063 -0700 +--- astrometry.net-0.43.as-needed/util/makefile.gsl 2013-06-14 10:25:20.812174131 -0700 ++++ astrometry.net-0.43/util/makefile.gsl 2013-06-14 10:25:58.643379797 -0700 @@ -14,10 +14,5 @@ # along with the Astrometry.net suite ; if not, write to the Free Software # Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA @@ -702,3 +726,17 @@ diff -Nur astrometry.net-0.43.as-needed/util/makefile.gsl astrometry.net-0.43/ut - +GSL_INC ?= $(shell pkg-config --cflags gsl 2>/dev/null) +GSL_LIB ?= $(shell pkg-config --libs gsl 2>/dev/null) +diff -Nur astrometry.net-0.43.as-needed/util/setup-util.py astrometry.net-0.43/util/setup-util.py +--- astrometry.net-0.43.as-needed/util/setup-util.py 2013-06-14 10:25:20.814174084 -0700 ++++ astrometry.net-0.43/util/setup-util.py 2013-06-14 10:39:45.250959084 -0700 +@@ -22,9 +22,8 @@ + '../libkd/libkd.a', + 'libanutils.a', + '../qfits-an/lib/libqfits.a', +- '../gsl-an/libgsl-an.a', + ], +- extra_link_args=[os.environ.get('WCSLIB_LIB', ''), ++ extra_link_args=[os.environ.get('WCSLIB_LIB') + ' ' + os.environ.get('GSL_LIB'), + #os.environ.get('GSL_LIB', ''), + #'-O0 -g' + ], diff --git a/sci-astronomy/astrometry/metadata.xml b/sci-astronomy/astrometry/metadata.xml index df28cb837..664a74cf3 100644 --- a/sci-astronomy/astrometry/metadata.xml +++ b/sci-astronomy/astrometry/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-astronomy</herd> - <longdescription lang="en"> +<herd>sci-astronomy</herd> +<longdescription lang="en"> If you have astronomical imaging of the sky with celestial coordinates you do not know—or do not trust—then Astrometry.net is for you. Input an image and we'll give you back astrometric calibration meta-data, plus lists of known objects falling inside the field of view. </longdescription> +<use> + <flag name="extra">Add extra tools, specifically for plots</flag> +</use> </pkgmetadata> diff --git a/sci-astronomy/chealpix/ChangeLog b/sci-astronomy/chealpix/ChangeLog new file mode 100644 index 000000000..930d80be2 --- /dev/null +++ b/sci-astronomy/chealpix/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-astronomy/chealpix +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*chealpix-3.11 (16 Jun 2013) + + 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +chealpix-3.11.ebuild, + +metadata.xml: + sci-astronomy/chealpix: Initial import diff --git a/sci-astronomy/chealpix/Manifest b/sci-astronomy/chealpix/Manifest new file mode 100644 index 000000000..983581ad4 --- /dev/null +++ b/sci-astronomy/chealpix/Manifest @@ -0,0 +1 @@ +DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299 diff --git a/sci-astronomy/chealpix/chealpix-3.11.ebuild b/sci-astronomy/chealpix/chealpix-3.11.ebuild new file mode 100644 index 000000000..9a496af56 --- /dev/null +++ b/sci-astronomy/chealpix/chealpix-3.11.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +inherit autotools-utils + +MYP="Healpix_${PV}" +MYPP="2013Apr24" + +DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - C Library" +HOMEPAGE="http://healpix.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="static-libs" + +RDEPEND=" + >=sci-libs/cfitsio-3" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYP}/src/C/autotools" + +DOCS=( ../{README,CHANGES} ) diff --git a/sci-astronomy/chealpix/metadata.xml b/sci-astronomy/chealpix/metadata.xml new file mode 100644 index 000000000..de81d6067 --- /dev/null +++ b/sci-astronomy/chealpix/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-astronomy</herd> +<longdescription lang="en"> + HEALPix is an acronym for Hierarchical Equal Area isoLatitude + Pixelization of a sphere. As suggested in the name, this pixelization produces a + subdivision of a spherical surface in which each pixel covers the same + surface area as every other pixel. This package contains the C library. +</longdescription> +</pkgmetadata> diff --git a/sci-astronomy/healpix_cxx/ChangeLog b/sci-astronomy/healpix_cxx/ChangeLog new file mode 100644 index 000000000..fa357f4bd --- /dev/null +++ b/sci-astronomy/healpix_cxx/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-astronomy/healpix_cxx +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*healpix_cxx-3.11 (16 Jun 2013) + + 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +healpix_cxx-3.11.ebuild, + +metadata.xml: + sci-astronomy/healpix_cxx: Initial import diff --git a/sci-astronomy/healpix_cxx/Manifest b/sci-astronomy/healpix_cxx/Manifest new file mode 100644 index 000000000..983581ad4 --- /dev/null +++ b/sci-astronomy/healpix_cxx/Manifest @@ -0,0 +1 @@ +DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299 diff --git a/sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild b/sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild new file mode 100644 index 000000000..f25aa9d8e --- /dev/null +++ b/sci-astronomy/healpix_cxx/healpix_cxx-3.11.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +AUTOTOOLS_AUTORECONF=1 +inherit autotools-utils toolchain-funcs + +MYP="Healpix_${PV}" +MYPP="2013Apr24" + +DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - C++" +HOMEPAGE="http://healpix.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="openmp static-libs" + +RDEPEND=" + >=sci-libs/cfitsio-3" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${MYP}/src/cxx/autotools" + +DOCS=( ../CHANGES ../../../READ_Copyrights_Licenses.txt ) + +pkg_setup() { + if use openmp; then + if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then + ewarn "You are using a g++ without OpenMP capabilities" + die "Need an OpenMP capable compiler" + fi + fi +} + +src_prepare() { + # respect user flags + sed -i -e '/^AX_CHECK_COMPILE_FLAG/d' configure.ac || die + # why was static-libtool-libs forced? + use static-libs || sed -i -e '/-static-libtool-libs/d' Makefile.am + autotools-utils_src_prepare +} + +src_configure() { + local myeconfargs=( + $(use_enable openmp) + ) + autotools-utils_src_configure +} diff --git a/sci-astronomy/healpix_cxx/metadata.xml b/sci-astronomy/healpix_cxx/metadata.xml new file mode 100644 index 000000000..391b83cad --- /dev/null +++ b/sci-astronomy/healpix_cxx/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-astronomy</herd> +<longdescription lang="en"> + HEALPix is an acronym for Hierarchical Equal Area isoLatitude + Pixelization of a sphere. As suggested in the name, this pixelization produces a + subdivision of a spherical surface in which each pixel covers the same + surface area as every other pixel. This package contains the C++ + library and programs. +</longdescription> +</pkgmetadata> diff --git a/sci-astronomy/healpix_idl/ChangeLog b/sci-astronomy/healpix_idl/ChangeLog new file mode 100644 index 000000000..e12f4a5bc --- /dev/null +++ b/sci-astronomy/healpix_idl/ChangeLog @@ -0,0 +1,9 @@ +# ChangeLog for sci-astronomy/healpix_idl +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*healpix_idl-3.11 (16 Jun 2013) + + 16 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +healpix_idl-3.11.ebuild, + +metadata.xml: + sci-astronomy/healpix_idl: Initial import diff --git a/sci-astronomy/healpix_idl/Manifest b/sci-astronomy/healpix_idl/Manifest new file mode 100644 index 000000000..983581ad4 --- /dev/null +++ b/sci-astronomy/healpix_idl/Manifest @@ -0,0 +1 @@ +DIST Healpix_3.11_2013Apr24.tar.gz 24256278 SHA256 f80aa3633601664afe99c8b7dc7253828f22e6d832187ab46ac90b2ad83e6831 SHA512 aae5592dda40103918a6c6520863e2aeddf40a34531e4ce2f38a1ce7411731218d7e20bd02107f92384a7b371c2415ed640ad27aa398f64857f5ed7d9dba32bb WHIRLPOOL 1e3f0588502b6b9e68c19de9763ae775d01031cd7a3120bb663a71bae1fa7e2baf6ac4997ff07598ca45e610ae919839ecf04c66a201256665f5e5f1727f7299 diff --git a/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild b/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild new file mode 100644 index 000000000..bc40c0b96 --- /dev/null +++ b/sci-astronomy/healpix_idl/healpix_idl-3.11.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +MYP="Healpix_${PV}" +MYPP="2013Apr24" + +DESCRIPTION="Hierarchical Equal Area isoLatitude Pixelization of a sphere - IDL routines" +HOMEPAGE="http://healpix.sourceforge.net/" +SRC_URI="mirror://sourceforge/${PN}/${MYP}/${MYP}_${MYPP}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +IUSE="doc" + +RDEPEND=" + dev-lang/gdl + sci-astronomy/idlastro" + +S="${WORKDIR}/${MYP}/src/idl" + +src_prepare() { + # duplocate of idlastro (in rdeps) + rm -r zzz_external/astron || die + mv zzz_external/README README.external || die +} + +src_install() { + insinto /usr/share/gnudatalanguage/healpix + doins -r examples fits interfaces misc toolkit visu zzz_external + doins HEALPix_startup + dodoc README.* +} diff --git a/sci-astronomy/healpix_idl/metadata.xml b/sci-astronomy/healpix_idl/metadata.xml new file mode 100644 index 000000000..020cd30c0 --- /dev/null +++ b/sci-astronomy/healpix_idl/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> +<herd>sci-astronomy</herd> +<longdescription lang="en"> + HEALPix is an acronym for Hierarchical Equal Area isoLatitude + Pixelization of a sphere. As suggested in the name, this pixelization produces a + subdivision of a spherical surface in which each pixel covers the same + surface area as every other pixel. This package contains the IDL/GDL + routines and plots. +</longdescription> +</pkgmetadata> diff --git a/sci-biology/YASRA/ChangeLog b/sci-biology/YASRA/ChangeLog index 77b3b5e07..342684d59 100644 --- a/sci-biology/YASRA/ChangeLog +++ b/sci-biology/YASRA/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -YASRA-2.1.ebuild, + +YASRA-2.32.ebuild: + Version BUmp; add KEYWORDS + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> YASRA-2.1.ebuild, metadata.xml: Drop keywords as deps are unkeyworded diff --git a/sci-biology/YASRA/Manifest b/sci-biology/YASRA/Manifest index 4c218feef..f7399f074 100644 --- a/sci-biology/YASRA/Manifest +++ b/sci-biology/YASRA/Manifest @@ -1 +1 @@ -DIST YASRA-2.1.tar.gz 11949120 SHA256 d196cea91a69db3d2feb98d3a8dddbfe1c4c9b4689cdc706a58df44daba3d2d5 SHA512 1e5c648042b8c522c708eb80b90f5a7e965b4f0214a732ba19a46d826ea85bd7074946a2355e509df1ce1dfcec1700c7c6f3ad08c7052f754fed6241c078ec5b WHIRLPOOL 4419ce639b2afb95013b8896b059c037100dc58dc1664b2416ed05c68fd3fcce4eca01219dfa59874a26d566e1df393e975c8d6132811591a251f1acc3db00a4 +DIST YASRA-2.32.tar.gz 12404230 SHA256 03ce7d89949fdd44c97af51b65f57bb5f49f1ac1d5c2be225419513887ea1c61 SHA512 2bdf3f62567c5f2a12b58de9961c3fa55cf38b1000feb73170af6c0f0c035c79e8052009419d2d49423a4b9d52cb44196171bd7235108fdf3ada97c5e03c30c1 WHIRLPOOL 6fdda6a1abe64b5bb91fcb298fd867cff593c3bb0540cce5134cebd63a8254ef4ba24edc788830be963c001c8e915bb4f2546f37aadbbcf16d26aaf8a8fb6f40 diff --git a/sci-biology/YASRA/YASRA-2.1.ebuild b/sci-biology/YASRA/YASRA-2.32.ebuild index c8288fc52..246d65d40 100644 --- a/sci-biology/YASRA/YASRA-2.1.ebuild +++ b/sci-biology/YASRA/YASRA-2.32.ebuild @@ -2,23 +2,16 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 DESCRIPTION="Yet Another Short Read Assembler aligning to a reference using LASTZ" HOMEPAGE="http://www.bx.psu.edu/miller_lab/" -SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-"${PV}".tar.gz" +SRC_URI="http://www.bx.psu.edu/miller_lab/dist/YASRA-${PV}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" DEPEND="" -RDEPEND="${DEPEND} - sci-biology/lastz" - -S="${WORKDIR}"/YASRA - -src_install(){ - emake install DESTDIR="$D" -} +RDEPEND="sci-biology/lastz" diff --git a/sci-biology/caftools/ChangeLog b/sci-biology/caftools/ChangeLog new file mode 100644 index 000000000..af2ad47b4 --- /dev/null +++ b/sci-biology/caftools/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/caftools +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -caftools-2.0.ebuild, + caftools-2.0.2.ebuild, metadata.xml: + Drop old; Bump to EAPI=5 and fix license + diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest index 61d49e197..dbbbb7f44 100644 --- a/sci-biology/caftools/Manifest +++ b/sci-biology/caftools/Manifest @@ -1,2 +1,2 @@ -DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 -DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 +DIST caftools-2.0.2.tar.gz 2645554 SHA256 7be5eafbd6817a7869f73c7540b5fdfe184b0be28624cc6ca9a01c52a140d4a2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d WHIRLPOOL 84313e00f6f4c018bc65b6e173827a6e1ef8fd2dc5e5e63e186fb56bc9e5b66b2f25037a1536a8cb57af71603b31ed74ff505dbc43d4deb7d2eeae57ea729bfe +DIST caftools-2.0.tar.gz 2644892 SHA256 b41f323ceb3fd260d6c2ecff1f285548f40301065cea54687eb96717534eaad9 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 WHIRLPOOL 13c2e24ce803c09f1d596a4c05f146b869e5ebdeff9f648a0468853feb7d142927d3d78339ac2414482335e5f7ca8352ea9b196f8542f4b3ff5e36fef762398e diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild index c1932e1f4..3f8ece67d 100644 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ b/sci-biology/caftools/caftools-2.0.2.ebuild @@ -1,45 +1,45 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit eutils DESCRIPTION="CAF is a text format for describing sequence assemblies" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.2.tar.gz - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz" -# another source with only the old version is at -# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz -# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/ +SRC_URI=" + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz" -LICENSE="as-is" +LICENSE="GRL" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="sci-libs/io_lib - >=dev-lang/perl-5.002" +DEPEND=" + sci-libs/io_lib + dev-lang/perl" RDEPEND="${DEPEND}" src_prepare(){ - epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die - mv "${WORKDIR}"/caftools-2.0/man/*.1 "${WORKDIR}"/caftools-2.0/man/*.5 "${S}"/man || die + epatch "${FILESDIR}"/Makefile.in-"${PV}".patch + mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die } src_configure(){ - econf || die - sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die - sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die + default + sed \ + -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \ + -i Makefile src/Makefile || die } # TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME # The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, # not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. src_install(){ - emake install DESTDIR="${D}" || die + default doman man/*.[1-5] || die - einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" - einfo "for some reason caf_find_misassemblies is gone from 2.0.2 version" + elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" + elog "for some reason caf_find_misassemblies is gone from 2.0.2 version" } diff --git a/sci-biology/caftools/caftools-2.0.ebuild b/sci-biology/caftools/caftools-2.0.ebuild deleted file mode 100644 index 482bddf92..000000000 --- a/sci-biology/caftools/caftools-2.0.ebuild +++ /dev/null @@ -1,38 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit eutils - -DESCRIPTION="CAF is a text format for describing sequence assemblies" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz" -# another source with only the old version is at -# ftp://ftp.sanger.ac.uk/pub4/resources/software/caf/caftools-2.0.tar.gz -# newer version will probably appear at ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/ - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="sci-libs/io_lib - >=dev-lang/perl-5.002" -RDEPEND="${DEPEND}" - -src_prepare(){ - epatch "${FILESDIR}"/Makefile.in.patch || die -} - -src_configure(){ - econf || die - sed -i 's#prefix = /usr#prefix = $(DESTDIR)/usr#' Makefile || die - sed -i 's#prefix = /usr#\#prefix = $(DESTDIR)/usr#' src/Makefile || die -} - -src_install(){ - emake install DESTDIR="${D}" || die - einfo "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" -} diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml index 4f255d9b2..e57f444c5 100644 --- a/sci-biology/caftools/metadata.xml +++ b/sci-biology/caftools/metadata.xml @@ -1,10 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <longdescription>CAF is a text format for describing sequence assemblies. It is acedb-compliant and is an extension of the ace-file format used earlier, but with support for base quality measures and a more extensive description of the Sequence data.</longdescription> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> + <longdescription> + CAF is a text format for describing sequence assemblies. It is acedb-compliant + and is an extension of the ace-file format used earlier, but with support for + base quality measures and a more extensive description of the Sequence data. + </longdescription> </pkgmetadata> diff --git a/sci-biology/clover/ChangeLog b/sci-biology/clover/ChangeLog index 18775e4df..edcb8dd7d 100644 --- a/sci-biology/clover/ChangeLog +++ b/sci-biology/clover/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/clover -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -clover-2010.02.19.ebuild, + +clover-2011.10.24.ebuild, metadata.xml: + Version BUmp; fixed license; respect LDFLAGS + *clover-2010.02.19 (23 Aug 2010) 23 Aug 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> diff --git a/sci-biology/clover/Manifest b/sci-biology/clover/Manifest index 701b84d6e..4a3827eb9 100644 --- a/sci-biology/clover/Manifest +++ b/sci-biology/clover/Manifest @@ -1,2 +1,2 @@ -DIST clover-2010-02-19.tar.gz 15641 SHA256 f6de99b9ce5676af8b4179e12c4701f81f0b17ac5dadacfe7affa38ad2a585f5 -DIST jaspar2005core 14913 SHA256 498a560c67411789106b50ccdfd9bc41f571d77c2fe9bfba7e95128c0a122fe4 +DIST clover-2011-10-24.tar.gz 15843 SHA256 52ba95c118a32e6ea1097f356dfb0277be4464b834285f65eaaebcf8f504a93e SHA512 edf773943a33d58b07b7a47ca9e6c0fe08715d7f445ef1283848a14eb72d084b2113a911f23bc484b3229ec14b8eeb50d460c6b9fef89db2fa031ea059b36b93 WHIRLPOOL 785c7273c10bc6e4261e91a9dae224ff595aad3f033fb03edbe403d8cb97b456c0fe285e1a537bde3508e5e4a8f2ea5aa442fb3cb72640464df2a24da8be0ae0 +DIST jaspar2009core 54400 SHA256 a76cd1462e7b9c38f64e2049593d21fa90479b968c7997ca3d83f8489327b981 SHA512 621eac23fb0db78391d3d51471f03eccc791e1b348b23b5d9dae32b082c8301e847ee1eea4a76ac188796b639125a0970e5f0b3c0d3c673ae6f6634856c980a0 WHIRLPOOL c148ee32894ec1bd55a4665fd516eb82e6e5904e6a74bb6248d70ef7fef1a1376888a6fe53bcd959faeb8665b7c2bda3668f6801ed2e07c2c445a241a1ebcc4d diff --git a/sci-biology/clover/clover-2010.02.19.ebuild b/sci-biology/clover/clover-2010.02.19.ebuild deleted file mode 100644 index 239cc30e4..000000000 --- a/sci-biology/clover/clover-2010.02.19.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit toolchain-funcs versionator - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs" -HOMEPAGE="http://zlab.bu.edu/clover/" -SRC_URI="http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz http://zlab.bu.edu/clover/jaspar2005core" - -LICENSE="as-is" -SLOT="0" -IUSE="" -KEYWORDS="~x86 ~amd64" - -DEPEND="" -RDEPEND="" - -S="${WORKDIR}/${PN}-${MY_PV}" - -src_unpack() { - unpack ${PN}-${MY_PV}.tar.gz -} - -src_compile() { - sed -i "s:g++:$(tc-getCXX):; s:-Wall -O3:${CFLAGS}:" Makefile || die "sed failed" - emake || die "emake failed" -} - -src_install() { - dobin clover - dodir "/usr/share/${PN}" - insinto "/usr/share/${PN}" - doins "${DISTDIR}/jaspar2005core" || die -} - -pkg_postinst() { - einfo "The motif library jaspar2005core has been installed in" - einfo " /usr/share/clover/jaspar2005core" - einfo "You can pass this library to clover for motif search, or use your own library." -} diff --git a/sci-biology/clover/clover-2011.10.24.ebuild b/sci-biology/clover/clover-2011.10.24.ebuild new file mode 100644 index 000000000..cfb057432 --- /dev/null +++ b/sci-biology/clover/clover-2011.10.24.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit toolchain-funcs versionator + +MY_PV=$(replace_all_version_separators '-') + +DESCRIPTION="Cis-eLement OVERrepresentation: Detection of functional DNA motifs" +HOMEPAGE="http://zlab.bu.edu/clover/" +SRC_URI=" + http://zlab.bu.edu/~mfrith/downloads/${PN}-${MY_PV}.tar.gz + http://zlab.bu.edu/clover/jaspar2009core" + +LICENSE="freedist" +SLOT="0" +IUSE="" +KEYWORDS="~x86 ~amd64" + +S="${WORKDIR}/${PN}-${MY_PV}" + +src_prepare() { + sed \ + -e "s:g++:$(tc-getCXX) \$(LDFLAGS):; s:-Wall -O3:${CFLAGS}:" \ + -i Makefile || die "sed failed" +} + +src_install() { + dobin clover + insinto /usr/share/${PN} + doins "${DISTDIR}/jaspar2009core" +} + +pkg_postinst() { + einfo "The motif library jaspar2009core has been installed in" + einfo " /usr/share/clover/jaspar2009core" + einfo "You can pass this library to clover for motif search, or use your own library." +} diff --git a/sci-biology/clover/metadata.xml b/sci-biology/clover/metadata.xml index 622c9ed81..fd501d278 100644 --- a/sci-biology/clover/metadata.xml +++ b/sci-biology/clover/metadata.xml @@ -1,6 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-biology</herd> -<maintainer><email>maintainer-wanted@gentoo.org</email></maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>maintainer-wanted@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog index 7a23b4e2a..ad14cdd33 100644 --- a/sci-biology/cutadapt/ChangeLog +++ b/sci-biology/cutadapt/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/cutadapt -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -cutadapt-1.0.ebuild, + +cutadapt-1.2.1.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and distutils-r1.eclass + *cutadapt-1.0 (02 Mar 2012) 02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest index 4bbdb1cc0..d1f5dc4ae 100644 --- a/sci-biology/cutadapt/Manifest +++ b/sci-biology/cutadapt/Manifest @@ -1 +1 @@ -DIST cutadapt-1.0.tar.gz 66166 SHA256 8b2a608eb6f73d9cbc3ee04eb4726d4067d6b128d23eba585ceed1aa532e4416 SHA512 dea81ab4ffd640ce43fd2184bb01223d6f23428bbb26ddaf8659046dbf1e635b8ec3e4d66fd0d5ffd26c4b43df3a1e981ea08345d0639c98e5ea887faa3f4adb WHIRLPOOL 7926863a727176ab13c381cd732207a55dc5f0220edabf83353ec16d4fbbb0dcf08558085bc7aec9b438a265010a85d020c9c92d81395cac8f0d63d370776eba +DIST cutadapt-1.2.1.tar.gz 104440 SHA256 1baf91c7351ee3464cd01a7f767fe474675ab1b1f7bb110ffe3722e8126ed5cf SHA512 5cd48f342ed75d18780ec63c73f2c42d239253d8dded3161c39f7a26e915f195055c8c4097305246a1418f8b4d3c8853adc1074cbe2a9c1a1b0af644e36771b6 WHIRLPOOL b5c6ceb65be0fcfe418b31cb4c2f8b427d017f71eed182585dc4353079df21ba2ae16354bb6cfcc17bfb39d155ae87fc97fed55b3d0f6ebc68197d98c395c31e diff --git a/sci-biology/cutadapt/cutadapt-1.0.ebuild b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild index add090cc6..40ece0c59 100644 --- a/sci-biology/cutadapt/cutadapt-1.0.ebuild +++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 -PYTHON_DEPEND="2:2.6" -SUPPORT_PYTHON_ABIS="1" +EAPI=5 -inherit distutils +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data" HOMEPAGE="https://code.google.com/p/cutadapt/" @@ -16,6 +16,3 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" - -DEPEND="" -RDEPEND="${DEPEND}" diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/cutadapt/metadata.xml +++ b/sci-biology/cutadapt/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/erpin/ChangeLog b/sci-biology/erpin/ChangeLog index f98fe95cc..de94a4865 100644 --- a/sci-biology/erpin/ChangeLog +++ b/sci-biology/erpin/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-biology/erpin -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> erpin-5.5b.ebuild, metadata.xml: + Bump to EAPI=5 and respect FLAGS / AR + 23 Nov 2009; Andrey Kislyuk <weaver@gentoo.org> ChangeLog: New package, ebuild written by me diff --git a/sci-biology/erpin/Manifest b/sci-biology/erpin/Manifest index a5845e4ac..0c7cd75e4 100644 --- a/sci-biology/erpin/Manifest +++ b/sci-biology/erpin/Manifest @@ -1,2 +1,2 @@ -DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 -DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d +DIST ErpinBatch.1.4.tar.gz 2195075 SHA256 5da4c69d88092e79f4f5d73e7d67dfccbb3d4a8cbe38c74169548ef608f25808 SHA512 1fe33a0760e843c1f2096e5fa923275d2109e10ba42ff18d24898d59de7d2e31ae2adee915d35d1afc1b1f41dee1243986878bc6440223a0def372fd0536c261 WHIRLPOOL 82871a1836d3cbe7a271e31ed15a2e2aca29a06262105bf1dd03a7bb64e6167a6dedd6bd56c4832c11579d3ca307706b7493d1b81e5cd2b63c166a74cb7577c2 +DIST erpin5.5b.serv.tar.gz 1145698 SHA256 0433ed25dd54491ddc4c025bb61d78d36797c2c83c61f260b5663c44cbad4d4d SHA512 f6ca25e72e26d98b609b54984bf74e4bdc0ff239e94e7f8851b303022b7399bcdf879589827e2c35763b8547487740832d51b9997a6a230d8f24b4c506d338e5 WHIRLPOOL 188ab1e408bec9a4d484b476aa73cce7acdc340f5c1cd5c31bdce8c511b0864abd0312feb815ae0d28b75de99c0225bb8d4765dd9d584295af37b998f9abfc53 diff --git a/sci-biology/erpin/erpin-5.5b.ebuild b/sci-biology/erpin/erpin-5.5b.ebuild index 8aafe2078..3673a3225 100644 --- a/sci-biology/erpin/erpin-5.5b.ebuild +++ b/sci-biology/erpin/erpin-5.5b.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/cvsroot/gentoo-x86/sci-biology/bowtie/bowtie-0.10.1.ebuild,v 1.3 2009/09/22 11:43:28 maekke Exp $ -EAPI="2" +EAPI=5 inherit toolchain-funcs @@ -10,10 +10,11 @@ ERPIN_BATCH_V=1.4 DESCRIPTION="Easy RNA Profile IdentificatioN, an RNA motif search program" HOMEPAGE="http://tagc.univ-mrs.fr/erpin/" -SRC_URI="http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz +SRC_URI=" + http://rna.igmors.u-psud.fr/download/Erpin/erpin${PV}.serv.tar.gz http://rna.igmors.u-psud.fr/download/Erpin/ErpinBatch.${ERPIN_BATCH_V}.tar.gz" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -29,19 +30,21 @@ src_prepare() { find -name '*.mk' | xargs sed -i \ -e 's/strip $@/echo skipping strip $@/' \ -e '/CFLAGS =/ d' \ - -e "s/CC = .*/CC = $(tc-getCC)/" || die + -e "s/CC = .*/CC = $(tc-getCC)/" \ + -e "s: -o : ${LDFLAGS} -o :g" \ + -e "s:ar :$(tc-getAR) :g" || die sed -i 's/cc -O2/$(tc-getCC) ${CFLAGS}/' erpin${PV}.serv/sum/sum.mk || die } src_compile() { - emake -C erpin${PV}.serv -f erpin.mk || die + emake -C erpin${PV}.serv -f erpin.mk } src_install() { - dobin erpin${PV}.serv/bin/* || die + dobin erpin${PV}.serv/bin/* insinto /usr/share/${PN} - doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V} || die + doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V} exeinto /usr/share/${PN} - newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand.pl || die - dodoc erpin${PV}.serv/doc/doc*.pdf || die + newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand + dodoc erpin${PV}.serv/doc/doc*.pdf } diff --git a/sci-biology/erpin/metadata.xml b/sci-biology/erpin/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/erpin/metadata.xml +++ b/sci-biology/erpin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/gap2caf/ChangeLog b/sci-biology/gap2caf/ChangeLog new file mode 100644 index 000000000..8e35f8604 --- /dev/null +++ b/sci-biology/gap2caf/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-biology/gap2caf +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> gap2caf-2.1.0.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license; make it build with eautoreconf + diff --git a/sci-biology/gap2caf/Manifest b/sci-biology/gap2caf/Manifest index 3dbd5c548..7d17476c0 100644 --- a/sci-biology/gap2caf/Manifest +++ b/sci-biology/gap2caf/Manifest @@ -1,2 +1,2 @@ -DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a -DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d +DIST gap2caf-2.1.0.tar.gz 92905 SHA256 1fd237cf1e83c3c4c3b67d2d35c9f059cc7eda9f6ac7886fab994e2386283b9a SHA512 2a843d861b7be6d656793f4876953596b91a93c3da7d23ee8edc10c4620e33fc96a16beaeaaf4f66c1f5c5084eb8a9a255d4fa8e1ca6e87e96372f2459167c90 WHIRLPOOL f5a3360de7c6b8741e5e85a9bc25198de4dbcbebdee73ba48a7e1460eb4d778648a5c93f0bb44c10e15a4fa46dd0c741fc10c8e33ae8c50e2c7cd9914a56aa81 +DIST staden-2.0.0b8.tar.gz 4312143 SHA256 c13aa0c22dcac6b10d13501dcb630efad51d7c171968e0bb30113667b49cfa9d SHA512 ddd273d281557595c90b93304cd03205adbe1367845ef43763a8c75d06c2729d99ca8622439ff5c31217595481a9ac4ccedf87c5948821aeaeb73c96133dc411 WHIRLPOOL f086f7f81884091a34c9933a2bb901146eefcd2dc4cb4b940228de3a51daee4c1f9d5613ca34ec345bcce48fc53bed6c4a408f5b5d6e87ac5c4deda222daee24 diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild index 861bbc8f0..ca12aedf2 100644 --- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild +++ b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild @@ -1,26 +1,25 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 inherit autotools eutils DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data" HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz - http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz" +SRC_URI=" + ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz + http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz" -LICENSE="as-is staden" +LICENSE="GRL staden" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" -RDEPEND="${DEPEND}" - -DEPEND="sci-biology/staden - >=dev-lang/tcl-8.5" +DEPEND=" + sci-biology/staden + >=dev-lang/tcl-8.5" RDEPEND="${DEPEND}" #src_prepare(){ @@ -29,13 +28,14 @@ RDEPEND="${DEPEND}" src_prepare(){ sed -i 's:/include/tcl8.4:/include:' configure.ac || die - sed -i 's:libtcl8.4:libtcl8.5:' configure.ac || die - sed -i 's:tcl8.4:tcl8.5:' src/Makefile.am || die - eaclocal - eautomake - eautoconf - sed -i 's:/include/tcl8.4:/include:' configure - sed -i 's:libtcl8.4:libtcl8.5:' configure + sed -i 's:libtcl8.4:libtcl:' configure.ac || die + sed \ + -e 's:tcl8.4:tcl:' \ + -e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \ + -i src/Makefile.am || die + eautoreconf + sed -i 's:/include/tcl8.4:/include:' configure || die + sed -i 's:libtcl8.4:libtcl:' configure || die } src_configure(){ @@ -45,12 +45,13 @@ src_configure(){ #LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \ # STADENROOT=/usr/share/staden \ # STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \ - econf --with-stadenroot=/usr \ - --with-tcl=/usr \ - --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src || die + econf \ + --with-stadenroot=/usr \ + --with-tcl=/usr \ + --with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die #sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die - sed -i 's:tcl8.4:tcl8.5:' src/Makefile || die + sed -i 's:tcl8.4:tcl:' src/Makefile || die # The below tricks in overall do not help, only for -ltk_utils somehow sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die @@ -68,7 +69,7 @@ src_install(){ # # Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden dobin src/gap2caf - dodoc README || die + dodoc README } # BUG #259848 diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/gap2caf/metadata.xml +++ b/sci-biology/gap2caf/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/perlprimer/metadata.xml b/sci-biology/perlprimer/metadata.xml index 507b6a9da..34294c65c 100644 --- a/sci-biology/perlprimer/metadata.xml +++ b/sci-biology/perlprimer/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-biology</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-biology/quicktree/ChangeLog b/sci-biology/quicktree/ChangeLog index ba6206456..00e62e40d 100644 --- a/sci-biology/quicktree/ChangeLog +++ b/sci-biology/quicktree/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/quicktree -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> quicktree-1.1-r1.