diff options
50 files changed, 23 insertions, 3209 deletions
diff --git a/app-doc/root-docs/ChangeLog b/app-doc/root-docs/ChangeLog deleted file mode 100644 index e7a39935d..000000000 --- a/app-doc/root-docs/ChangeLog +++ /dev/null @@ -1,108 +0,0 @@ -# ChangeLog for app-doc/root-docs -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*root-docs-5.34.13 (05 Dec 2013) - - 05 Dec 2013; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.34.13.ebuild: - Version bump. - - 07 Oct 2013; Andrew Savchenko <bircoph@gmail.com> root-docs-5.34.10.ebuild: - Omit unneeded howto messages. - -*root-docs-5.34.10 (04 Oct 2013) - - 04 Oct 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.09.ebuild, - +root-docs-5.34.10.ebuild: - Version bump per bug 486620. Remove old. - -*root-docs-5.34.09 (29 Jun 2013) - - 29 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.08.ebuild, - +root-docs-5.34.09.ebuild: - Version bump. - -*root-docs-5.34.08 (08 Jun 2013) - - 08 Jun 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.07.ebuild, - +root-docs-5.34.08.ebuild: - Version bump. - -*root-docs-5.34.07 (28 May 2013) - - 28 May 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.05.ebuild, - +root-docs-5.34.07.ebuild, -files/root-docs-5.32-makehtml.patch: - Fix sandbox violation on DRI systems: use addpredict instead of - switching to Xong GL interface. Remove old. - -*root-docs-5.34.05 (23 Feb 2013) - - 23 Feb 2013; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.32.04.ebuild, - -root-docs-5.34.03.ebuild, +root-docs-5.34.05.ebuild, root-docs-9999.ebuild: - Version bump. Remove old. Do not compress files (mostly headers) as - this renders them unusable from html pages. - -*root-docs-5.34.03 (25 Oct 2012) - - 25 Oct 2012; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.34.02.ebuild, - +root-docs-5.34.03.ebuild: - Version bump. - -*root-docs-5.34.02 (19 Oct 2012) -*root-docs-5.32.04 (19 Oct 2012) - - 19 Oct 2012; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.32.04.ebuild, - +files/root-docs-5.32-makehtml.patch, +root-docs-5.34.02.ebuild: - Version bump for patch releases in 5.32 and 5.34 branches. - -*root-docs-5.34.01 (22 Jul 2012) - - 22 Jul 2012; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.34.01.ebuild, - +files/root-docs-5.34.01-makehtml.patch, root-docs-9999.ebuild, - -files/root-docs-9999-makehtml.patch: - Version bump. - - 21 Jul 2012; Andrew Savchenko <bircoph@gmail.com> - -files/root-docs-5.32-makehtml.patch, -files/root-docs-5.34-makehtml.patch, - root-docs-9999.ebuild, +files/root-docs-9999-makehtml.patch: - Update patching for live ebuild. Remove old. - - 06 Jul 2012; Justin Lecher <jlec@gentoo.org> -root-docs-5.32.03.ebuild, - metadata.xml: - Dropped in tree version - -*root-docs-5.32.03 (20 Jun 2012) - - 20 Jun 2012; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.32.ebuild, - +root-docs-5.32.03.ebuild, +files/root-docs-5.32-makehtml.patch: - Backport htmldoc generation fixes for 5.32 branch. - -*root-docs-5.34.00 (19 Jun 2012) - - 19 Jun 2012; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.34.00.ebuild: - Version bump based on live ebuild. - -*root-docs-9999 (19 Jun 2012) - - 19 Jun 2012; Andrew Savchenko <bircoph@gmail.com> - +files/root-docs-5.34-makehtml.patch, +root-docs-9999.ebuild: - htmldoc generation for root must be separated, because it is - supposed to be run only root was installed to the live - filesystem. It can't be faked easily in the sandbox environment, - because ROOTSYS is not respected when --prefix or --*dir are - used for configure script. - -*root-docs-5.32 (03 Dec 2011) - - 03 Dec 2011; Andrew Savchenko <bircoph@gmail.com> -root-docs-5.30.ebuild, - +root-docs-5.32.ebuild: - Version bump. - Remove useless html/html32/ patch chunk, thus html files will be - installed directly into /usr/share/doc/${PF}/. - -*root-docs-5.30 (02 Aug 2011) - - 02 Aug 2011; Andrew Savchenko <bircoph@gmail.com> +root-docs-5.30.ebuild, - +metadata.xml: - Version bump. - diff --git a/app-doc/root-docs/Manifest b/app-doc/root-docs/Manifest deleted file mode 100644 index 512e92ea7..000000000 --- a/app-doc/root-docs/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST root_v5.34.10.source.tar.gz 66685508 SHA256 a70c46f382e6557765c4741a367bded9b4041f669e9c313c4201ef66f1ae5d9d SHA512 c51cab511ab771d174f8d6c5ea6d3a047179e9412c508ec31f5a501f71309799dbe863e2d6e72c234a2c973201e3e5131f538c153c5fe68e8a998fe5a59fde11 WHIRLPOOL 677bfeb4bfed1f39be9a7292ab80a2fd1e58e89a4090d4c3b7799397fcb140c5c5f7c421d591e78999218c250f40f232775f7b3a3e680b251d54d5efe5704dc8 -DIST root_v5.34.13.source.tar.gz 67650443 SHA256 15ee741ca2766ee4c7bacadfca64ae9c3f53ddba2ea28728554d78a088ee0043 SHA512 d30365bde0170cb3d2bec93efa73abd0a75f4363f4351c74c62076bd1b4cc282425fbd06236a6ada757df1171450357c36b6bcf53a08108ce5c29cd57cd6039f WHIRLPOOL 