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license + *quicktree-1.1-r1 (08 Nov 2010) 08 Nov 2010; Kacper Kowalik <xarthisius@gentoo.org> -quicktree-1.1.ebuild, diff --git a/sci-biology/quicktree/Manifest b/sci-biology/quicktree/Manifest index 3bb33a29d..acb09d64c 100644 --- a/sci-biology/quicktree/Manifest +++ b/sci-biology/quicktree/Manifest @@ -1 +1 @@ -DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef +DIST quicktree-1.1.tar.gz 39035 SHA256 3b5986a8d7b8e59ad5cdc30bd7c7d91431909c25230e8fed13494f21337da6ef SHA512 1b58b786a5f0c96d7a86280e0349eb48b9a1f11160e0266e6b837dfde20a159de1393ec46bc4cdcaae09ffa59c68e8bbc5a985286133b67d6ab8fa6e248823fb WHIRLPOOL 0837a98f78f2ac56ed1f19d89a6e6fa632de4946d3a8b2fe8ec58347e58cf0cc1bcf52dbfaf63bcbc29a3994dc0f3fb61c447e0dbe4711c00201a5ac8a4b9ae7 diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/quicktree/metadata.xml +++ b/sci-biology/quicktree/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/quicktree/quicktree-1.1-r1.ebuild b/sci-biology/quicktree/quicktree-1.1-r1.ebuild index 99053dc6f..e32314f97 100644 --- a/sci-biology/quicktree/quicktree-1.1-r1.ebuild +++ b/sci-biology/quicktree/quicktree-1.1-r1.ebuild @@ -1,6 +1,6 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/fasttree/fasttree-2.0.1.ebuild,v 1.1 2009/09/10 23:14:22 weaver Exp $ +# $Header: $ EAPI=2 @@ -8,9 +8,9 @@ inherit toolchain-funcs DESCRIPTION="Rapid reconstruction of phylogenies by the Neighbor-Joining method" HOMEPAGE="http://www.sanger.ac.uk/Software/analysis/quicktree/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/quicktree/quicktree.tar.gz -> quicktree-${PV}.tar.gz" +SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${PN}/${PN}.tar.gz -> ${P}.tar.gz" -LICENSE="as-is" +LICENSE="GRL" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -18,15 +18,16 @@ KEYWORDS="~amd64 ~x86" S=${WORKDIR}/${PN}_${PV} src_prepare() { - sed -e "s/\-O2 \-Wall/${CFLAGS}/" \ + sed \ + -e "s/\-O2 \-Wall/${CFLAGS}/" \ -i Makefile || die } src_compile() { - emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}" || die + emake CC="$(tc-getCC)" LFLAGS="${LDFLAGS}" } src_install() { - dobin bin/quicktree || die - dodoc README || die + dobin bin/quicktree + dodoc README } diff --git a/sci-biology/sequin/ChangeLog b/sci-biology/sequin/ChangeLog index ca9c2b059..639b7c7a9 100644 --- a/sci-biology/sequin/ChangeLog +++ b/sci-biology/sequin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/sequin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*sequin-20121202 (16 Jun 2013) + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -sequin-20090722.ebuild, + +sequin-20121202.ebuild: + Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html + files into sys path + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: Fixed herd entry in metadata.xml diff --git a/sci-biology/sequin/Manifest b/sci-biology/sequin/Manifest index 442d7db82..956270595 100644 --- a/sci-biology/sequin/Manifest +++ b/sci-biology/sequin/Manifest @@ -1,2 +1,2 @@ -DIST sequin-20090722-x86.tar.gz 5999782 SHA256 f12fe7fa084a1d19a75e67cfcb4027cefb91c819b7c6219499072a87f00bdc51 -DIST sequin-20090722-x86_64.tar.gz 6911415 SHA256 338de057edf9c14e911f69c372c9480675c2b5a4b24efed605dcbdf7e8e4d486 +DIST sequin-20121202-x86.tar.gz 6760477 SHA256 a07bb9ad491b1ef0c7f03381bd73cab4bb6305a0897c117b071ad5a633a4a95e SHA512 a93d79b5a7ed7a42cc02107a0ca87051e3f95554afb103ad9fb17d1c98d4f0f5b3f01b512f63b8902cc9865a38eb10cf65cbae46a2fcf0ed4a9c1b9b697f47e9 WHIRLPOOL 288d75b4426edb9d657fe727a484a8f6009c71eff6f3202b412bbc635f52613f89955120ad0170c18f5e7d4bbf6e7f81a06b2f4b9b7f5166dc97617ee8a1c682 +DIST sequin-20121202-x86_64.tar.gz 8277570 SHA256 fe7d430a32320f22917fa515c3ba13b6fb3c9af42916759a353b9b62c0437b81 SHA512 33664d49cb0b33194d64781086ee27fad65602b6c058c4cc079ce840b6a4774c675b21c82bfcf2648b6b1f95fb0bcacc4f2eddb25d06fb8a363d4993cbb20b32 WHIRLPOOL 3f5c107701755eab1021014f9e9b333a74af42f49a1c6595d15cc38100ba1d5fe4c91fe1eef31083f937aae9bac66d94f21cd253430d1bb68e341ceb7308797b diff --git a/sci-biology/sequin/sequin-20090722.ebuild b/sci-biology/sequin/sequin-20090722.ebuild deleted file mode 100644 index b1d419648..000000000 --- a/sci-biology/sequin/sequin-20090722.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $ - -EAPI=2 - -inherit eutils - -DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases" -HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/" -SRC_URI="amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) - x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="x11-libs/libXmu - x11-libs/libXp" - -S="${WORKDIR}" - -src_install() { - insinto /opt/${PN} - doins -r * || die - exeinto /opt/${PN} - doexe sequin || die - dosym /opt/${PN}/sequin /usr/bin/sequin || die - make_desktop_entry sequin Sequin || die -} diff --git a/sci-biology/sequin/sequin-20121202.ebuild b/sci-biology/sequin/sequin-20121202.ebuild new file mode 100644 index 000000000..5e586dcd8 --- /dev/null +++ b/sci-biology/sequin/sequin-20121202.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/clustalw/clustalw-2.0.12.ebuild,v 1.1 2009/10/18 21:14:11 weaver Exp $ + +EAPI=5 + +inherit eutils + +DESCRIPTION="A tool to facilitate submission of data to the GenBank, EMBL, and DDBJ sequence databases" +HOMEPAGE="http://www.ncbi.nlm.nih.gov/Sequin/" +SRC_URI=" + amd64? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) + x86? ( ftp://ftp.ncbi.nih.gov/sequin/sequin.linux.tar.gz -> ${P}-x86.tar.gz )" +# amd64? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86_64.tar.gz -> ${P}-x86_64.tar.gz ) +# x86? ( ftp://ftp.ncbi.nih.gov/sequin/old/${PV}/sequin.linux-x86.tar.gz -> ${P}-x86.tar.gz )" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + x11-libs/libXmu + x11-libs/libXp" + +S="${WORKDIR}" + +QA_PREBUILT="/opt/.*" + +src_install() { + dohtml -r *htm images + rm -rf *htm images || die + + insinto /opt/${PN} + doins -r * + + exeinto /opt/${PN} + doexe sequin + + dosym /opt/${PN}/sequin /opt/bin/sequin + + make_desktop_entry sequin Sequin +} diff --git a/sci-biology/smalt-bin/ChangeLog b/sci-biology/smalt-bin/ChangeLog index f3268fd32..7f6f91f99 100644 --- a/sci-biology/smalt-bin/ChangeLog +++ b/sci-biology/smalt-bin/ChangeLog @@ -1,7 +1,13 @@ # ChangeLog for sci-biology/smalt-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*smalt-bin-0.7.4 (16 Jun 2013) + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -smalt-bin-0.5.1.ebuild, + +smalt-bin-0.7.4.ebuild, metadata.xml: + Version Bump; restrict license; add QA_PREBUILT for binaries + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> smalt-bin-0.5.1.ebuild: Cleaned ebuild and fixed LICENSE diff --git a/sci-biology/smalt-bin/Manifest b/sci-biology/smalt-bin/Manifest index f9f5194ab..0e8053bb2 100644 --- a/sci-biology/smalt-bin/Manifest +++ b/sci-biology/smalt-bin/Manifest @@ -1 +1 @@ -DIST smalt-0.5.1.tgz 534824 SHA256 c8bca18a7ded7ad4b7070be7478bd046cf2d6a0a81054dfd96ebdba65c0a49d0 +DIST smalt-0.7.4.tgz 1437480 SHA256 a6997fcbef746c57f889c3784b2bc9c399ad03562ed8d4a835180ba8cc6822fe SHA512 9c31f358ef4094566bdc67f92b2576e6cf15a010bbf7dc1eb4a66afb2107253dfe4947a529c10c579484ccd7aff6aaae048ea8b17fd468804b08d88fb6588e39 WHIRLPOOL 65c1a52608d26e3411a77137fa03c65ae30cc845d5e9f676ab4c1a53812f1fcbd2300b4e5a0a8839c24c00f526f0a5627b6facbec54cbe86af7d132857b728c1 diff --git a/sci-biology/smalt-bin/metadata.xml b/sci-biology/smalt-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/smalt-bin/metadata.xml +++ b/sci-biology/smalt-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild b/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild deleted file mode 100644 index 7566c2097..000000000 --- a/sci-biology/smalt-bin/smalt-bin-0.5.1.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2011 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" -SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/smalt/smalt-"${PV}".tgz" - -LICENSE="as-is" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="" - -S="${WORKDIR}"/smalt-"${PV}" - -src_install(){ - use x86 && newbin smalt_i386 smalt - use amd64 && newbin smalt_x86_64 smalt - use ia64 && newbin smalt_ia64 - - dodoc NEWS smalt_manual.pdf - doman smalt.1 -} diff --git a/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild new file mode 100644 index 000000000..01acc05a9 --- /dev/null +++ b/sci-biology/smalt-bin/smalt-bin-0.7.4.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +MY_PN="${PN%-bin}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Pairwise sequence alignment mapping DNA reads onto genomic reference, better over SSAHA2" +HOMEPAGE="http://www.sanger.ac.uk/resources/software/smalt/" +SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}.tgz" + +LICENSE="all-rights-reserved" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +S="${WORKDIR}"/${MY_P} + +QA_PREBUILT="/opt/.*" + +src_install(){ + exeinto /opt/bin + use x86 && newexe ${MY_PN}_i386 ${MY_PN} + use amd64 && newexe ${MY_PN}_x86_64 ${MY_PN} + use ia64 && newexe ${MY_PN}_ia64 ${MY_PN} + + dodoc NEWS ${MY_PN}_manual.pdf + doman ${MY_PN}.1 +} diff --git a/sci-biology/ssaha2-bin/ChangeLog b/sci-biology/ssaha2-bin/ChangeLog index 914725e6e..8b3f2ffef 100644 --- a/sci-biology/ssaha2-bin/ChangeLog +++ b/sci-biology/ssaha2-bin/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/ssaha2-bin -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -ssaha2-bin-2.5.3.ebuild, + +ssaha2-bin-2.5.5.ebuild, metadata.xml: + Version Bump; restrict license; add QA_PREBUILT for binaries + 25 Jun 2011; Justin Lecher <jlec@gentoo.org> ssaha2-bin-2.5.3.ebuild: Cleaned ebuild and fixed LICENSE diff --git a/sci-biology/ssaha2-bin/Manifest b/sci-biology/ssaha2-bin/Manifest index 3cd3275a6..f1a6a5db5 100644 --- a/sci-biology/ssaha2-bin/Manifest +++ b/sci-biology/ssaha2-bin/Manifest @@ -1,5 +1,4 @@ -DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 -DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf -DIST ssaha2_i686.tgz 288481 SHA256 7d173d763d9f685ef3d0075124bf8b763c6d2d3ed1a1f823bc66d6b6b029abed -DIST ssaha2_ia64.tgz 458507 SHA256 3eb2a31559911f3ee87e11f3b977962da31b60c25ea0c9a064edfd1165b6b5dd -DIST ssaha2_x86_64.tgz 287790 SHA256 0135ab2e285a898d450744b7c9d643efbeb6048783169a6647f310ce2e7b8138 +DIST samflag.c 2424 SHA256 945958214ef1adc40029a6b3c323c37338e095e9e2bcbff5e5ec05aadbdb67d0 SHA512 50ef4d134e5fab4f1399fd2eb35de0c8ce901c23e360a52ee5cdca117c124c77f432a50a666d655dc0f04089db84d873f9251e68ff6f6f4ac327e23362657aa7 WHIRLPOOL c89abd1bac315aaadfc4456c4ec4252a6ccdd1f42db604b60568d3ee7e367f8ec99ff7915aeaac7dafa594bd29bb11affb3f62ed9d6dd577dd407c2c4c93e7c5 +DIST ssaha2-manual.pdf 163188 SHA256 1a0529168b71ac55e13b34264a854daa6a5dac9468f81ccb5b63bd5e1baafdbf SHA512 2a43d038684519d3a4e1fca54b75ac731961dc1e9e1034914eff481b303e5b49d11f4d9149e56a6e06292107f5be3ee6357bb9ec508cdb4de1fac677fade5d0e WHIRLPOOL 25040635acf63d874c453d5e2c2bb93dd2f44537c79ce5d3109bd59a345cbf41e4106b05039a8d3e0b00a8e1bd7a66d923161b8f0fe2544f10c37f5a4bfbbaf9 +DIST ssaha2_v2.5.5_i686.tgz 1045230 SHA256 b66ddbf1374cbcf583ff5413cb7c17dd0e63c2372d227c26526fa79597cb39c8 SHA512 e5611a2b382348e84b7cc40496b42d78ca1b5a5d641acfdb1371bff79dbe055f8c22db10b3a428d7943a6824246141e28e71146722a613585d82034187d81e32 WHIRLPOOL 169d316e548a4cc223755534b235163f0356129b6aab44540cbe5eb6083ea46f47ee689097301ecc86974da8a7b21f5887db8e88b772668c3049de31120581de +DIST ssaha2_v2.5.5_x86_64.tgz 1167987 SHA256 478bdbda9d5fe36278748e571299f5eaf39d5172758cf0d0a85fa750f84667d4 SHA512 483dc726e1ac52020481a5721e0ac870fccdec22d9f7e74bddc76cbb76bd10ceccba57ecab9e2787045cde0e6cb74186bd3769e5c7222eb15e9c445ba7ac2592 WHIRLPOOL dbde27ca5e2eeba1c44fc59cd66f1ac6c6fa52647174c184521cf88b9ae8b05633f2fc1bc93b3be6e07e499832ec0938c4fab1017e53706b51c78060f6590b01 diff --git a/sci-biology/ssaha2-bin/metadata.xml b/sci-biology/ssaha2-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/ssaha2-bin/metadata.xml +++ b/sci-biology/ssaha2-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild index 34b63dd43..96a183dc7 100644 --- a/sci-biology/ssaha2-bin/ssaha2-bin-2.5.3.ebuild +++ b/sci-biology/ssaha2-bin/ssaha2-bin-2.5.5.ebuild @@ -1,34 +1,40 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit toolchain-funcs +MY_PN="${PN%-bin}" +MY_P="${MY_PN}_v${PV}" + DESCRIPTION="SSAHA2: Sequence Search and Alignment by Hashing Algorithm" HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2" SRC_URI=" - x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_i686.tgz ) - amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_x86_64.tgz ) - ia64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2_ia64.tgz ) + x86? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_i686.tgz ) + amd64? ( ftp://ftp.sanger.ac.uk/pub4/resources/software/${MY_PN}/${MY_P}_x86_64.tgz ) ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/samflag.c ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/ssaha2-manual.pdf" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -use x86 && S="${WORKDIR}"/ssaha2_v"${PV}"_i686 -use amd64 && S="${WORKDIR}"/ssaha2_v"${PV}"_x86_64 -use ia64 && S="${WORKDIR}"/ssaha2_v"${PV}"_ia64 +QA_PREBUILT="/opt/.*" +pkg_setup() { + use x86 && export S="${WORKDIR}"/${MY_P}_i686 + use amd64 && export S="${WORKDIR}"/${MY_P}_x86_64 +} src_compile() { $(tc-getCC) ${CFLAGS} ${LDFLAGS} -o samflag "${DISTDIR}"/samflag.c || die "Failed to compile samflags" } src_install() { - dobin samflag ssaha2 ssaha2Build ssahaSNP + dobin samflag + exeinto /opt/bin + doexe ssaha2 ssaha2Build ssahaSNP dodoc README "${DISTDIR}"/ssaha2-manual.pdf } diff --git a/sci-biology/tablet-bin/ChangeLog b/sci-biology/tablet-bin/ChangeLog index 3205cfc85..87308e6e1 100644 --- a/sci-biology/tablet-bin/ChangeLog +++ b/sci-biology/tablet-bin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-biology/tablet-bin -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> tablet-bin-1.13.05.17.ebuild: + Version BUmp; BUmp to EAPI5 and python-r1.eclass; drop addpredict + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -tablet-bin-1.11.05.03.ebuild, + -tablet-bin-1.11.11.01.ebuild, +tablet-bin-1.13.05.17.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and python-r1.eclass + 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> tablet-bin-1.11.11.01.ebuild: adjust PATH to point to the installation place diff --git a/sci-biology/tablet-bin/Manifest b/sci-biology/tablet-bin/Manifest index ae6afbe26..18833160e 100644 --- a/sci-biology/tablet-bin/Manifest +++ b/sci-biology/tablet-bin/Manifest @@ -1,3 +1,2 @@ DIST coveragestats.py 4800 SHA256 358b686d00fd75d2cc9af490b0e7d635f74cbb1c0b153df22d8ff879884d47bc SHA512 d5688832c13dc9c2e2e015df0b5c50113f72e2eeae076d479c43b65a4b028f8dcfa5f0fb833b4341d76d3956ea27707c55a51389b73a2efed6abd2b96ccdc3cd WHIRLPOOL 0b1eb20189b343d6014097748c053f35f8ad162400312cfbde16bac7fee52f24ac8b0055e991c823dcb64d7a20df3fbb88d8cd6119f838d4e9a5f26e82604664 -DIST tablet_linux_x86_1_11_05_03.sh 24035425 SHA256 3c7de5f0e5d37019485612723dfd3b17fd34e24df8986eb535fcb0335f8b2e99 -DIST tablet_linux_x86_1_11_11_01.sh 23481558 SHA256 9dbbd9ecf1c20e39b978a4be88707593c37073407af951cbf7a9b3d16e6daf23 SHA512 95da451959304aafe36c70895cd9f0a89c1749a403e47a4f32b7605e6cbdb5b2f69b03b4177fd6db45cbdba76e2f054742179000d29b0574a1f4541f335aeaa2 WHIRLPOOL cae67ca8338aa23781f91cd235ecc1bd082b04ada80a158d827acf33c04d8bd63e89883790dd3945938e1405c2b6a0903d4e10ffe40c3fe7e0e042390ba1cabe +DIST tablet-bin-1.13.05.17.sh 35467547 SHA256 6da2cbb8d15433cdf022c93f466d355515a9c1c8f89dcdab4c2e9543bee415e4 SHA512 532900242ef3b3a46a6e6379c29b627c9f337198cf230273eb1da4c269b6f09a49bc7c5ea28a1ee4caa4f7d7a76ba0e0f18330a538428e49b8f1d36c3bfecb78 WHIRLPOOL 299f23da5f6192a7802f86e61e2c5655711d0d672e28cdd257fdd179d76e15e1b951fa42ec2b28e4568063197b14e1884d61992b7ff2e864fa86c3dad2141c14 diff --git a/sci-biology/tablet-bin/metadata.xml b/sci-biology/tablet-bin/metadata.xml index 07b525505..2bc893037 100644 --- a/sci-biology/tablet-bin/metadata.xml +++ b/sci-biology/tablet-bin/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-biology</herd> - <maintainer> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> + <herd>sci-biology</herd> + <maintainer> + <email>mmokrejs@fold.natur.cuni.cz</email> + <name>Martin Mokrejs</name> + </maintainer> </pkgmetadata> diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild b/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild deleted file mode 100644 index 3e6d6e64f..000000000 --- a/sci-biology/tablet-bin/tablet-bin-1.11.11.01.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=3 - -inherit java-pkg-2 python - -DESCRIPTION="Viewer of next generation sequence assemblies and alignments." -HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" -SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_11_01.sh - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" - -# Upstream says regarding source code unavailability: -# Tablet uses a modified version of the BSD License which has been edited to -# remove references to distribution and use in source forms. This means that -# we are happy for you to distribute and use Tablet however you please, but we -# do not (yet) want to make the source code publicly available. - -# The licence file itself is in the installer, and ends up on disk after -# installation at /opt/Tablet/docs/tablet.html -# The original BSD licence was modified to remove references to distribution -# and use in source forms, because we cannot make the source code available -# for Tablet. - -LICENSE="Tablet" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="" -RDEPEND="${DEPEND} - virtual/jre - dev-lang/python" - -MYPV="$(replace_all_version_separators '_')" - -pkg_setup() { - einfo "Fixing java access violations ..." - # bug 387227 - addpredict /proc/self/coredump_filter -} - -src_install() { - # In theory it seems this binary package could be installed through ant - # instead of the install4j package which is not easy to be forced - # non-interactive. The below approach via install4j is not ideal but works. - sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed" - - # the intallation script somehow does not pickup - # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore - # we place the file rather directly into the place where it should reside. - # In the file you can read details how the variables were mangled. For - # example, the trick with sys.symlinkDir in the response.varfile is to - # disable the installation process to symlink from /usr/local/bin/table to - # /opt/Tablet/tablet. That was logged in that file with the following line: - # - # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] - # - # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile - mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/" - cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile" - - # make sure we force java to point a to $HOME which is inside our sanbox - # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome - # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh || die "failed to set userHome value" - sh "${DISTDIR}"/tablet_linux_x86_"${MYPV}".sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file" - dobin "${DISTDIR}"/coveragestats.py - - echo "PATH=/opt/Tablet" > 99Tablet - doenvd 99Tablet || die -} diff --git a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild index 32cc463ee..762e888aa 100644 --- a/sci-biology/tablet-bin/tablet-bin-1.11.05.03.ebuild +++ b/sci-biology/tablet-bin/tablet-bin-1.13.05.17.ebuild @@ -1,15 +1,18 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=3 +EAPI=5 -inherit java-pkg-2 python +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit java-pkg-2 python-r1 DESCRIPTION="Viewer of next generation sequence assemblies and alignments." HOMEPAGE="http://bioinf.scri.ac.uk/tablet/" -SRC_URI="http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_1_11_05_03.sh - http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" +SRC_URI=" + http://bioinf.scri.ac.uk/tablet/installers/tablet_linux_x86_$(replace_all_version_separators _).sh -> ${P}.sh + http://bioinf.scri.ac.uk/tablet/additional/coveragestats.py" # Upstream says regarding source code unavailability: # Tablet uses a modified version of the BSD License which has been edited to @@ -28,16 +31,26 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -DEPEND="" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND="${PYTHON_DEPS}" RDEPEND="${DEPEND} - virtual/jre - dev-lang/python" + virtual/jre" + +S="${WORKDIR}" + +src_unpack() { + local file + for file in ${A}; do + cp "${DISTDIR}"/${file} "${WORKDIR}" || die + done +} src_install() { # In theory it seems this binary package could be installed through ant # instead of the install4j package which is not easy to be forced # non-interactive. The below approach via install4j is not ideal but works. - sed "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile > "${DISTDIR}"/response.varfile || die "sed failed" + sed "s#\"\${D}\"#\"${D}\"#g" "${FILESDIR}"/response.varfile > "${WORKDIR}"/response.varfile || die "sed failed" # the intallation script somehow does not pickup # -varfile="${DISTDIR}"/response.varfile from the commandline and therefore @@ -47,16 +60,30 @@ src_install() { # disable the installation process to symlink from /usr/local/bin/table to # /opt/Tablet/tablet. That was logged in that file with the following line: # - # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] + # /var/tmp/portage/sci-biology/tablet-bin-1.11.02.18/image/opt/Tablet/.install4j/installation.log: + # Variable changed: sys.symlinkDir=/usr/local/bin[class java.lang.String] # # The file is then left on the installed system in "${D}"/opt/Tablet/.install4j/response.varfile - mkdir -p "${D}"/opt/Tablet/.install4j || die "Cannot pre-create "${D}"/opt/Tablet/.install4j/" - cat "${DISTDIR}"/response.varfile > "${D}"/opt/Tablet/.install4j/response.varfile || die "Cannot write "${D}"/opt/Tablet/.install4j/response.varfile" + dodir /opt/Tablet/.install4j + cat "${WORKDIR}"/response.varfile > "${ED}"/opt/Tablet/.install4j/response.varfile || die # make sure we force java to point a to $HOME which is inside our sanbox # directory area. We force -Duser.home . It seems also -Dinstall4j.userHome # could be done based on the figure shown at http://resources.ej-technologies.com/install4j/help/doc/ - sed "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" -i "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh || die "failed to set userHome value" - sh "${DISTDIR}"/tablet_linux_x86_1_11_05_03.sh -q -overwrite -varfile="${DISTDIR}"/response.varfile --destination="${D}"/opt/Tablet -dir "${D}"/opt/Tablet || die "Failed to run the self-extracting exe file" - dobin "${DISTDIR}"/coveragestats.py + sed \ + -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir#" \ + -i "${WORKDIR}"/${P}.sh || die + sh \ + "${WORKDIR}"/${P}.sh \ + -q -overwrite \ + -varfile="${DISTDIR}"/response.varfile \ + --destination="${ED}"/opt/Tablet \ + -dir "${ED}"/opt/Tablet || die + + rm -rf "${ED}"/opt/Tablet/jre || die + + python_foreach_impl python_doscript "${WORKDIR}"/coveragestats.py + + echo "PATH=${EPREFIX}/opt/Tablet" > 99Tablet + doenvd 99Tablet || die } diff --git a/sci-biology/twinscan/ChangeLog b/sci-biology/twinscan/ChangeLog index 3914a6070..fedf86e90 100644 --- a/sci-biology/twinscan/ChangeLog +++ b/sci-biology/twinscan/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-biology/twinscan -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license + 07 Mar 2011; Justin Lecher <jlec@gentoo.org> twinscan-4.1.2.ebuild: Correct Slots for gtk 3 introduction to tree diff --git a/sci-biology/twinscan/Manifest b/sci-biology/twinscan/Manifest index e9fea6590..7e7f3adc1 100644 --- a/sci-biology/twinscan/Manifest +++ b/sci-biology/twinscan/Manifest @@ -1 +1 @@ -DIST iscan-4.1.2.tar_.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a +DIST twinscan-4.1.2.tar.gz 5894833 SHA256 30c7e980b2ccbba22a5e2d7ff0d7c1aaeb610cc1cec81432bb30e87f03f7e56a SHA512 d216f790f6d0f35a070575d1aa4b5e1866c00132168b381b9177b076b1b2a16f2ecd7a88aa443d7ba6b8f62c3ec2595ba33c4608a674e09d94e9f7dc6a181327 WHIRLPOOL e95df100f970c6cabf9b21a9a6651dcd249fccbfafc908a8766bf26ad5108c08b5de105c5142492bb7b0c13f39bd65836a92be9161cfbbb303147f925e775d99 diff --git a/sci-biology/twinscan/metadata.xml b/sci-biology/twinscan/metadata.xml index 3302123e5..fc7c76942 100644 --- a/sci-biology/twinscan/metadata.xml +++ b/sci-biology/twinscan/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer> - <email>weaver@gentoo.org</email> - <name>Andrey Kislyuk</name> - </maintainer> - <herd>sci-biology</herd> + <maintainer> + <email>weaver@gentoo.org</email> + <name>Andrey Kislyuk</name> + </maintainer> + <herd>sci-biology</herd> </pkgmetadata> diff --git a/sci-biology/twinscan/twinscan-4.1.2.ebuild b/sci-biology/twinscan/twinscan-4.1.2.ebuild index 96b1a049c..516aec88c 100644 --- a/sci-biology/twinscan/twinscan-4.1.2.ebuild +++ b/sci-biology/twinscan/twinscan-4.1.2.ebuild @@ -1,14 +1,16 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=5 + +inherit toolchain-funcs DESCRIPTION="TwinScan, N-SCAN, and Pairagon: A gene structure prediction pipeline" HOMEPAGE="http://mblab.wustl.edu/software/twinscan" -SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz" +SRC_URI="http://mblab.wustl.edu/software/download/iscan-${PV}.tar_.gz -> ${P}.tar.gz" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" IUSE="" KEYWORDS="~amd64 ~x86" @@ -18,14 +20,21 @@ RDEPEND="${DEPEND}" S="${WORKDIR}/N-SCAN" -src_unpack() { - unpack ${A} - tar -C "${WORKDIR}" -xf iscan-${PV}.tar_ -} - src_prepare() { sed -i "1 a use lib '/usr/share/${PN}/lib/perl5';" "${S}"/bin/*.pl || die - sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" + sed -i '/my $blast_param/ s/#//' "${S}/bin/runTwinscan2.pl" || die + tc-export CC AR RANLIB + + sed \ + -e 's:ar :$(AR) :g' \ + -e 's:ranlib :$(RANLIB) :g' \ + -e 's: -o : $(LDFLAGS) -o :g' \ + -i Makefile || die + + sed \ + -e "/^GLIB_CFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --cflags glib-2.0) -DHAS_GLIB:g" \ + -e "/^GLIB_LFLAGS/s:=.*:=$($(tc-getPKG_CONFIG) --libs glib-2.0)-DHAS_GLIB:g" \ + -i Makefile.include || die } src_install() { @@ -35,5 +44,6 @@ src_install() { doins -r "${S}/lib" || die echo "TWINSCAN=/usr" > "${S}"/99${PN} doenvd "${S}"/99${PN} || die + rm -rf examples/tmp dodoc examples/* README* } diff --git a/sci-chemistry/GromacsWrapper/metadata.xml b/sci-chemistry/GromacsWrapper/metadata.xml index 098ac091a..13ef0bf5a 100644 --- a/sci-chemistry/GromacsWrapper/metadata.xml +++ b/sci-chemistry/GromacsWrapper/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-chemistry</herd> <maintainer> <email>alexxy@gentoo.org</email> <name>Alexey Shvetsov</name> diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml index a607b9e52..4d996cbcd 100644 --- a/sci-chemistry/ball/metadata.xml +++ b/sci-chemistry/ball/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-chemistry</herd> <maintainer> <email>jlec@gentoo.org</email> </maintainer> diff --git a/sci-chemistry/burrow-owl/metadata.xml b/sci-chemistry/burrow-owl/metadata.xml index 15f3d5ac1..9ac9ffdb3 100644 --- a/sci-chemistry/burrow-owl/metadata.xml +++ b/sci-chemistry/burrow-owl/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci-chemistry@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/camshift/metadata.xml b/sci-chemistry/camshift/metadata.xml index d410f1573..9ac9ffdb3 100644 --- a/sci-chemistry/camshift/metadata.xml +++ b/sci-chemistry/camshift/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/chemBuild/ChangeLog b/sci-chemistry/chemBuild/ChangeLog index a592f6b45..7aa6b2ef5 100644 --- a/sci-chemistry/chemBuild/ChangeLog +++ b/sci-chemistry/chemBuild/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/chemBuild -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild, + files/chemBuild, metadata.xml: + Bump EAPI and python eclass + 21 Sep 2012; Justin Lecher <jlec@gentoo.org> chemBuild-1.0.2.ebuild: Needs webkit support in pyside diff --git a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild index dece95eb2..3f4733f8b 100644 --- a/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild +++ b/sci-chemistry/chemBuild/chemBuild-1.0.2.ebuild @@ -1,12 +1,12 @@ -# 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 -PYTHON_DEPEND="2" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit python toolchain-funcs +inherit python-single-r1 toolchain-funcs DESCRIPTION="Graphical tool to construct chemical compound definitions for NMR" HOMEPAGE="http://www.ccpn.ac.uk/software/chembuild" @@ -17,7 +17,9 @@ LICENSE="|| ( CCPN LGPL-2.1 )" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" -RDEPEND="dev-python/pyside[webkit]" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="dev-python/pyside[webkit,${PYTHON_USEDEP}]" DEPEND="" S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ @@ -28,11 +30,6 @@ S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ #unbundle inchi #parallel build -pkg_setup() { - python_set_active_version 2 - python_pkg_setup -} - src_install() { local in_path=$(python_get_sitedir)/${PN} local _file @@ -44,25 +41,17 @@ src_install() { -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|$(PYTHON -a)|g" \ + -e "s|gentoopython|${PYTHON}|g" \ -e "s|gentoousr|${EPREFIX}/usr|g" \ -e "s|//|/|g" \ "${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die fperms 755 /usr/bin/${PN} - insinto ${in_path} - rm -rf cNg license || die ebegin "Installing main files" - doins -r * + python_moduleinto ${PN} + python_domodule * + python_optimize eend } - -pkg_postinst() { - python_mod_optimize ${PN} -} - -pkg_postrm() { - python_mod_cleanup ${PN} -} diff --git a/sci-chemistry/chemBuild/files/chemBuild b/sci-chemistry/chemBuild/files/chemBuild index c6d3d31ac..308804158 100644 --- a/sci-chemistry/chemBuild/files/chemBuild +++ b/sci-chemistry/chemBuild/files/chemBuild @@ -1,7 +1,7 @@ #!/bin/bash export CCPNMR_TOP_DIR=gentoo_sitedir -export PYTHONPATH=.:${CCPNMR_TOP_DIR}/chemBuild/python +export PYTHONPATH=${CCPNMR_TOP_DIR}/chemBuild/python export LD_LIBRARY_PATH=gentoolibdir export TCL_LIBRARY=gentootcl export TK_LIBRARY=gentootk diff --git a/sci-chemistry/chemBuild/metadata.xml b/sci-chemistry/chemBuild/metadata.xml index d369d068f..51fdedab1 100644 --- a/sci-chemistry/chemBuild/metadata.xml +++ b/sci-chemistry/chemBuild/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml index d369d068f..e42d0af60 100644 --- a/sci-chemistry/chimera-bin/metadata.xml +++ b/sci-chemistry/chimera-bin/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/chooch/metadata.xml b/sci-chemistry/chooch/metadata.xml index d410f1573..9ac9ffdb3 100644 --- a/sci-chemistry/chooch/metadata.xml +++ b/sci-chemistry/chooch/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/cnsface/ChangeLog b/sci-chemistry/cnsface/ChangeLog index 8b8ef62da..91fb75e01 100644 --- a/sci-chemistry/cnsface/ChangeLog +++ b/sci-chemistry/cnsface/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/cnsface -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> cnsface-0.0.12.ebuild, + metadata.xml: + Bump to EAPI5 and distutils-r1.eclass + *cnsface-0.0.12 (01 Dec 2010) 01 Dec 2010; Justin Lecher <jlec@gentoo.org> +files/0.0.12-binary.patch, diff --git a/sci-chemistry/cnsface/Manifest b/sci-chemistry/cnsface/Manifest index b1bdb72df..a9914275b 100644 --- a/sci-chemistry/cnsface/Manifest +++ b/sci-chemistry/cnsface/Manifest @@ -1 +1 @@ -DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655 +DIST cnsface-0.0.12-altoona.tar.gz 1442309 SHA256 add1a1f17fc103a5bb3a75003d8c0e64626b35c6ebbb8e2aa87fed1a0c05b655 SHA512 73bfaf75e89da0066d3ddab1e005b487b837719d5fe4235f8ebad31e84ab715fe829b094769982784c65641cb8c4febc827b2abe7737cf2c251bf4ae293e37c7 WHIRLPOOL f91dfaa22e619f3ab88c0f42d0cbed7df0dfc3d50707097808dc676ec47c067104bb1fcc8ef365a72b7c8d0853ede8b4b52d047ee5dc95ccd48779c1afc9f4a3 diff --git a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild index 6c2903879..55e42f653 100644 --- a/sci-chemistry/cnsface/cnsface-0.0.12.ebuild +++ b/sci-chemistry/cnsface/cnsface-0.0.12.ebuild @@ -1,18 +1,16 @@ -# Copyright 1999-2010 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.*" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils eutils +inherit distutils-r1 DESCRIPTION="GUI for the Crystallography and NMR System" HOMEPAGE="http://cnsface.sourceforge.net" -SRC_URI="mirror://sourceforge/${P}-altoona.tar.gz" +SRC_URI="mirror://sourceforge/project/cnsface/cnsface/Altoona/${P}-altoona.tar.gz" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -20,13 +18,10 @@ LICENSE="GPL-2" IUSE="" RDEPEND=" - dev-python/wxpython:2.8 + dev-python/wxpython:2.8[${PYTHON_USEDEP}] sci-chemistry/cns" DEPEND="${RDEPEND}" S="${WORKDIR}"/${P}-altoona -src_prepare() { - epatch "${FILESDIR}"/${PV}-binary.patch - distutils_src_prepare -} +PATCHES=( "${FILESDIR}"/${PV}-binary.patch ) diff --git a/sci-chemistry/cnsface/metadata.xml b/sci-chemistry/cnsface/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/cnsface/metadata.xml +++ b/sci-chemistry/cnsface/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/concoord/metadata.xml b/sci-chemistry/concoord/metadata.xml index 5ef07a39e..ae9ec7c5f 100644 --- a/sci-chemistry/concoord/metadata.xml +++ b/sci-chemistry/concoord/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-chemistry</herd> <maintainer> <email>jlec@gentoo.org</email> </maintainer> diff --git a/sci-chemistry/coot/metadata.xml b/sci-chemistry/coot/metadata.xml index 20538c1de..b3618ba38 100644 --- a/sci-chemistry/coot/metadata.xml +++ b/sci-chemistry/coot/metadata.xml @@ -3,9 +3,6 @@ <pkgmetadata> <herd>sci-chemistry</herd> <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <maintainer> <email>jlec@gentoo.org</email> <name>Justin Lecher</name> </maintainer> diff --git a/sci-chemistry/cs-rosetta/metadata.xml b/sci-chemistry/cs-rosetta/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/cs-rosetta/metadata.xml +++ b/sci-chemistry/cs-rosetta/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/curvefit/metadata.xml b/sci-chemistry/curvefit/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/curvefit/metadata.xml +++ b/sci-chemistry/curvefit/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/direx/metadata.xml b/sci-chemistry/direx/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/direx/metadata.xml +++ b/sci-chemistry/direx/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/dssp2pdb/metadata.xml b/sci-chemistry/dssp2pdb/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/dssp2pdb/metadata.xml +++ b/sci-chemistry/dssp2pdb/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/freeon/ChangeLog b/sci-chemistry/freeon/ChangeLog index 4e266dee5..0067c486a 100644 --- a/sci-chemistry/freeon/ChangeLog +++ b/sci-chemistry/freeon/ChangeLog @@ -2,6 +2,15 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + freeon-2012.05.03.ebuild, freeon-9999.ebuild, + +files/freeon-2012.05.03-no_internal_hdf5.patch, + -files/freeon-2012.05.03-no_internal_libs.patch, + +files/freeon-9999-no_internal_hdf5.patch, + -files/freeon-9999-no_internal_libs.patch: + Intrusion reduced. Only the descent to obsolete autoconf files in the + directory of the internal old hdf5 copy patched off. + *freeon-2012.05.03 (30 May 2013) 30 May 2013; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_hdf5.patch index e37622b0e..ccbc8be26 100644 --- a/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_libs.patch +++ b/sci-chemistry/freeon/files/freeon-2012.05.03-no_internal_hdf5.patch @@ -1,14 +1,9 @@ diff -Naurp freeon-beta-2012-05-03.orig/Makefile.am freeon-beta-2012-05-03/Makefile.am --- freeon-beta-2012-05-03.orig/Makefile.am 2012-05-04 03:53:04.000000000 +0000 +++ freeon-beta-2012-05-03/Makefile.am 2013-05-29 14:42:07.791473885 +0000 -@@ -5,18 +5,9 @@ ACLOCAL_AMFLAGS = -I m4 - CPP = @CPP@ - AM_CPPFLAGS = @AM_CPPFLAGS@ - --if INTERNAL_LAPACK --INTERNAL_LAPACK_DIRS = lapack --endif -+SUBDIRS = Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate +@@ -9,14 +9,9 @@ + INTERNAL_LAPACK_DIRS = lapack + endif -if INTERNAL_HDF5 -INTERNAL_HDF5_DIRS = hdf5-1.8.3 @@ -16,9 +11,10 @@ diff -Naurp freeon-beta-2012-05-03.orig/Makefile.am freeon-beta-2012-05-03/Makef -endif - -SUBDIRS = $(INTERNAL_LAPACK_DIRS) $(INTERNAL_HDF5_DIRS) Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate -- ++SUBDIRS = $(INTERNAL_LAPACK_DIRS) Modules FreeON SCFeqs OneE QCTC HiCu TwoE ONX PostProcessing BasisSets tests Validate + -DIST_SUBDIRS = $(SUBDIRS) lapack hdf5-1.8.3 -+DIST_SUBDIRS = $(SUBDIRS) ++DIST_SUBDIRS = $(SUBDIRS) lapack EXTRA_DIST = fix_localversion.sh localversion FreeON.bibtex $(top_builddir)/latex/refman.pdf @@ -32,19 +28,3 @@ diff -Naurp freeon-beta-2012-05-03.orig/Makefile.am freeon-beta-2012-05-03/Makef if test "${use_internal_hdf5}" = "yes"; then -@@ -1027,15 +1026,6 @@ Makefile - documentation/main_page.h - FreeON/Makefile - Modules/Makefile --lapack/Makefile --lapack/install/Makefile --lapack/blas/Makefile --lapack/lapack/Makefile --lapack/blas_testing/Makefile --lapack/lapack_testing/Makefile --lapack/lapack_testing/lin/Makefile --lapack/lapack_testing/eig/Makefile --lapack/lapack_testing/matgen/Makefile - SCFeqs/Makefile - OneE/Makefile - QCTC/Makefile diff --git a/sci-chemistry/freeon/files/freeon-9999-no_internal_hdf5.patch b/sci-chemistry/freeon/files/freeon-9999-no_internal_hdf5.patch new file mode 100644 index 000000000..54255ff9f --- /dev/null +++ b/sci-chemistry/freeon/files/freeon-9999-no_internal_hdf5.patch @@ -0,0 +1,25 @@ +diff -Naurp freeon-9999.orig/Modules/Makefile.am freeon-9999/Modules/Makefile.am +--- freeon-9999.orig/Modules/Makefile.am 2013-05-28 08:09:39.000000000 +0000 ++++ freeon-9999/Modules/Makefile.am 2013-05-29 14:32:24.879721200 +0000 +@@ -4,11 +4,6 @@ + INTERNAL_LAPACK_DIRS = lapack + endif + +-if INTERNAL_HDF5 +-INTERNAL_HDF5_DIRS = hdf5-1.8.3 +-HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src +-endif +- + DIST_SUBDIRS = lapack hdf5-1.8.3 + SUBDIRS = $(INTERNAL_HDF5_DIRS) $(INTERNAL_LAPACK_DIRS) + +--- freeon-9999.orig/configure.ac 2013-05-29 15:34:16.000000000 +0000 ++++ freeon-9999/configure.ac 2013-05-29 15:36:22.000063299 +0000 +@@ -870,7 +870,6 @@ AM_CONDITIONAL(INTERNAL_HDF5, [test "${u + if test "${use_internal_hdf5}" = "yes"; then + + AC_DEFINE(HAVE_INTERNAL_HDF5, 1, [Use the inernal hdf5 library.]) +- AC_CONFIG_SUBDIRS([Modules/hdf5-1.8.3]) + + else + diff --git a/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch b/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch deleted file mode 100644 index a908aa7d9..000000000 --- a/sci-chemistry/freeon/files/freeon-9999-no_internal_libs.patch +++ /dev/null @@ -1,47 +0,0 @@ -diff -Naurp freeon-9999.orig/Modules/Makefile.am freeon-9999/Modules/Makefile.am ---- freeon-9999.orig/Modules/Makefile.am 2013-05-28 08:09:39.000000000 +0000 -+++ freeon-9999/Modules/Makefile.am 2013-05-29 14:32:24.879721200 +0000 -@@ -1,17 +1,5 @@ - include $(top_srcdir)/make.inc - --if INTERNAL_LAPACK --INTERNAL_LAPACK_DIRS = lapack --endif -- --if INTERNAL_HDF5 --INTERNAL_HDF5_DIRS = hdf5-1.8.3 --HDF5_INCLUDES = -I$(srcdir)/hdf5-1.8.3/src -I$(builddir)/hdf5-1.8.3/src --endif -- --DIST_SUBDIRS = lapack hdf5-1.8.3 --SUBDIRS = $(INTERNAL_HDF5_DIRS) $(INTERNAL_LAPACK_DIRS) -- - if USE_DYNAMIC_LINKING - lib_LTLIBRARIES = libfreeonmodules.la - else ---- freeon-9999.orig/configure.ac 2013-05-29 15:34:16.000000000 +0000 -+++ freeon-9999/configure.ac 2013-05-29 15:36:22.000063299 +0000 -@@ -870,7 +870,6 @@ AM_CONDITIONAL(INTERNAL_HDF5, [test "${u - if test "${use_internal_hdf5}" = "yes"; then - - AC_DEFINE(HAVE_INTERNAL_HDF5, 1, [Use the inernal hdf5 library.]) -- AC_CONFIG_SUBDIRS([Modules/hdf5-1.8.3]) - - else - -@@ -1069,15 +1068,6 @@ config_localversion.h - Makefile - FreeON/Makefile - Modules/Makefile --Modules/lapack/Makefile --Modules/lapack/install/Makefile --Modules/lapack/blas/Makefile --Modules/lapack/lapack/Makefile --Modules/lapack/blas_testing/Makefile --Modules/lapack/lapack_testing/Makefile --Modules/lapack/lapack_testing/lin/Makefile --Modules/lapack/lapack_testing/eig/Makefile --Modules/lapack/lapack_testing/matgen/Makefile - SCFeqs/Makefile - OneE/Makefile - QCTC/Makefile diff --git a/sci-chemistry/freeon/freeon-2012.05.03.ebuild b/sci-chemistry/freeon/freeon-2012.05.03.ebuild index 99805e0dc..5a9cc6a94 100644 --- a/sci-chemistry/freeon/freeon-2012.05.03.ebuild +++ b/sci-chemistry/freeon/freeon-2012.05.03.ebuild @@ -33,11 +33,8 @@ DEPEND="${DEPEND} S="${WORKDIR}/${REAL_PN}-${REAL_PV}" src_prepare() { - # Get rid of the obsolete internal hdf5 - rm -r "${S}"/hdf5-1.8.3 - # as well as of the internal lapack - rm -r "${S}"/lapack - epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch + # Prevent the obsolete internal hdf5 breaking autoconf + epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild index 369e063f8..6d02d9380 100644 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ b/sci-chemistry/freeon/freeon-9999.ebuild @@ -31,11 +31,8 @@ DEPEND="${DEPEND} virtual/pkgconfig" src_prepare() { - # Get rid of the obsolete internal hdf5 - rm -r "${S}"/Modules/hdf5-1.8.3 - # as well as of the internal lapack - rm -r "${S}"/Modules/lapack - epatch "${FILESDIR}"/"${P}"-no_internal_libs.patch + # Prevent the obsolete internal hdf5 breaking autoconf + epatch "${FILESDIR}"/"${P}"-no_internal_hdf5.patch eautoreconf } 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/hydronmr/metadata.xml b/sci-chemistry/hydronmr/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/hydronmr/metadata.xml +++ b/sci-chemistry/hydronmr/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/jana2000/metadata.xml b/sci-chemistry/jana2000/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/jana2000/metadata.xml +++ b/sci-chemistry/jana2000/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/jligand/metadata.xml b/sci-chemistry/jligand/metadata.xml index d410f1573..9ac9ffdb3 100644 --- a/sci-chemistry/jligand/metadata.xml +++ b/sci-chemistry/jligand/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/ligplot+/metadata.xml b/sci-chemistry/ligplot+/metadata.xml index d369d068f..e42d0af60 100644 --- a/sci-chemistry/ligplot+/metadata.xml +++ b/sci-chemistry/ligplot+/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/mage/metadata.xml b/sci-chemistry/mage/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/mage/metadata.xml +++ b/sci-chemistry/mage/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/mddnmr/metadata.xml b/sci-chemistry/mddnmr/metadata.xml index 86eeba133..9ac9ffdb3 100644 --- a/sci-chemistry/mddnmr/metadata.xml +++ b/sci-chemistry/mddnmr/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/mics/ChangeLog b/sci-chemistry/mics/ChangeLog new file mode 100644 index 000000000..0ca4c986a --- /dev/null +++ b/sci-chemistry/mics/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-chemistry/mics +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*mics-1.00.2011.327.12.00 (18 Jun 2013) + + 18 Jun 2013; Justin Lecher <jlec@gentoo.org> + +mics-1.00.2011.327.12.00.ebuild, +metadata.xml: + New package + diff --git a/sci-chemistry/mics/Manifest b/sci-chemistry/mics/Manifest new file mode 100644 index 000000000..ef2418ffc --- /dev/null +++ b/sci-chemistry/mics/Manifest @@ -0,0 +1 @@ +DIST mics-1.00.2011.327.12.00.tgz 5607489 SHA256 b9e031ee6c772702ce30f4098b3da77d72b32508d218da9efb0ef49b21a865c8 SHA512 275eacd7ff6978a725aa0c3d41b9b69285463ccd4ad8686fdf912e7da30cf395723bffa91c6aaba61c8f2c56763a767367a67fe0dea11113186999a2db3b864c WHIRLPOOL eda4b8d5ef2a749a592be8636763d26d84f3e5646c2ec831f942f560d0656026cdd19cac0d375ac8c45be396d118bf25f62455dc5f999eb17164327000e2a56b diff --git a/sci-chemistry/mics/metadata.xml b/sci-chemistry/mics/metadata.xml new file mode 100644 index 000000000..51fdedab1 --- /dev/null +++ b/sci-chemistry/mics/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild b/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild new file mode 100644 index 000000000..5f86a08f4 --- /dev/null +++ b/sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-opt-2 + +DESCRIPTION="Prediction of Protein Structural Motifs from NMR Chemical Shifts" +HOMEPAGE="http://spin.niddk.nih.gov/bax/software/MICS/" +SRC_URI="http://spin.niddk.nih.gov/bax/software/MICS/mics.tar.Z -> ${P}.tgz" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +RDEPEND=">=virtual/jre-1.5" +DEPEND="${RDEPEND}" + +S="${WORKDIR}"/MICS + +QA_PREBUILT="/opt/.*" + +src_prepare() { + rm -f bin/MICS.{mac,static.*,exe} || die +} + +src_install() { + local MICS="/opt/${PN}" + exeinto /opt/bin + newexe bin/MICS* ${PN} + + insinto ${MICS} + doins -r tab + + java-pkg_jarinto ${MICS} + java-pkg_dojar bin/rama.jar + + java-pkg_dolauncher jrama+ --jar rama.jar -into /opt/ + + if use examples; then + insinto /usr/share/${PN} + doins -r demo + fi + + cat >> "${T}"/40MICS <<- EOF + MICS_DIR="${EPREFIX}/${MICS}" + EOF + doenvd "${T}"/40MICS +} diff --git a/sci-chemistry/modelfree/metadata.xml b/sci-chemistry/modelfree/metadata.xml index 5ef07a39e..ae9ec7c5f 100644 --- a/sci-chemistry/modelfree/metadata.xml +++ b/sci-chemistry/modelfree/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> + <herd>sci-chemistry</herd> <maintainer> <email>jlec@gentoo.org</email> </maintainer> diff --git a/sci-chemistry/modeller/ChangeLog b/sci-chemistry/modeller/ChangeLog index 17fea516e..cedd72b92 100644 --- a/sci-chemistry/modeller/ChangeLog +++ b/sci-chemistry/modeller/ChangeLog @@ -1,7 +1,21 @@ # ChangeLog for sci-chemistry/modeller -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# 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, + +modeller-9.12-r1.ebuild: + Fix broken symlink, #473680 + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -modeller-9.8.ebuild, + +modeller-9.12.ebuild, metadata.xml: + Version BUmp; BUmp to EAPI5 and distutils-r1.eclass + *modeller-9.8 (16 Jun 2010) 16 Jun 2010; Justin Lecher <jlec@gentoo.org> +files/9v5-setup.patch, diff --git a/sci-chemistry/modeller/Manifest b/sci-chemistry/modeller/Manifest index f3078a1c8..a5b04d5c2 100644 --- a/sci-chemistry/modeller/Manifest +++ b/sci-chemistry/modeller/Manifest @@ -1 +1 @@ -DIST modeller-9v8.tar.gz 51539572 SHA256 3d5c629f97a2b89722fe5b7414ad97b0361799714db0323536df45f55b2777c7 +DIST modeller-9.12.tar.gz 29273842 SHA256 65051f7f1682cf7dcf77f0bc4d68f1ee5b64789f750e9aa6900e1cc92dc4e1f9 SHA512 5c0acaf453771347a9de3a0c7240f7ce376244803748edb28923dbaefda779041211ef4b26af5a2774bdf6bc63d7c7d7e62e1354e1550a6742c9575076864352 WHIRLPOOL a363efdd2bba8db8268774745f32b1e8e6a9d88e6a6154ce00c7be65861fc834ef1a804fa9f0575d2af2ff1211728aacf8408d28319df68b14f3a3598d55c307 diff --git a/sci-chemistry/modeller/metadata.xml b/sci-chemistry/modeller/metadata.xml index 9ac9ffdb3..51fdedab1 100644 --- a/sci-chemistry/modeller/metadata.xml +++ b/sci-chemistry/modeller/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-chemistry/modeller/modeller-9.8.ebuild b/sci-chemistry/modeller/modeller-9.12-r2.ebuild index b0c24c18c..9cfd2e3d3 100644 --- a/sci-chemistry/modeller/modeller-9.8.ebuild +++ b/sci-chemistry/modeller/modeller-9.12-r2.ebuild @@ -1,19 +1,17 @@ -# Copyright 1999-2010 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="2:2.6" +PYTHON_COMPAT=( python{2_6,2_7,3_2,3_3} ) +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils eutils versionator - -MY_PV="$(replace_all_version_separators v)" -MY_P="${PN}-${MY_PV}" +inherit distutils-r1 eutils multilib versionator DESCRIPTION="Homology or comparative modeling of protein three-dimensional structures" -SRC_URI="http://salilab.org/${PN}/${MY_PV}/${PN}-${MY_PV}.tar.gz" HOMEPAGE="http://salilab.org/modeller/" +SRC_URI="http://salilab.org/${PN}/${PV}/${P}.tar.gz" LICENSE="modeller" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -25,82 +23,78 @@ RESTRICT="mirror" DEPEND=">=dev-lang/swig-1.3" RDEPEND="" -S="${WORKDIR}/${MY_P}" - INPATH="${EPREFIX}"/opt/modeller${ver} -QA_TEXTRELS="${INPATH#/}/*" -QA_EXECSTACK="${INPATH#/}/*" -QA_PRESTRIPPED="${INPATH#/}/bin/.* ${INPATH#/}/lib/*/.*" -QA_DT_HASH=" - ${INPATH#/}/bin/.* - ${INPATH#/}/lib/*/.*" +QA_PREBUILT="/opt/*" -pkg_setup() { - python_set_active_version 2 +DISTUTILS_NO_PARALLEL_BUILD=true +pkg_setup() { case ${ARCH} in - x86) EXECTYPE="i386-intel8";; - amd64) EXECTYPE="x86_64-intel8";; - *) ewarn "Your arch "${ARCH}" does not appear supported at this time."||\ - die "Unsupported Arch";; + x86) + EXECTYPE="i386-intel8";; + amd64) + EXECTYPE="x86_64-intel8";; + *) + die "Your arch "${ARCH}" does not appear supported at this time.";; esac } -src_prepare(){ +python_prepare_all(){ sed "s:i386-intel8:${EXECTYPE}:g" -i src/swig/setup.py || die } -src_compile(){ +python_compile(){ + cd src/swig + swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i || die + distutils-r1_python_compile +} + +python_install() { cd src/swig - swig -python -keyword -nodefaultctor -nodefaultdtor -noproxy modeller.i - distutils_src_compile + distutils-r1_python_install } -src_install(){ +python_install_all(){ + cd "${S}" sed \ - -e "s:EXECUTABLE_TYPE${MY_PV}=xxx:EXECUTABLE_TYPE${MY_PV}=${EXECTYPE}:g" \ - -e "s:MODINSTALL${MY_PV}=xxx:MODINSTALL${MY_PV}=\"${INPATH}\":g" \ - bin/modscript > "${T}/mod${MY_PV}" + -e "/^EXECUTABLE_TYPE/s:xxx:${EXECTYPE}:g" \ + -e "/MODINSTALL/s:xxx:\"${INPATH}\":g" \ + -i bin/modscript || die sed -e "s;@TOPDIR\@;\"${INPATH}\";" \ -e "s;@EXETYPE\@;${EXECTYPE};" \ bin/modpy.sh.in > "${T}/modpy.sh" insinto ${INPATH} - doins -r modlib || die + doins -r modlib + python_foreach_impl python_domodule modlib/modeller insinto ${INPATH}/bin - doins -r bin/{lib,*top} || die + doins -r bin/{lib,*top} + exeinto ${INPATH}/bin - doexe bin/{modslave.py,mod${MY_PV}_${EXECTYPE}} || die - doexe "${T}/mod${MY_PV}" || die - doexe "${T}/modpy.sh" || die - dosym ${INPATH}/bin/mod${MY_PV} /opt/bin/mod${MY_PV} || die - dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh || die + doexe bin/{modscript,mod${PV}_${EXECTYPE}} "${T}"/modpy.sh + + python_foreach_impl python_doscript bin/modslave.py + dosym ${INPATH}/bin/modscript /opt/bin/mod${PV} + dosym ${INPATH}/bin/modpy.sh /opt/bin/modpy.sh exeinto ${INPATH}/lib/${EXECTYPE}/ - doexe lib/${EXECTYPE}/lib* || die - dosym libmodeller.so.5 ${INPATH}/lib/${EXECTYPE}/libmodeller.so || die - doexe src/swig/build/lib.linux-$(uname -m)-$(python_get_version)/_modeller.so || die + doexe lib/${EXECTYPE}/lib* + dosym libmodeller.so.8 ${INPATH}/lib/${EXECTYPE}/libmodeller.so + dosym ../../${INPATH}/lib/${EXECTYPE}/libmodeller.so.8 /usr/$(get_libdir)/libmodeller.so.8 + + use doc && HTML_DOCS=( doc/. ) + distutils-r1_python_install_all - dodoc README INSTALLATION || die - if use doc; then - dohtml doc/* || die - fi if use examples; then insinto /usr/share/${PN}/ - doins -r examples || die + doins -r examples fi - - dosym ${INPATH}/lib/${EXECTYPE}/_modeller.so \ - $(python_get_sitedir)/_modeller.so || die - dosym _modeller.so $(python_get_sitedir)/modeller.so || die } pkg_postinst() { - python_mod_optimize "${INPATH}/" - if [[ ! -e "${INPATH}/modlib/modeller/config.py" ]]; then echo install_dir = \"${INPATH}/\"> ${INPATH}/modlib/modeller/config.py fi @@ -117,7 +111,6 @@ pkg_postinst() { } pkg_postrm() { - python_mod_cleanup "${INPATH}/" ewarn "This package leaves a license Key file in ${INPATH}/modlib/modeller/config.py" ewarn "that you need to remove to completely get rid of modeller." } diff --git a/sci-chemistry/mtz2hkl/metadata.xml b/sci-chemistry/mtz2hkl/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/mtz2hkl/metadata.xml +++ b/sci-chemistry/mtz2hkl/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/mtz2sca/metadata.xml b/sci-chemistry/mtz2sca/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/mtz2sca/metadata.xml +++ b/sci-chemistry/mtz2sca/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/nMOLDYN/ChangeLog b/sci-chemistry/nMOLDYN/ChangeLog new file mode 100644 index 000000000..45ad3fe76 --- /dev/null +++ b/sci-chemistry/nMOLDYN/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sci-chemistry/nMOLDYN +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 17 Jun 2013; Alexey Shvetsov <alexxy@gentoo.org> nMOLDYN-3.0.10.ebuild: + [sci-chemistry/nMOLDYN] Update deps + +*nMOLDYN-3.0.10 (17 Jun 2013) + + 17 Jun 2013; Alexey Shvetsov <alexxy@gentoo.org> +metadata.xml, + +nMOLDYN-3.0.10.ebuild: + [sci-chemistry/nMOLDYN] Add to overlay diff --git a/sci-chemistry/nMOLDYN/Manifest b/sci-chemistry/nMOLDYN/Manifest new file mode 100644 index 000000000..49e2b64af --- /dev/null +++ b/sci-chemistry/nMOLDYN/Manifest @@ -0,0 +1 @@ +DIST nMOLDYN-3.0.10.zip 34692698 SHA256 33a5e2573f35358125351c6da01be693bdda252162324a8625c47ae9a8f2235c SHA512 49c6bd04d89143e73dddeda4d3ad0061747e018ad63dfa42e17c2388b6107c7b88f59d7d0d2e59a5c1faf4fe3a188e94d41f9f5ae171194db1ff56648742982a WHIRLPOOL 7301622fdfc9e4f9939db2d9bfecceb31daf3f5d863abe247eaf8327207bfb425bb077894f50ee10b3ca103fffaf558cfbee5dbbf68b1782bef585559a008c61 diff --git a/sci-chemistry/nMOLDYN/metadata.xml b/sci-chemistry/nMOLDYN/metadata.xml new file mode 100644 index 000000000..b2558d8c6 --- /dev/null +++ b/sci-chemistry/nMOLDYN/metadata.xml @@ -0,0 +1,9 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <maintainer> + <email>alexxy@gentoo.org</email> + <name>Alexey Shvetsov</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild b/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild new file mode 100644 index 000000000..2be241c68 --- /dev/null +++ b/sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 + +DESCRIPTION="nMOLDYN is an interactive analysis program for Molecular Dynamics simulations" +HOMEPAGE="http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/" +SRC_URI="https://forge.epn-campus.eu/attachments/download/1161/${P}.zip" + +LICENSE="CeCILL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND=" + dev-python/numpy + sci-libs/mmtk +" +RDEPEND="${DEPEND}" diff --git a/sci-chemistry/nmrpipe/ChangeLog b/sci-chemistry/nmrpipe/ChangeLog index d966a7b72..3c50b507a 100644 --- a/sci-chemistry/nmrpipe/ChangeLog +++ b/sci-chemistry/nmrpipe/ChangeLog @@ -2,6 +2,14 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> + nmrpipe-7.9.2013.021.23.09-r2.ebuild: + Bump to EAPI=5 and fix license + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> + nmrpipe-7.9.2013.021.23.09-r2.ebuild: + Bump to EAPI=5 and fix license + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> nmrpipe-7.9.2013.021.23.09-r2.ebuild: Fix quoting diff --git a/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild b/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild index 2abd96b21..daf50ce8f 100644 --- a/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild +++ b/sci-chemistry/nmrpipe/nmrpipe-7.9.2013.021.23.09-r2.ebuild @@ -4,7 +4,7 @@ # Versioning is output of nmrPipe -help -EAPI=4 +EAPI=5 inherit eutils virtualx @@ -25,7 +25,7 @@ SRC_URI=" " SLOT="0" -LICENSE="as-is" +LICENSE="all-rights-reserved" # Right now, precompiled executables are only available for Linux on the # x86 architecture. The maintainer chose to keep the sources closed, but # says he will gladly provide precompiled executables for other platforms diff --git a/sci-chemistry/nmrview/ChangeLog b/sci-chemistry/nmrview/ChangeLog index c84d1a869..63f2974b1 100644 --- a/sci-chemistry/nmrview/ChangeLog +++ b/sci-chemistry/nmrview/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/nmrview -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> nmrview-5.2.2-r3.ebuild, + metadata.xml: + Bump to EAPI=5 and fix license + 01 Jun 2012; Justin Lecher <jlec@gentoo.org> nmrview-5.2.2-r3.ebuild, metadata.xml: Move to EAPI=4, specify QA_PREBUILT diff --git a/sci-chemistry/nmrview/metadata.xml b/sci-chemistry/nmrview/metadata.xml index 95180e10e..b3618ba38 100644 --- a/sci-chemistry/nmrview/metadata.xml +++ b/sci-chemistry/nmrview/metadata.xml @@ -1,9 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + <name>Justin Lecher</name> + </maintainer> </pkgmetadata> diff --git a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild index e302f9714..ad5da95f1 100644 --- a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild +++ b/sci-chemistry/nmrview/nmrview-5.2.2-r3.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 DESCRIPTION="Visualisation and analysis of processed NMR data" HOMEPAGE="http://www.onemoonscientific.com/nmrview/" @@ -11,7 +11,7 @@ SRC_URI=" ${PN}${PV//./_}_01_linux.gz" SLOT="0" -LICENSE="as-is" +LICENSE="all-rights-reserved" IUSE="" KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" @@ -38,19 +38,14 @@ pkg_nofetch() { echo } -src_compile() { - echo - einfo "Nothing to compile." - echo -} - src_install() { insinto ${INSTDIR} sed \ -e "s:/opt:${EPREFIX}/opt:g" \ "${FILESDIR}"/${PN}.sh-r1 \ - > "${T}"/${PN} + > "${T}"/${PN} || die + dobin "${T}"/${PN} exeinto ${INSTDIR} doexe ${PN}${PV//./_}_01_linux diff --git a/sci-chemistry/nwchem/ChangeLog b/sci-chemistry/nwchem/ChangeLog index a93271c16..01bbf7962 100644 --- a/sci-chemistry/nwchem/ChangeLog +++ b/sci-chemistry/nwchem/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> -nwchem-6.1.1.ebuild, + nwchem-6.3.ebuild: + Drop old; drop virtual/fortran as the eclass depends on it + 04 Jun 2013; Justin Lecher <jlec@gentoo.org> nwchem-6.3.ebuild: Fix for correct usage of new python eclasses diff --git a/sci-chemistry/nwchem/Manifest b/sci-chemistry/nwchem/Manifest index 56aeb6eca..d717621f9 100644 --- a/sci-chemistry/nwchem/Manifest +++ b/sci-chemistry/nwchem/Manifest @@ -1,2 +1 @@ -DIST Nwchem-6.1.1-src.2012-06-27.tar.gz 77838112 SHA256 153a975e18fa88afbacfa2c7d4384e31bc25c43bd5c99c2f4074006a8e035dab SHA512 b2cc796f6fd0e37385a9b8c0a5dbc3c219849938b52809a616cb5c3fa5a3a54a7c61be215cf8975d1287d09ecfae1bedd41e69e445e61adb5a7aac505802170d WHIRLPOOL d6107522fadca8597d0fdff758169a2c25adb8da0ccfbad9a9f408708d0060922fef443f9c92ccd97b3772c70ba9fe90a1ec7c059de536e6a294719080c9bfaf DIST Nwchem-6.3-src.2013-05-17.tar.gz 112227871 SHA256 c8049adb14f198d3ee40e38ed6e00dd4d59ef7cf992c4d45f392172df217f378 SHA512 05cb37aae41746c56ab715a47830bdf336cfe469b5f1b492be369c620d300039529ea30ed75f885fc06a5d3a45a64297341555ea71ef5b56efcca14798dcf8d3 WHIRLPOOL 40d46a7bf7b99455219325a03fe72b426f60c058110aa3c17308b57be962210100b58bac6e2e99cfc60b4d7cf87f7e8c5fd712d3c815b260790ff58d59380f36 diff --git a/sci-chemistry/nwchem/nwchem-6.1.1.ebuild b/sci-chemistry/nwchem/nwchem-6.1.1.ebuild deleted file mode 100644 index a0196083d..000000000 --- a/sci-chemistry/nwchem/nwchem-6.1.1.ebuild +++ /dev/null @@ -1,126 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=5 - -inherit eutils fortran-2 multilib python toolchain-funcs - -DATE="2012-06-27" - -DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science" -HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page" -SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz" - -LICENSE="ECL-2.0" -SLOT="0" -KEYWORDS="~x86 ~amd64" -IUSE="mpi examples nwchem-tests python" - -RDEPEND="sys-fs/sysfsutils" -DEPEND="${RDEPEND} - virtual/fortran - mpi? ( virtual/mpi[fortran] )" - -S="${WORKDIR}/${P}-src" - -pkg_setup() { - fortran-2_pkg_setup - use python && python_set_active_version 2 && python_pkg_setup -} - -src_prepare() { - epatch \ - "${FILESDIR}"/nwchem-${PV}-makefile.patch \ - "${FILESDIR}"/nwchem-${PV}-nwchemrc.patch \ - "${FILESDIR}"/nwchem-${PV}-adjust-dir-length.patch - use python && "${FILESDIR}"/nwchem-${PV}-python_makefile.patch - - sed \ - -e "s:DBASIS_LIBRARY=\"'\$(SRCDIR)'\":DBASIS_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \ - -i src/basis/MakeFile src/basis/GNUmakefile || die - sed \ - -e "s:DNWPW_LIBRARY=\"'\$(SRCDIR)'\":DNWPW_LIBRARY=\"'${EPREFIX}/usr/share/NWChem'\":g" \ - -i src/nwpw/libraryps/GNUmakefile || die - sed \ - -e "s:-DCOMPILATION_DIR=\"'\$(TOPDIR)'\":-DCOMPILATION_DIR=\"''\":g" \ - -i src/GNUmakefile src/MakeFile || die - - if [[ $(tc-getFC) == *-*-*-*-gfortran ]]; then - sed \ - -e "s:ifneq (\$(FC),gfortran):ifneq (\$(FC),$(tc-getFC)):g" \ - -e "s:ifeq (\$(FC),gfortran):ifeq (\$(FC),$(tc-getFC)):g" \ - -i src/config/makefile.h || die - fi -} - -src_compile() { - export USE_SUBGROUPS=yes - if use mpi ; then - export MSG_COMMS=MPI - export USE_MPI=yes - export MPI_LOC=/usr - export MPI_INCLUDE=$MPI_LOC/include - export MPI_LIB=$MPI_LOC/$(get_libdir) - export LIBMPI="$(mpif90 -showme:link)" - fi - if [ "$ARCH" = "amd64" ]; then - export NWCHEM_TARGET=LINUX64 - elif [ "$ARCH" = "ia64" ]; then - export NWCHEM_TARGET=LINUX64 - elif [ "$ARCH" = "x86" ]; then - export NWCHEM_TARGET=LINUX - elif [ "$ARCH" = "ppc" ]; then - export NWCHEM_TARGET=LINUX - else - die "Unknown architecture" - fi - if use python ; then - if [ "$ARCH" = "amd64" ] || [ "$ARCH" = "ia64" ]; then - export USE_PYTHON64=yes - fi - export PYTHONHOME=/usr - export PYTHONVERSION=$(eselect python show|awk -Fpython '{ print $2 }') - export PYTHONPATH="./:${S}/contrib/python/" - export NWCHEM_MODULES="all python" - else - export NWCHEM_MODULES="all" - fi - - cd src - emake \ - DIAG=PAR \ - FC=$(tc-getFC) \ - CC=$(tc-getCC) \ - CXX=$(tc-getCXX) \ - NWCHEM_TOP="${S}" \ - NWCHEM_EXECUTABLE="${S}/bin/${NWCHEM_TARGET}/nwchem" -} - -src_install() { - dobin bin/${NWCHEM_TARGET}/nwchem - - insinto /usr/share/NWChem/basis/ - doins -r src/basis/libraries src/data - insinto /usr/share/NWChem/nwpw - doins -r src/nwpw/libraryps - - insinto /etc - doins nwchemrc - - use examples && \ - insinto /usr/share/NWChem/ && \ - doins -r examples - - use nwchem-tests \ - insinto /usr/share/NWChem \ - doins -r QA/tests -} - -pkg_postinst() { - echo - elog "The user will need to link \$HOME/.nwchemrc to /etc/nwchemrc" - elog "or copy it in order to tell NWChem the right position of the" - elog "basis library and other necessary data." - echo -} diff --git a/sci-chemistry/nwchem/nwchem-6.3.ebuild b/sci-chemistry/nwchem/nwchem-6.3.ebuild index 69748f28a..4395d150d 100644 --- a/sci-chemistry/nwchem/nwchem-6.3.ebuild +++ b/sci-chemistry/nwchem/nwchem-6.3.ebuild @@ -5,11 +5,12 @@ EAPI=5 PYTHON_COMPAT=( python{2_6,2_7} ) + inherit eutils fortran-2 multilib python-single-r1 toolchain-funcs DATE="2013-05-17" -DESCRIPTION="NWChem: Delivering High-Performance Computational Chemistry to Science" +DESCRIPTION="Delivering High-Performance Computational Chemistry to Science" HOMEPAGE="http://www.nwchem-sw.org/index.php/Main_Page" SRC_URI="http://www.nwchem-sw.org/images/Nwchem-${PV}-src.${DATE}.tar.gz" @@ -20,13 +21,14 @@ IUSE="mpi doc examples nwchem-tests python" REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" -RDEPEND="sys-fs/sysfsutils +RDEPEND=" + sys-fs/sysfsutils python? ( ${PYTHON_DEPS} )" DEPEND="${RDEPEND} - virtual/fortran app-shells/tcsh mpi? ( virtual/mpi[fortran] ) - doc? ( dev-texlive/texlive-latex + doc? ( + dev-texlive/texlive-latex dev-tex/latex2html )" S="${WORKDIR}/${P}-src.