22ece4608126500ecaf3cf89a659d5b3ff5b1b24e183d7504d649a03d6a33179ee66370924c0de27a96f91a676e135827a8345bf5c614f8e6d2df46ccaf66e4e diff --git a/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch b/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch deleted file mode 100644 index b339226c8..000000000 --- a/app-doc/root-docs/files/root-docs-5.34.01-makehtml.patch +++ /dev/null @@ -1,51 +0,0 @@ ---- root/Makefile.orig 2012-07-13 13:42:46.000000000 +0400 -+++ root/Makefile 2012-07-22 00:15:03.282994389 +0400 -@@ -1087,16 +1087,7 @@ - - ifeq ($(BUILDX11),yes) - ifeq ($(BUILDASIMAGE),yes) --html: rootexecs postbin changelog releasenotes --ifneq ($(USECONFIG),FALSE) -- @if [ "x`which root.exe`" != "x$(DESTDIR)$(BINDIR)/root.exe" ] \ -- || [ "`which root.exe`" -ot "bin/root.exe" ]; then \ -- echo 'ERROR: root.exe has not been installed by this build.'; \ -- echo ' Run "make install" before running "make html".'; \ -- exit 1; \ -- fi --endif -- @$(MAKELOGHTML) -+html: compiledata releasenotes - @$(MAKEHTML) - else - html: ---- root/build/unix/makehtml.sh.orig 2012-06-28 11:33:36.000000000 +0400 -+++ root/build/unix/makehtml.sh 2012-07-22 00:18:58.705804436 +0400 -@@ -1,16 +1,16 @@ - #! /bin/sh - - dir=`pwd` --ROOT=$dir/bin/root -+ROOT=root - cd tutorials - # we need tutorials/hsimple.root - if [ ! -f hsimple.root ]; then -- $ROOT -l -b -q hsimple.C -+ $ROOT -l -b -q hsimple.C && exit 1 - fi - cd tree - # we need tutorials/tree/cernstaff.root - if [ ! -f cernstaff.root ]; then -- $ROOT -l -b -q cernbuild.C -+ $ROOT -l -b -q cernbuild.C || exit 1 - fi - cd $dir - -@@ -20,7 +20,7 @@ - - # To generate the full documentation, we do need to - # use the graphics engine, so do not use '-b'. --$ROOT -l <<makedoc -+$ROOT -l <<makedoc || exit 1 - THtml h; - h.LoadAllLibs(); - h.MakeAll(); diff --git a/app-doc/root-docs/metadata.xml b/app-doc/root-docs/metadata.xml deleted file mode 100644 index 8d64e524d..000000000 --- a/app-doc/root-docs/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<maintainer> - <email>bircoph@gmail.com</email> - <name>Andrew Savchenko</name> - <description>Maintainer. Assign bugs to him</description> -</maintainer> -<herd>sci-physics</herd> -<longdescription lang="en"> - This package contains the automatically generated ROOT class - documentation. -</longdescription> -</pkgmetadata> diff --git a/app-doc/root-docs/root-docs-5.34.10.ebuild b/app-doc/root-docs/root-docs-5.34.10.ebuild deleted file mode 100644 index 3a039f113..000000000 --- a/app-doc/root-docs/root-docs-5.34.10.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.07.ebuild,v 1.1 2013/05/23 23:50:00 bicatali Exp $ - -EAPI=5 - -ROOT_PN="root" -PATCH_PV="5.34.01" - -if [[ ${PV} == "9999" ]] ; then - _GIT=git-2 - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -inherit eutils multilib toolchain-funcs virtualx ${_GIT} - -DESCRIPTION="API documentation for ROOT (An Object-Oriented Data Analysis Framework)" -HOMEPAGE="http://root.cern.ch/" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="" - -S="${WORKDIR}/${ROOT_PN}" -VIRTUALX_REQUIRED="always" - -DEPEND=" - ~sci-physics/root-${PV}[X,doc,graphviz,htmldoc,opengl] - virtual/pkgconfig - ${_GIT_DEP}" -RDEPEND="" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-${PATCH_PV}-makehtml.patch -} - -src_configure() { - # we need only to setup paths here, html docs doesn't depend on USE flags - ./configure \ - --prefix="${EPREFIX}"/usr \ - --etcdir="${EPREFIX}"/etc/root \ - --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ - --docdir="${EPREFIX}"/usr/share/doc/${PF} \ - --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ - --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ - --with-cc=$(tc-getCC) \ - --with-cxx=$(tc-getCXX) \ - --with-f77=$(tc-getFC) \ - --with-ld=$(tc-getCXX) \ - --with-afs-shared=yes \ - --with-llvm-config="${EPREFIX}"/usr/bin/llvm-config \ - --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \ - --nohowto -} - -src_compile() { - # video drivers may want to access hardware devices - cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g') - [[ -n "${cards}" ]] && addpredict "${cards}" - - ROOTSYS="${S}" Xemake html - # if root.exe crashes, return code will be 0 due to gdb attach, - # so we need to check if last html file was generated; - # this check is volatile and can't catch crash on the last file. - [[ -f htmldoc/timespec.html ]] || die "looks like html doc generation crashed" -} - -src_install() { - dodir /usr/share/doc/${PF} - # too large data to copy - mv htmldoc/* "${ED}usr/share/doc/${PF}/" - docompress -x "${EPREFIX}/usr/share/doc/${PF}/" -} diff --git a/app-doc/root-docs/root-docs-5.34.13.ebuild b/app-doc/root-docs/root-docs-5.34.13.ebuild deleted file mode 100644 index 3a039f113..000000000 --- a/app-doc/root-docs/root-docs-5.34.13.ebuild +++ /dev/null @@ -1,77 