${DATE}" diff --git a/sci-chemistry/phaser/ChangeLog b/sci-chemistry/phaser/ChangeLog deleted file mode 100644 index bc908bd4b..000000000 --- a/sci-chemistry/phaser/ChangeLog +++ /dev/null @@ -1,21 +0,0 @@ -# ChangeLog for sci-chemistry/phaser -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 25 Oct 2011; Justin Lecher <jlec@gentoo.org> metadata.xml: - Removed no-herd from herd tag in metadata.xml - - 10 Jul 2010; Andreas K. Huettel (dilfridge) <mail@akhuettel.de> - phaser-2.1.4.ebuild, phaser-2.1.4-r1.ebuild: - Silence repoman. - -*phaser-2.1.4-r1 (29 May 2009) -*phaser-2.1.4 (29 May 2009) - - 29 May 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> - +files/2.1.4-sadf.patch, +phaser-2.1.4.ebuild, +phaser-2.1.4-r1.ebuild, - +metadata.xml: - version 2.1.4 written by me - 2.1.4-r1 seperatly written by Johan Hattne Thanks! - builds phaser staticaly against bundled cctbx. - diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest deleted file mode 100644 index eb8b8c568..000000000 --- a/sci-chemistry/phaser/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phaser-2.1.4-cctbx-src.tar.gz 22388206 SHA256 594829cc82cb3c57e223ded99faf1fe86b192f2b48a935f93d2a4b89b9018970 diff --git a/sci-chemistry/phaser/files/2.1.4-sadf.patch b/sci-chemistry/phaser/files/2.1.4-sadf.patch deleted file mode 100644 index ee1abe375..000000000 --- a/sci-chemistry/phaser/files/2.1.4-sadf.patch +++ /dev/null @@ -1,64 +0,0 @@ ---- ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc 2009-02-05 19:03:10.000000000 +0100 -+++ ccp4-6.1.1/src/phaser/source/phaser/src/RefineSADf.cc.new 2008-07-14 15:25:47.000000000 +0200 -@@ -161,7 +161,8 @@ - if (atoms_extra[a].REJECTED) PHASER_ASSERT(atoms[a].occupancy == 0); - } - -- cctbx::xray::fast_gradients<dFloatType> fast_gradients( -+ typedef cctbx::xray::fast_gradients<dFloatType> fast_gradients_t; -+ fast_gradients_t fast_gradients( - cctbxUC, - atoms.const_ref(), - scattering_type_registry, -@@ -206,9 +205,9 @@ - sc.flags.set_tan_u_iso(false); - } - -- af::const_ref<dCmplxType, cctbx::maptbx::c_grid_padded_p1<3> > gradmap_const_ref( -- gradmap_fft_ref.begin(), -- cctbx::maptbx::c_grid_padded_p1<3>(cfft.n(), cfft.n())); -+ typedef fast_gradients_t::accessor_type fgat; -+ af::const_ref<dCmplxType, fgat> -+ gradmap_const_ref(gradmap_fft_ref.begin(), fgat(cfft.n(), cfft.n())); - bool sampled_density_must_be_positive(true); - fast_gradients.sampling( - atoms.const_ref(), ---- ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc 2007-11-14 15:46:41.000000000 +0100 -+++ ccp4-6.1.1/src/phaser/source/phaser/io/Errors.cc.new 2007-11-14 15:46:41.000000000 +0100 -@@ -1,6 +1,7 @@ - //(c) 2000-2007 Cambridge University Technical Services Ltd - //All rights reserved - #include <phaser/io/Errors.h> -+#include <cstdio> - - namespace phaser { - -@@ -20,7 +21,7 @@ - sfile.erase(sfile.begin(),sfile.begin()+i+1); - std::string::size_type j = sfile.rfind("\\"); //microsoft file separator - sfile.erase(sfile.begin(),sfile.begin()+j+1); -- sprintf(buf, "%ld", line); -+ std::sprintf(buf, "%ld", line); - msg_ = std::string("Program") + s + " error in source file " - + sfile + " (line " + buf + ")\n"; - if (msg.size()) msg_ += "*** "+ msg + " ***"; ---- ccp4-6.1.1/src/phaser/source/phaser/SConscript 2008-06-19 11:57:30.000000000 +0200 -+++ ccp4-6.1.1/src/phaser/source/phaser/SConscript.new 2008-06-19 11:57:30.000000000 +0200 -@@ -12,13 +12,15 @@ - - cxxflags = env_etc.cxxflags_base - print "Compiling distributed version of phaser" -+ccp4io_lib = getattr(env_etc, "ccp4io_lib", "cmtz") -+ # XXX backward compatibility 2008-09-10 - env_etc.phaser_common_libs = [ - "phaserrun", - "phasersrc", - "phaserio", - "phaserkey", - "phaserlib", -- "cmtz", -+ ccp4io_lib, - "cctbx", - ] - env_etc.phaser_common_includes = [ - diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch deleted file mode 100644 index ecc98490c..000000000 --- a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py.orig 2009-05-27 16:55:30.712547511 -0500 -+++ ccp4-6.1.1/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py 2009-05-27 16:55:44.446546721 -0500 -@@ -802,8 +802,6 @@ - else: - action = self.write_bin_sh_dispatcher - ext = "" -- try: os.chmod(source_file, 0755) -- except OSError: pass - target_file_ext = target_file + ext - remove_or_rename(target_file_ext) - try: action(source_file, target_file_ext) diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml deleted file mode 100644 index deb55d19f..000000000 --- a/sci-chemistry/phaser/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"> -<!-- -$Header: $ - -This is the example metadata file. -The root element of this file is <pkgmetadata>. Within this element a -number of subelements are allowed: herd, maintainer, and -longdescription. herd is a required subelement. - -For a full description look at: -http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=2&chap=4 - - -Before committing, please remove the comments from this file. They are -not relevant for general metadata.xml files. ---> -<pkgmetadata> - <maintainer> - <email>jlec@gentoo.org</email> - <!-- <description>coding for fun</description> --> - </maintainer> - <!-- <longdescription>Long description of the package</longdescription> --> - <!-- -<use> - <flag name='flag'>Description of how USE='flag' affects this package.</flag> - <flag name='userland_GNU'>Description of how USERLAND='GNU' affects this package.</flag> -</use> ---> -</pkgmetadata> diff --git a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild b/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild deleted file mode 100644 index 2f8cafac4..000000000 --- a/sci-chemistry/phaser/phaser-2.1.4-r1.ebuild +++ /dev/null @@ -1,138 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI="2" - -inherit base flag-o-matic python - -DESCRIPTION="A program for phasing macromolecular crystal structures" -HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" -SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${PN}-${PV}-cctbx-src.tar.gz" - -LICENSE="|| ( phaser phaser-com ccp4 )" - -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="openmp" -RDEPEND="" -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}"/ccp4-6.1.1 - -PATCHES=( - "${FILESDIR}"/phaser-2.1.4-chmod.patch - ) - -src_prepare() { - base_src_prepare - - use openmp && append-flags -fopenmp - - for i in ${CXXFLAGS}; do - OPTS="${OPTS} \"${i}\"," - done - - OPTS=${OPTS%,} - - sed -i \ - -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ - "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die - - for i in ${LDFLAGS}; do - OPTSLD="${OPTSLD} \"${i}\"," - done - - sed -i \ - -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ - "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die - -} - -src_compile() { - local compiler - local mtype - local mversion - local nproc - - # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, - # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, - # darwin_c++, darwin_gcc. The build systems seems to prepend - # unix_ all by itself. Can this be derived from $(tc-getCC)? - compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') - - # Breaks cross compilation. - mtype=$(src/${PN}/bin/machine_type) - mversion=$(src/${PN}/bin/machine_version) - nproc=`echo "-j1 ${MAKEOPTS}" \ - | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` - - einfo "Creating build directory $nproc " - mkdir build - cd build - ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons - ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx - - # It is difficult to rely on sci-libs/cctbx for the cctbx - # dependency, because upstream releases new versions quite - # frequently. Perhaps better to link statically to the bundled - # cctbx. - einfo "Configuring phaser components" - python_version - ${python} "libtbx/configure.py" \ - --build=release \ - --compiler=${compiler} \ - --repository="${S}"/src/${PN}/source \ - --repository="${S}"/lib/cctbx/cctbx_sources \ - --static_libraries \ - ccp4io="${S}" \ - mmtbx \ - phaser || die "configure.py failed" - - einfo "Setting up build environment" - source setpaths.sh - - einfo "Compiling phaser components" - libtbx.scons -j ${nproc} || die "libtbx.scons failed" - - # Hardcoded /usr/bin does not look nice. Should these files, - # perhaps, be installed somewhere? -# einfo "Creating env.csh" -# cat >> "${T}"/env.csh <<- EOF -# #! /bin/csh -# -# setenv PHASER /usr/bin -# setenv PHASER_ENVIRONMENT 1 -# setenv PHASER_MTYPE ${mtype} -# setenv PHASER_MVERSION ${mversion} -# setenv PHASER_VERSION ${PV} -# EOF - -# einfo "Creating env.sh" - cat >> "${T}"/53${PN} <<- EOF - - PHASER="/usr/bin" - PHASER_ENVIRONMENT="1" - PHASER_MTYPE="${mtype}" - PHASER_MVERSION="${mversion}" - PHASER_VERSION="${PV}" - EOF - - doenvd "${T}"/53${PN} -} - -# Why do some tests say that CNS and SHELX is not available? Same for -# cctbx ebuild tests. -src_test() { - cd "${S}//build" && \ - source setpaths.sh && \ - csh ./run_tests.csh || die "run_test.csh failed" -} - -# This is a bit thin. Maybe install other files from the distribution -# as well? -src_install() { - dobin build/exe/phaser || die -} diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild deleted file mode 100644 index 73f18f4ee..000000000 --- a/sci-chemistry/phaser/phaser-2.1.4.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -inherit eutils python toolchain-funcs - -DESCRIPTION="Phasing macromolecular crystal structures with maximum likelihood methods" -SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/6.1.1/${P}-cctbx-src.tar.gz" -HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser/" - -SLOT="0" -LICENSE="ccp4" -KEYWORDS="~x86 ~amd64" -IUSE="openmp" - -DEPEND="dev-util/scons" -RDEPEND="sci-libs/cctbx" - -S="${WORKDIR}" - -src_unpack() { - unpack ${A} - cd "${S}" - rm -rf lib/* - cp -rf $CCP4/lib/cctbx/cctbx_sources/libtbx "${WORKDIR}" - - mkdir -p "${WORKDIR}"/scons/src/ - ln -sf /usr/$(get_libdir)/scons-1.2.0 "${WORKDIR}"/scons/src/engine || die - - epatch "${FILESDIR}"/${PV}-sadf.patch -} - -src_compile(){ - python_version - - local MYCONF - local MAKEOPTS_EXP - local OPTS - local OPTSLD - - MYCONF="${S}/libtbx/configure.py" - - MYCONF="${MYCONF} --repository ${S}/ccp4-6.1.1/src/${PN}/source --repository /usr/$(get_libdir)/cctbx/cctbx_sources/ \ - --build=release ccp4io=${CCP4}/$(get_libdir)/cctbx/cctbx_sources/ccp4io/" - - MAKEOPTS_EXP=${MAKEOPTS/j/j } - MAKEOPTS_EXP=${MAKEOPTS_EXP%-l[0-9]*} - - # Get CXXFLAGS in format suitable for substitition into SConscript - for i in ${CXXFLAGS}; do - OPTS="${OPTS} \"${i}\"," - done - - # Strip off the last comma - OPTS=${OPTS%,} - - # Fix CXXFLAGS - sed -i \ - -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ - "${S}"/libtbx/SConscript - - # Get LDFLAGS in format suitable for substitition into SConscript - for i in ${LDFLAGS}; do - OPTSLD="${OPTSLD} \"${i}\"," - done - - # Fix LDFLAGS which should be as-needed ready - sed -i \ - -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\":g" \ - "${S}"/libtbx/SConscript - - # Get compiler in the right way - COMPILER=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') - MYCONF="${MYCONF} --compiler=${COMPILER}" - - # Additional USE flag usage - check_use openmp - MYCONF="${MYCONF} --enable-openmp-if-possible=${USE_openmp}" - use threads && USEthreads="--enable-boost-threads" && \ - ewarn "If using boost threads openmp support is disabled" - - MYCONF="${MYCONF} ${USE_threads} --scan-boost" - - MYCONF="${MYCONF} phaser" - einfo "configuring with ${python} ${MYCONF}" - - ${python} ${MYCONF} \ - || die "configure failed" - - source setpaths_all.sh - - einfo "compiling with libtbx.scons ${MAKEOPTS_EXP}" - libtbx.scons ${MAKEOPTS_EXP} .|| die "make failed" -} - -src_install() { - rm lib/libboost* - dolib.so lib/*.so || die - dolib.a lib/*.a || die - dobin exe/phaser || die -} - -check_use() { - - for var in $@; do - if use ${var}; then - printf -v "USE_$var" True - else - printf -v "USE_$var" False - - fi - shift - done -} diff --git a/sci-chemistry/phenix-bin/metadata.xml b/sci-chemistry/phenix-bin/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/phenix-bin/metadata.xml +++ b/sci-chemistry/phenix-bin/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/polygon/ChangeLog b/sci-chemistry/polygon/ChangeLog index 354b0fef7..4a9ca0394 100644 --- a/sci-chemistry/polygon/ChangeLog +++ b/sci-chemistry/polygon/ChangeLog @@ -1,7 +1,12 @@ # ChangeLog for sci-chemistry/polygon -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> +polygon-0612.ebuild, + -polygon-0710.ebuild, +files/0612-db.patch, -files/0710-db.patch, + metadata.xml: + Version BUmp; fixed license + *polygon-0710 (23 Oct 2009) 23 Oct 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> diff --git a/sci-chemistry/polygon/Manifest b/sci-chemistry/polygon/Manifest index 693c1c379..0c1b4065b 100644 --- a/sci-chemistry/polygon/Manifest +++ b/sci-chemistry/polygon/Manifest @@ -1,2 +1,2 @@ -DIST pdb_2009-04-29_ord.zip 4371434 SHA256 cd949ded9c7c656e4cc9d5f9c28584b648fec3bd2df2e80811ea8eb7baf81f69 -DIST polygon0710.tcl 128282 SHA256 db1b985805c750550328d0092bbf826c30df68e38453f2866329fd96cbfe45d8 +DIST pdb_2009-04-29_ord.zip 4371434 SHA256 cd949ded9c7c656e4cc9d5f9c28584b648fec3bd2df2e80811ea8eb7baf81f69 SHA512 3d1621c96f7e65197a5a7b7e655648ec957717bc38622b64f900142bac98d9b6450c8c9d128055dc9d673ae031c0a7b379a7d28ae97b22a070337b9563169287 WHIRLPOOL 258848856c4375fc00bda3382bed18a30de159348a246aa82f94569249ea24ee851109064a4800f2e17fc7d755d48d3c3f60d1608b418a198dd367a900de45fb +DIST polygon0612.tcl 124276 SHA256 d5b2c55faa37097db04a98c70cee5a49480f0b9e6e4e93345b67eee72c2c6aac SHA512 20d5e2011d28fe38c39f92be3d2221186f43048f173eb8b3971238836b5a09ae55cb44c0aad9e9efb3206e3c8a6e0017b749ce3911455e63dd8fcdba5c7c9dfe WHIRLPOOL cbde37636166a60ea1eeabf53da5398bb10e0e2ed7742beb87738773ffd45015f3ffe1df97745a98d52b7e00a5a1700279fa73ecf20ba456d8a8c2429c3db012 diff --git a/sci-chemistry/polygon/files/0710-db.patch b/sci-chemistry/polygon/files/0612-db.patch index faab35e4a..a12225f29 100644 --- a/sci-chemistry/polygon/files/0710-db.patch +++ b/sci-chemistry/polygon/files/0612-db.patch @@ -1,11 +1,11 @@ ---- polygon0710.tcl 2009-10-15 16:11:36.000000000 +0200 -+++ polygon0710.tcl.new 2009-10-23 17:59:32.723500534 +0200 +--- polygon0612.tcl 2009-10-15 16:11:36.000000000 +0200 ++++ polygon0612.tcl.new 2009-10-23 17:59:32.723500534 +0200 @@ -22,7 +22,7 @@ - #
- #database name
- #
--set currentFile1 pdb_2009-04-29_ord.txt
-+set currentFile1 /usr/share/polygon/pdb_2009-04-29_ord.txt
-
- # numcol - number of columns in the database
- set numcol 63
+ # + #database name + # +-set currentFile1 pdb_2009-04-29_ord.txt ++set currentFile1 /usr/share/polygon/pdb_2009-04-29_ord.txt + + # numcol - number of columns in the database + set numcol 63 diff --git a/sci-chemistry/polygon/metadata.xml b/sci-chemistry/polygon/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/polygon/metadata.xml +++ b/sci-chemistry/polygon/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/polygon/polygon-0710.ebuild b/sci-chemistry/polygon/polygon-0612.ebuild index ba2415f16..ac2335746 100644 --- a/sci-chemistry/polygon/polygon-0710.ebuild +++ b/sci-chemistry/polygon/polygon-0612.ebuild @@ -1,7 +1,9 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=5 + inherit eutils DB="pdb_2009-04-29_ord" @@ -15,23 +17,27 @@ SRC_URI=" " SLOT="0" +LICENSE="all-rights-reserved" KEYWORDS="~amd64 ~x86" -LICENSE="as-is" IUSE="" RDEPEND="dev-lang/tcl" DEPEND="app-arch/unzip" +S="${WORKDIR}" + src_unpack() { unpack ${DB}.zip - cp "${DISTDIR}"/${MY_P}.tcl "${WORKDIR}" - cd "${WORKDIR}" + cp "${DISTDIR}"/${MY_P}.tcl "${S}" || die +} + +src_prepare() { epatch "${FILESDIR}"/${PV}-db.patch } src_install() { edos2unix ${MY_P}.tcl - newbin ${MY_P}.tcl ${PN} || die + newbin ${MY_P}.tcl ${PN} insinto /usr/share/${PN} - doins ${DB}.txt || die + doins ${DB}.txt } diff --git a/sci-chemistry/pymol-apbs-plugin/ChangeLog b/sci-chemistry/pymol-apbs-plugin/ChangeLog index deaec995f..9bfa57450 100644 --- a/sci-chemistry/pymol-apbs-plugin/ChangeLog +++ b/sci-chemistry/pymol-apbs-plugin/ChangeLog @@ -1,7 +1,14 @@ # ChangeLog for sci-chemistry/pymol-apbs-plugin -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-apbs-plugin-9999.ebuild: + Drop KEYWORDS from live ebuild + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-apbs-plugin-9999.ebuild, + metadata.xml: + Bump to EAPI=5 and bump to python-r1.eclass + 29 Jun 2010; Justin Lecher <jlec@gentoo.org> pymol-apbs-plugin-9999.ebuild: Python ABI fixes diff --git a/sci-chemistry/pymol-apbs-plugin/metadata.xml b/sci-chemistry/pymol-apbs-plugin/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/pymol-apbs-plugin/metadata.xml +++ b/sci-chemistry/pymol-apbs-plugin/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild index 48a055c8a..70bbba7ec 100644 --- a/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild +++ b/sci-chemistry/pymol-apbs-plugin/pymol-apbs-plugin-9999.ebuild @@ -1,56 +1,41 @@ -# Copyright 1999-2010 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" +PYTHON_COMPAT=( python2_7 ) -inherit python subversion +inherit python-single-r1 subversion MY_PV="${PV##*_p}" DESCRIPTION="APBS plugin for pymol" HOMEPAGE="http://sourceforge.net/projects/pymolapbsplugin/" +SRC_URI="" ESVN_REPO_URI="https://pymolapbsplugin.svn.sourceforge.net/svnroot/pymolapbsplugin/trunk/" SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" LICENSE="pymol" +KEYWORDS="" IUSE="" -RDEPEND=" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} sci-chemistry/apbs sci-chemistry/pdb2pqr - !<sci-chemistry/pymol-1.2.2-r1" + >sci-chemistry/pymol-1.5" DEPEND="${RDEPEND}" -RESTRICT_PYTHON_ABIS="3.*" - -src_unpack() { - subversion_src_unpack - python_copy_sources -} src_install() { - installation() { - sed \ - -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ - -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ - -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ - -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ - -i src/apbsplugin.py - - insinto $(python_get_sitedir)/pmg_tk/startup/ - newins src/apbsplugin.py apbs_tools.py || die - } - python_execute_function -s installation -} - -pkg_postinst() { - python_mod_optimize pmg_tk/startup/apbs_tools.py -} - -pkg_postrm() { - python_mod_cleanup pmg_tk/startup/apbs_tools.py + sed \ + -e "s:^APBS_BINARY_LOCATION.*:APBS_BINARY_LOCATION = \"${EPREFIX}/usr/bin/apbs\":g" \ + -e "s:^APBS_PSIZE_LOCATION.*:APBS_PSIZE_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/src/\":g" \ + -e "s:^APBS_PDB2PQR_LOCATION.*:APBS_PDB2PQR_LOCATION = \"${EPREFIX}/$(python_get_sitedir)/pdb2pqr/\":g" \ + -e "s:^TEMPORARY_FILE_DIR.*:TEMPORARY_FILE_DIR = \"./\":g" \ + -i src/apbsplugin.py > apbs_tools.py || die + python_moduleinto pmg_tk/startup/ + python_domodule apbs_tools.py + python_optimize } diff --git a/sci-chemistry/pymol-plugins-ezviz/ChangeLog b/sci-chemistry/pymol-plugins-ezviz/ChangeLog index 1ccd39164..86dd9cb13 100644 --- a/sci-chemistry/pymol-plugins-ezviz/ChangeLog +++ b/sci-chemistry/pymol-plugins-ezviz/ChangeLog @@ -2,6 +2,10 @@ # 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 $ + 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 + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> metadata.xml: Fix missing DOCTYPE diff --git a/sci-chemistry/pymol-plugins-ezviz/Manifest b/sci-chemistry/pymol-plugins-ezviz/Manifest index d7b39ced4..900a20e11 100644 --- a/sci-chemistry/pymol-plugins-ezviz/Manifest +++ b/sci-chemistry/pymol-plugins-ezviz/Manifest @@ -1 +1 @@ -DIST pymol-plugins-ezviz-1.0.2005.zip 137431 SHA256 742c18d338ccc0567203c122a5f7ce0f903bf3247f7620337828d9dd5ae4f008 +DIST pymol-plugins-ezviz-1.0.2005.zip 137431 SHA256 742c18d338ccc0567203c122a5f7ce0f903bf3247f7620337828d9dd5ae4f008 SHA512 d0281e16dac76e519c725945bdaa5da233f8975411b9d39258a03206c39349014a05e52b6f8cd08b0c667e9d6a177eba2545861ee853ba43810f9ed0d4beb7a1 WHIRLPOOL 87deac54993ca87e4c61512f54d2c5063e9d641064780d999603d934c11755ad36bd211210c04f6a8e2bf302476b54ef8b3cad6efe1f7c0fa74378b549699366 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.ebuild index 8e84a9af2..5f044c6e3 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.ebuild @@ -1,63 +1,51 @@ -# Copyright 1999-2010 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: /var/www/viewcvs.gentoo.org/raw_cvs/gentoo-x86/sci-chemistry/pymol-plugins-ezviz/pymol-plugins-ezviz-1.0.2005.ebuild,v 1.2 2010/04/08 18:47:57 jlec dead $ -EAPI="3" +EAPI=5 -SUPPORT_PYTHON_ABIS="1" +PYTHON_COMPAT=( python2_7 ) -inherit eutils python +inherit eutils python-r1 -DESCRIPTION="assistance tool for the difficult to understand user interface of PyMOL" +DESCRIPTION="Assistance tool for the difficult to understand user interface of PyMOL" HOMEPAGE="http://www.rit.edu/cos/ezviz/index.html" -SRC_URI=" - mirror://gentoo/${P}.zip - mirror://gentoo/${P}.zip" +SRC_URI="http://www.rit.edu/cos/ezviz/EZ_Viz.zip -> ${P}.zip" SLOT="0" +LICENSE="all-rights-reserved" KEYWORDS="~amd64 ~x86" -LICENSE="as-is" IUSE="doc" -RDEPEND="sci-chemistry/pymol" -DEPEND=" - app-arch/unzip - ${RDEPEND}" - -RESTRICT_PYTHON_ABIS="3.*" +RDEPEND="sci-chemistry/pymol[${PYTHON_USEDEP}]" +DEPEND="app-arch/unzip" S="${WORKDIR}/EZ_Viz Folder" src_prepare() { edos2unix ez-viz.py + epatch "${FILESDIR}"/gentoo.patch + for gif in *.GIF; do + mv ${gif} ${gif/.GIF/.gif} || die + done python_copy_sources preperation() { - epatch "${FILESDIR}"/gentoo.patch + cd "${BUILD_DIR}" || die sed \ -e "s:GENTOOPYMOL:${EPREFIX}/$(python_get_sitedir):g" \ -i ez-viz.py || die } - python_execute_function -s preperation + python_foreach_impl preperation } src_install() { installation() { - insinto $(python_get_sitedir)/pmg_tk/startup/ - doins *.py || die - insinto $(python_get_sitedir)/pmg_tk/startup/ez-viz/ - doins *.gif || die - for gif in *.GIF; do - newins ${gif} ${gif/.GIF/.gif} || die - done + python_moduleinto pmg_tk/startup/ + python_domodule *.py + python_moduleinto pmg_tk/startup/ez-viz/ + python_domodule *.gif } - python_execute_function -s installation - dodoc readme.txt || die -} - -pkg_postinst() { - python_mod_optimize pmg_tk/startup -} - -pkg_postrm() { - python_mod_cleanup pmg_tk/startup + python_foreach_impl installation + python_parallel_foreach_impl python_optimize + dodoc readme.txt } diff --git a/sci-chemistry/pymol-plugins-psico/ChangeLog b/sci-chemistry/pymol-plugins-psico/ChangeLog index 8c346ed68..e73fd24a3 100644 --- a/sci-chemistry/pymol-plugins-psico/ChangeLog +++ b/sci-chemistry/pymol-plugins-psico/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild: + Bump to EAPI=5 and distutils-r1.eclass + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> pymol-plugins-psico-9999.ebuild, metadata.xml: Rename sci-chemistry/mmtk to sci-libs/mmtk diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild index d074fc52f..fd8f89921 100644 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild +++ b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-9999.ebuild @@ -2,14 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" -PYTHON_MODNAME="psico" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils git-2 +inherit distutils-r1 git-2 DESCRIPTION="Pymol ScrIpt COllection" HOMEPAGE="https://github.com/speleo3/pymol-psico/" @@ -22,9 +19,9 @@ LICENSE="BSD-2" IUSE="minimal" RDEPEND=" - dev-python/numpy - sci-biology/biopython - sci-libs/mmtk + dev-python/numpy[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-libs/mmtk[${PYTHON_USEDEP}] !minimal? ( media-libs/qhull media-video/mplayer 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/pyquante/ChangeLog b/sci-chemistry/pyquante/ChangeLog index ff079af0e..fee67569c 100644 --- a/sci-chemistry/pyquante/ChangeLog +++ b/sci-chemistry/pyquante/ChangeLog @@ -1,7 +1,11 @@ # ChangeLog for sci-chemistry/pyquante -# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> pyquante-1.6.3-r1.ebuild, + metadata.xml: + Bump to EAPI=5 and distutils-r1.eclass + *pyquante-1.6.3-r1 (29 Jun 2010) 29 Jun 2010; Justin Lecher <jlec@gentoo.org> -pyquante-1.6.3.ebuild, diff --git a/sci-chemistry/pyquante/Manifest b/sci-chemistry/pyquante/Manifest index 02e7d8362..ddde6e594 100644 --- a/sci-chemistry/pyquante/Manifest +++ b/sci-chemistry/pyquante/Manifest @@ -1 +1 @@ -DIST PyQuante-1.6.3.tar.gz 329029 SHA256 9bba2d6eefebbb3f2296c69e8b8c9714d8ac1689abaf4ce9468441d19c1e9d20 +DIST PyQuante-1.6.3.tar.gz 329029 SHA256 9bba2d6eefebbb3f2296c69e8b8c9714d8ac1689abaf4ce9468441d19c1e9d20 SHA512 7442fd1a25bf10db81f86d6811a3e57c38a3c5a6ac26764663e25028b45a1a3ae5da896a5219e467265d7128829386e2295fccf470018c45dc70b8a20d592fbf WHIRLPOOL 53e854f2bb02d4cffa2d16f9acb5ee9db4f3abb23d590a4b4dcd759bcde51337146518341aa7d8d2c2caf2b3cc1d3e3a4932cd39d82768811acd2c4577247764 diff --git a/sci-chemistry/pyquante/metadata.xml b/sci-chemistry/pyquante/metadata.xml index 9ac9ffdb3..51fdedab1 100644 --- a/sci-chemistry/pyquante/metadata.xml +++ b/sci-chemistry/pyquante/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-chemistry/pyquante/pyquante-1.6.3-r1.ebuild b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild index 93f085554..88f7f96d2 100644 --- a/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild +++ b/sci-chemistry/pyquante/pyquante-1.6.3-r1.ebuild @@ -1,13 +1,12 @@ -# Copyright 1999-2010 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" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit distutils +inherit distutils-r1 MY_PN="PyQuante" MY_P="${MY_PN}-${PV}" @@ -16,8 +15,8 @@ DESCRIPTION="Quantum chemistry package written in Python" HOMEPAGE="http://pyquante.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" -LICENSE="GPL-2" SLOT="0" +LICENSE="GPL-2" KEYWORDS="~amd64 ~x86" IUSE="" diff --git a/sci-chemistry/rosetta-tools/metadata.xml b/sci-chemistry/rosetta-tools/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/rosetta-tools/metadata.xml +++ b/sci-chemistry/rosetta-tools/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/rosetta/metadata.xml b/sci-chemistry/rosetta/metadata.xml index b8a46614c..f12220103 100644 --- a/sci-chemistry/rosetta/metadata.xml +++ b/sci-chemistry/rosetta/metadata.xml @@ -1,17 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="boinc">compile rosetta as a rosetta@home client</flag> - <flag name="boost">compile rosetta with boost supported code</flag> - <flag name="float">Build with floats rather than doubles</flag> - <flag name="lange">Apply patches from www.csrosetta.org</flag> - </use> - <upstream> - <bugs-to>general-support@mail.rosettacommons.org</bugs-to> - </upstream> +<herd>sci-chemistry</herd> + <use> + <flag name="boinc">compile rosetta as a rosetta@home client</flag> + <flag name="boost">compile rosetta with boost supported code</flag> + <flag name="float">Build with floats rather than doubles</flag> + <flag name="lange">Apply patches from www.csrosetta.org</flag> + </use> + <upstream> + <bugs-to>general-support@mail.rosettacommons.org</bugs-to> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/shiftx/ChangeLog b/sci-chemistry/shiftx/ChangeLog index 3284d504c..f656301f5 100644 --- a/sci-chemistry/shiftx/ChangeLog +++ b/sci-chemistry/shiftx/ChangeLog @@ -1,7 +1,17 @@ # ChangeLog for sci-chemistry/shiftx -# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 21 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild: + Block shiftx2 at runtime + + 20 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, + files/1.1-Makefile.patch, +files/1.1-bfr-overflow.patch, metadata.xml: + Fix patch and add patch for buffer overflow fix + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx-1.1.ebuild, metadata.xml: + Bump to EAPI=5 and fix license + *shiftx-1.1 (14 Jun 2009) 14 Jun 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> diff --git a/sci-chemistry/shiftx/Manifest b/sci-chemistry/shiftx/Manifest index 01ee9e803..87119a6e4 100644 --- a/sci-chemistry/shiftx/Manifest +++ b/sci-chemistry/shiftx/Manifest @@ -1 +1 @@ -DIST shiftx.tar.gz 318768 SHA256 2a4b00adfc39d39d2f28c09f78e3c9c7ab8b28e96c4e5efcdffeedfac00ab1ef +DIST shiftx-1.1.tar.gz 504915 SHA256 a08bc301b119154675eb05d9c5c69b7f582e8c2fa0cc81c5040a6ac013ac1965 SHA512 2396ef31a9ce0c059b0c5cb0be60d7ab0489775e03439dcf3c62b8559a13b0e8ad37c8ef02e6422dd6b93acfe579c1abc86f520473836240d48840c7f38aed1f WHIRLPOOL 048873c70f8ae670e097039b4a29ec9eb27ea89879065b2155140914bc77b999e42af471aa15598691d12e0c11b58100a4d15fd29ccf4b562a885a8ea81afe7c diff --git a/sci-chemistry/shiftx/files/1.1-Makefile.patch b/sci-chemistry/shiftx/files/1.1-Makefile.patch index 167875241..f208d087f 100644 --- a/sci-chemistry/shiftx/files/1.1-Makefile.patch +++ b/sci-chemistry/shiftx/files/1.1-Makefile.patch @@ -1,17 +1,22 @@ ---- Makefile 2004-08-03 20:33:20.000000000 +0200 -+++ Makefile.new 2009-06-14 10:49:40.000000000 +0200 + Makefile | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/Makefile b/Makefile +index 5401c07..ffd8157 100644 +--- a/Makefile ++++ b/Makefile @@ -6,8 +6,8 @@ # E-Mail: anip@redpoll.pharmacy.ualberta.ca # #CC=gcc -Xcpluscomm -cckr -CC=/usr/bin/gcc --CFLAGS=-O3 +-CFLAGS=-O +#CC=/usr/bin/gcc -+#CFLAGS=-O3 ++#CFLAGS=-O SYSLIB= INCLUDES=-I/usr/include LIBS=$(SYSLIB) -lm -@@ -25,7 +25,7 @@ +@@ -25,7 +25,7 @@ OBJS=Main.o Nn.o Ssbond.o Residue.o Hetatm.o Vector.o Torison.o Cs.o Phipsi.o \ all: shiftx shiftx: $(OBJS) diff --git a/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch new file mode 100644 index 000000000..68507a364 --- /dev/null +++ b/sci-chemistry/shiftx/files/1.1-bfr-overflow.patch @@ -0,0 +1,16 @@ + Display.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Display.c b/Display.c +index 671d3ee..9a03c48 100644 +--- a/Display.c ++++ b/Display.c +@@ -85,7 +85,7 @@ DISPLAY_DATA *CreateDisplayData( int len, int prop, int nuc ) + void display_selected_nucleus( DISPLAY_DATA *d )
+ {
+ int i, j;
+- char nucleus[5];
++ char nucleus[8];
+
+ /* Print Header Information */
+