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.07.ebuild,v 1.1 2013/05/23 23:50:00 bicatali Exp $ - -EAPI=5 - -ROOT_PN="root" -PATCH_PV="5.34.01" - -if [[ ${PV} == "9999" ]] ; then - _GIT=git-2 - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -inherit eutils multilib toolchain-funcs virtualx ${_GIT} - -DESCRIPTION="API documentation for ROOT (An Object-Oriented Data Analysis Framework)" -HOMEPAGE="http://root.cern.ch/" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="" - -S="${WORKDIR}/${ROOT_PN}" -VIRTUALX_REQUIRED="always" - -DEPEND=" - ~sci-physics/root-${PV}[X,doc,graphviz,htmldoc,opengl] - virtual/pkgconfig - ${_GIT_DEP}" -RDEPEND="" - -src_prepare() { - epatch "${FILESDIR}"/${PN}-${PATCH_PV}-makehtml.patch -} - -src_configure() { - # we need only to setup paths here, html docs doesn't depend on USE flags - ./configure \ - --prefix="${EPREFIX}"/usr \ - --etcdir="${EPREFIX}"/etc/root \ - --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ - --docdir="${EPREFIX}"/usr/share/doc/${PF} \ - --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ - --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ - --with-cc=$(tc-getCC) \ - --with-cxx=$(tc-getCXX) \ - --with-f77=$(tc-getFC) \ - --with-ld=$(tc-getCXX) \ - --with-afs-shared=yes \ - --with-llvm-config="${EPREFIX}"/usr/bin/llvm-config \ - --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \ - --nohowto -} - -src_compile() { - # video drivers may want to access hardware devices - cards=$(echo -n /dev/dri/card* /dev/ati/card* /dev/nvidiactl* | sed 's/ /:/g') - [[ -n "${cards}" ]] && addpredict "${cards}" - - ROOTSYS="${S}" Xemake html - # if root.exe crashes, return code will be 0 due to gdb attach, - # so we need to check if last html file was generated; - # this check is volatile and can't catch crash on the last file. - [[ -f htmldoc/timespec.html ]] || die "looks like html doc generation crashed" -} - -src_install() { - dodir /usr/share/doc/${PF} - # too large data to copy - mv htmldoc/* "${ED}usr/share/doc/${PF}/" - docompress -x "${EPREFIX}/usr/share/doc/${PF}/" -} diff --git a/app-doc/root-docs/root-docs-9999.ebuild b/app-doc/root-docs/root-docs-9999.ebuild deleted file mode 100644 index 8b170c66a..000000000 --- a/app-doc/root-docs/root-docs-9999.ebuild +++ /dev/null @@ -1,97 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/app-doc/root-docs/root-docs-5.34.00.ebuild,v 1.2 2012/06/27 17:31:12 bicatali Exp $ - -EAPI=5 - -ROOT_PN="root" -PATCH_PV="5.34.01" - -if [[ ${PV} == "9999" ]] ; then - _SVN_DEP="dev-vcs/subversion" - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${ROOT_PN}/${ROOT_PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -inherit eutils multilib toolchain-funcs virtualx - -DESCRIPTION="API documentation for ROOT (An Object-Oriented Data Analysis Framework)" -HOMEPAGE="http://root.cern.ch/" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="" - -S="${WORKDIR}/${ROOT_PN}" -VIRTUALX_REQUIRED="always" - -DEPEND=" - ~sci-physics/root-${PV}[X,doc,graphviz,htmldoc,opengl] - virtual/pkgconfig - ${_SVN_DEP}" -RDEPEND="" - -pkg_setup() { - # sandboxed user can't access video hardware, so xorg-x11 implementation - # should be used - GL_IMPLEM=$(eselect opengl show) - eselect opengl set xorg-x11 -} - -src_unpack() { - # can't use subversion eclass functions, - # we need to svn export the same root tree: - # 1) svn revisions for root and root-docs must be the same; - # 2) no need to abuse server twice. - if [[ ${PV} == "9999" ]] ; then - addpredict "${PORTAGE_ACTUAL_DISTDIR:-${DISTDIR}}/svn-src/${ROOT_PN}/trunk/.svn" - svn export "${PORTAGE_ACTUAL_DISTDIR:-${DISTDIR}}/svn-src/${ROOT_PN}/trunk" \ - "${S}" || die "svn export failed" - else - default - fi -} - -src_prepare() { - epatch "${FILESDIR}"/${PN}-${PATCH_PV}-makehtml.patch -} - -src_configure() { - # we need only to setup paths here, html docs doesn't depend on USE flags - ./configure \ - --prefix="${EPREFIX}"/usr \ - --etcdir="${EPREFIX}"/etc/root \ - --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ - --docdir="${EPREFIX}"/usr/share/doc/${PF} \ - --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ - --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ - --with-cc=$(tc-getCC) \ - --with-cxx=$(tc-getCXX) \ - --with-f77=$(tc-getFC) \ - --with-ld=$(tc-getCXX) \ - --with-afs-shared=yes \ - --with-llvm-config="${EPREFIX}"/usr/bin/llvm-config \ - --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps -} - -src_compile() { - ROOTSYS="${S}" Xemake html - # if root.exe crashes, return code will be 0 due to gdb attach, - # so we need to check if last html file was generated; - # this check is volatile and can't catch crash on the last file. - [[ -f htmldoc/timespec.html ]] || die "looks like html doc generation crashed" -} - -src_install() { - dodir /usr/share/doc/${PF} - # too large data to copy - mv htmldoc/* "${ED}usr/share/doc/${PF}/" - docompress -x "${EPREFIX}/usr/share/doc/${PF}/" -} - -pkg_postinst() { - eselect opengl set ${GL_IMPLEM} -} diff --git a/dev-java/joda-convert/ChangeLog b/dev-java/joda-convert/ChangeLog deleted file mode 100644 index 2c2bbe4b6..000000000 --- a/dev-java/joda-convert/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for dev-java/joda-convert -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*joda-convert-1.2 (14 May 2012) - - 14 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +files/1.2-build.xml, - +joda-convert-1.2.ebuild, +metadata.xml: - dev-java/joda-convert: import from the java overlay - diff --git a/dev-java/joda-convert/Manifest b/dev-java/joda-convert/Manifest deleted file mode 100644 index 5cc6d7868..000000000 --- a/dev-java/joda-convert/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST joda-convert-1.2-dist.tar.gz 124723 SHA256 510e15e9174a33af6bf8f52b4f24c14a2b02afdf8808cdb969bc18c3092b3fff SHA512 841b38558ee6a4ae4f781d2bef3720efa4a87fa001c3c9b4fda2cd8a3cc332c2bf2e91fa8ab8675d5b06d5c5368ea0634542c7bedee977f89b39731082dd4ab3 WHIRLPOOL b71db44ea79d3f0e6cca05f1f962b8391b25a06ccfb6ecb738d6cbcb6bb150b847540fcc4bb82fbff876838d622f989450c027cce63de391809a9125b1a7d796 diff --git a/dev-java/joda-convert/files/1.2-build.xml b/dev-java/joda-convert/files/1.2-build.xml deleted file mode 100644 index 07fe6e0ad..000000000 --- a/dev-java/joda-convert/files/1.2-build.xml +++ /dev/null @@ -1,99 +0,0 @@ -<?xml version="1.0"?> -<project name="Joda convert" default="all" basedir="."> - <target name="init" description="Sets build properties"> - <!-- package configuration --> - <property name="package.version" value="devel"/> - <!-- directory locations --> - <property name="src" value="${basedir}/src"/> - <property name="src.lib" value="${src}/main/java"/> - <property name="src.test" value="${src}/test/java"/> - <property name="build" value="${basedir}/build"/> - <property name="build.lib" value="${build}/lib"/> - <property name="build.test" value="${build}/test"/> - <property name="doc" value="${basedir}/doc"/> - <property name="doc.api" value="${doc}/api"/> - <!-- external dependencies --> - <property name="junit.jar" value="junit.jar"/> - <!-- classpaths --> - <path id="project.class.path"> - </path> - <path id="test.class.path"> - <!--pathelement location="${junit.jar}"/--> <!-- handled by Gentoo's ANT_TASKS --> - </path> - <path id="build.lib.class.path"> - <pathelement location="${build.lib}"/> - </path> - <path id="build.test.class.path"> - <pathelement location="${build.test}"/> - </path> - </target> - <target name="all" depends="jar,javadoc" - description="Pseudo-target that builds JAR and Javadoc"/> - <target name="build-lib" depends="init" - description="Compiles the library classes"> - <mkdir dir="${build.lib}"/> - <javac destdir="${build.lib}" srcdir="${src.lib}" debug="true" - deprecation="true" includeantruntime="false"> - <classpath refid="project.class.path"/> - <classpath refid="build.lib.class.path"/> - <!--compilerarg line="-Xlint:unchecked"/--> - </javac> - <!--copy todir="${build}"> - <mappedresources> - <fileset dir="${src}" includes="**/test/test.fits*"/> - <globmapper from="*" to="*"/> - </mappedresources> - </copy--> - </target> - <target name="build-tests" depends="build-lib" - description="Compiles the test classes"> - <mkdir dir="${build.test}"/> - <javac destdir="${build.test}" srcdir="${src.test}" debug="true" - deprecation="true" includeantruntime="false"> - <classpath refid="project.class.path"/> - <classpath refid="test.class.path"/> - <classpath refid="build.lib.class.path"/> - </javac> - </target> - <target name="build" depends="build-lib" - description="Alias for build-lib"/> - <target name="test" depends="build-tests"> - <junit> - <classpath refid="project.class.path"/> - <classpath refid="test.class.path"/> - <classpath refid="build.lib.class.path"/> - <classpath refid="build.test.class.path"/> - <formatter type="brief" usefile="false" /> - <batchtest> - <fileset dir="${build.test}"> - <include name="**/*.class" /> - <exclude name="**/*$*.class" /> - </fileset> - </batchtest> - </junit> - </target> - <target name="javadoc" depends="init" - description="Generates Javadoc API documentation"> - <mkdir dir="${doc.api}"/> - <javadoc packagenames="*" - sourcepath="${src.lib}" destdir="${doc.api}" - author="true" version="true" - use="true" private="true"/> - </target> - <target name="jar" depends="build-lib" - description="Builds a project JAR file"> - <jar basedir="${build.lib}" jarfile="${build}/joda-convert.jar"> - <manifest> - <attribute name="Version" value="${package.version}"/> - </manifest> - </jar> - </target> - <target name="clean" depends="init" - description="Erase all generated files and dirs"> - <delete dir="${build}" verbose="true"/> - <delete dir="${doc}" verbose="true"/> - <delete verbose="true"> - <fileset dir="${basedir}" includes="*.jar"/> - </delete> - </target> -</project> diff --git a/dev-java/joda-convert/joda-convert-1.2.ebuild b/dev-java/joda-convert/joda-convert-1.2.ebuild deleted file mode 100644 index 303b05201..000000000 --- a/dev-java/joda-convert/joda-convert-1.