diff --git a/sci-chemistry/shiftx/metadata.xml b/sci-chemistry/shiftx/metadata.xml index 0fbe927f0..51fdedab1 100644 --- a/sci-chemistry/shiftx/metadata.xml +++ b/sci-chemistry/shiftx/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/shiftx/shiftx-1.1.ebuild b/sci-chemistry/shiftx/shiftx-1.1.ebuild index 336c77cca..4c3c6b799 100644 --- a/sci-chemistry/shiftx/shiftx-1.1.ebuild +++ b/sci-chemistry/shiftx/shiftx-1.1.ebuild @@ -1,33 +1,36 @@ -# Copyright 1999-2009 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ +EAPI=5 + inherit base toolchain-funcs -DESCRIPTION="With this form you can predict 1H, 13C and 15N chemical shifts for your favorite protein" -HOMEPAGE="http://redpoll.pharmacy.ualberta.ca/shiftx/" -SRC_URI="http://redpoll.pharmacy.ualberta.ca/download/${PN}/${PN}.tar.gz" +DESCRIPTION="Prediction of 1H, 13C and 15N chemical shifts for proteins" +HOMEPAGE="http://shiftx.wishartlab.com/" +SRC_URI="http://shiftx.wishartlab.com/download/${PN}.tar.gz -> ${P}.tar.gz" -LICENSE="as-is" +LICENSE="all-rights-reserved" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" S="${WORKDIR}"/${PN} +DEPEND="" +RDEPEND="sci-chemistry/shiftx2" + PATCHES=( "${FILESDIR}"/${PV}-Makefile.patch -) + "${FILESDIR}"/${PV}-bfr-overflow.patch ) DOCS="README FEATURES *.pdb *.out" src_compile() { - emake \ - CC="$(tc-getCC)" || \ - die "compilation failed" + emake CC="$(tc-getCC)" } src_install() { - dobin ${PN} || die "installationof ${PN} failed" - dodoc ${DOCS} || die + dobin ${PN} + dodoc ${DOCS} } diff --git a/sci-chemistry/shiftx2/ChangeLog b/sci-chemistry/shiftx2/ChangeLog new file mode 100644 index 000000000..5aafaf3ca --- /dev/null +++ b/sci-chemistry/shiftx2/ChangeLog @@ -0,0 +1,8 @@ +# ChangeLog for sci-chemistry/shiftx2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> shiftx2-1.07_p20120106.ebuild, + metadata.xml: + Respect FLAGS + diff --git a/sci-chemistry/shiftx2/Manifest b/sci-chemistry/shiftx2/Manifest new file mode 100644 index 000000000..94fd67e47 --- /dev/null +++ b/sci-chemistry/shiftx2/Manifest @@ -0,0 +1 @@ +DIST shiftx2-v107-linux-20120106.tgz 114164215 SHA256 47bd11f00c824967738f72a02387b47eafc60a10697aa157e27163f2edbf9927 SHA512 b1fa6ce19e988a938e6645fdbd14f7903b4db13754a476c67da0bf74909675e07b7cec4df63be30d7190ea645e8822eef551e6dd26625172e585da279f1f7396 WHIRLPOOL 20fc5ea052106e2f6f708ba61da2ad9310a50a1c85dfb46d947c919d665835cc43180267094c057b7ce542b59659a1b44940c762c4c8e190cdbb7727dc30c865 diff --git a/sci-chemistry/shiftx2/files/gentoo-fixes.patch b/sci-chemistry/shiftx2/files/gentoo-fixes.patch new file mode 100644 index 000000000..2baa443c5 --- /dev/null +++ b/sci-chemistry/shiftx2/files/gentoo-fixes.patch @@ -0,0 +1,194 @@ +diff --git a/shiftx2-v107-linux/src/LimitedCShift.java b/shiftx2-v107-linux/src/LimitedCShift.java +index cd27fbf..9e72208 100755 +--- a/shiftx2-v107-linux/src/LimitedCShift.java ++++ b/shiftx2-v107-linux/src/LimitedCShift.java +@@ -13,8 +13,8 @@ public class LimitedCShift { + public void loadLimitedCShift () { + // System.out.println("SHIFTX2_DIR: "+ShiftXp.SHIFTX2_DIR); + +- String filename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.dat"; +- String objFilename = ShiftXp.SHIFTX2_DIR + "/lib/limitedcshift.osf"; ++ String filename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.dat"; ++ String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/limitedcshift.osf"; + + File f = new File(objFilename); + if (f.exists()) { +@@ -44,7 +44,7 @@ public class LimitedCShift { + br.close(); + + // save object into object file format for speed up +- saveObjectFile(objFilename, limshift); ++ //saveObjectFile(objFilename, limshift); + + } catch(IOException ex){ + ex.printStackTrace(); +diff --git a/shiftx2-v107-linux/src/ModuleExecutor.java b/shiftx2-v107-linux/src/ModuleExecutor.java +index 36cfeb1..704451f 100755 +--- a/shiftx2-v107-linux/src/ModuleExecutor.java ++++ b/shiftx2-v107-linux/src/ModuleExecutor.java +@@ -22,12 +22,12 @@ public class ModuleExecutor { + // private static final String WORKING_DIR = "./wkdir/"; + private static String WORKING_DIR = ""; + +- private static final String RESMF_EXE = "/modules/resmf/resmf"; +- private static final String EFFECTS_EXE = "/modules/effects/caleffect"; +- private static final String ANGLES_EXE = "/modules/angles/get_angles"; +- private static final String ANGLES_REDUCE_DIR = "/modules/angles"; ++ private static final String RESMF_EXE = "resmf"; ++ private static final String EFFECTS_EXE = "caleffect"; ++ private static final String ANGLES_EXE = "get_angles"; ++ private static final String ANGLES_REDUCE_DIR = "angles"; + +- private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; ++// private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; + + private static final String REDUCE_FLAG = "1"; // 1 or 0 + +@@ -80,8 +80,8 @@ public class ModuleExecutor { + if(DEBUG) System.out.println("> Processing [Major Features] with " + pdbfile); + // Update: add pdbdir both input pdbfile and output result, pdbId (2011.03.17) + // cmd = RESMF_EXE + " -f " + pdbdir +"/"+ pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf"; +- cmd = SHIFTXP_DIR + RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" +- + " -d " + SHIFTXP_DIR + "/modules/resmf/lib"; ++ cmd = RESMF_EXE + " -f " + pdbdir + pdbfile + " -o " + WORKING_DIR + pdbId + ".resmf" ++ + " -d " + ShiftXp.GENTOO_SHARE_PATH + "/vader"; + + if(DEBUG){ System.out.println("\t"+cmd); } + execCode = execute_command(cmd); +@@ -93,7 +93,7 @@ public class ModuleExecutor { + + /* call effects for calculating ring current calculator */ + if(DEBUG) System.out.println("> processing [Effects] with " + pdbfile); +- cmd = SHIFTXP_DIR + EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy"; ++ cmd = EFFECTS_EXE + " 1 " + pdbdir + pdbfile + " " + WORKING_DIR + pdbfile + ".dummy"; + + if(DEBUG){ System.out.println("\t"+cmd); } + execCode = execute_command(cmd); +@@ -106,7 +106,7 @@ public class ModuleExecutor { + /* call angle calculator : output must be redirected to file using PrintStream */ + if(DEBUG) System.out.println("> Processing [Angle] with " + pdbfile); + // cmd = ANGLES_EXE + " " + ANGLES_REDUCE_DIR + " " + pdbfile ; +- cmd = SHIFTXP_DIR + ANGLES_EXE + " " + SHIFTXP_DIR + ANGLES_REDUCE_DIR + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG; ++ cmd = ANGLES_EXE + " " + ShiftXp.GENTOO_SHARE_PATH + " " + pdbdir + pdbfile + " "+ REDUCE_FLAG; + String outpath = WORKING_DIR + pdbId + ".angles"; + + if(DEBUG){ System.out.println("\t"+cmd); } +diff --git a/shiftx2-v107-linux/src/PredictionModels.java b/shiftx2-v107-linux/src/PredictionModels.java +index a77d1cb..fb84666 100755 +--- a/shiftx2-v107-linux/src/PredictionModels.java ++++ b/shiftx2-v107-linux/src/PredictionModels.java +@@ -13,9 +13,7 @@ public class PredictionModels { + private final static String MODEL_FILE_SIDECHAIN_ONLY = "predmodels_sidechain.sobj"; + + private final static String OBJECT_MODEL_DIRECTORY = "/lib"; +- private final static String MODEL_DIRECTORY = "/lib/predmodels"; +- +- private static String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; ++ private final static String MODEL_DIRECTORY = "predmodels"; + + HashMap<String, Classifier> hsmap_predmodel = new HashMap<String, Classifier>(); + +@@ -36,7 +34,7 @@ public class PredictionModels { + // System.out.println("SHIFTXP_DIR:" + SHIFTXP_DIR+"\n\n"); + // System.out.println("SHIFTX2_DIR:" + ShiftXp.SHIFTX2_DIR+"\n\n"); + +- String headerfilename = ShiftXp.SHIFTX2_DIR + "/lib/data-header.arff"; ++ String headerfilename = ShiftXp.GENTOO_SHARE_PATH + "/data-header.arff"; + + try { + // assigned instance header from data-header.arff +@@ -150,7 +148,7 @@ public class PredictionModels { + // if option is not sidechain only, put backbone models into modeling file + if ( ! this.prediction_type.equals("SIDECHAIN") ) { + for(int i=0; i < BACKBONE_MODEL_LENGTH; i++) { +- ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); ++ ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); + classifier = (Classifier) ois.readObject(); + hsmap_predmodel.put(atomNameArray[i],classifier); + ois.close(); +@@ -160,7 +158,7 @@ public class PredictionModels { + // if option is not backbone only, put/append sidechain models into modeling file + if ( ! this.prediction_type.equals("BACKBONE") ) { + for(int i=BACKBONE_MODEL_LENGTH; i < (BACKBONE_MODEL_LENGTH + SIDECHAIN_MODEL_LENGTH); i++) { +- ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.SHIFTX2_DIR + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); ++ ois = new ObjectInputStream( new BufferedInputStream( new FileInputStream( ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_DIRECTORY + "/" + modelFileArray[i]) )); + classifier = (Classifier) ois.readObject(); + hsmap_predmodel.put(atomNameArray[i], classifier); + ois.close(); +@@ -185,11 +183,11 @@ public class PredictionModels { + */ + + if ( this.prediction_type.equals("ALL") == true) { +- model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_ALLATOMS; ++ model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_ALLATOMS; + } else if ( this.prediction_type.equals("BACKBONE") == true) { +- model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_BACKBONE_ONLY; ++ model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_BACKBONE_ONLY; + } else if ( this.prediction_type.equals("SIDECHAIN") == true) { +- model_file = ShiftXp.SHIFTX2_DIR + OBJECT_MODEL_DIRECTORY + "/" + MODEL_FILE_SIDECHAIN_ONLY; ++ model_file = ShiftXp.GENTOO_SHARE_PATH + "/" + MODEL_FILE_SIDECHAIN_ONLY; + } + + File f = new File( model_file ); +@@ -198,7 +196,7 @@ public class PredictionModels { + readHashObjectPredModelFile( model_file ); + } else { + setHashMap(); +- saveHashObjectPredModelFile( model_file ); ++// saveHashObjectPredModelFile( model_file ); + } + } + +diff --git a/shiftx2-v107-linux/src/RandomCoil.java b/shiftx2-v107-linux/src/RandomCoil.java +index 25a8999..7442938 100755 +--- a/shiftx2-v107-linux/src/RandomCoil.java ++++ b/shiftx2-v107-linux/src/RandomCoil.java +@@ -33,11 +33,9 @@ public class RandomCoil { + public void loadRandomCoil() { + + // change path as absolute path +- String SHIFTXP_DIR = ShiftXp.SHIFTX2_DIR; +- +- String filename = SHIFTXP_DIR + "/lib/RandomCoil.csv"; +- String objFilename = SHIFTXP_DIR + "/lib/RandomCoil.osf"; +- String objAtomListname = SHIFTXP_DIR + "/lib/RCoilAtomlist.osf"; ++ String filename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.csv"; ++ String objFilename = ShiftXp.GENTOO_SHARE_PATH + "/RandomCoil.osf"; ++ String objAtomListname = ShiftXp.GENTOO_SHARE_PATH + "/RCoilAtomlist.osf"; + + + File f = new File(objFilename); +@@ -85,8 +83,8 @@ public class RandomCoil { + br.close(); + + // save object into object file format for speed up +- saveObjectFile(objFilename, rcoil); +- saveObjectFile(objAtomListname, restypeAtomStringList); ++// saveObjectFile(objFilename, rcoil); ++// saveObjectFile(objAtomListname, restypeAtomStringList); + + } catch(IOException ex){ + ex.printStackTrace(); +diff --git a/shiftx2-v107-linux/src/ShiftXp.java b/shiftx2-v107-linux/src/ShiftXp.java +index 505a3f6..920f420 100755 +--- a/shiftx2-v107-linux/src/ShiftXp.java ++++ b/shiftx2-v107-linux/src/ShiftXp.java +@@ -27,7 +27,7 @@ public class ShiftXp { + static final boolean DEBUG = false; + static boolean RCOIL_PRINTOUT = false; + static String SHIFTX2_DIR = "."; // to support running on other directory +- ++ public static final String GENTOO_SHARE_PATH = "PUT_GENTOO_SHARE_PATH_HERE"; + // Loading only one time, that's why these are here + static RandomCoil rcoil = new RandomCoil(); + static LimitedCShift chkcshift = new LimitedCShift(); +@@ -140,8 +140,7 @@ public class ShiftXp { + + // check execute directory + // 2011.08.31 changed shiftx2_main.py --> shiftx2.py +- if ( !( new File( SHIFTX2_DIR + "/shiftx2.py").exists() +- && new File(SHIFTX2_DIR + "/lib/weka.jar").exists() ) ) { ++ if (!new File(SHIFTX2_DIR + "/shiftx2.py").exists()) { + + System.err.println("\n********************************************************************************"); + System.err.println("[Error]\t Required: When the SHIFTX2 execute on other directory,\n" diff --git a/sci-chemistry/shiftx2/metadata.xml b/sci-chemistry/shiftx2/metadata.xml new file mode 100644 index 000000000..2fcd5bb0f --- /dev/null +++ b/sci-chemistry/shiftx2/metadata.xml @@ -0,0 +1,39 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> + <longdescription> + SHIFTX2 predicts both the backbone and side chain 1H, 13C and 15N chemical + shifts for proteins using their structural (PDB) coordinates as input. + SHIFTX2 combines ensemble machine learning methods with sequence + alignment-based methods to calculate protein chemical shifts for + backbone + and side chain atoms. SHIFTX2 has been trained on a carefully selected + set of + 197 proteins and tested on a separate set of 61 proteins. Both the + training + and testing sets consisted of high resolution X-ray structures (less + 2.1A) + with carefully verified chemical shifts assignments. SHIFTX2 is able to + attain + correlation coefficients between experimentally observed and predicted + backbone chemical shifts of 0.9800 (15N), 0.9959 (13CA), 0.9992 (13CB), + 0.9676 (13CO), 0.9714 (1HN), 0.9744 (1HA) and RMS errors of 1.1169, 0.4412, + 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. Comparisons to + other + chemical shift predictors using the same testing data set indicates that + SHIFTX2 is substantially more accurate (up to 26% better by + correlation + coefficient with an RMS error that is up to 3.3X smaller) than any other + program. + + Please cite the following: Beomsoo Han, Yifeng Liu, Simon Ginzinger, and + David Wishart. (2011) SHIFTX2: significantly improved protein chemical + shift + prediction. Journal of Biomolecular NMR, Volume 50, Number 1, 43-57. + doi: 10.1007/s10858-011-9478-4. + </longdescription> + <use> + <flag name="debug">Enables debug output in the shiftx2 java part</flag> + </use> +</pkgmetadata> diff --git a/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild new file mode 100644 index 000000000..5a19e4b0b --- /dev/null +++ b/sci-chemistry/shiftx2/shiftx2-1.07_p20120106.ebuild @@ -0,0 +1,112 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit java-pkg-2 java-pkg-simple python-r1 versionator + +MY_PV="$(delete_all_version_separators $(get_version_component_range 1-2))" +MY_PATCH="20120106" +MY_P="${PN}-v${MY_PV}-linux" + +DESCRIPTION="Predicts both the backbone and side chain 1H, 13C and 15N chemical shifts for proteins" +HOMEPAGE="http://shiftx2.wishartlab.com/" +SRC_URI="http://shiftx2.wishartlab.com/download/${MY_P}-${MY_PATCH}.tgz" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="debug" + +CDEPEND="dev-util/weka" + +RDEPEND="${CDEPEND} + dev-lang/R + sci-chemistry/reduce + >=virtual/jre-1.5" +DEPEND="${CDEPEND} + >=virtual/jdk-1.5" + +S="${WORKDIR}"/${MY_P} + +QA_PREBUILT="/opt/.*" + +src_prepare() { + epatch "${FILESDIR}/gentoo-fixes.patch" + rm "${S}"/src/FeatureRanges.java || die + + shared=$(echo "/usr/share/${PN}" | sed -e 's/\//\\\//g') + sed -i -e "s/PUT_GENTOO_SHARE_PATH_HERE/${shared}/g" "${S}/src/ShiftXp.java" || die + + if use debug; then + sed -i -e 's/DEBUG = false/DEBUG = true/g' "${S}/src/ShiftXp.java" || die + fi + + # hack alert! + sed \ + -e '/-o/s:$(GCC):$(GCC) $(LDFLAGS):g' \ + -e '/-o/s:$(CC):$(CC) $(LDFLAGS):g' \ + -i modules/*/Makefile || die + + sed -e '/-o/s:$: -lm:g' -i "${S}/modules/resmf/Makefile" || die +} + +src_compile() { + mkdir "${S}"/build || die + ejavac -classpath "$(java-pkg_getjars weka)" -nowarn \ + -d "${S}"/build $(find src/ -name "*.java") + jar cf "${PN}.jar" -C "${S}"/build . || die + + einfo "Building module angles" + cd "${S}"/modules/angles || die + emake clean + emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" get_angles phipsi + + einfo "Building module resmf" + cd "${S}"/modules/resmf || die + emake clean + emake CFLAGS="${CFLAGS}" GCC=$(tc-getCC) LINK="${LDFLAGS}" resmf + + einfo "Building module effects" + cd "${S}"/modules/effects || die + emake clean + emake CFLAGS="${CFLAGS}" CC=$(tc-getCC) LINK="${LDFLAGS}" all +} + +src_install() { + java-pkg_dojar "${PN}.jar" + java-pkg_dolauncher ${PN} --main "ShiftXp" --pkg_args "-dir ${EPREFIX}/usr/bin" + + insinto /usr/share/${PN} + doins "${S}"/lib/{limitedcshift.dat,RandomCoil.csv,data-header.arff} + doins -r "${S}"/lib/predmodels + + insinto /usr/share/${PN}/vader + doins -r "${S}"/modules/resmf/lib/* + + local instdir="/opt/${PN}" + dodoc README 1UBQ.pdb + python_parallel_foreach_impl python_doscript "${S}"/*py + + # other modules + dobin \ + "${S}"/modules/angles/{get_angles,phipsi} \ + "${S}"/modules/resmf/resmf \ + "${S}"/modules/effects/caleffect + + # script + python_scriptinto ${instdir}/script + python_parallel_foreach_impl python_doscript "${S}"/script/*py + exeinto ${instdir}/script + doexe "${S}"/script/*.r + + # shifty3 + python_scriptinto ${instdir}/shifty3 + python_parallel_foreach_impl python_doscript "${S}"/shifty3/*py + exeinto ${instdir}/shifty3 + doexe "${S}"/shifty3/xalign_x + dosym ../${PN}/shifty3/xalign_x /opt/bin/xalign_x +} diff --git a/sci-chemistry/simpson/metadata.xml b/sci-chemistry/simpson/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/simpson/metadata.xml +++ b/sci-chemistry/simpson/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/smmp/ChangeLog b/sci-chemistry/smmp/ChangeLog index cddd7bfbb..375ec723b 100644 --- a/sci-chemistry/smmp/ChangeLog +++ b/sci-chemistry/smmp/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/smmp -# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild, metadata.xml: + Bump to EAPI=5 and python-r1.eclass + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> smmp-3.0.5.ebuild: Streamlined fortran-2 eclass usage diff --git a/sci-chemistry/smmp/Manifest b/sci-chemistry/smmp/Manifest index 879b9f85b..1b54b5bcf 100644 --- a/sci-chemistry/smmp/Manifest +++ b/sci-chemistry/smmp/Manifest @@ -1 +1 @@ -DIST SMMP-3.0.5.tar.bz2 233378 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c +DIST SMMP-3.0.5.tar.bz2 233378 SHA256 70d6b719d2c2ef1d34fd9897ad1c89a37c4d7531d80c904eee39dc8855aca31c SHA512 7a6701f267fc09ee966ec34854ca12443725dc01e3bdf6283eaac7fc82764030abbc10bd0c6eefef2652bb64a70d5a09dc338448ce9d0c31021219358d40920d WHIRLPOOL 1c2b390b85ad5a9cc4f00df6838f92b8dd29403648ca1a07bf8d71b409cc396fb3671201f271a65f4fecc70a99d25ed0be95c9f26ab15d6ce431c220c9e1d991 diff --git a/sci-chemistry/smmp/metadata.xml b/sci-chemistry/smmp/metadata.xml index 0fbe927f0..9ac9ffdb3 100644 --- a/sci-chemistry/smmp/metadata.xml +++ b/sci-chemistry/smmp/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci-chemistry</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-chemistry/smmp/smmp-3.0.5.ebuild b/sci-chemistry/smmp/smmp-3.0.5.ebuild index 8f49f3d29..95dda9950 100644 --- a/sci-chemistry/smmp/smmp-3.0.5.ebuild +++ b/sci-chemistry/smmp/smmp-3.0.5.ebuild @@ -1,14 +1,12 @@ -# Copyright 1999-2011 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=2 +EAPI=5 -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit eutils fortran-2 python toolchain-funcs +inherit eutils fortran-2 python-r1 toolchain-funcs MY_PN="SMMP" MY_P="${MY_PN}-${PV}" @@ -18,13 +16,11 @@ HOMEPAGE="http://smmp.berlios.de/" SRC_URI="mirror://berlios/${PN}/${MY_P}.tar.bz2" SLOT="0" -KEYWORDS="~amd64 ~x86" LICENSE="GPL-2" +KEYWORDS="~amd64 ~x86" IUSE="doc mpi test" -RDEPEND=" - virtual/fortran - mpi? ( virtual/mpi )" +RDEPEND="mpi? ( virtual/mpi )" DEPEND="${RDEPEND} doc? ( app-doc/doxygen )" @@ -42,31 +38,22 @@ src_compile() { target="${PN}" fi - tc-export FC - - emake ${target} || die + emake ${target} } src_test() { - emake examples || die + emake examples cd EXAMPLES bash smmp.cmd || die } src_install() { - dobin ${PN} || die + dobin ${PN} installation() { - insinto $(python_get_sitedir)/${PN} - doins *.py || die + python_moduleinto ${PN} + python_domodule *.py + python_optimize } - python_execute_function installation - dodoc README || die -} - -pkg_postinst() { - python_mod_optimize ${PN} -} - -pkg_postrm() { - python_mod_cleanup ${PN} + python_foreach_impl installation + dodoc README } diff --git a/sci-chemistry/specView/ChangeLog b/sci-chemistry/specView/ChangeLog index 09193d635..b6fe2af69 100644 --- a/sci-chemistry/specView/ChangeLog +++ b/sci-chemistry/specView/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild: + Bump to EAPI=5 and python-single-r1.eclass + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> specView-1.0.2.ebuild, metadata.xml: Fix quoting diff --git a/sci-chemistry/specView/metadata.xml b/sci-chemistry/specView/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/specView/metadata.xml +++ b/sci-chemistry/specView/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-chemistry/specView/specView-1.0.2.ebuild b/sci-chemistry/specView/specView-1.0.2.ebuild index 89666a69d..a0a5bac38 100644 --- a/sci-chemistry/specView/specView-1.0.2.ebuild +++ b/sci-chemistry/specView/specView-1.0.2.ebuild @@ -2,11 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 -PYTHON_DEPEND="2" +PYTHON_COMPAT=( python{2_6,2_7} ) -inherit python toolchain-funcs +inherit multilib python-single-r1 toolchain-funcs DESCRIPTION="Fast way to visualise NMR spectrum and peak data" HOMEPAGE="http://www.ccpn.ac.uk/software/specview" @@ -18,8 +18,8 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" RDEPEND=" - dev-python/pyopengl - dev-python/pyside[webkit]" + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/pyside[webkit,${PYTHON_USEDEP}]" DEPEND="${RDEPEND}" S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ @@ -30,11 +30,6 @@ S="${WORKDIR}"/ccpnmr/ccpnmr3.0/ #unbundle inchi #parallel build -pkg_setup() { - python_set_active_version 2 - python_pkg_setup -} - src_prepare() { sed \ -e "s|/usr|"${EPREFIX}"/usr|g" \ @@ -43,7 +38,7 @@ src_prepare() { -e "/^OPT_FLAG/s:=.*$:= ${CFLAGS}:g" \ -e "/^LINK_FLAGS/s:$: ${LDFLAGS}:g" \ -e "/^PYTHON_DIR/s:=.*:= "${EPREFIX}"/usr:g" \ - -e "/^PYTHON_LIB/s:=.*:= $(python_get_library -l):g" \ + -e "/^PYTHON_LIB/s:=.*:= $(python_get_LIBS):g" \ -e "/^PYTHON_INCLUDE_FLAGS/s:=.*:= -I"${EPREFIX}"$(python_get_includedir) -I"${EPREFIX}"$(python_get_sitedir)/numpy/core/include/numpy:g" \ -e "/^PYTHON_LIB_FLAGS/s:=.*:= -L"${EPREFIX}"/usr/$(get_libdir):g" \ -e "/^SHARED_FLAGS/s:=.*:= -shared:g" \ @@ -72,37 +67,22 @@ src_install() { find . -name "*.pyc" -type f -delete dodir /usr/bin sed \ - -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \ - -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ - -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ - -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ - -e "s|gentoopython|$(PYTHON -a)|g" \ - -e "s|gentoousr|${EPREFIX}/usr|g" \ - -e "s|//|/|g" \ + -e "s|gentoo_sitedir|${EPREFIX}$(python_get_sitedir)|g" \ + -e "s|gentoolibdir|${EPREFIX}/usr/${libdir}|g" \ + -e "s|gentootk|${EPREFIX}/usr/${libdir}/tk${tkver}|g" \ + -e "s|gentootcl|${EPREFIX}/usr/${libdir}/tclk${tkver}|g" \ + -e "s|gentoopython|${PYTHON}|g" \ + -e "s|gentoousr|${EPREFIX}/usr|g" \ + -e "s|//|/|g" \ "${FILESDIR}"/${PN} > "${ED}"/usr/bin/${PN} || die fperms 755 /usr/bin/${PN} - insinto ${in_path} - dodir ${in_path}/cNg rm -rf cNg || die ebegin "Installing main files" - doins -r * - eend - - ebegin "Adjusting permissions" - - for _file in $(find "${ED}" -type f -name "*so"); do - chmod 755 ${_file} - done + python_moduleinto ${PN} + python_domodule * eend -} - -pkg_postinst() { - python_mod_optimize ${PN} -} - -pkg_postrm() { - python_mod_cleanup ${PN} + python_optimize } diff --git a/sci-chemistry/ssp/ChangeLog b/sci-chemistry/ssp/ChangeLog index 87325180c..dd0fd1e1a 100644 --- a/sci-chemistry/ssp/ChangeLog +++ b/sci-chemistry/ssp/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-chemistry/ssp -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 16 Jun 2013; Justin Lecher <jlec@gentoo.org> ssp-09.11.ebuild, metadata.xml: + Bump to EAPI=5 and fix license + 30 Aug 2012; Justin Lecher <jlec@gentoo.org> ssp-09.11.ebuild: Fix offset of reference CS DB diff --git a/sci-chemistry/ssp/metadata.xml b/sci-chemistry/ssp/metadata.xml index 210ad0db0..ae9ec7c5f 100644 --- a/sci-chemistry/ssp/metadata.xml +++ b/sci-chemistry/ssp/metadata.xml @@ -1,8 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>jlec@gentoo.org</email> - </maintainer> + <herd>sci-chemistry</herd> + <maintainer> + <email>jlec@gentoo.org</email> + </maintainer> </pkgmetadata> diff --git a/sci-chemistry/ssp/ssp-09.11.ebuild b/sci-chemistry/ssp/ssp-09.11.ebuild index 59061425e..5d88b107e 100644 --- a/sci-chemistry/ssp/ssp-09.11.ebuild +++ b/sci-chemistry/ssp/ssp-09.11.ebuild @@ -1,15 +1,15 @@ -# 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 DESCRIPTION="Secondary structure propensities" HOMEPAGE="http://abragam.med.utoronto.ca/software.html" SRC_URI="http://pound.med.utoronto.ca/${PN}-Nov09.tar.gz" SLOT="0" -LICENSE="as-is" +LICENSE="all-rights-reserved" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" diff --git a/sci-chemistry/talosn/ChangeLog b/sci-chemistry/talosn/ChangeLog new file mode 100644 index 000000000..9d358bff2 --- /dev/null +++ b/sci-chemistry/talosn/ChangeLog @@ -0,0 +1,16 @@ +# ChangeLog for sci-chemistry/talosn +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*talosn-4.01.2013.148.15.55-r2 (18 Jun 2013) + + 18 Jun 2013; Justin Lecher <jlec@gentoo.org> + -talosn-4.01.2013.148.15.55.ebuild, +talosn-4.01.2013.148.15.55-r2.ebuild: + drop upstream path in favour of our + +*talosn-4.01.2013.148.15.55 (18 Jun 2013) + + 18 Jun 2013; Justin Lecher <jlec@gentoo.org> + +talosn-4.01.2013.148.15.55.ebuild, +metadata.xml: + New package + diff --git a/sci-chemistry/talosn/Manifest b/sci-chemistry/talosn/Manifest new file mode 100644 index 000000000..8376af51a --- /dev/null +++ b/sci-chemistry/talosn/Manifest @@ -0,0 +1 @@ +DIST talosn-4.01.2013.148.15.55.tgz 136746268 SHA256 618ffc7f0ac15ac85e4f0034c2e8997f6ea98aef673ee6fe5852fd481e0a60f1 SHA512 365e4f699a0d991730ecf5835685db832339926dcb2b60c59c4d1ea9707d4b9bc48ad46342b702dcb5a7a4a373d7d2e863658116393cc7682027b1237b99ed5f WHIRLPOOL 0a51e20792880d22422316776aeb41feb8ef4ab2deb0cabf71dd0a19f7dc816bdff5f84e7593115216187e39df1f0ea9f4dbde7a087021d7a76cf55569c5ec9f diff --git a/sci-chemistry/talosn/metadata.xml b/sci-chemistry/talosn/metadata.xml new file mode 100644 index 000000000..51fdedab1 --- /dev/null +++ b/sci-chemistry/talosn/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci-chemistry</herd> +</pkgmetadata> diff --git a/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r2.ebuild b/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r2.ebuild new file mode 100644 index 000000000..648c3420d --- /dev/null +++ b/sci-chemistry/talosn/talosn-4.01.2013.148.15.55-r2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-opt-2 + +DESCRIPTION="Prediction of Protein Backbone and Sidechain Torsion Angles from NMR Chemical Shifts" +HOMEPAGE="http://spin.niddk.nih.gov/bax/software/TALOS-N/" +SRC_URI="http://spin.niddk.nih.gov/bax/software/TALOS-N/talosn.tZ -> ${P}.tgz" + +SLOT="0" +LICENSE="all-rights-reserved" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="examples" + +DEPEND=">=virtual/jre-1.5" +RDEPEND="${DEPEND} + app-shells/tcsh + sci-biology/ncbi-tools" + +S="${WORKDIR}" + +QA_PREBUILT="/opt/.*" + +src_prepare() { + local s64 + use amd64 || s64="_x64" + rm -f bin/TALOSN.{linux,mac,static.*,winxp,linux9${s64}} || die + + sed \ + -e '/setenv TALOSN_DIR/d' \ + -e "/set BLAST/s:=.*:= \"${EPREFIX}/usr/bin/blastpgp\":g" \ + -e '/set NR_DBNAME/s:=.*:= ${BLASTDB}:g' \ + -i talosn_ss || die +} + +src_install() { + local TALOSN="/opt/${PN}" + exeinto ${TALOSN}/bin + doexe bin/* + + exeinto ${TALOSN}/com + doexe com/* + + exeinto /opt/bin + doexe talosn{,_ss} + + insinto ${TALOSN} + doins -r tab + + java-pkg_jarinto ${TALOSN} + java-pkg_dojar rama.jar + + java-pkg_dolauncher jrama --jar rama.jar -into /opt/ + + if use examples; then + insinto /usr/share/${PN} + doins -r demo + fi + + cat >> "${T}"/40talosn <<- EOF + TALOSN_DIR="${EPREFIX}/${TALOSN}" + #BLASTDB= + EOF + doenvd "${T}"/40talosn +} 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/metadata.xml b/sci-chemistry/ucsf-tools/metadata.xml index 897aa2e6b..51fdedab1 100644 --- a/sci-chemistry/ucsf-tools/metadata.xml +++ b/sci-chemistry/ucsf-tools/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</herd> + <herd>sci-chemistry</herd> </pkgmetadata> 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-chemistry/unio/metadata.xml b/sci-chemistry/unio/metadata.xml index 86eeba133..9ac9ffdb3 100644 --- a/sci-chemistry/unio/metadata.xml +++ b/sci-chemistry/unio/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-chemistry</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-libs/Cgraph/metadata.xml b/sci-libs/Cgraph/metadata.xml index 4bf6dbc6b..b229aec85 100644 --- a/sci-libs/Cgraph/metadata.xml +++ b/sci-libs/Cgraph/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/bigdft-abi/ChangeLog b/sci-libs/bigdft-abi/ChangeLog new file mode 100644 index 000000000..8b17f1fa5 --- /dev/null +++ b/sci-libs/bigdft-abi/ChangeLog @@ -0,0 +1,29 @@ +# ChangeLog for sci-libs/bigdft-abi +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-abi-1.0.4.ebuild: + Filter LDFLAGS for cuda use not to break nvcc. + + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-abi-1.0.4.ebuild: + Added dev-util/gdbus-codegen to dependencies. + + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-abi-1.0.4.ebuild: + Spaces in the testing snippet of fortran code in + sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting. + + 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-abi-1.0.4.ebuild: + The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. + +*bigdft-abi-1.0.4 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + +bigdft-abi-1.0.4.ebuild, +files/bigdft-abi-1.0.4-tests.tar.bz2: + sci-libs/bigdft-abi-1.0.4 added. Replaces sci-libs/bigdft as a library of + sci-physics/abinit. Based on former sci-libs/bigdft ebuilds, usage of + LIBDIR/finclude abandoned in favour of /usr/include, as used upstream. + diff --git a/sci-libs/bigdft-abi/Manifest b/sci-libs/bigdft-abi/Manifest new file mode 100644 index 000000000..e8a8b973e --- /dev/null +++ b/sci-libs/bigdft-abi/Manifest @@ -0,0 +1 @@ +DIST bigdft-abi-1.0.4.tar.gz 8982260 SHA256 345cf49da92275710252d50b4ac8364f2f3c33e8f28d84d7b13ccf6fd0c69310 SHA512 556001d1ffd08be70b97f07a8a150d5d033a4611957180a7a25b41963754e0e3d2bb2a4e9d5b6beb8ff6fb1eb6f4ae9b51633cfe3d7f5a8ed20a85be21031c35 WHIRLPOOL b7c58732b538306f2b9b89b1310d9212cc1bb038fded782e6707e54679013ebc8376d54b5bd1bd51464dc7878fa05102fcba8f70a5d38b4571720c8d57ee3af1 diff --git a/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild new file mode 100644 index 000000000..51f1e48c6 --- /dev/null +++ b/sci-libs/bigdft-abi/bigdft-abi-1.0.4.ebuild @@ -0,0 +1,165 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_5 python2_6 python2_7 ) + +inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs + + +DESCRIPTION="A DFT electronic structure code using a wavelet basis set" +HOMEPAGE="http://www.abinit.org/downloads/plug-in-sources" +SRC_URI="http://forge.abinit.org/fallbacks/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" + +RDEPEND=" + >=sci-libs/libxc-1.2.0-r1[fortran] + virtual/blas + virtual/fortran + virtual/lapack + dev-libs/libyaml + mpi? ( virtual/mpi ) + cuda? ( dev-util/nvidia-cuda-sdk ) + opencl? ( virtual/opencl ) + etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) + netcdf? ( || ( + sci-libs/netcdf[fortran] + sci-libs/netcdf-fortran + ) + )" +DEPEND="${RDEPEND} + virtual/pkgconfig + >=sys-devel/autoconf-2.59 + doc? ( virtual/latex-base ) + ${PYTHON_DEPS} + dev-python/pyyaml[libyaml] + dev-util/gdbus-codegen + app-arch/tar + app-arch/gzip" + +DOCS=( README INSTALL ChangeLog AUTHORS NEWS ) + +FORTRAN_STANDARD=90 + +pkg_setup() { + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + else + tc-export FC F77 CC + fi + + # This should be correct. + # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. + # Should a bug be filed against toolchain-funcs.eclass? + # if use openmp; then + # tc-has-openmp || \ + # die "Please select an openmp capable compiler like gcc[openmp]" + # fi + # + # Luckily Abinit is a fortran package. + # fortran-2.eclass has its own test for OpenMP support, + # more general than toolchain-funcs.eclass + # The test itself proceeds inside fortran-2_pkg_setup + if use openmp; then FORTRAN_NEED_OPENMP=1; fi + + fortran-2_pkg_setup + python-any-r1_pkg_setup +} + +src_prepare() { + tar -xjf "${FILESDIR}"/"${P}"-tests.tar.bz2 -C "${S}"/tests/DFT/ + eautoreconf +} + +src_configure() { + local openmp="" + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local fcode=ebuild-openmp-flags.f + local _fc=$(tc-getFC) + + cat <<- EOF > "${fcode}" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${_fc} ${openmp} "${fcode}" -o "${fcode}.x" && break + done + + rm -f "${fcode}.*" + fi + local modules="${EPREFIX}/usr/include" +# local Imodules="-I${modules}" + local Imodules="" + local netcdff_libs="-lnetcdff" + filter-flags '-m*' '-O*' "-pipe" + local nvcflags="${CFLAGS}" + _filter-var nvcflags '-m*' '-O*' "-pipe" "-W*" + use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*" + local myeconfargs=( + $(use_enable mpi) + --enable-optimised-convolution + --enable-pseudo + --enable-libbigdft + --enable-binaries + --disable-minima-hopping + --disable-internal-libyaml + --enable-internal-libabinit + --with-moduledir="${modules}" + --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \ + $($(tc-getPKG_CONFIG) --libs-only-l blas)" + --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \ + $($(tc-getPKG_CONFIG) --libs-only-L blas)" + --with-libxc="yes" + --disable-internal-libxc + $(use_enable cuda cuda-gpu) + $(use_with cuda cuda-path /opt/cuda) + $(use_with cuda nvcc-flags "${nvcflags}") + $(use_enable opencl) + $(use_with etsf_io etsf-io) + "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" + PKG_CONFIG="$(tc-getPKG_CONFIG)" + FCFLAGS="${FCFLAGS} ${openmp} ${Imodules}" + LD="$(tc-getLD)" + CPP="$(tc-getCPP)" + ) + autotools-utils_src_configure +} + +src_compile() { + #autotools-utils_src_compile() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + emake -j1 + sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc + popd > /dev/null + + #autotools-utils_src_compile + use doc && autotools-utils_src_compile doc +} + +src_test() { + if use test; then + #autotools-utils_src_test() expanded + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + # Run default src_test as defined in ebuild.sh + cd tests + emake -j1 check + popd > /dev/null + fi +} + +src_install() { + autotools-utils_src_install +} diff --git a/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-tests.tar.bz2 b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-tests.tar.bz2 Binary files differnew file mode 100644 index 000000000..40f7ca5ac --- /dev/null +++ b/sci-libs/bigdft-abi/files/bigdft-abi-1.0.4-tests.tar.bz2 diff --git a/sci-libs/bigdft/metadata.xml b/sci-libs/bigdft/metadata.xml index 71f04f476..fcc220851 100644 --- a/sci-libs/bigdft/metadata.xml +++ b/sci-libs/bigdft/metadata.xml @@ -1,17 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="cuda">Add cuda support</flag> - </use> - <use> - <flag name="etsf_io">Undocumented USE</flag> - </use> - <use> - <flag name="opencl">Undocumented USE</flag> - </use> +<herd>sci</herd> +<use> + <flag name="cuda">Add cuda support</flag> + <flag name="etsf_io">Undocumented USE</flag> + <flag name="opencl">Undocumented USE</flag> +</use> </pkgmetadata> diff --git a/sci-libs/cnsface-scripts/metadata.xml b/sci-libs/cnsface-scripts/metadata.xml index efb490d78..b229aec85 100644 --- a/sci-libs/cnsface-scripts/metadata.xml +++ b/sci-libs/cnsface-scripts/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-libs/coinor-clp/ChangeLog b/sci-libs/coinor-clp/ChangeLog index 96afefed4..1d7d59e4b 100644 --- a/sci-libs/coinor-clp/ChangeLog +++ b/sci-libs/coinor-clp/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*coinor-clp-1.15.1 (19 Jun 2013) + + 19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +coinor-clp-1.15.1.ebuild, + +files/coinor-clp-1.15.1-mpi-header.patch, -coinor-clp-1.15.0.ebuild: + sci-libs/coinor-clp: Version bump and patch for mpi + *coinor-clp-1.15.0 (26 May 2013) 26 May 2013; Sébastien Fabbro <bicatali@gentoo.org> +coinor-clp-1.15.0.ebuild, diff --git a/sci-libs/coinor-clp/Manifest b/sci-libs/coinor-clp/Manifest index 64742b106..116810cc2 100644 --- a/sci-libs/coinor-clp/Manifest +++ b/sci-libs/coinor-clp/Manifest @@ -1 +1 @@ -DIST Clp-1.15.0.tgz 5587043 SHA256 e1a50e048f55b669a0858b3fc3abd0dfe52e24178ff62f7d168cb1bb3038e57d SHA512 03b5540cba4a274d8991c241095df033a24bb613b951849b35ce1e1d6162f20da59c6f81f31dd5a4f4b3ba504640822bdce8329d75b21a4c37d97032ff88175b WHIRLPOOL d53f8558dda965d769aee3cb280056094503e4f4b65cccbc9ed8bb9f0f8041f20e66c5944305ec3f0a9690200573af6037ba0105d7b9f2b860d58d25eb3f4203 +DIST Clp-1.15.1.tgz 5636624 SHA256 bd6ba2a0b96ff4bd91d8dad1ce1dfb60a730eae52eb9b9059d25effa4ec13b3d SHA512 59de666afc1143c621fed810c214c4f35e635f57bcade27c5be4da5844e6271f75e1df9a6ac6241ff374749a0607ccc8edc895cddfc26e5dbe8e73e88303deb8 WHIRLPOOL e0edeeec290549567308e17ec4bbb1ab7e48d27b31dd0defe324271850f134a7443e9351eedf259c762345adb8c0688021b149cbb2156ab767e06dcd7efff234 diff --git a/sci-libs/coinor-clp/coinor-clp-1.15.0.ebuild b/sci-libs/coinor-clp/coinor-clp-1.15.1.ebuild index a745ae296..a5630cb53 100644 --- a/sci-libs/coinor-clp/coinor-clp-1.15.0.ebuild +++ b/sci-libs/coinor-clp/coinor-clp-1.15.1.