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 -JAVA_PKG_IUSE="doc source test" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java library for conversion between Object and String" -HOMEPAGE="http://joda-convert.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}-dist.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND=">=virtual/jdk-1.5 - dev-java/junit:4 - test? ( - dev-java/ant-junit4 - dev-java/hamcrest-core - )" -RDEPEND=">=virtual/jre-1.5" - -JAVA_PKG_WANT_SOURCE="5" -EANT_EXTRA_ARGS="-Dpacakge.version=${PV}" -EANT_GENTOO_CLASSPATH="junit-4" -JAVA_ANT_REWRITE_CLASSPATH="true" - -src_prepare() { - cp "${FILESDIR}"/${PV}-build.xml build.xml -} - -src_test() { - ANT_TASKS="ant-junit4" eant test -} - -src_install() { - java-pkg_newjar build/${PN}.jar ${PN}.jar - dodoc NOTICE.txt RELEASE-NOTES.txt - use doc && java-pkg_dojavadoc doc/api - use source && java-pkg_dosrc src/main/java/* -} diff --git a/dev-java/joda-convert/metadata.xml b/dev-java/joda-convert/metadata.xml deleted file mode 100644 index b229aec85..000000000 --- a/dev-java/joda-convert/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -</pkgmetadata> diff --git a/dev-java/joda-time/ChangeLog b/dev-java/joda-time/ChangeLog deleted file mode 100644 index 27d441760..000000000 --- a/dev-java/joda-time/ChangeLog +++ /dev/null @@ -1,10 +0,0 @@ -# ChangeLog for dev-java/joda-time -# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - -*joda-time-2.1 (14 May 2012) - - 14 May 2012; Sébastien Fabbro <bicatali@gentoo.org> +joda-time-2.1.ebuild, - +metadata.xml: - dev-java/joda-time: import from wtk overlay - diff --git a/dev-java/joda-time/Manifest b/dev-java/joda-time/Manifest deleted file mode 100644 index afd91527b..000000000 --- a/dev-java/joda-time/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST joda-time-2.1-dist.tar.gz 3405364 SHA256 abcfc6b444a62a266ddc4d0325191d59af6d0bc099f6c050b41906f42b6cb351 SHA512 83cfc67696f30eefdde640c6ba57ba68e87279b750c2ba54d43a0e0f8234aeb9d5e3af675718364c2722cdc32158ff456749f0050afcee11296f4097fc92eaaa WHIRLPOOL e473c7816134f3441bf118bd1ae71169d00eea98980cce63d471911bef6b911ede31db9f256f01fbcb26ea31fc1f4002e4746ff3eee29f7c860bc9db02e29966 diff --git a/dev-java/joda-time/joda-time-2.1.ebuild b/dev-java/joda-time/joda-time-2.1.ebuild deleted file mode 100644 index 1877c4d32..000000000 --- a/dev-java/joda-time/joda-time-2.1.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=4 -JAVA_PKG_IUSE="doc examples source test" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Replacement for the Java Date and Time classes" -HOMEPAGE="http://joda-time.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}-dist.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -CDEPEND="dev-java/joda-convert" -DEPEND=">=virtual/jdk-1.5 - test? ( dev-java/ant-junit4 ) - ${CDEPEND}" -RDEPEND=">=virtual/jre-1.5 - ${CDEPEND}" - -JAVA_PKG_WANT_SOURCE="5" -# chokes on static inner class making instance of non-static inner class -EANT_FILTER_COMPILER="jikes" -# Keep ant from trying to use maven internally -EANT_EXTRA_ARGS="-Djunit.ant=1 -Djunit.present=1 -Djodaconvert.present=1" -EANT_GENTOO_CLASSPATH="joda-convert" -JAVA_ANT_REWRITE_CLASSPATH="true" - -src_test() { - ANT_TASKS="ant-junit" eant \ - -Djunit.jar="$(java-pkg_getjar junit-4 junit.jar)" \ - -Djodaconvert.jar="$(java-pkg_getjar joda-convert joda-convert.jar)" \ - test -} - -src_install() { - java-pkg_newjar build/${P}.jar ${PN}.jar - dodoc NOTICE.txt RELEASE-NOTES.txt ToDo.txt - use doc && java-pkg_dojavadoc build/docs - use examples && java-pkg_doexamples src/example - use source && java-pkg_dosrc src/java/org -} diff --git a/dev-java/joda-time/metadata.xml b/dev-java/joda-time/metadata.xml deleted file mode 100644 index b229aec85..000000000 --- a/dev-java/joda-time/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> -<herd>sci</herd> -</pkgmetadata> diff --git a/sci-biology/amos/ChangeLog b/sci-biology/amos/ChangeLog index 22c5625b3..7d1df6d02 100644 --- a/sci-biology/amos/ChangeLog +++ b/sci-biology/amos/ChangeLog @@ -2,6 +2,12 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: $ + 29 Dec 2013; Justin Lecher <jlec@gentoo.org> -amos-3.1.0-r1.ebuild, + amos-9999.ebuild, -files/amos-3.1.0-gcc-4.7.patch, + -files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch, + -files/amos.m4.patch: + Move to tree + *amos-3.1.0-r1 (11 Sep 2013) 11 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> diff --git a/sci-biology/amos/Manifest b/sci-biology/amos/Manifest deleted file mode 