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit autotools-utils multilib toolchain-funcs +inherit autotools-utils eutils multilib toolchain-funcs MYPN=Clp @@ -39,7 +39,7 @@ src_prepare() { sed -i \ -e 's:\(libClp_la_LIBADD.*=\).*:\1 @CLPLIB_LIBS@:g' \ src/Makefile.in || die - + epatch "${FILESDIR}"/${P}-mpi-header.patch if has_version sci-libs/mumps[-mpi]; then ln -s "${EPREFIX}"/usr/include/mpiseq/mpi.h src/mpi.h elif has_version sci-libs/mumps[mpi]; then diff --git a/sci-libs/coinor-clp/files/coinor-clp-1.15.1-mpi-header.patch b/sci-libs/coinor-clp/files/coinor-clp-1.15.1-mpi-header.patch new file mode 100644 index 000000000..7ad03e8c7 --- /dev/null +++ b/sci-libs/coinor-clp/files/coinor-clp-1.15.1-mpi-header.patch @@ -0,0 +1,12 @@ +--- src/ClpCholeskyMumps.cpp.orig 2013-06-19 09:58:02.834485943 -0700 ++++ src/ClpCholeskyMumps.cpp 2013-06-19 09:57:39.013355095 -0700 +@@ -14,8 +14,8 @@ + #define USE_COMM_WORLD -987654 + extern "C" { + #include "dmumps_c.h" +-#include "mpi.h" + } ++#include "mpi.h" + + #include "ClpCholeskyMumps.hpp" + #include "ClpMessage.hpp" diff --git a/sci-libs/driftwood/metadata.xml b/sci-libs/driftwood/metadata.xml index efb490d78..9ac9ffdb3 100644 --- a/sci-libs/driftwood/metadata.xml +++ b/sci-libs/driftwood/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-libs/etsf_io/ChangeLog b/sci-libs/etsf_io/ChangeLog index 19ac5b64a..073dcb921 100644 --- a/sci-libs/etsf_io/ChangeLog +++ b/sci-libs/etsf_io/ChangeLog @@ -1,7 +1,18 @@ # ChangeLog for sci-libs/etsf_io -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + etsf_io-1.0.3-r2.ebuild: + The announced, but forgotten, change actually done. + +*etsf_io-1.0.3-r2 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -etsf_io-1.0.3-r1.ebuild, +etsf_io-1.0.3-r2.ebuild: + Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used + upstream. + *etsf_io-1.0.3-r1 (19 Jun 2012) 19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz> diff --git a/sci-libs/etsf_io/etsf_io-1.0.3-r1.ebuild b/sci-libs/etsf_io/etsf_io-1.0.3-r2.ebuild index a3c62340d..65827b343 100644 --- a/sci-libs/etsf_io/etsf_io-1.0.3-r1.ebuild +++ b/sci-libs/etsf_io/etsf_io-1.0.3-r2.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 inherit fortran-2 multilib @@ -32,5 +32,5 @@ src_configure() { $(use_enable examples build-tutorials) \ --prefix="${EPREFIX}/usr" \ --with-netcdf-ldflags="-L${EPREFIX}/usr/$(get_libdir) -lnetcdff" \ - --with-moduledir="${EPREFIX}/usr/$(get_libdir)/finclude" + --with-moduledir="${EPREFIX}/usr/include" } diff --git a/sci-libs/etsf_io/metadata.xml b/sci-libs/etsf_io/metadata.xml index d747d72a2..b229aec85 100644 --- a/sci-libs/etsf_io/metadata.xml +++ b/sci-libs/etsf_io/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/fox/ChangeLog b/sci-libs/fox/ChangeLog index 1d50ca61b..1945a75a1 100644 --- a/sci-libs/fox/ChangeLog +++ b/sci-libs/fox/ChangeLog @@ -1,7 +1,19 @@ # ChangeLog for sci-libs/fox -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + files/4.1.2-r2-install-customizations.patch: + The announced, but forgotten, change actually done. + +*fox-4.1.2-r2 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -fox-4.1.2-r1.ebuild, + +fox-4.1.2-r2.ebuild, -files/4.0.4-install-customizations.patch, + +files/4.1.2-r2-install-customizations.patch: + Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used by most + other packages. + 22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> fox-4.1.2-r1.ebuild: [sci-libs/fox] make it prefix aware diff --git a/sci-libs/fox/files/4.0.4-install-customizations.patch b/sci-libs/fox/files/4.1.2-r2-install-customizations.patch index 0ea77314c..15bb837f0 100644 --- a/sci-libs/fox/files/4.0.4-install-customizations.patch +++ b/sci-libs/fox/files/4.1.2-r2-install-customizations.patch @@ -6,10 +6,10 @@ diff -Naur tmp-old/Makefile tmp-new/Makefile # install: objsdir $(BUILD_TARGETS) - $(MKDIR_P) $(install_prefix)/lib $(install_prefix)/finclude $(install_prefix)/bin -+ $(MKDIR_P) $(install_prefix)/lib $(install_prefix)/lib/finclude $(install_prefix)/bin ++ $(MKDIR_P) $(install_prefix)/lib $(install_prefix)/include $(install_prefix)/bin $(INSTALL) objs/lib/* $(install_prefix)/lib - $(INSTALL) -m 644 objs/finclude/* $(install_prefix)/finclude -+ $(INSTALL) -m 644 objs/finclude/* $(install_prefix)/lib/finclude ++ $(INSTALL) -m 644 objs/finclude/* $(install_prefix)/include $(INSTALL) FoX-config $(install_prefix)/bin # examples_build: diff --git a/sci-libs/fox/fox-4.1.2-r1.ebuild b/sci-libs/fox/fox-4.1.2-r2.ebuild index 20856c8da..c856fcb2c 100644 --- a/sci-libs/fox/fox-4.1.2-r1.ebuild +++ b/sci-libs/fox/fox-4.1.2-r2.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 inherit eutils @@ -30,7 +30,7 @@ S="${WORKDIR}/${MY_P}" FORTRAN_STANDARD=90 src_prepare() { - epatch "${FILESDIR}"/4.0.4-install-customizations.patch + epatch "${FILESDIR}"/4.1.2-r2-install-customizations.patch } src_configure() { @@ -50,13 +50,13 @@ src_compile() { } src_test() { - emake -j1 check || die "make check failed" + emake -j1 check || ewarn "make check failed" einfo "Please look at the last few RESULT lines for a summary." } src_install() { sed -i -e's%^comp_prefix=.*$%comp_prefix=${EPREFIX}/usr%' \ - -e's%comp_prefix/finclude%comp_prefix/lib/finclude%' \ + -e's%comp_prefix/finclude%comp_prefix/include%' \ -e's%\$libdir/lib\([^ ]\+\)\.a\>%-l\1%g' \ -e's%\(echo\( -I"$moddir"\)\?\) \$LIBS%\1 -L"$libdir" $LIBS%' \ FoX-config diff --git a/sci-libs/fox/metadata.xml b/sci-libs/fox/metadata.xml index 0d10e1027..9f1573b8e 100644 --- a/sci-libs/fox/metadata.xml +++ b/sci-libs/fox/metadata.xml @@ -1,16 +1,13 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="dom">Compile the W3C document object model module</flag> - <flag name="fast">Compile with best known optimization flags</flag> - <flag name="sax">Compile the streaming, validating parser based on java's Simple API for XML</flag> - <flag name="wcml">Compile the module for a subset of the Chemical Markup Language</flag> - <flag name="wkml">Compile the module for the creation of KML documents used by applications such as Google Earth</flag> - <flag name="wxml">Compile the XML writer used to sequentially create arbitrary XML documents quickly with minimal memory requirements</flag> +<herd>sci</herd> +<use> + <flag name="dom">Compile the W3C document object model module</flag> + <flag name="fast">Compile with best known optimization flags</flag> + <flag name="sax">Compile the streaming, validating parser based on java's Simple API for XML</flag> + <flag name="wcml">Compile the module for a subset of the Chemical Markup Language</flag> + <flag name="wkml">Compile the module for the creation of KML documents used by applications such as Google Earth</flag> + <flag name="wxml">Compile the XML writer used to sequentially create arbitrary XML documents quickly with minimal memory requirements</flag> </use> </pkgmetadata> diff --git a/sci-libs/libxc/ChangeLog b/sci-libs/libxc/ChangeLog index 291d4ae5f..4bf38b928 100644 --- a/sci-libs/libxc/ChangeLog +++ b/sci-libs/libxc/ChangeLog @@ -1,7 +1,16 @@ # ChangeLog for sci-libs/libxc -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*libxc-2.0.1 (17 Jun 2013) +*libxc-1.2.0-r1 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -libxc-1.1.0-r1.ebuild, -libxc-1.2.0.ebuild, +libxc-1.2.0-r1.ebuild, + +libxc-2.0.1.ebuild, libxc-9999.ebuild: + Version bumped to 2.0.1. Usage of LIBDIR/finclude abandoned in favour of + /usr/include, as used upstream. Old files cleaned up. + 22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> libxc-1.1.0-r1.ebuild, libxc-1.2.0.ebuild: [sci-libs/libxc] add ~amd64-linux diff --git a/sci-libs/libxc/Manifest b/sci-libs/libxc/Manifest index fa863cf20..a85ebc898 100644 --- a/sci-libs/libxc/Manifest +++ b/sci-libs/libxc/Manifest @@ -1,2 +1,2 @@ -DIST libxc-1.1.0.tar.gz 543168 SHA256 b75fb2a73a9e2d75e250cc77b71d5485c8e9b11c3b25c91899c366e217283c57 SHA512 a5ed3a4a7a7abaa11321fe877d01ff00132eab976205213e578cd57fbd2073eea00ce3a3afc188e30ebbd31deb32468c4472313df9992e8d9e3148e6f619936b WHIRLPOOL 8ff70acb2ee65b3373942b71e350fe146f1c205aa4c09dbb22adc04227ba6888482ce412b3e843a9402efd51f9cf6f478f9c65b97305b2035185e59b35484d9f DIST libxc-1.2.0.tar.gz 895527 SHA256 ee441c3cde2e2bd87828186aa17f6e4438d17b38634c5d29bb12d3b7554461fb SHA512 3ac0fd07e40db4feb0f0a4ebe1358fdd4de0fff21f6dd369895c658a14cd3bafedbbc374b89f68320401dfcfe16a6230e05403fdaccfcbebb98349ca06593125 WHIRLPOOL 66439bf65a656567c0e52a4ee20b206658a9185bdbd3e045daca00bf01ba0199ccbedea3e5034cf90fbc36dbc04d9666cde8bde46e2577ffd160800f1718bd2a +DIST libxc-2.0.1.tar.gz 1062846 SHA256 c332f08648ec2bc7ccce83e45a84776215aa5dfebc64fae2a23f2ac546d41ea4 SHA512 c7d87134911fdfd91d985397a3fa990a63cc05d0752f0e2522e41dae0c2f39c43f9bd87ee6eb1972ab92b1aedeefad55a33ad84b1c66032e61ca03c87db02c5b WHIRLPOOL 16a5b999bb60177fde1371421f41f35736af4fcf8df123318ea438ffd34f487dcbadc95124ab9cf6ab2edeadd7983c56e0ca9d84bf528254de1f2a003addd402 diff --git a/sci-libs/libxc/libxc-1.2.0.ebuild b/sci-libs/libxc/libxc-1.2.0-r1.ebuild index 0d9fc78f4..7f4ab188d 100644 --- a/sci-libs/libxc/libxc-1.2.0.ebuild +++ b/sci-libs/libxc/libxc-1.2.0-r1.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 inherit autotools-utils fortran-2 multilib @@ -15,7 +15,7 @@ SRC_URI="http://www.tddft.org/programs/octopus/download/${PN}/${P}.tar.gz" LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="fortran static-libs" +IUSE="fortran static-libs -test" S="${WORKDIR}"/${MY_P} @@ -37,17 +37,19 @@ src_configure() { ## Upstream recommends not running the test suite because it requires ## human expert interpretation to determine whether output is an error or ## expected under certain circumstances. -# src_test() { :; } +# The autotools src_test function modified not to die. Runs emake check in build directory. +src_test() { + debug-print-function ${FUNCNAME} "$@" + + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + ewarn "This will fail if any test fails, no matter how dealt with in the ebuild." + make check || ewarn "Make check failed. See above for details." + einfo "emake check done" + popd > /dev/null || die +} src_install() { autotools-utils_src_install - if use fortran; then - # argument for this: --with-moduledir from etsf_io/bigdft - insinto /usr/$(get_libdir)/finclude - pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null - doins *.mod || die - rm -f "${D}"/usr/include/*.mod || die - popd >/dev/null - fi } diff --git a/sci-libs/libxc/libxc-1.1.0-r1.ebuild b/sci-libs/libxc/libxc-2.0.1.ebuild index 0d9fc78f4..47b17a3da 100644 --- a/sci-libs/libxc/libxc-1.1.0-r1.ebuild +++ b/sci-libs/libxc/libxc-2.0.1.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 inherit autotools-utils fortran-2 multilib @@ -15,7 +15,7 @@ SRC_URI="http://www.tddft.org/programs/octopus/download/${PN}/${P}.tar.gz" LICENSE="LGPL-3" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux" -IUSE="fortran static-libs" +IUSE="fortran static-libs -test" S="${WORKDIR}"/${MY_P} @@ -36,18 +36,19 @@ src_configure() { ## Upstream recommends not running the test suite because it requires ## human expert interpretation to determine whether output is an error or -## expected under certain circumstances. -# src_test() { :; } +## expected under certain circumstances. Nevertheless, experts might want the option. +# The autotools src_test function modified not to die. Runs emake check in build directory. +src_test() { + debug-print-function ${FUNCNAME} "$@" + + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + make check || ewarn "Make check failed. See above for details." + einfo "emake check done" + popd > /dev/null || die +} src_install() { autotools-utils_src_install - if use fortran; then - # argument for this: --with-moduledir from etsf_io/bigdft - insinto /usr/$(get_libdir)/finclude - pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null - doins *.mod || die - rm -f "${D}"/usr/include/*.mod || die - popd >/dev/null - fi } diff --git a/sci-libs/libxc/libxc-9999.ebuild b/sci-libs/libxc/libxc-9999.ebuild index baf29d429..2432915ed 100644 --- a/sci-libs/libxc/libxc-9999.ebuild +++ b/sci-libs/libxc/libxc-9999.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 inherit autotools-utils fortran-2 multilib subversion @@ -14,7 +14,7 @@ ESVN_BOOTSTRAP="eautoreconf -i" LICENSE="LGPL-3" SLOT="0" KEYWORDS="" -IUSE="fortran static-libs" +IUSE="fortran static-libs -test" MAKEOPTS+=" -j1" @@ -31,14 +31,21 @@ src_configure() { autotools-utils_src_configure } +## Upstream recommends not running the test suite because it requires +## human expert interpretation to determine whether output is an error or +## expected under certain circumstances. Nevertheless, experts might want the option. +# The autotools src_test function modified not to die. Runs emake check in build directory. +src_test() { + debug-print-function ${FUNCNAME} "$@" + + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + make check || ewarn "Make check failed. See above for details." + einfo "emake check done" + popd > /dev/null || die +} + src_install() { autotools-utils_src_install - if use fortran; then - insinto /usr/$(get_libdir)/finclude - pushd "${AUTOTOOLS_BUILD_DIR}"/src >/dev/null - doins *.mod || die - rm -f "${D}"/usr/include/*.mod || die - popd >/dev/null - fi } diff --git a/sci-libs/libxc/metadata.xml b/sci-libs/libxc/metadata.xml index d747d72a2..b229aec85 100644 --- a/sci-libs/libxc/metadata.xml +++ b/sci-libs/libxc/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> 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/med/metadata.xml b/sci-libs/med/metadata.xml index 3e42177c3..b229aec85 100644 --- a/sci-libs/med/metadata.xml +++ b/sci-libs/med/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <!--<maintainer>--> - <!-- <email>sci@gentoo.org</email>--> - <!--</maintainer>--> +<herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/msms/metadata.xml b/sci-libs/msms/metadata.xml index d747d72a2..9ac9ffdb3 100644 --- a/sci-libs/msms/metadata.xml +++ b/sci-libs/msms/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-chemistry</herd> </pkgmetadata> diff --git a/sci-libs/mumps/ChangeLog b/sci-libs/mumps/ChangeLog index 6eba45347..46b5d6d03 100644 --- a/sci-libs/mumps/ChangeLog +++ b/sci-libs/mumps/ChangeLog @@ -1,7 +1,10 @@ # ChangeLog for sci-libs/mumps -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 17 Jun 2013; Justin Bronder <jsbronder@gentoo.org> mumps-4.10.0-r2.ebuild: + Don't let openmpi override malloc, works around sandbox issue in #462602 + *mumps-4.10.0-r2 (11 Dec 2012) 11 Dec 2012; Sébastien Fabbro <bicatali@gentoo.org> +mumps-4.10.0-r2.ebuild, diff --git a/sci-libs/mumps/mumps-4.10.0-r2.ebuild b/sci-libs/mumps/mumps-4.10.0-r2.ebuild index 0d63d75cf..0aa195e30 100644 --- a/sci-libs/mumps/mumps-4.10.0-r2.ebuild +++ b/sci-libs/mumps/mumps-4.10.0-r2.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2012 Gentoo Foundation +# Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 # $Header: $ @@ -122,6 +122,9 @@ src_configure() { } src_compile() { + # Workaround #462602 + export FAKEROOTKEY=1 + # -j1 because of static archive race emake -j1 alllib PIC="-fPIC" if ! use mpi; then diff --git a/sci-libs/pagmo/metadata.xml b/sci-libs/pagmo/metadata.xml index ce5ca8e2f..f406e118a 100644 --- a/sci-libs/pagmo/metadata.xml +++ b/sci-libs/pagmo/metadata.xml @@ -1,12 +1,9 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="kepler">Automatically generated description for kepler</flag> - <flag name="nlopt">Automatically generated description for nlopt</flag> - </use> +<herd>sci-astronomy</herd> +<use> + <flag name="kepler">Automatically generated description for kepler</flag> + <flag name="nlopt">Automatically generated description for nlopt</flag> +</use> </pkgmetadata> diff --git a/sci-libs/starparse/metadata.xml b/sci-libs/starparse/metadata.xml index 4bf6dbc6b..b229aec85 100644 --- a/sci-libs/starparse/metadata.xml +++ b/sci-libs/starparse/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/trilinos/ChangeLog b/sci-libs/trilinos/ChangeLog index c05bfebf0..7f1ee3d96 100644 --- a/sci-libs/trilinos/ChangeLog +++ b/sci-libs/trilinos/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*trilinos-11.2.3 (19 Jun 2013) + + 19 Jun 2013; Sébastien Fabbro <bicatali@gentoo.org> +trilinos-11.2.3.ebuild, + metadata.xml: + sci-libs/trilinos: Version bump and rewrite + 12 Jun 2013; Justin Lecher <jlec@gentoo.org> -trilinos-10.10.1.ebuild, trilinos-11.0.3.ebuild: Drop old, fix handling of qt support @@ -25,4 +31,3 @@ 8 Apr 2012; Andrea Arteaga <andyspiros@gmail.com> +trilinos-10.10.1.ebuild +metadata.xml: Initial ebuild. - diff --git a/sci-libs/trilinos/metadata.xml b/sci-libs/trilinos/metadata.xml index fbde4bfd0..46351c51e 100644 --- a/sci-libs/trilinos/metadata.xml +++ b/sci-libs/trilinos/metadata.xml @@ -11,14 +11,30 @@ of large-scale, complex multi-physics engineering and scientific problems. </longdescription> <use> + <flag name="adolc">Undocumented USE</flag> <flag name="arprec">Undocumented USE</flag> <flag name="boost">Undocumented USE</flag> + <flag name="clp">Undocumented USE</flag> + <flag name="cppunit">Undocumented USE</flag> <flag name="cuda">Undocumented USE</flag> + <flag name="eigen">Undocumented USE</flag> + <flag name="glpk">Undocumented USE</flag> + <flag name="gtest">Undocumented USE</flag> <flag name="hwloc">Undocumented USE</flag> + <flag name="hypre">Undocumented USE</flag> + <flag name="metis">Undocumented USE</flag> + <flag name="mkl">Undocumented USE</flag> + <flag name="mumps">Undocumented USE</flag> + <flag name="petsc">Undocumented USE</flag> <flag name="qd">Undocumented USE</flag> + <flag name="scalapack">Undocumented USE</flag> <flag name="scotch">Undocumented USE</flag> + <flag name="sparse">Undocumented USE</flag> + <flag name="superlu">Undocumented USE</flag> <flag name="taucs">Undocumented USE</flag> <flag name="tbb">Undocumented USE</flag> + <flag name="tvmet">Undocumented USE</flag> <flag name="umfpack">Undocumented USE</flag> + <flag name="yaml">Undocumented USE</flag> </use> </pkgmetadata> diff --git a/sci-libs/trilinos/trilinos-11.2.3.ebuild b/sci-libs/trilinos/trilinos-11.2.3.ebuild new file mode 100644 index 000000000..b22fa5882 --- /dev/null +++ b/sci-libs/trilinos/trilinos-11.2.3.ebuild @@ -0,0 +1,186 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit cmake-utils toolchain-funcs multilib toolchain-funcs + +DESCRIPTION="Scientific library collection for large scale problems" +HOMEPAGE="http://trilinos.sandia.gov/" +SRC_URI="${P}-Source.tar.bz2" + +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +LICENSE="BSD LGPL-2.1" +SLOT="0" + +IUSE=" + adolc arprec boost clp cppunit cuda eigen glpk gtest + hdf5 hwloc hypre metis mkl mumps netcdf petsc qd qt4 + scalapack scotch sparse superlu taucs tbb test threads + tvmet yaml zlib +" + +# TODO: fix export cmake function for tests +RESTRICT="test" + +RDEPEND=" + virtual/blas + virtual/lapack + virtual/mpi + adolc? ( sci-libs/adolc ) + arprec? ( sci-libs/arprec ) + boost? ( dev-libs/boost ) + clp? ( sci-libs/coinor-clp ) + cuda? ( >=dev-util/nvidia-cuda-toolkit-3.2 ) + eigen? ( dev-cpp/eigen:3 ) + gtest? ( dev-cpp/gtest ) + hdf5? ( sci-libs/hdf5[mpi] ) + hypre? ( sci-libs/hypre ) + hwloc? ( sys-apps/hwloc ) + mkl? ( sci-libs/mkl ) + metis? ( || ( sci-libs/parmetis sci-libs/metis ) ) + mumps? ( sci-libs/mumps ) + netcdf? ( sci-libs/netcdf ) + petsc? ( sci-libs/petsc ) + qd? ( sci-libs/qd ) + qt4? ( dev-qt/qtgui:4 ) + scalapack? ( virtual/scalapack ) + scotch? ( sci-libs/scotch ) + sparse? ( sci-libs/cxsparse sci-libs/umfpack ) + superlu? ( sci-libs/superlu ) + taucs? ( sci-libs/taucs ) + tbb? ( dev-cpp/tbb ) + tvmet? ( dev-libs/tvmet ) + yaml? ( dev-cpp/yaml-cpp ) + zlib? ( sys-libs/zlib )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${P}-Source" + +trilinos_conf() { + local dirs libs d + for d in $($(tc-getPKG_CONFIG) --libs-only-L $1); do + dirs="${dirs};${d:2}" + done + [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_DIRS=${dirs:1}" ) + for d in $($(tc-getPKG_CONFIG) --libs-only-l $1); do + libs="${libs};${d:2}" + done + [[ -n ${libs} ]] && mycmakeargs+=( "-D${2}_LIBRARY_NAMES=${libs:1}" ) + dirs="" + for d in $($(tc-getPKG_CONFIG) --cflags-only-I $1); do + dirs="${dirs};${d:2}" + done + [[ -n ${dirs} ]] && mycmakeargs+=( "-D${2}_INCLUDE_DIRS=${dirs:1}" ) +} + +trilinos_enable() { + cmake-utils_use $1 TPL_ENABLE_${2:-${1^^}} +} + +src_configure() { + + local mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DCMAKE_INSTALL_PREFIX="${EPREFIX}" + -DTrilinos_ENABLE_ALL_PACKAGES=ON + -DTrilinos_INSTALL_INCLUDE_DIR="${EPREFIX}/usr/include/trilinos" + -DTrilinos_INSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)/trilinos" + -DTPL_ENABLE_BinUtils=ON + -DTPL_ENABLE_MPI=ON + -DTPL_ENABLE_BLAS=ON + -DTPL_ENABLE_LAPACK=ON + $(cmake-utils_use test Trilinos_ENABLE_TESTS) + $(trilinos_enable adolc) + $(trilinos_enable arprec) + $(trilinos_enable boost Boost) + $(trilinos_enable boost BoostLib) + $(trilinos_enable cppunit Cppunit) + $(trilinos_enable clp Clp) + $(trilinos_enable cuda) + $(trilinos_enable cuda CUSPARSE) + $(trilinos_enable cuda Thrust) + $(trilinos_enable eigen Eigen) + $(trilinos_enable gtest gtest) + $(trilinos_enable glpk) + $(trilinos_enable hdf5) + $(trilinos_enable hwloc) + $(trilinos_enable hypre) + $(trilinos_enable metis) + $(trilinos_enable mkl) + $(trilinos_enable mkl PARDISO_MKL) + $(trilinos_enable mumps) + $(trilinos_enable netcdf Netcdf) + $(trilinos_enable petsc) + $(trilinos_enable qd) + $(trilinos_enable qt4 QT) + $(trilinos_enable scalapack) + $(trilinos_enable scalapack BLACS) + $(trilinos_enable scotch Scotch) + $(trilinos_enable sparse AMD) + $(trilinos_enable sparse CSparse) + $(trilinos_enable sparse UMFPACK) + $(trilinos_enable superlu SuperLU) + $(trilinos_enable taucs) + $(trilinos_enable tbb) + $(trilinos_enable threads Pthread) + $(trilinos_enable tvmet) + $(trilinos_enable yaml yaml-cpp) + $(trilinos_enable zlib Zlib) + ) + + use eigen && \ + mycmakeargs+=( + -DEigen_INCLUDE_DIRS="${EPREFIX}/usr/include/eigen3" + ) + use hypre && \ + mycmakeargs+=( + -DHYPRE_INCLUDE_DIRS="${EPREFIX}/usr/include/hypre" + ) + use scotch && \ + mycmakeargs+=( + -DScotch_INCLUDE_DIRS="${EPREFIX}/usr/include/scotch" + ) + + # cxsparse is a rewrite of csparse + extras + use sparse && \ + mycmakeargs+=( + -DCSparse_LIBRARY_NAMES="cxsparse" + ) + + # mandatory blas and lapack + trilinos_conf blas BLAS + trilinos_conf lapack LAPACK + use superlu && trilinos_conf superlu SuperLU + use metis && trilinos_conf metis METIS + + # blacs library is included in scalapack these days + if use scalapack; then + trilinos_conf scalapack SCALAPACK + mycmakeargs+=( + -DBLACS_LIBRARY_NAMES="scalapack" + -DBLACS_INCLUDE_DIRS="${EPREFIX}/usr/include/blacs" + ) + fi + + # TODO: do we need that line? + export CC=mpicc CXX=mpicxx && tc-export CC CXX + + # cmake-utils eclass patches the base directory CMakeLists.txt + # which does not work for complex Trilinos CMake modules + CMAKE_BUILD_TYPE=RELEASE cmake-utils_src_configure + + # TODO: + # python bindings with python-r1 + # fix hypre bindings + # fix hdf5 + # cuda/thrust is untested + # do we always need mpi? and for all packages: blah[mpi] ? + # install docs, examples + # see what packages are related, do we need REQUIRED_USE + # proper use flags description + # add more use flags/packages ? +} diff --git a/sci-libs/wannier90/ChangeLog b/sci-libs/wannier90/ChangeLog index dfe5c7a0c..bb0da8817 100644 --- a/sci-libs/wannier90/ChangeLog +++ b/sci-libs/wannier90/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*wannier90-1.2-r1 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -wannier90-1.2.ebuild, +wannier90-1.2-r1.ebuild: + Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used by most + packages. + 22 Feb 2013; Justin Lecher <jlec@gentoo.org> wannier90-1.2.ebuild, metadata.xml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml index 4bf6dbc6b..b229aec85 100644 --- a/sci-libs/wannier90/metadata.xml +++ b/sci-libs/wannier90/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/sci-libs/wannier90/wannier90-1.2.ebuild b/sci-libs/wannier90/wannier90-1.2-r1.ebuild index 252792245..252792245 100644 --- a/sci-libs/wannier90/wannier90-1.2.ebuild +++ b/sci-libs/wannier90/wannier90-1.2-r1.ebuild diff --git a/sci-mathematics/alt-ergo/metadata.xml b/sci-mathematics/alt-ergo/metadata.xml index 02dfb1fc6..70209e070 100644 --- a/sci-mathematics/alt-ergo/metadata.xml +++ b/sci-mathematics/alt-ergo/metadata.xml @@ -1,19 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Alt-Ergo is an open source automatic theorem prover dedicated to program verification. - It is an SMT solver based on CC(X): a congruence closure algorithm parameterized by an - equational theory X. Alt-Ergo is based on a home-made SAT-solver and implements an - instantiation mechanism for quantified formulas. Its architecture is summarized by the - the following picture. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="gtk">?gtk?</flag> - <flag name="ocamlopt">?ocamlopt?</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + Alt-Ergo is an open source automatic theorem prover dedicated to program verification. + It is an SMT solver based on CC(X): a congruence closure algorithm parameterized by an + equational theory X. Alt-Ergo is based on a home-made SAT-solver and implements an + instantiation mechanism for quantified formulas. Its architecture is summarized by the + the following picture. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/apron/metadata.xml b/sci-mathematics/apron/metadata.xml index 49895e201..75f2ae704 100644 --- a/sci-mathematics/apron/metadata.xml +++ b/sci-mathematics/apron/metadata.xml @@ -1,21 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - The APRON library is dedicated to the static analysis of the numerical - variables of a program by Abstract Interpretation. The aim of such an - analysis is to infer invariants about these variables. The APRON library - is intended to be a common interface to various underlying - libraries/abstract domains and to provide additional services that can - be implemented independently from the underlying library/abstract - domain, as shown by the poster on the right (presented at the SAS 2007 - conference. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="ppl">Enable optional interface to the Parma Polyhedra Library</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + The APRON library is dedicated to the static analysis of the numerical + variables of a program by Abstract Interpretation. The aim of such an + analysis is to infer invariants about these variables. The APRON library + is intended to be a common interface to various underlying + libraries/abstract domains and to provide additional services that can + be implemented independently from the underlying library/abstract + domain, as shown by the poster on the right (presented at the SAS 2007 + conference. +</longdescription> +<use> + <flag name="ppl">Enable optional interface to the Parma Polyhedra Library</flag> +</use> </pkgmetadata> diff --git a/sci-mathematics/flocq/metadata.xml b/sci-mathematics/flocq/metadata.xml index 03b6dd3bd..dad568b86 100644 --- a/sci-mathematics/flocq/metadata.xml +++ b/sci-mathematics/flocq/metadata.xml @@ -1,14 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Flocq (Floats for Coq) is a floating-point formalization for the Coq - system. It provides a comprehensive library of theorems on a multi-radix - multi-precision arithmetic. It also supports efficient numerical - computations inside Coq. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-mathematics</herd> +<longdescription> + Flocq (Floats for Coq) is a floating-point formalization for the Coq + system. It provides a comprehensive library of theorems on a multi-radix + multi-precision arithmetic. It also supports efficient numerical + computations inside Coq. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/frama-c/metadata.xml b/sci-mathematics/frama-c/metadata.xml index 59797bca3..e429e6192 100644 --- a/sci-mathematics/frama-c/metadata.xml +++ b/sci-mathematics/frama-c/metadata.xml @@ -1,22 +1,14 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Frama-C is a suite of tools dedicated to the analysis of the source code - of software written in C. It gathers several static analysis techniques - in a single collaborative framework. The collaborative approach of - Frama-C allows static analyzers to build upon the results already - computed by other analyzers in the framework. Thanks to this approach, - Frama-C provides sophisticated tools, such as a slicer and dependency - analysis. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="doc">?doc?</flag> - <flag name="gtk">?gtk?</flag> - <flag name="ocamlopt">?ocamlopt?</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + Frama-C is a suite of tools dedicated to the analysis of the source code + of software written in C. It gathers several static analysis techniques + in a single collaborative framework. The collaborative approach of + Frama-C allows static analyzers to build upon the results already + computed by other analyzers in the framework. Thanks to this approach, + Frama-C provides sophisticated tools, such as a slicer and dependency + analysis. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/gap-guava/metadata.xml b/sci-mathematics/gap-guava/metadata.xml index e8b1fe068..5a2f1c7b8 100644 --- a/sci-mathematics/gap-guava/metadata.xml +++ b/sci-mathematics/gap-guava/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-mathematics</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-mathematics</herd> </pkgmetadata> diff --git a/sci-mathematics/gappa/metadata.xml b/sci-mathematics/gappa/metadata.xml index 5f9d1b74f..2b01d6b84 100644 --- a/sci-mathematics/gappa/metadata.xml +++ b/sci-mathematics/gappa/metadata.xml @@ -1,18 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Gappa is a tool intended to help verifying and formally proving - properties on numerical programs dealing with floating-point or - fixed-point arithmetic. It has been used to write robust floating-point - filters for CGAL and it is used to certify elementary functions in - CRlibm. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="doc">?doc?</flag> - </use> +<herd>sci-mathematics</herd> +<longdescription> + Gappa is a tool intended to help verifying and formally proving + properties on numerical programs dealing with floating-point or + fixed-point arithmetic. It has been used to write robust floating-point + filters for CGAL and it is used to certify elementary functions in + CRlibm. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/gappalib-coq/metadata.xml b/sci-mathematics/gappalib-coq/metadata.xml index f2cbd1ccf..657327897 100644 --- a/sci-mathematics/gappalib-coq/metadata.xml +++ b/sci-mathematics/gappalib-coq/metadata.xml @@ -1,13 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - While Gappa is intended to be used directly, it can also act as a - backend prover for the Why software verification plateform or as an - automatic tactic for the Coq proof assistant. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-mathematics</herd> +<longdescription> + While Gappa is intended to be used directly, it can also act as a + backend prover for the Why software verification plateform or as an + automatic tactic for the Coq proof assistant. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/giac/metadata.xml b/sci-mathematics/giac/metadata.xml index c28cb6d59..f2342ef59 100644 --- a/sci-mathematics/giac/metadata.xml +++ b/sci-mathematics/giac/metadata.xml @@ -1,20 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Giac is a free computer algebra system that can be used to perform - computer algebra, function graphs, interactive geometry (2-d and 3-d), - spreadsheet and statistics, programmation. It may be used as a replacement - for high end graphic calculators for example on netbooks (for about - the same price as a calculator but with much more performances). - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="doc">?doc?</flag> - <flag name="examples">?examples?</flag> - <flag name="fltk">?fltk?</flag> - </use> +<herd>sci</herd> +<longdescription> + Giac is a free computer algebra system that can be used to perform + computer algebra, function graphs, interactive geometry (2-d and 3-d), + spreadsheet and statistics, programmation. It may be used as a replacement + for high end graphic calculators for example on netbooks (for about + the same price as a calculator but with much more performances). +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/ltl2ba/metadata.xml b/sci-mathematics/ltl2ba/metadata.xml index efb490d78..b229aec85 100644 --- a/sci-mathematics/ltl2ba/metadata.xml +++ b/sci-mathematics/ltl2ba/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> diff --git a/sci-mathematics/pff/metadata.xml b/sci-mathematics/pff/metadata.xml index 03cc14266..0a23bf26c 100644 --- a/sci-mathematics/pff/metadata.xml +++ b/sci-mathematics/pff/metadata.xml @@ -1,14 +1,11 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - PFF (Preuves Formelles sur les Flottants = Formal Proofs about Floats) - is a repository of a Coq library about floating-point arithmetic. It - contains both definitions and proofs of basic facts, old and new - properties and algorithms. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-mathematics</herd> +<longdescription> + PFF (Preuves Formelles sur les Flottants = Formal Proofs about Floats) + is a repository of a Coq library about floating-point arithmetic. It + contains both definitions and proofs of basic facts, old and new + properties and algorithms. +</longdescription> </pkgmetadata> diff --git a/sci-mathematics/why/metadata.xml b/sci-mathematics/why/metadata.xml index 1aaaa1bfb..43f4d4f50 100644 --- a/sci-mathematics/why/metadata.xml +++ b/sci-mathematics/why/metadata.xml @@ -1,23 +1,19 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <longdescription> - Why is a software verification platform. It contains a general-purpose - verification condition generator (VCG) which is used as a back-end - by other verification tools but it can also be used directly to verify - programs. It also provides Krakatoa, a tool or the verification of Java - programs and Caduceus, a tool for the verification of C programs. - </longdescription> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="apron">?apron?</flag> - <flag name="coq">?coq?</flag> - <flag name="gappa">?gappa?</flag> - <flag name="jessie">?jessie?</flag> - <flag name="gtk">?gtk?</flag> - <flag name="pff">?pff?</flag> +<herd>sci-mathematics</herd> +<longdescription> + Why is a software verification platform. It contains a general-purpose + verification condition generator (VCG) which is used as a back-end + by other verification tools but it can also be used directly to verify + programs. It also provides Krakatoa, a tool or the verification of Java + programs and Caduceus, a tool for the verification of C programs. +</longdescription> +<use> + <flag name="apron">Support for <pkg>sci-mathematics/apron</pkg></flag> + <flag name="coq">Support for <pkg>sci-mathematics/coq</pkg></flag> + <flag name="gappa">Support for <pkg>sci-mathematics/gappa</pkg></flag> + <flag name="jessie">Support for <pkg>sci-mathematics/frama-c</pkg></flag> + <flag name="pff">Support for <pkg>sci-mathematics/pff</pkg></flag> </use> </pkgmetadata> diff --git a/sci-physics/LoopTools/metadata.xml b/sci-physics/LoopTools/metadata.xml index 8752705f7..9f73933b9 100644 --- a/sci-physics/LoopTools/metadata.xml +++ b/sci-physics/LoopTools/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-physics</herd> <maintainer> <email>maintainer-wanted@gentoo.org</email> </maintainer> diff --git a/sci-physics/abinit/ChangeLog b/sci-physics/abinit/ChangeLog index 72028dd6b..a46d8e53a 100644 --- a/sci-physics/abinit/ChangeLog +++ b/sci-physics/abinit/ChangeLog @@ -2,6 +2,22 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 20 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + +files/6.12.3-gui-makefiles.tbz: + files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake. + + 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> abinit-7.2.2.ebuild: + The dependency on sci-libs/libxc modified to allow for 1.2.0-r1. + +*abinit-7.2.2 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> -abinit-7.0.4.ebuild, + -abinit-7.0.5.ebuild, +abinit-7.2.2.ebuild, -files/6.0.3-fftw.patch, + -files/6.12.1-libabinit_options.patch, -files/6.12.3-gui-makefiles.tbz: + Version bumped to 7.2.2. Switched from sci-libs/bigdft to + sci-libs/bigdft-abi. Usage of LIBDIR/finclude abandoned in favour of + /usr/include, as used upstream. Old files cleaned up. + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> -abinit-6.12.3-r2.ebuild: Drop old diff --git a/sci-physics/abinit/Manifest b/sci-physics/abinit/Manifest index dee036578..f000cdcd5 100644 --- a/sci-physics/abinit/Manifest +++ b/sci-physics/abinit/Manifest @@ -1,2 +1 @@ -DIST abinit-7.0.4.tar.gz 61715030 SHA256 b3ad895b75b92b3ff05e873d42d0b26f6e6113b9de4579966f7b6d1b49d6004e SHA512 8edfe4019c968e6f912d0678fe331fc8a6ce2848f1b16973336d4181d010a776ed1ea2c5500499dac895d9d773d72165e20524705cf8928f91ede873272b0417 WHIRLPOOL 35da8681a68e435b460a11112e6cf6990fdf141d53d5849be45225d50e803e2bfc65cb05e5e576c704411be5734e47ed2e4ccca1fd1689311bd4febea937f0f8 -DIST abinit-7.0.5.tar.gz 61711550 SHA256 b16556aa05448781d872ab18f76ca6446a52be9eeed8d22015a0b63f4adf0f54 SHA512 007292cc7cdf459a5d62e907b29009d9496955952b5f491fa9183a5abb86dbf48020eb435b784d74037e381d65d2255a2b9a130322ee9bfecbff8ca075488ecd WHIRLPOOL 74d83a3a05817eaca402ace1b7ec3c3a6db3697a7ca0166549aee8155edfa2a7c8d516e2ae210a6f0e855f72617d704785bbb10e3a3ee262140964913608a307 +DIST abinit-7.2.2.tar.gz 63683267 SHA256 96f83e3af63e993cb886d9d6cd1c4fac04d50b5e460d5620330441050a909533 SHA512 fbc4898ae4625e12ea22d8f2da63e037eb947320fedf800bd40bd7e0015633ce54b7cb224cee3fc931d015774c51df5f8594ebe26a409cb0325e7a3ab0bf5e4a WHIRLPOOL a149d7ecea9b2b19b94b4e873f1924ce5fe221e037c642d6428727b552dc0c428b288551dda708286995da26080171c385a3ef3ad3766e065073139d4ef0f2e8 diff --git a/sci-physics/abinit/abinit-7.0.5.ebuild b/sci-physics/abinit/abinit-7.0.5.ebuild deleted file mode 100644 index 3bfaa809f..000000000 --- a/sci-physics/abinit/abinit-7.0.5.ebuild +++ /dev/null @@ -1,356 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 - -inherit autotools-utils eutils flag-o-matic fortran-2 multilib toolchain-funcs - -DESCRIPTION="Find total energy, charge density and electronic structure using density functional theory" -HOMEPAGE="http://www.abinit.org/" -SRC_URI="http://ftp.abinit.org/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc" - -RDEPEND="~sci-libs/bigdft-1.7_pre12 - =sci-libs/libxc-1*[fortran] - sci-physics/atompaw[libxc] - etsf_io? ( sci-libs/etsf_io ) - fox? ( >=sci-libs/fox-4.1.2-r1[sax] ) - netcdf? ( - || ( - sci-libs/netcdf[fortran] - sci-libs/netcdf-fortran - ) - hdf5? ( - sci-libs/netcdf[hdf5] - ) - ) - hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 - virtual/blas - virtual/lapack - gsl? ( sci-libs/gsl ) - fftw? ( - sci-libs/fftw:3.0 - fftw-threads? ( sci-libs/fftw:3.0[threads] ) - ) - mpi? ( virtual/mpi ) - python? ( dev-python/numpy ) - cuda? ( dev-util/nvidia-cuda-sdk )" -DEPEND="${RDEPEND} - virtual/pkgconfig - gui? ( >=virtual/jdk-1.6.0 - app-arch/sharutils - sys-apps/gawk ) - dev-perl/Text-Markdown" - -S=${WORKDIR}/${P%[a-z]} - -lat1loc="" - -DOCS=( AUTHORS ChangeLog COPYING INSTALL KNOWN_PROBLEMS NEWS PACKAGING - README README.ChangeLog README.GPU README.xlf RELNOTES THANKS ) - -FORTRAN_STANDARD=90 - -pkg_setup() { - # Doesn't compile with gcc-4.0, only >=4.1 - if [[ $(tc-getFC) == *gfortran ]]; then - if [[ $(gcc-major-version) -eq 4 ]] \ - && [[ $(gcc-minor-version) -lt 1 ]]; then - die "Requires gcc-4.1 or newer" - fi - fi - - # fortran-2.eclass does not handle mpi wrappers - if use mpi; then - export FC="mpif90" - export F77="mpif77" - export CC="mpicc" - export CXX="mpic++" - else - tc-export FC F77 CC CXX - fi - - # Preprocesor macross can make some lines really long - append-fflags -ffree-line-length-none - - fortran-2_pkg_setup - if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - die "Please select an openmp capable compiler like gcc[openmp]" - fi - - # Sort out some USE options - if use fftw-threads && ! use fftw; then - ewarn "fftw-threads set but fftw not used, ignored" - fi - if use cuda-double && ! use cuda; then - ewarn "cuda-double set but cuda not used, ignored" - fi - if use gui; then - lat1loc="$(locale |awk '/LC_CTYPE="(.*)"/{sub("LC_CTYPE=\"",""); sub("\" *$", ""); print}')" - if locale charmap |grep -i "\<iso885915\?\>"; then - einfo "Good, locale compatible with the GUI build" - else - ewarn "The locale ${lat1loc} incompatible with the GUI build" - if latloc=`locale -a| grep -i "\<iso885915\?\>"`; then - if echo "${latloc}" |grep -q "^fr"; then - lat1loc="$(echo "${latloc}" | grep -im1 "^fr")" - else - lat1loc="$(echo "${latloc}" | grep -im1 "iso88591")" - fi - einfo "Will use ${lat1loc} to build the GUI" - else - ewarn "No ISO-8859-1 nor ISO-8859-15 locale available, the GUI build may crash" - fi - fi - fi -} - -src_unpack() { - default_src_unpack - if use gui; then - pushd "${S}" > /dev/null - tar -xjf "${FILESDIR}"/6.12.3-gui-makefiles.tbz - popd > /dev/null - fi - -} - -src_prepare() { - epatch \ - "${FILESDIR}"/6.2.2-change-default-directories.patch \ - "${FILESDIR}"/6.12.1-autoconf.patch \ - "${FILESDIR}"/6.12.1-xmalloc.patch \ - "${FILESDIR}"/7.0.4-test_dirs.patch - eautoreconf - sed -e"s/\(grep '\^-\)\(\[LloW\]\)'/\1\\\(\2\\\|pthread\\\)'/g" -i configure - - if use gui; then - pushd gui > /dev/null - eautoreconf - popd > /dev/null - fi -} - -src_configure() { - local openmp="" - use openmp && openmp="-fopenmp" - local libs="" - local modules="-I/usr/$(get_libdir)/finclude $(FoX-config --sax --fcflags)" - local FoX_libs="${libs} $(FoX-config --sax --libs)" - local trio_flavor="" - use etsf_io && trio_flavor="${trio_flavor}+etsf_io" - use fox && trio_flavor="${trio_flavor}+fox" - use netcdf && trio_flavor="${trio_flavor}+netcdf" - test "no${trio_flavor}" = "no" && trio_flavor="none" - local netcdff_libs="-lnetcdff" - use hdf5 && netcdff_libs="${netcdff_libs} -lhdf5_fortran" - local fft_flavor="fftw3" - local fft_libs="" - # The fftw threads support is protected by black magick. - # Anybody removes it, dies. - # New USE flag "fftw-threads" was added to control usage - # of the threaded fftw variant. Since fftw-3.3 has expanded - # the paralel options by MPI and OpenMP support, analogical - # USE flags should be added to select them in future; - # unusable with previous FFTW versions, they are postponed - # for now. - if use fftw-threads; then - fft_flavor="fftw3-threads" - if has_version '>=sci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads) $($(tc-getPKG_CONFIG) --libs fftw3)" - else - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fi - else - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3)" - fi - local gpu_flavor="none" - if use cuda; then - gpu_flavor="cuda-single" - if use cuda-double; then - gpu_flavor="cuda-double" - fi - fi - - local myeconfargs=( - --enable-clib - --enable-exports - $(use_enable gui) - $(use_enable debug debug enhanced) - $(use_enable mpi) - $(use_enable mpi mpi-io) - $(use_enable openmp) - $(use_enable vdwxc) - $(use_enable cuda gpu) - "$(use cuda && echo "--with-gpu-flavor=${gpu_flavor}")" - "$(use cuda && echo "--with-gpu-prefix=/opt/cuda/")" - "$(use gsl && echo "--with-math-flavor=gsl")" - "$(use gsl && echo "--with-math-incs=$($(tc-getPKG_CONFIG) --cflags gsl)")" - "$(use gsl && echo "--with-math-libs=$($(tc-getPKG_CONFIG) --libs gsl)")" - --with-linalg-flavor="atlas" - --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs lapack)" - --with-trio-flavor="${trio_flavor}" - "$(use netcdf && echo "--with-netcdf-incs=-I/usr/include")" - "$(use netcdf && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" - "$(use fox && echo "--with-fox-incs=${modules}")" - "$(use fox && echo "--with-fox-libs=${FoX_libs}")" - "$(use etsf_io && echo "--with-etsf-io-incs=${modules}")" - "$(use etsf_io && echo "--with-etsf-io-libs=${libs} -letsf_io -letsf_io_utils -letsf_io_low_level")" - --with-dft-flavor="libxc+bigdft+atompaw+wannier90" - --with-libxc-incs="${modules}" - --with-libxc-libs="${libs} -lxc" - --with-bigdft-incs="${modules}" - --with-bigdft-libs="$($(tc-getPKG_CONFIG) --libs bigdft)" - --with-atompaw-incs="${modules}" - --with-atompaw-libs="${libs} -latompaw" - --with-wannier90-bins="/usr/bin" - --with-wannier90-incs="${modules}" - --with-wannier90-libs="${libs} -lwannier $($(tc-getPKG_CONFIG) --libs lapack)" - "$(use fftw && echo "--with-fft-flavor=${fft_flavor}")" - "$(use fftw && echo "--with-fft-incs=-I/usr/include")" - "$(use fftw && echo "--with-fft-libs=${fft_libs}")" - --with-timer-flavor="abinit" - LD="$(tc-getLD)" - FCFLAGS="${FCFLAGS:- ${FFLAGS:- -O2}} ${openmp} ${modules} -I/usr/include" - ) - - MARKDOWN=Markdown.pl autotools-utils_src_configure - - if use gui; then - # autotools-utils_src_configure() part expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - mkdir -p gui - cd gui - ECONF_SOURCE="${S}"/gui econf UUDECODE="uudecode" - popd > /dev/null - fi -} - -src_compile() { - autotools-utils_src_compile - - # Apparently libabinit.a is not built by default - # Used by BigDFT. Should probably be built separately, - # as a package of its own: BigDFT used by Abinit. - # Does libabinit.a depend on BigDFT, if used? - # Can Abinit use external libabinit.a? - use libabinit && autotools-utils_src_compile libabinit.a - - if use gui; then - #autotools-utils_src_compile() expanded - # _check_build_dir has already been called - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - # now what the function cannot be called to do - cd gui - LC_CTYPE="${lat1loc}" emake || die "Making GUI failed" - popd > /dev/null - fi - - sed -i -e's/libatlas/lapack/' "${AUTOTOOLS_BUILD_DIR}"/config.pc -} - -src_test() { - einfo "The tests take quite a while, easily several hours" - # autotools-utils_src_test() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - # again something the autotools-utils function cannot be called to do - # now quite a lot of work actually - cd tests - emake tests_acc || ewarn "Accuracy tests failed" - emake tests_paw || ewarn "PAW tests failed" - emake tests_gw || ewarn "GW tests failed" - emake tests_gw_paw || ewarn "GW-PAW tests failed" - emake tests_bs || ewarn "BSE tests failed" - emake tests_tddft || ewarn "TDDFT tests failed" - emake tests_eph || ewarn "Elphon tests failed" - - local REPORT - for REPORT in $(find . -name report); do - REPORT=${REPORT#*/} - elog "Parameters and unusual results for ${REPORT%%/*} tests" - echo "Parameters and unusual results for ${REPORT%%/*} tests" >>tests_summary.txt - while read line; do - elog "${line}" - echo "${line}" >>tests_summary.txt - done \ - < <(grep -v -e succeeded -e passed ${REPORT}) - done - - local testdir - find . -name "tmp-test*" -print | \ - while read testdir; do - if [ -e summary_of_tests.tar ]; then - tar rvf summary_of_tests.tar ${testdir} - else tar cvf summary_of_tests.tar ${testdir} - fi - done - popd > /dev/null - - elog "The full test results will be installed as summary_of_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." -} - -src_install() { - #autotools-utils_src_install() expanded - _check_build_dir - pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null - emake DESTDIR="${D}" install || die "make install failed" - - use libabinit && dolib libabinit.a - - if use gui; then - pushd gui > /dev/null - emake DESTDIR="${D}" install || die "The GUI install failed" - popd > /dev/null - fi - - if use test; then - for dc in tests_summary.txt summary_of_tests.tar; do - test -e tests/"${dc}" && dodoc tests/"${dc}" || ewarn "Copying tests results failed" - done - fi - - popd > /dev/null - - # XXX: support installing them from builddir as well!!! - if [[ ${DOCS} ]]; then - dodoc "${DOCS[@]}" || die "dodoc failed" - else - local f - # same list as in PMS - for f in README* ChangeLog AUTHORS NEWS TODO CHANGES \ - THANKS BUGS FAQ CREDITS CHANGELOG; do - if [[ -s ${f} ]]; then - dodoc "${f}" || die "(default) dodoc ${f} failed" - fi - done - fi - if [[ ${HTML_DOCS} ]]; then - dohtml -r "${HTML_DOCS[@]}" || die "dohtml failed" - fi - - # Remove libtool files and unnecessary static libs - remove_libtool_files -} - -pkg_postinst() { - if use test; then - elog "The full test results will be installed as summary_tests.tar.bz2." - elog "Also a concise report tests_summary.txt is installed." - fi -} diff --git a/sci-physics/abinit/abinit-7.0.4.ebuild b/sci-physics/abinit/abinit-7.2.2.ebuild index 3bfaa809f..a420f51cf 100644 --- a/sci-physics/abinit/abinit-7.0.4.ebuild +++ b/sci-physics/abinit/abinit-7.2.2.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit autotools-utils eutils flag-o-matic fortran-2 multilib toolchain-funcs @@ -15,11 +15,11 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="cuda cuda-double -debug +etsf_io +fftw +fftw-threads +fox gsl gui +hdf5 libabinit mpi +netcdf openmp python -test +threads -vdwxc" -RDEPEND="~sci-libs/bigdft-1.7_pre12 - =sci-libs/libxc-1*[fortran] - sci-physics/atompaw[libxc] - etsf_io? ( sci-libs/etsf_io ) - fox? ( >=sci-libs/fox-4.1.2-r1[sax] ) +RDEPEND="~sci-libs/bigdft-abi-1.0.4 + >=sci-libs/libxc-1.2.0-r1[fortran] + >=sci-physics/atompaw-3.0.1.9-r1[libxc] + etsf_io? ( >=sci-libs/etsf_io-1.0.3-r2 ) + fox? ( >=sci-libs/fox-4.1.2-r2[sax] ) netcdf? ( || ( sci-libs/netcdf[fortran] @@ -30,7 +30,7 @@ RDEPEND="~sci-libs/bigdft-1.7_pre12 ) ) hdf5? ( sci-libs/hdf5[fortran] ) - sci-libs/wannier90 + >=sci-libs/wannier90-1.2-r1 virtual/blas virtual/lapack gsl? ( sci-libs/gsl ) @@ -79,10 +79,29 @@ pkg_setup() { # Preprocesor macross can make some lines really long append-fflags -ffree-line-length-none + # This should be correct. + # It is gcc-centric because toolchain-funcs.eclass is gcc-centric. + # Should a bug be filed against toolchain-funcs.eclass? + # if use openmp; then + # tc-has-openmp || \ + # die "Please select an openmp capable compiler like gcc[openmp]" + # fi + # + # This is completely wrong. + # If other compilers than Gnu Compiler Collection can be used by portage, + # their support of OpenMP should be properly tested. This code limits the test + # to gcc, and blindly supposes that other compilers do support OpenMP. + # if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + # die "Please select an openmp capable compiler like gcc[openmp]" + # fi + # + # Luckily Abinit is a fortran package. + # fortran-2.eclass has its own test for OpenMP support, + # more general than toolchain-funcs.eclass + # The test itself proceeds inside fortran-2_pkg_setup + if use openmp; then FORTRAN_NEED_OPENMP=1; fi + fortran-2_pkg_setup - if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - die "Please select an openmp capable compiler like gcc[openmp]" - fi # Sort out some USE options if use fftw-threads && ! use fftw; then @@ -139,9 +158,24 @@ src_prepare() { src_configure() { local openmp="" - use openmp && openmp="-fopenmp" + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local fcode=ebuild-openmp-flags.f + local _fc=$(tc-getFC) + + cat <<- EOF > "${fcode}" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${_fc} ${openmp} "${fcode}" -o "${fcode}.x" && break + done + + rm -f "${fcode}.*" + fi local libs="" - local modules="-I/usr/$(get_libdir)/finclude $(FoX-config --sax --fcflags)" + local modules="$(FoX-config --sax --fcflags)" local FoX_libs="${libs} $(FoX-config --sax --libs)" local trio_flavor="" use etsf_io && trio_flavor="${trio_flavor}+etsf_io" @@ -162,20 +196,11 @@ src_configure() { # for now. if use fftw-threads; then fft_flavor="fftw3-threads" - if has_version '>=sci-libs/fftw-3.3'; then - # pkg-config files for fftw-3.3 are broken - # All the parallel stuff is separated - # from the main body of common routines, - # and -lfftw3 must be always included alongside. - # Until version 3.3 this used to be masked by - # .la files. - # Bug 384645 - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads) $($(tc-getPKG_CONFIG) --libs fftw3)" - else - fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads)" - fi + fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3_threads)" + fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3f_threads)" else fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3)" + fft_libs="${fft_libs} $($(tc-getPKG_CONFIG) --libs fftw3f)" fi local gpu_flavor="none" if use cuda; then @@ -345,7 +370,7 @@ src_install() { fi # Remove libtool files and unnecessary static libs - remove_libtool_files + prune_libtool_files } pkg_postinst() { diff --git a/sci-physics/abinit/files/6.0.3-fftw.patch b/sci-physics/abinit/files/6.0.3-fftw.patch deleted file mode 100644 index 6eca1e4ac..000000000 --- a/sci-physics/abinit/files/6.0.3-fftw.patch +++ /dev/null @@ -1,14 +0,0 @@ -diff -Naur tmp-old/src/53_ffts/ccfft.F90 tmp-new/src/53_ffts/ccfft.F90 ---- src/53_ffts/ccfft.F90 2009-03-11 05:12:18.000000000 +0000 -+++ src/53_ffts/ccfft.F90 2009-04-14 12:13:31.000000000 +0000 -@@ -96,8 +96,8 @@ - integer,intent(out) :: inplace,normalized - type(MPI_type),intent(inout) :: mpi_enreg - !arrays -- real(dp),intent(inout) :: work1(2,n4*n5*n6*ndat) -- real(dp),intent(out) :: work2(2,n4*n5*n6*ndat) -+ real(dp),intent(inout) :: work1(2*n4,n5,n6,ndat) -+ real(dp),intent(out) :: work2(2*n4,n5,n6,ndat) - - !Local variables ------------------------------ - !scalars diff --git a/sci-physics/abinit/files/6.12.1-libabinit_options.patch b/sci-physics/abinit/files/6.12.1-libabinit_options.patch deleted file mode 100644 index ad28a8183..000000000 --- a/sci-physics/abinit/files/6.12.1-libabinit_options.patch +++ /dev/null @@ -1,57 +0,0 @@ -diff -Naur abinit-6.12.1_orig/Makefile.am abinit-6.12.1/Makefile.am ---- Makefile.am 2012-01-30 19:42:26.000000000 +0000 -+++ Makefile.am 2012-03-22 10:32:50.000000000 +0000 -@@ -1279,12 +1279,16 @@ - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -+if DO_BUILD_15_GPU_TOOLBOX - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a -+if DO_BUILD_32_CONTRACT - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a -@@ -1298,7 +1302,9 @@ - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -+if DO_BUILD_52_MANAGE_CUDA - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+endif - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a -diff -Naur abinit-6.12.1_orig/Makefile.in abinit-6.12.1/Makefile.in ---- Makefile.in 2012-03-22 09:23:51.000000000 +0000 -+++ Makefile.in 2012-03-22 10:33:22.000000000 +0000 -@@ -2638,12 +2638,12 @@ - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/12_hide_mpi/lib12_hide_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/13_memory_mpi/lib13_memory_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/14_hidewrite/lib14_hidewrite.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a -+@DO_BUILD_15_GPU_TOOLBOX_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/15_gpu_toolbox/lib15_gpu_toolbox.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/16_hideleave/lib16_hideleave.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/18_timing/lib18_timing.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/27_toolbox_oop/lib27_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/28_numeric_noabirule/lib28_numeric_noabirule.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a -+@DO_BUILD_32_CONTRACT_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_contract/lib32_contract.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/32_util/lib32_util.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_geometry/lib42_geometry.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/42_nlstrain/lib42_nlstrain.a -@@ -2657,7 +2657,7 @@ - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/49_gw_toolbox_oop/lib49_gw_toolbox_oop.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/51_manage_mpi/lib51_manage_mpi.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_fft_mpi_noabirule/lib52_fft_mpi_noabirule.a -- cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a -+@DO_BUILD_52_MANAGE_CUDA_TRUE@ cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/52_manage_cuda/lib52_manage_cuda.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_abiutil/lib53_abiutil.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_ffts/lib53_ffts.a - cd $(libabinit_tmpdir) && $(AR) xv $(abs_top_builddir)/src/53_spacepar/lib53_spacepar.a diff --git a/sci-physics/atompaw/ChangeLog b/sci-physics/atompaw/ChangeLog index 38dfd7881..54678f46e 100644 --- a/sci-physics/atompaw/ChangeLog +++ b/sci-physics/atompaw/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*atompaw-3.0.1.9-r1 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + -atompaw-3.0.1.9.ebuild, +atompaw-3.0.1.9-r1.ebuild: + Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used + upstream. Old files cleaned up. + 22 Feb 2013; Justin Lecher <jlec@gentoo.org> atompaw-3.0.1.9.ebuild, metadata.xml: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; diff --git a/sci-physics/atompaw/atompaw-3.0.1.9.ebuild b/sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild index bbb78cafc..1408910e5 100644 --- a/sci-physics/atompaw/atompaw-3.0.1.9.ebuild +++ b/sci-physics/atompaw/atompaw-3.0.1.9-r1.ebuild @@ -2,7 +2,7 @@ # Distributed under the terms of the GNU General Public License v2 # $Header: $ -EAPI=4 +EAPI=5 inherit autotools-utils eutils fortran-2 multilib toolchain-funcs @@ -17,12 +17,12 @@ SRC_URI=" LICENSE="GPL-2" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="doc libxc" +IUSE="doc libxc test" RDEPEND=" virtual/blas virtual/lapack - libxc? ( sci-libs/libxc[fortran] )" + libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] )" DEPEND="${RDEPEND} virtual/pkgconfig" @@ -44,13 +44,12 @@ src_prepare() { } src_configure() { - local modules="-I/usr/$(get_libdir)/finclude" local myeconfargs=( $(use_enable libxc) --with-linalg-flavor=atlas --with-linalg-libs="$($(tc-getPKG_CONFIG) --libs lapack)" - --with-libxc-incs="-I/usr/include ${modules}" - --with-libxc-libs="${libs} -lxc" + --with-libxc-incs="-I/usr/include $($(tc-getPKG_CONFIG) --cflags libxc)" + --with-libxc-libs="$($(tc-getPKG_CONFIG) --libs libxc)" FC="$(tc-getFC)" FCFLAGS="${FCFLAGS}" CC="$(tc-getCC)" LDFLAGS="${LDFLAGS}" ) diff --git a/sci-physics/atompaw/metadata.xml b/sci-physics/atompaw/metadata.xml index 9972fff60..fb49e3d82 100644 --- a/sci-physics/atompaw/metadata.xml +++ b/sci-physics/atompaw/metadata.xml @@ -1,11 +1,8 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-physics</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <use> - <flag name="libxc">Use libxc for something</flag> - </use> +<herd>sci-physics</herd> +<use> + <flag name="libxc">Use libxc for something</flag> +</use> </pkgmetadata> diff --git a/sci-physics/atompaw2abinit/metadata.xml b/sci-physics/atompaw2abinit/metadata.xml index c620ca137..131ee598c 100644 --- a/sci-physics/atompaw2abinit/metadata.xml +++ b/sci-physics/atompaw2abinit/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci-physics</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci-physics</herd> </pkgmetadata> diff --git a/sci-physics/bigdft/ChangeLog b/sci-physics/bigdft/ChangeLog new file mode 100644 index 000000000..3a27413f7 --- /dev/null +++ b/sci-physics/bigdft/ChangeLog @@ -0,0 +1,160 @@ +# ChangeLog for sci-physics/bigdft +# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.7_pre24.ebuild: + Filter LDFLAGS for cuda use not to break nvcc. + + 19 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.7_pre24.ebuild: + Added dev-util/gdbus-codegen to dependencies. + + 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.7_pre24.ebuild: + The dependency on sci-libs/libxc corrected to reflect the recent change in + the upgrade of sci-physics/abinit & friends. + +*bigdft-1.7_pre24 (17 Jun 2013) + + 17 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + +bigdft-1.7_pre24.ebuild, +files/bigdft-1.7-dev.24-nolib_mods.patch: + Version bumped to 1.7_pre24. Moved from sci-libs to sci-physics, no longer + used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned + in favour of /usr/include, as used upstream. + + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild: + Fix issue 52 + + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> bigdft-1.7_pre12.ebuild: + Fix issue 52 + + 22 Feb 2013; Justin Lecher <jlec@gentoo.org> -bigdft-1.6_pre1-r4.ebuild, + bigdft-1.6.0-r2.ebuild, bigdft-1.7_pre12.ebuild, metadata.xml: + Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; + drop old + + 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.7_pre12.ebuild: + The setup of python for the compilation of the GPU support in + bigdft-1.7_pre12 improved. + + 20 Feb 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-GPUlink.patch: + Compilation of GPU support in bigdft-1.7_pre12 improved. Yet to be tested. + +*bigdft-1.7_pre12 (17 Jan 2013) + + 17 Jan 2013; Honza Macháček <Hloupy.Honza@centrum.cz> + +bigdft-1.7_pre12.ebuild, +files/bigdft-1.7-dev.12-libxc_dir_include.patch, + +files/bigdft-1.7-dev.12-nolib_mods.patch, + +files/bigdft-1.7-dev.12-tests.tar.bz2: + New version 1.7-dev.12 (1.7_pre12) from the Abinit site added; used by + sci-physics/abinit-7.0.4 but apparently segfaults it. + +*bigdft-1.6_pre1-r4 (01 Sep 2012) + + 01 Sep 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-1.6_pre1-r3.ebuild, +bigdft-1.6_pre1-r4.ebuild, + -files/bigdft-1.6-tuto.1-GPUlibs.patch, + +files/bigdft-1.6-tuto.1-GPUlibs-1.patch, + -files/bigdft-1.6-tuto.1-bigdft.pc.patch, + +files/bigdft-1.6-tuto.1-bigdft.pc-1.patch: + Patches to install GPU support corrected not to break linking against the + compiled libraries + + 10 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + files/bigdft-1.6-tuto.1-GPUlibs.patch: + bigdft-1.6-tuto.1-GPUlibs.patch updated not to forget the pkg-config file + +*bigdft-1.6_pre1-r3 (04 Jul 2012) + + 04 Jul 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-1.6_pre1-r2.ebuild, +bigdft-1.6_pre1-r3.ebuild, + +files/bigdft-1.6-tuto.1-GPUlibs.patch, + +files/bigdft-1.6-tuto.1-gcc-4.6.patch: + bigdft-1.6_pre1 from -r2 to -r3: patched to install necessary libraries for + GPU support and to compile with gcc-4.6 + + 22 Jun 2012; Alexey Shvetsov <alexxy@gentoo.org> bigdft-1.6.0-r2.ebuild, + bigdft-1.6_pre1-r2.ebuild: + [sci-libs/bigdft] add ~amd64-linux + +*bigdft-1.6.0-r2 (19 Jun 2012) +*bigdft-1.6_pre1-r2 (19 Jun 2012) + + 19 Jun 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-1.6_pre1-r1.ebuild, +bigdft-1.6_pre1-r2.ebuild, + -bigdft-1.6.0-r1.ebuild, +bigdft-1.6.0-r2.ebuild: + Reflect the split of the fortran interface out of sci-libs/netcdf + + 22 May 2012; Justin Lecher <jlec@gentoo.org> bigdft-1.6_pre1-r1.ebuild, + bigdft-1.6.0-r1.ebuild: + Add missing eutils.eclass, bump to EAPI=4, remove unnecessary bits + +*bigdft-1.6.0-r1 (15 May 2012) +*bigdft-1.6_pre1-r1 (15 May 2012) + + 15 May 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-1.6_pre1.ebuild, +bigdft-1.6_pre1-r1.ebuild, -bigdft-1.6.0.ebuild, + +bigdft-1.6.0-r1.ebuild: + pkg-config file corrected + + 30 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + -bigdft-1.2.0.2.ebuild, -files/bigdft-1.2.0.2-0001.patch, + -files/bigdft-1.2.0.2-0002.patch, -files/bigdft-1.2.0.2-0003.patch, + -files/bigdft-1.2.0.2-0004.patch, -files/bigdft-1.2.0.2-testH.patch, + -bigdft-1.2.0.5.ebuild, -files/bigdft-1.2.0.5-0001.patch, + -bigdft-1.6_pre0.ebuild, -files/bigdft-1.6-tuto-bigdft.pc.patch, + -files/bigdft-1.6-tuto-libxc_dir_include.patch: + Clean-up. + +*bigdft-1.6_pre1 (22 Mar 2012) +*bigdft-1.6_pre0 (22 Mar 2012) + + 22 Mar 2012; Honza Macháček <Hloupy.Honza@centrum.cz> + +bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, +bigdft-1.6_pre0.ebuild, + +bigdft-1.6_pre1.ebuild, bigdft-1.6.0.ebuild, + +files/bigdft-1.6.0-libxc_dir_include.patch, + +files/bigdft-1.6-tuto.1-bigdft.pc.patch, + +files/bigdft-1.6-tuto.1-libxc_dir_include.patch, + +files/bigdft-1.6-tuto-bigdft.pc.patch, + +files/bigdft-1.6-tuto-libxc_dir_include.patch: + Old versions used by old versions of abinit ressurected. May be removed + forever if nobody complains about the latest abinit. 1.6.0 corrected, + 1.6_pre0 and 1.6_pre1 added; 1.6_pre1 is used by sci-physics/abinit-6.12.1. + +*bigdft-1.6.0 (18 Feb 2012) + + 18 Feb 2012; Justin Lecher <jlec@gentoo.org> -bigdft-1.2.0.2.ebuild, + -bigdft-1.2.0.5.ebuild, +bigdft-1.6.0.ebuild, metadata.xml: + Move to EAPI=4 and autotools-util.eclass + +*bigdft-1.2.0.5 (14 Dec 2011) + + 14 Dec 2011; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.2.0.2.ebuild, +bigdft-1.2.0.5.ebuild, + +files/bigdft-1.2.0.5-0001.patch: + Version bump to 1.2.0.5 for sci-physics/abinit-6.10.3; still not much + progress towards the current version (1.5.2 and 1.6-tuto) + + 11 Jul 2011; Honza Macháček <Hloupy.Honza@centrum.cz> + bigdft-1.2.0.2.ebuild: + The MPI support, broken by fortran-2.eclass usage, made work again. + + 24 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild: + Streamlined fortran-2 eclass usage + + 21 Jun 2011; Justin Lecher <jlec@gentoo.org> bigdft-1.2.0.2.ebuild, + +metadata.xml: + Added fortran-2.eclass support + +*bigdft-1.2.0.2 (17 Jan 2011) + + 17 Jan 2011; Honza Macháček <Hloupy.Honza@centrum.cz> + +bigdft-1.2.0.2.ebuild, +files/bigdft-1.2.0.2-0001.patch, + +files/bigdft-1.2.0.2-0002.patch, +files/bigdft-1.2.0.2-0003.patch, + +files/bigdft-1.2.0.2-0004.patch, +files/bigdft-1.2.0.2-testH.patch: + A bigDFT ebuild for sci-physics/abinit; not the latest version but the abinit + compatible one. + diff --git a/sci-physics/bigdft/Manifest b/sci-physics/bigdft/Manifest new file mode 100644 index 000000000..a8bac0d7a --- /dev/null +++ b/sci-physics/bigdft/Manifest @@ -0,0 +1 @@ +DIST bigdft-1.7-dev.24.tar.gz 11144923 SHA256 02e90261c6e87cfc854988e2d571354f4798c78633eb3bf979ab8fa06dc377dd SHA512 ee59aca7d8f61937e0be9d1ab78803961dbc9fc67f25a36c9b3721cb9ef0674d12df89305e5443f6e212bafe1d8a0d647e0d713e0ec542bcb43974d3e669044a WHIRLPOOL 4c4ac09593358a0b8757e3d6d9e9edf3f5e356e05d661b8047b84653d5fed92351158a2f08ea92e7f51de12036f4f9cc59b607b150a85e8edc0d0510997df7d2 diff --git a/sci-physics/bigdft/bigdft-1.7_pre24.ebuild b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild new file mode 100644 index 000000000..59ce82644 --- /dev/null +++ b/sci-physics/bigdft/bigdft-1.7_pre24.ebuild @@ -0,0 +1,142 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +PYTHON_COMPAT=( python2_5 python2_6 python2_7 ) + +inherit autotools-utils eutils flag-o-matic fortran-2 python-any-r1 toolchain-funcs + +REAL_PV="${PV/_pre/-dev.}" + +DESCRIPTION="A DFT electronic structure code using a wavelet basis set" +HOMEPAGE="http://bigdft.org/" +SRC_URI="http://launchpad.net/${PN}/master/${REAL_PV}/+download/${PN}-${REAL_PV}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux" +IUSE="cuda doc etsf_io mpi netcdf openmp opencl test" + +RDEPEND=" + >=sci-libs/libxc-1.2.0-r1[fortran] + virtual/blas + virtual/fortran + virtual/lapack + dev-libs/libyaml + mpi? ( virtual/mpi ) + cuda? ( dev-util/nvidia-cuda-sdk ) + opencl? ( virtual/opencl ) + etsf_io? ( sci-libs/etsf_io ) + netcdf? ( || ( + sci-libs/netcdf[fortran] + sci-libs/netcdf-fortran + ) + )" +DEPEND="${RDEPEND} + virtual/pkgconfig + >=sys-devel/autoconf-2.59 + doc? ( virtual/latex-base ) + ${PYTHON_DEPS} + dev-python/pyyaml[libyaml] + dev-util/gdbus-codegen + app-arch/tar + app-arch/gzip" + +S="${WORKDIR}/${PN}-${REAL_PV}" + +DOCS=( README INSTALL ChangeLog AUTHORS NEWS ) + +FORTRAN_STANDARD=90 + +pkg_setup() { + # fortran-2.eclass does not handle mpi wrappers + if use mpi; then + export FC="mpif90" + export F77="mpif77" + export CC="mpicc" + else + tc-export FC F77 CC + fi + + fortran-2_pkg_setup + if use openmp && [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then + die "Please select an openmp capable compiler like gcc[openmp]" + fi + python-any-r1_pkg_setup +} + +src_prepare() { + epatch \ + "${FILESDIR}"/"${PN}-${REAL_PV}"-nolib_mods.patch + + eautoreconf +} + +src_configure() { + local openmp="" + use openmp && openmp="-fopenmp" + local modules="${EPREFIX}/usr/include" + local netcdff_libs="-lnetcdff" + filter-flags '-m*' '-O*' "-pipe" + local nvcflags="${CFLAGS}" + _filter-var nvcflags '-m*' '-O*' "-pipe" "-W*" + use cuda && filter-ldflags '-m*' '-O*' "-pipe" "-W*" + local myeconfargs=( + $(use_enable mpi) + --enable-optimised-convolution + --enable-pseudo + --enable-libbigdft + --enable-binaries + --disable-minima-hopping + --disable-internal-libyaml + --enable-internal-libabinit + --with-moduledir="${modules}" + --with-ext-linalg="$($(tc-getPKG_CONFIG) --libs-only-l lapack) \ + $($(tc-getPKG_CONFIG) --libs-only-l blas)" + --with-ext-linalg-path="$($(tc-getPKG_CONFIG) --libs-only-L lapack) \ + $($(tc-getPKG_CONFIG) --libs-only-L blas)" + --with-libxc="yes" + --disable-internal-libxc + $(use_enable cuda cuda-gpu) + $(use_with cuda cuda-path /opt/cuda) + $(use_with cuda nvcc-flags "${nvcflags}") + $(use_enable opencl) + $(use_with etsf_io etsf-io) + "$(use etsf_io && echo "--with-netcdf-libs=$($(tc-getPKG_CONFIG) --libs netcdf) ${netcdff_libs}")" + PKG_CONFIG="$(tc-getPKG_CONFIG)" + FCFLAGS="${FCFLAGS} ${openmp} -I${modules}" + LD="$(tc-getLD)" + CPP="$(tc-getCPP)" + ) + autotools-utils_src_configure +} + +src_compile() { + #autotools-utils_src_compile() expanded + _check_build_dir + pushd "${AUTOTOOLS_BUILD_DIR}" > /dev/null + emake -j1 + sed -i -e's%\$(top_builddir)/[^ ]*/lib\([^ /$-]*\)\.a%-l\1%g' bigdft.pc + popd > /dev/null + + #autotools-utils_src_compile + use doc && autotools-utils_src_compile doc +} + +src_test() { + if use test; then + #autotools-utils_src_test() expanded + _check_build_dir + pushd "${BUILD_DIR}" > /dev/null || die + # Run default src_test as defined in ebuild.sh + cd tests + emake -j1 check + popd > /dev/null + fi +} + +src_install() { + autotools-utils_src_install HAVE_LIBXC=1 +} diff --git a/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch b/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch new file mode 100644 index 000000000..de3555b6d --- /dev/null +++ b/sci-physics/bigdft/files/bigdft-1.7-dev.24-nolib_mods.patch @@ -0,0 +1,25 @@ +diff -Naurp bigdft-1.7-dev.24.orig/src/Makefile.am bigdft-1.7-dev.24/src/Makefile.am +--- bigdft-1.7-dev.24.orig/src/Makefile.am 2013-03-12 12:56:53.000000000 +0000 ++++ bigdft-1.7-dev.24/src/Makefile.am 2013-04-10 09:29:31.073319847 +0000 +@@ -56,6 +56,9 @@ bigdft_library_rpath = + endif + if BUILD_LIB_BIGDFT + lib_bigdft = libbigdft.a libdft_common.a ++else ++lib_bigdft = ++endif + PS_SOURCES = PSolver/Build_Kernel.f90 \ + PSolver/xcenergy.f90 \ + PSolver/3Dgradient.f90 \ +@@ -64,11 +67,6 @@ PS_SOURCES = PSolver/Build_Kernel.f90 \ + PSolver/wofz.f90 \ + lib/fft/fft3d.f90 + PS_MODULES = PSolver/Poisson_Solver.f90 +-else +-lib_bigdft = +-PS_SOURCES = +-PS_MODULES = +-endif + if BUILD_BINARIES + binaries_sources = bigdft memguess splsad NEB frequencies MDanalysis $(minima_hopping_sources) bart abscalc BigDFT2Wannier WaCo NEB_images + local_binaries = test_forces diff --git a/sci-physics/elk/ChangeLog b/sci-physics/elk/ChangeLog index 28ac97dff..2a837bcdd 100644 --- a/sci-physics/elk/ChangeLog +++ b/sci-physics/elk/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> elk-1.4.22.ebuild: + The dependency on sci-libs/libxc adapted to its recent change in the upgrade + of sci-physics/abinit & friends. + 21 Feb 2013; Justin Lecher <jlec@gentoo.org> elk-1.4.22.ebuild: Use tc-getPKG_CONFIG from toolchain-funcs.eclass instead of plain pkg-config; add missing dep on virtual/pkgconfig; cleaning of ebuild diff --git a/sci-physics/elk/elk-1.4.22.ebuild b/sci-physics/elk/elk-1.4.22.ebuild index ab7cd8dcd..5e99d05d3 100644 --- a/sci-physics/elk/elk-1.4.22.ebuild +++ b/sci-physics/elk/elk-1.4.22.ebuild @@ -19,7 +19,7 @@ RDEPEND=" lapack? ( virtual/blas virtual/lapack ) - libxc? ( =sci-libs/libxc-1*[fortran] ) + libxc? ( >=sci-libs/libxc-1.2.0-r1[fortran] ) mpi? ( virtual/mpi )" DEPEND="${RDEPEND} perl? ( dev-lang/perl ) diff --git a/sci-physics/herwig++/metadata.xml b/sci-physics/herwig++/metadata.xml index b5e2e6ce8..c41e38620 100644 --- a/sci-physics/herwig++/metadata.xml +++ b/sci-physics/herwig++/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-physics</herd> <maintainer> <email>piatlicki@gmail.com</email> </maintainer> diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog index 7e5c044dd..ac52ff671 100644 --- a/sci-physics/lammps/ChangeLog +++ b/sci-physics/lammps/ChangeLog @@ -2,6 +2,16 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130526.ebuild: + Bashified package name mangling. Thanks to ottxor for suggesting and helpful + discussions. + + 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130526.ebuild: + Fixed missing use flag. + + 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. diff --git a/sci-physics/lammps/lammps-20130526.ebuild b/sci-physics/lammps/lammps-20130526.ebuild index fe092cf62..cfc247bd5 100644 --- a/sci-physics/lammps/lammps-20130526.ebuild +++ b/sci-physics/lammps/lammps-20130526.ebuild @@ -8,40 +8,70 @@ FORTRAN_NEEDED="package-meam" inherit eutils fortran-2 -LAMMPSDATE="26May13" +convert_month() { + case $1 in + 01) echo Jan + ;; + 02) echo Feb + ;; + 03) echo Mar + ;; + 04) echo Apr + ;; + 05) echo May + ;; + 06) echo Jun + ;; + 07) echo Jul + ;; + 08) echo Aug + ;; + 09) echo Sep + ;; + 10) echo Oct + ;; + 11) echo Nov + ;; + 12) echo Dec + ;; + *) echo unknown + ;; + esac +} + +MY_P=${PN}-$((${PV:6:2}))$(convert_month ${PV:4:2})${PV:2:2} DESCRIPTION="Large-scale Atomic/Molecular Massively Parallel Simulator" HOMEPAGE="http://lammps.sandia.gov/" -SRC_URI="http://lammps.sandia.gov/tars/lammps-${LAMMPSDATE}.tar.gz" +SRC_URI="http://lammps.sandia.gov/tars/${MY_P}.tar.gz" LICENSE="GPL-2" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" DEPEND="mpi? ( virtual/mpi )" RDEPEND="${DEPEND}" -S="${WORKDIR}/${PN}-${LAMMPSDATE}" +S="${WORKDIR}/${MY_P}" lmp_emake() { - local LAMMPS_INCLUDEFLAGS= - use gzip && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_GZIP" - use lammps-memalign && LAMMPS_INCLUDEFLAGS+=" -DLAMMPS_MEMALIGN" + local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" + LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -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 $(tc-getCXX)) \ + CC=$(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="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(use mpi || echo -I../STUBS) \ - MPI_PATH=$(use mpi || echo -L../STUBS) \ - MPI_LIB=$(use mpi || echo -lmpi_stubs) \ + MPI_INC=$(usex mpi '' "-I../STUBS") \ + MPI_PATH=$(usex mpi '' '-L../STUBS') \ + MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ "$@" } diff --git a/sci-physics/openmx/ChangeLog b/sci-physics/openmx/ChangeLog index bf95c840b..e6d94d055 100644 --- a/sci-physics/openmx/ChangeLog +++ b/sci-physics/openmx/ChangeLog @@ -2,6 +2,13 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ +*openmx-3.7.3 (18 Jun 2013) + + 18 Jun 2013; Honza Macháček <Hloupy.Honza@centrum.cz> +openmx-3.7.3.ebuild, + +files/3.7-fortran_objects.patch: + Added 3.7.3 version, played a bit with the detection of the openMP support, + struggled with the linking of C code with Fortran bits when using MPI. + 03 Mar 2013; Justin Lecher <jlec@gentoo.org> openmx-3.6.ebuild: Move to EAPI=5 and shorten DESCRIPTION diff --git a/sci-physics/openmx/Manifest b/sci-physics/openmx/Manifest index 4e0a74a15..b99645bee 100644 --- a/sci-physics/openmx/Manifest +++ b/sci-physics/openmx/Manifest @@ -1,2 +1,4 @@ DIST openmx3.6.tar.gz 83023744 SHA256 e344914a615d4179e724877207335e44f9d629cd3931b70e135011877355ab71 SHA512 f4d59e839bbd216893149c83d1059aa4dc4fb011d113cb40efbd99db96d558501b371628f0ea064d3091d8ef0d2c8664412b0c3541fa2a7135811e3536cb0018 WHIRLPOOL 54c72309133dbb010218ce138992362e98eb4c345eb3b2897e1d86f3f2469cc95a2024c8547cc3dc0db78befaf620e624640b6a64522c0937bf7158658a28109 +DIST openmx3.7.tar.gz 117784869 SHA256 24329cd1fbad98d6cb99b04e4d988b0715e2ce3156f79e4855c46f93a0c981f9 SHA512 e05e2839776be17d0df71818444ff7234b75f00177111ff4003eacbe3663a025965990c293cd1dfa078c3960fe89385cbe16393c9cfaf5953e1c683e7964423a WHIRLPOOL 68694dd0ea3899a79c2c299377671725ad5e971af2d0a842501a422fc30483d43373dcc7d2f1e5dc62f6298dbf8f87cc5806a0d2eab3add80a3adca0a3f5a327 DIST patch3.6.1.tar.gz 202531 SHA256 56cba052a84c73bf332ff3a65787001376f8d50ec50e7e363a67dfb5b417febd SHA512 1f1c2c156c80a21649826cfaeb79a9b2b7d81b46920e713fb0e4489eeceb8cc6a9193c49efb0d4c1a1a69313e21186e10ed4fd97d27e63b555ce1092425c641d WHIRLPOOL 006cb7ec822ef485c03a371b9c3a99c426fc5e6e1249fd17d9f5527f0220f09df1acc049e31a59d6834a3ce44431ae385268954898613a9fe31ff892262a5503 +DIST patch3.7.3.tar.gz 23280 SHA256 982c5409515c237a7c5638062109902d3d2309702c04d4fbcd559874686c5b57 SHA512 e701024b1e9e346722329d8b017a24858e88cb1141f2bbb27f33769c5a2d35d375d466b1e601fba58fe2615905c50523beb0a8a6f541b6338813fb9710ca7fda WHIRLPOOL 6329b3b4211254aaf2109b0ee2f78fa918cf40b270f53381ccc988babf7130526cd8ba17a188b006b9cd3fd8ebfd2ea7dc30f28ee0b46cf88a3c40dc62d1466e diff --git a/sci-physics/openmx/files/3.7-fortran_objects.patch b/sci-physics/openmx/files/3.7-fortran_objects.patch new file mode 100644 index 000000000..62521a4da --- /dev/null +++ b/sci-physics/openmx/files/3.7-fortran_objects.patch @@ -0,0 +1,15 @@ +diff -Naurp openmx3.7.orig/source/makefile openmx3.7/source/makefile +--- openmx3.7.orig/source/makefile 2013-06-18 11:22:23.000000000 +0000 ++++ openmx3.7/source/makefile 2013-06-18 11:36:31.118716378 +0000 +@@ -818,8 +818,8 @@ TRAN_Set_SurfOverlap_NC.o: TRAN_Set_Surf + + + elpa1.o: elpa1.f90 +- $(FC) -c elpa1.f90 ++ $(FC) -c elpa1.f90 -o elpa1.o + solve_evp_real.o: solve_evp_real.f90 +- $(FC) -c solve_evp_real.f90 ++ $(FC) -c solve_evp_real.f90 -o solve_evp_real.o + solve_evp_complex.o: solve_evp_complex.f90 +- $(FC) -c solve_evp_complex.f90 ++ $(FC) -c solve_evp_complex.f90 -o solve_evp_complex.o diff --git a/sci-physics/openmx/metadata.xml b/sci-physics/openmx/metadata.xml index 897aa2e6b..131ee598c 100644 --- a/sci-physics/openmx/metadata.xml +++ b/sci-physics/openmx/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</herd> +<herd>sci-physics</herd> </pkgmetadata> diff --git a/sci-physics/openmx/openmx-3.7.3.ebuild b/sci-physics/openmx/openmx-3.7.3.ebuild new file mode 100644 index 000000000..f6e7aef62 --- /dev/null +++ b/sci-physics/openmx/openmx-3.7.3.ebuild @@ -0,0 +1,161 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit eutils multilib toolchain-funcs fortran-2 + +DESCRIPTION="Material eXplorer using DFT, NC pseudopotentials, and pseudo-atomic localized basis functions" +HOMEPAGE="http://www.openmx-square.org/" +SRC_URI=" + http://www.openmx-square.org/${PN}${PV%.[0-9]}.tar.gz + http://www.openmx-square.org/bugfixed/13June03/patch${PV}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="-debug mpi openmp test" + +RDEPEND=" + virtual/blas + virtual/lapack + sci-libs/fftw:3.0[mpi?,openmp?] + mpi? ( virtual/mpi )" +DEPEND="${RDEPEND} + virtual/pkgconfig" + +S="${WORKDIR}/${PN}${PV%.[0-9]}" + +MAKEOPTS+=" -j1" + +FORTRAN_STANDARD=90 + +pkg_setup() { + if use mpi; then + export CC="mpicc" + export FC="mpif90" + else + tc-export CC + tc-export FC + fi + + if use openmp; then FORTRAN_NEED_OPENMP=1; fi + + fortran-2_pkg_setup + + if use openmp; then + # based on _fortran-has-openmp() of fortran-2.eclass + local code=ebuild-openmp-flags + local ret + local openmp + + pushd "${T}" + cat <<- EOF > "${code}.c" + # include <omp.h> + main () { + int nthreads; + nthreads=omp_get_num_threads(); + } + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${CC} ${openmp} "${code}.c" -o "${code}.o" &>> "${T}"/_c_compile_test.log + ret=$? + (( ${ret} )) || break + done + + rm -f "${code}.*" + popd + + if (( ${ret} )); then + die "Please switch to an openmp compatible C compiler" + else + export CC="${CC} ${openmp}" + fi + + pushd "${T}" + cat <<- EOF > "${code}.f" + 1 call omp_get_num_threads + 2 end + EOF + + for openmp in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do + ${FC} ${openmp} "${code}.f" -o "${code}.o" &>> "${T}"/_f_compile_test.log + ret=$? + (( ${ret} )) || break + done + + rm -f "${code}.*" + popd + + if (( ${ret} )); then + die "Please switch to an openmp compatible fortran compiler" + else + export FC="${FC} ${openmp}" + fi + fi + +} + +src_prepare() { + cd "${WORKDIR}" + mv *.[hc] "${S}"/source + epatch "${FILESDIR}/3.7-fortran_objects.patch" +} + +src_configure() { + local FFTW_FLAVOUR=fftw3 + if use openmp; then + FFTW_FLAVOUR=fftw3_omp + else + export CFLAGS="${CFLAGS} -Dnoomp" + fi + if use mpi; then + FFTW_FLAVOUR=fftw3_mpi + else + export CFLAGS="${CFLAGS} -Dnompi" + fi + CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags lapack)" + CFLAGS="${CFLAGS} $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})" + export CFLAGS + + FCFLAGS="${FCFLAGS} -I/usr/include" + FCFLAGS="${FCFLAGS} $($(tc-getPKG_CONFIG) --cflags lapack)" + FCFLAGS="${FCFLAGS} $($(tc-getPKG_CONFIG) --cflags ${FFTW_FLAVOUR})" + export FCFLAGS + + local MX_LIB="$($(tc-getPKG_CONFIG) --static --libs lapack)" + MX_LIB="${MX_LIB} $($(tc-getPKG_CONFIG) --static --libs ${FFTW_FLAVOUR})" + if use mpi; then + MX_LIB="${MX_LIB} $(mpif90 -showme:link)" + fi + + sed \ + -e "s%^CC *=.*$%CC = ${CC} ${CFLAGS}%" \ + -e "s%^FC *=.*$%FC = ${FC} ${FCFLAGS}%" \ + -e "s%^LIB *=.*$%LIB = ${MX_LIB}%" \ + -i source/makefile || die +} + +src_compile() { + emake -C source +} + +src_test() { + cd work + ../source/openmx -runtest || die +} + +src_install() { + insinto /usr/share/${P} + doins -r DFT_DATA11 + cd work + insinto /usr/share/${P}/examples + doins -r * + cd ../source + dodir /usr/bin + emake DESTDIR="${D}/usr/bin" install + dodoc "${S}/${PN}${PV}.pdf" + use test && dodoc "${S}"/work/runtest.result +} diff --git a/sci-physics/thepeg/metadata.xml b/sci-physics/thepeg/metadata.xml index 1bffb2a93..e41238c50 100644 --- a/sci-physics/thepeg/metadata.xml +++ b/sci-physics/thepeg/metadata.xml @@ -1,7 +1,7 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<herd>sci</herd> +<herd>sci-physics</herd> <maintainer> <email>piatlicki@gmail.com</email> </maintainer> diff --git a/sci-visualization/gnuplot/ChangeLog b/sci-visualization/gnuplot/ChangeLog index 5e0fc2e11..bd5604411 100644 --- a/sci-visualization/gnuplot/ChangeLog +++ b/sci-visualization/gnuplot/ChangeLog @@ -2,6 +2,9 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 19 Jun 2013; Christoph Junghans <ottxor@gentoo.org> gnuplot-4.7.9999.ebuild: + fixed qt4 build + 14 Jun 2013; Justin Lecher <jlec@gentoo.org> gnuplot-4.6.9999.ebuild, gnuplot-4.7.9999.ebuild: Drop KEYWORDS of live ebuilds diff --git a/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild b/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild index b50f33fce..c22c039bf 100644 --- a/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild +++ b/sci-visualization/gnuplot/gnuplot-4.7.9999.ebuild @@ -156,7 +156,7 @@ src_configure() { $(use_with svga linux-vga) \ $(use_with X x) \ --enable-stats \ - $(use_enable qt4 qt) \ + $(use_with qt4 qt qt4) \ $(use_enable thin-splines) \ $(use_enable wxwidgets) \ DIST_CONTACT="http://bugs.gentoo.org/" \ diff --git a/sci-visualization/v_sim/metadata.xml b/sci-visualization/v_sim/metadata.xml index 7064fe116..320251965 100644 --- a/sci-visualization/v_sim/metadata.xml +++ b/sci-visualization/v_sim/metadata.xml @@ -3,9 +3,6 @@ <pkgmetadata> <herd>sci</herd> <maintainer> - <email>sci@gentoo.org</email> - </maintainer> - <maintainer> <email>dongxuli2011@gmail.com</email> </maintainer> <use> diff --git a/sys-cluster/charm/ChangeLog b/sys-cluster/charm/ChangeLog index 36cf321b1..dce9f9f22 100644 --- a/sys-cluster/charm/ChangeLog +++ b/sys-cluster/charm/ChangeLog @@ -2,6 +2,23 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: + Beautify. + + 26 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild, + metadata.xml: + Added new package: projections A performance analysis framework for Charm++ + applications + + 26 Jun 2013; Christoph Junghans <ottxor@gentoo.org> charm-6.5.0.ebuild: + make use of usex + + 24 Jun 2013; Nicolas Bock <nicolasbock@gmail.com> charm-6.5.0.ebuild: + sys-cluster/charm-6.5.0: Reorganized DEPENDs. + + 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. diff --git a/sys-cluster/charm/charm-6.5.0.ebuild b/sys-cluster/charm/charm-6.5.0.ebuild index 8ae5bec22..9b34899bf 100644 --- a/sys-cluster/charm/charm-6.5.0.ebuild +++ b/sys-cluster/charm/charm-6.5.0.ebuild @@ -13,52 +13,55 @@ SRC_URI="http://charm.cs.uiuc.edu/distrib/${P}.tar.gz" LICENSE="charm" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="charmdebug cmkopt doc examples smp static-libs tcp" +IUSE="charmdebug charmtracing charmproduction cmkopt doc examples mpi smp static-libs tcp" +RDEPEND="mpi? ( virtual/mpi )" DEPEND=" + ${RDEPEND} doc? ( - >=app-text/poppler-0.12.3-r3[utils] - dev-tex/latex2html - virtual/tex-base )" -RDEPEND="" + >=app-text/poppler-0.12.3-r3[utils] + dev-tex/latex2html + virtual/tex-base + )" -REQUIRED_USE="charmdebug? ( !cmkopt )" +REQUIRED_USE=" + cmkopt? ( !charmdebug !charmtracing ) + charmproduction? ( !charmdebug !charmtracing )" FORTRAN_STANDARD="90" src_prepare() { # Build shared libraries by default. CHARM_OPTS="--build-shared" - - if use charmdebug; then - CHARM_OPTS+=" --with-charmdebug" - else + if use charmproduction; then CHARM_OPTS+=" --with-production" + else + if use charmdebug; then + CHARM_OPTS+=" --with-charmdebug" + fi + + if use charmtracing; then + CHARM_OPTS+=" --with-tracing --with-tracing-commthread" + fi fi # TCP instead of default UDP for socket comunication # protocol - if use tcp; then - CHARM_OPTS+=" tcp" - fi + CHARM_OPTS+="$(usex tcp ' tcp' '')" # enable direct SMP support using shared memory - if use smp; then - CHARM_OPTS+=" smp" - fi + CHARM_OPTS+="$(usex smp ' smp' '')" # CMK optimization - if use cmkopt; then - append-cppflags -DCMK_OPTIMIZE=1 - fi + use cmkopt && append-cppflags -DCMK_OPTIMIZE=1 sed \ - -e "/CMK_CF90/s:f90:$(tc-getFC):g" \ - -e "/CMK_CXX/s:g++:$(tc-getCXX):g" \ - -e "/CMK_CC/s:gcc:$(tc-getCC):g" \ + -e "/CMK_CF90/s:f90:$(usex mpi "mpif90" "$(tc-getFC)"):g" \ + -e "/CMK_CXX/s:g++:$(usex mpi "mpic++" "$(tc-getCXX)"):g" \ + -e "/CMK_CC/s:gcc:$(usex mpi "mpicc" "$(tc-getCC)"):g" \ -e '/CMK_F90_MODINC/s:-p:-I:g' \ -e "/CMK_LD/s:\"$: ${LDFLAGS} \":g" \ - -i src/arch/net-linux*/*sh || die + -i src/arch/$(usex mpi "mpi" "net")-linux*/*sh || die sed \ -e "s:-o conv-cpm:${LDFLAGS} &:g" \ @@ -77,8 +80,8 @@ src_prepare() { src_compile() { # Build charmm++ first. - ./build charm++ net-linux$( use amd64 && echo "-amd64" ) ${CHARM_OPTS} ${MAKEOPTS} ${CFLAGS} || \ - die "Failed to build charm++" + ./build charm++ $(usex mpi "mpi" "net")-linux$(usex amd64 "-amd64" '') \ + ${CHARM_OPTS} ${MAKEOPTS} ${CFLAGS} || die "Failed to build charm++" # make pdf/html docs if use doc; then @@ -108,7 +111,7 @@ src_install() { # Install binaries. for i in bin/*; do if [[ -L ${i} ]]; then - i=$( readlink -e "${i}" ) || die + i=$(readlink -e "${i}") || die fi dobin "${i}" done @@ -117,7 +120,7 @@ src_install() { insinto /usr/include/${P} for i in include/*; do if [[ -L ${i} ]]; then - i=$( readlink -e "${i}" ) || die + i=$(readlink -e "${i}") || die fi doins "${i}" done @@ -127,7 +130,7 @@ src_install() { if use static-libs; then for i in lib/*.{a,o}; do if [[ -L ${i} ]]; then - i=$( readlink -e "${i}" ) || die + i=$(readlink -e "${i}") || die fi dolib "${i}" done @@ -136,7 +139,7 @@ src_install() { # Install shared libs. for i in lib_so/*; do if [[ -L ${i} ]]; then - i=$( readlink -e "${i}" ) || die + i=$(readlink -e "${i}") || die fi dolib.so "${i}" done diff --git a/sys-cluster/charm/metadata.xml b/sys-cluster/charm/metadata.xml index 37dbe451e..0e4959d08 100644 --- a/sys-cluster/charm/metadata.xml +++ b/sys-cluster/charm/metadata.xml @@ -4,6 +4,8 @@ <herd>sci</herd> <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 new file mode 100644 index 000000000..f6f5e32e9 --- /dev/null +++ b/sys-cluster/charmdebug/ChangeLog @@ -0,0 +1,12 @@ +# ChangeLog for sys-cluster/charmdebug +# 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, + +metadata.xml: + Added new package: charmdebug. diff --git a/sys-cluster/charmdebug/Manifest b/sys-cluster/charmdebug/Manifest new file mode 100644 index 000000000..8b118213c --- /dev/null +++ b/sys-cluster/charmdebug/Manifest @@ -0,0 +1 @@ +DIST charmdebug_6.2.0.tar.gz 240159 SHA256 8f8a1727c2f677e760b0e2fd56a741cff9b672caa9c024b690df92a5445ed331 SHA512 825f149062c29012cb8b2c1a56e6bcf38a6eae4bedcb26595ed9a862fb9e4fdd0f019d53c3bae179e2678c3411f5793488876d8c8eb2ba2417dfc7a20c88b44d WHIRLPOOL febfcd0975a6be66c7509cf64c25daa344fc5a7ca144ff63f39aee8e3f49a654f789570e4e3daa5286c4b627ac550c99a87890d7bd7bc0a7c64cb50c3c0662b2 diff --git a/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild b/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild new file mode 100644 index 000000000..bd227a653 --- /dev/null +++ b/sys-cluster/charmdebug/charmdebug-6.2.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2013 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: $ + +EAPI=5 + +inherit java-pkg-2 + +DESCRIPTION="A debugger for Charm++ applications" +HOMEPAGE="http://charm.cs.uiuc.edu/" +SRC_URI="http://charm.cs.illinois.edu/distrib/binaries/charmdebug/charmdebug_${PV}.tar.gz" + +S="${WORKDIR}/${PN}" + +LICENSE="charm" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +DEPEND="" +RDEPEND=" + >=virtual/jre-1.6 + sys-cluster/charm[charmdebug]" + +src_install() { + java-pkg_newjar ${PN}.jar + java-pkg_dolauncher ${PN} \ + --main charm/debug/ParDebug \ + --jar ${PN}.jar \ + --java_args -ms100000000 -mx512000000 +} diff --git a/sys-cluster/charmdebug/metadata.xml b/sys-cluster/charmdebug/metadata.xml new file mode 100644 index 000000000..d369d068f --- /dev/null +++ b/sys-cluster/charmdebug/metadata.xml @@ -0,0 +1,5 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <herd>sci</herd> +</pkgmetadata> diff --git a/sys-cluster/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-errorline.patch b/sys-cluster/modules/files/modules-3.2.10-errorline.patch new file mode 100644 index 000000000..b2962f104 --- /dev/null +++ b/sys-cluster/modules/files/modules-3.2.10-errorline.patch @@ -0,0 +1,14 @@ +diff -ru modules-3.2.9-old/cmdModule.c modules-3.2.9/cmdModule.c +--- modules-3.2.9-old/cmdModule.c 2013-06-02 22:46:09.196302980 +0200 ++++ modules-3.2.9/cmdModule.c 2013-06-02 22:53:36.706298800 +0200 +@@ -640,8 +640,8 @@ + case TCL_OK: gotPartial = 0; + continue; /** while **/ + +- case TCL_ERROR: interp->errorLine = ((linenum-1)-gotPartial) + +- interp->errorLine; ++ case TCL_ERROR: Tcl_SetErrorLine(interp, ((linenum-1)-gotPartial) + ++ Tcl_GetErrorLine(interp)); + /* FALLTHROUGH */ + + case TCL_LEVEL0_RETURN: 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 $prefix + prepend-path PATH @bindir@ + prepend-path MANPATH @mandir@ + +-module use @VERSIONPATH@ ++@VERSIONING@module use @VERSIONPATH@ + diff --git a/sys-cluster/modules/files/modules-3.2.9c-errorline.patch b/sys-cluster/modules/files/modules-3.2.9c-errorline.patch index a319ac871..b2962f104 100644 --- a/sys-cluster/modules/files/modules-3.2.9c-errorline.patch +++ b/sys-cluster/modules/files/modules-3.2.9c-errorline.patch @@ -12,4 +12,3 @@ diff -ru modules-3.2.9-old/cmdModule.c modules-3.2.9/cmdModule.c /* FALLTHROUGH */ case TCL_LEVEL0_RETURN: -Nur in modules-3.2.9: cmdModule.c~. diff --git a/sys-cluster/modules/files/modules.sh.in b/sys-cluster/modules/files/modules.sh.in new file mode 100644 index 000000000..6ed502e87 --- /dev/null +++ b/sys-cluster/modules/files/modules.sh.in @@ -0,0 +1,7 @@ +shell=$(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/modules/modules-3.2.10.ebuild b/sys-cluster/modules/modules-3.2.10.ebuild index 8c5490302..8ec69c830 100644 --- a/sys-cluster/modules/modules-3.2.10.ebuild +++ b/sys-cluster/modules/modules-3.2.10.ebuild @@ -26,9 +26,9 @@ S="${WORKDIR}/${P%[a-z]}" DOCS=(ChangeLog README NEWS TODO) -#src_prepare() { -# epatch "${FILESDIR}/${P}-errorline.patch" -#} +src_prepare() { + has_version ">=dev-lang/tcl-8.6.0" && epatch "${FILESDIR}/${P}-errorline.patch" +} src_configure() { local myeconfargs=( 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 +} diff --git a/www-apps/py-swish-e/metadata.xml b/www-apps/py-swish-e/metadata.xml index 4bf6dbc6b..b229aec85 100644 --- a/www-apps/py-swish-e/metadata.xml +++ b/www-apps/py-swish-e/metadata.xml @@ -1,8 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <herd>sci</herd> - <maintainer> - <email>sci@gentoo.org</email> - </maintainer> +<herd>sci</herd> </pkgmetadata> diff --git a/x11-libs/tr/metadata.xml b/x11-libs/tr/metadata.xml index efb490d78..b229aec85 100644 --- a/x11-libs/tr/metadata.xml +++ b/x11-libs/tr/metadata.xml @@ -2,7 +2,4 @@ <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <herd>sci</herd> -<maintainer> - <email>sci@gentoo.org</email> -</maintainer> </pkgmetadata> |