100644 index 27ad50ff2..000000000 --- a/sci-biology/amos/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST amos-3.1.0.tar.gz 2094268 SHA256 2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b SHA512 7a416b9a0438b47425355383b709491a58f38c8d834df29e43c942170e710c6ea7e3bc8c509a58421b1340ad6eece9ea2da357ce5cd1d41ce08375676ee30491 WHIRLPOOL df9b547fcc0b7bf0149641fd8df9e4558f61bb6c17ded0facfeecde25d3a6307b40414e7cb8b2f021fa8cc192ee956672c26e0fc287981f4733a393739e80b61 diff --git a/sci-biology/amos/amos-3.1.0-r1.ebuild b/sci-biology/amos/amos-3.1.0-r1.ebuild deleted file mode 100644 index f1e0470b8..000000000 --- a/sci-biology/amos/amos-3.1.0-r1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/amos/amos-3.1.0.ebuild,v 1.8 2013/03/19 07:41:20 jlec Exp $ - -EAPI=4 - -inherit eutils - -DESCRIPTION="A Modular, Open-Source whole genome assembler" -HOMEPAGE="http://amos.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="qt4" - -DEPEND="qt4? ( dev-qt/qtcore:4 )" -RDEPEND="${DEPEND} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -MAKEOPTS+=" -j1" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch -} diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild index 67180f85f..29ae041f3 100644 --- a/sci-biology/amos/amos-9999.ebuild +++ b/sci-biology/amos/amos-9999.ebuild @@ -4,11 +4,9 @@ EAPI=5 -[ "$PV" == "9999" ] && VCS=git-2 - AUTOTOOLS_AUTORECONF=true -inherit autotools-utils ${VCS} +inherit autotools-utils git-r3 DESCRIPTION="Genome assembly package live cvs sources" HOMEPAGE="http://sourceforge.net/projects/amos" @@ -24,5 +22,5 @@ DEPEND=" dev-libs/boost dev-qt/qtcore:4" RDEPEND="${DEPEND} - dev-perl/DBI - sci-biology/mummer" + dev-perl/DBI + sci-biology/mummer" diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch deleted file mode 100644 index de2a41184..000000000 --- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/Align/find-tandem.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc -index ddf1cab..a29e21e 100644 ---- a/src/Align/find-tandem.cc -+++ b/src/Align/find-tandem.cc -@@ -7,6 +7,7 @@ - #include <vector> - #include <ctime> - #include <sys/time.h> -+#include <unistd.h> - using namespace std; - - const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch deleted file mode 100644 index 97a8f59d0..000000000 --- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch +++ /dev/null @@ -1,25 +0,0 @@ ---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 -+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 -@@ -1,7 +1,7 @@ - #pipeline script for assembly + Bambus 2 - #contributed by Todd J Treangen - --import string, sys, os, subprocess#, spincursor -+import sys, os, subprocess#, spincursor - - RED = "\033[0;31m" - GREEN = "\033[0;32m" -@@ -360,7 +360,7 @@ - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) - -- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) -+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) - - if xopt_dict["verbose"] == 1: - print "10) running OutputResults" -@@ -388,4 +388,3 @@ - else: - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) --) diff --git a/sci-biology/amos/files/amos.m4.patch b/sci-biology/amos/files/amos.m4.patch deleted file mode 100644 index 3c811b3ed..000000000 --- a/sci-biology/amos/files/amos.m4.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- config/amos.m4.ori 2010-12-05 17:33:13.000000000 +0100 -+++ config/amos.m4 2010-12-05 17:46:26.000000000 +0100 -@@ -219,7 +219,7 @@ - ); then - - if test x"$amos_qt_dir" = x; then -- amos_qt_dir="$amos_qt_bin_dir" -+ amos_qt_dir= - fi - if test x"$amos_qt_include_dir" = x; then - amos_qt_include_dir="$amos_qt_dir/include" -@@ -279,16 +279,6 @@ - QT_LIBS="$amos_qt_LIBS" - # If amos_qt_dir is defined, utilities are expected to be in the - # bin subdirectory -- if test x"$amos_qt_dir" != x; then -- if test -x "$amos_qt_dir/bin/uic"; then -- QT_UIC="$amos_qt_dir/bin/uic" -- else -- # Old versions of Qt don't have uic -- QT_UIC= -- fi -- QT_MOC="$amos_qt_dir/bin/moc" -- else -- # Or maybe we are told where to look for the utilities - if test x"$amos_qt_bin_dir" != x; then - if test -x "$amos_qt_bin_dir/uic"; then - QT_UIC="$amos_qt_bin_dir/uic" -@@ -297,11 +287,19 @@ - QT_UIC= - fi - QT_MOC="$amos_qt_bin_dir/moc" -- else -+ if test x"$QT_MOC" = "x/moc"; then - # Last possibility is that they are in $PATH - QT_UIC="`which uic`" - QT_MOC="`which moc`" - fi -+ elif test x"$amos_qt_dir" != x; then -+ if test -x "$amos_qt_dir/bin/uic"; then -+ QT_UIC="$amos_qt_dir/bin/uic" -+ else -+ # Old versions of Qt don't have uic -+ QT_UIC= -+ fi -+ QT_MOC="$amos_qt_dir/bin/moc" - fi - # All variables are defined, report the result - AC_MSG_RESULT([$have_qt]) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog deleted file mode 100644 index baf3b3a19..000000000 --- a/sci-biology/biopython/ChangeLog +++ /dev/null @@ -1,346 +0,0 @@ -# ChangeLog for sci-biology/biopython -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.72 2013/09/17 16:07:56 jlec Exp $ - -*biopython-1.62-r1 (25 Sep 2013) - - 25 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> - +biopython-1.62-r1.ebuild, +files/biopython-1.51-flex.patch, - +files/biopython-1.62-SffIO.patch, +files/SeqRecord.py.patch, - +files/adjust-trimpoints.patch, +metadata.xml: - Upstream accidentally dropped some of my patch chunks while preparing 1.62 - release. Bringing them back myself at least through sci overlay. - -*biopython-1.62 (17 Sep 2013) - - 17 Sep 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.62.ebuild: - Version Bump - - 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild: - Fix deps for python - - 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild: - Keyword ~-linux - -*biopython-1.61 (26 Apr 2013) - - 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild, - metadata.xml: - Version Bump - - 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> biopython-1.57.ebuild, - biopython-1.58.ebuild, biopython-1.59.ebuild: - Update LICENSE, HPND according to LICENSE file. - -*biopython-1.59 (27 Feb 2012) - - 27 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.59.ebuild: - Version bump - - 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild: - Version bump - -*biopython-1.58 (26 Dec 2011) - - 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild: - Version bump - - 23 Jun 2011; Markos Chandras <hwoarang@gentoo.org> -biopython-1.56.ebuild: - Remove old ebuilds. Requested by Arfrever - - 28 May 2011; Brent Baude <ranger@gentoo.org> biopython-1.57.ebuild: - Marking biopython-1.57 ppc for bug 365877 - - 24 May 2011; Markus Meier <maekke@gentoo.org> biopython-1.57.ebuild: - x86 stable, bug #365877 - - 06 May 2011; Justin Lecher <jlec@gentoo.org> biopython-1.56.ebuild, - biopython-1.57.ebuild: - Cleaned DESCRIPTION - - 05 May 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.57.ebuild: - Stable on amd64 wrt bug #365877 - -*biopython-1.57 (03 Apr 2011) - - 03 Apr 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - +biopython-1.57.ebuild: - Version bump. - - 30 Jan 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - -biopython-1.55.ebuild: - Delete. - - 30 Jan 2011; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild, - biopython-1.56.ebuild: - Drop alpha/sparc keywords - - 15 Jan 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org> - biopython-1.56.ebuild: - x86 stable wrt bug #351498 - - 14 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.56.ebuild: - stable ppc, bug 351498 - - 13 Jan 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.56.ebuild: - Stable on amd64 wrt bug #351498 - - 06 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.55.ebuild: - Marking biopython-1.55 ppc for bug 341519 - -*biopython-1.56 (13 Dec 2010) - - 13 Dec 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild: - Version bump. - - 31 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild: - alpha/sparc stable wrt #341519 - - 21 Oct 2010; Thomas Kahle <tomka@gentoo.org> biopython-1.55.ebuild: - x86 stable per bug 341519 - - 19 Oct 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.55.ebuild: - Stable on amd64 wrt bug #341519 - - 15 Oct 2010; Brent Baude <ranger@gentoo.org> biopython-1.54.ebuild: - stable ppc, bug 327151 - - 10 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.54.ebuild: - sparc stable wrt #327151 - -*biopython-1.55 (17 Sep 2010) - - 17 Sep 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - +biopython-1.55.ebuild: - Version bump. - - 12 Sep 2010; Tobias Klausmann <klausman@gentoo.org> biopython-1.54.ebuild: - Stable on alpha, bug #327151 - - 12 Jul 2010; Christian Faulhammer <fauli@gentoo.org> - biopython-1.54.ebuild: - stable x86, bug 327151 - - 06 Jul 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.54.ebuild: - Stable on amd64 wrt bug #327151 - -*biopython-1.54 (05 Jun 2010) - - 05 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - -biopython-1.49.ebuild, -files/biopython-1.49-flex.patch, - -biopython-1.51.ebuild, -biopython-1.52.ebuild, +biopython-1.54.ebuild: - Version bump. - - 13 Feb 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.53.ebuild: - alpha/sparc stable wrt #301964 - - 07 Feb 2010; Markus Meier <maekke@gentoo.org> biopython-1.53.ebuild: - amd64/x86 stable, bug #301964 - - 24 Jan 2010; Brent Baude <ranger@gentoo.org> biopython-1.53.ebuild: - stable ppc, bug 301964 - -*biopython-1.53 (21 Dec 2009) - - 21 Dec 2009; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org> - +biopython-1.53.ebuild: - Version bump. Set SUPPORT_PYTHON_ABIS. - - 31 Oct 2009; Markus Meier <maekke@gentoo.org> biopython-1.52.ebuild: - amd64/x86 stable, bug #290931 - -*biopython-1.52 (23 Sep 2009) - - 23 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.52.ebuild: - Version bump - -*biopython-1.51 (09 Sep 2009) - - 09 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> - +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild: - Version bump - - 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> metadata.xml: - remove now unused flag description - - 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> - -biopython-1.42.ebuild, -files/biopython-1.43-buildkdtree.patch, - -biopython-1.44.ebuild, -files/biopython-1.44-sequtils-complement.patch, - -biopython-1.47.ebuild, -files/biopython-1.47-kdtree.patch: - clean up - - 26 Aug 2009; Tobias Klausmann <klausman@gentoo.org> biopython-1.49.ebuild: - Stable on alpha, bug #277822 - - 02 Aug 2009; nixnut <nixnut@gentoo.org> biopython-1.49.ebuild: - ppc stable #277822 - - 20 Jul 2009; Jeremy Olexa <darkside@gentoo.org> biopython-1.49.ebuild: - amd64 stable, bug 277822 - - 17 Jul 2009; Ferris McCormick <fmccor@gentoo.org> biopython-1.49.ebuild: - Sparc stable --- bug #277822 --- ran tests successfully. - - 14 Jul 2009; Christian Faulhammer <fauli@gentoo.org> - biopython-1.49.ebuild: - stable x86, bug 277822 - - 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Giving up maintainership of this package. - -*biopython-1.49 (16 Jan 2009) - - 16 Jan 2009; Olivier Fisette <ribosome@gentoo.org> - +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild: - Version bump. Thanks to Juan Aguado <juantxorena@gmail.com> for his work. - Fixes bug #248799. - - 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml: - Add USE flag description to metadata wrt GLEP 56. - - 14 Jul 2008; nixnut <nixnut@gentoo.org> biopython-1.44.ebuild: - Stable on ppc wrt bug 221159 - - 07 Jul 2008; Raúl Porcel <armin76@gentoo.org> biopython-1.44.ebuild: - alpha/sparc/x86 stable wrt #221159 - -*biopython-1.47 (06 Jul 2008) - - 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> - +files/biopython-1.47-kdtree.patch, +biopython-1.47.ebuild: - New version. Better documentation installation. Added scripts and test - suite. KDTree now enabled by default (requires switching to EAPI 1). - - 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.44.ebuild: - Stable on amd64. - - 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.42.ebuild, - biopython-1.44.ebuild: - Q.A.: Quoted variables. - - 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> -biopython-1.43.ebuild: - Removed buggy version (see bug #202602). - -*biopython-1.44 (30 Jan 2008) - - 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> - +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild: - Fixed six_frame_translations function. Thanks to JTRiley - <justin.t.riley@gmail.com> for his patch. (Fixes bug #202606.) - -*biopython-1.43 (17 May 2007) - - 17 May 2007; Olivier Fisette <ribosome@gentoo.org> - +files/biopython-1.43-buildkdtree.patch, -biopython-1.40b.ebuild, - +biopython-1.43.ebuild: - New upstream version. Ebuild clean-up. Pruned old version. - - 16 May 2007; Raúl Porcel <armin76@gentoo.org> biopython-1.42.ebuild: - alpha stable wrt #153774 - - 05 Nov 2006; Christian Faulhammer <opfer@gentoo.org> - biopython-1.42.ebuild: - stabled x86, bug #153774 - - 03 Nov 2006; <blubb@gentoo.org> biopython-1.42.ebuild: - stable on amd64 - - 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -biopython-1.41.ebuild: - Pruned old version. - - 02 Nov 2006; nixnut <nixnut@gentoo.org> biopython-1.42.ebuild: - Stable on ppc wrt bug 153774 - - 02 Nov 2006; Jason Wever <weeve@gentoo.org> biopython-1.42.ebuild: - Stable on SPARC wrt bug #153774. - - 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml: - Taking over maintainership. - -*biopython-1.42 (12 Sep 2006) - - 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +biopython-1.42.ebuild: - New upstream version. - - 19 Jan 2006; George Shapovalov <george@gentoo.org> +biopython-1.41.ebuild: - new version, cleaned up install - - 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.24.ebuild, - -biopython-1.30.ebuild: - Removed obsolete versions. - - 12 Jun 2005; Bryan Østergaard <kloeri@gentoo.org> biopython-1.40b.ebuild: - Stable on alpha. - - 21 May 2005; Jason Wever <weeve@gentoo.org> biopython-1.40b.ebuild: - Stable on SPARC. - - 13 May 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.10.ebuild, - -biopython-1.21.ebuild, -biopython-1.23.ebuild, biopython-1.40b.ebuild: - Removed obsolete versions. Added 1.40b to x86. - -*biopython-1.40b (19 Feb 2005) - - 19 Feb 2005; Olivier Fisette <ribosome@gentoo.org> - +biopython-1.40b.ebuild: - New version. Should fix bug #82498. - - 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> : - Change encoding to UTF-8 for GLEP 31 compliance - -*biopython-1.23 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml, - +biopython-1.10.ebuild, +biopython-1.21.ebuild, +biopython-1.23.ebuild, - +biopython-1.24.ebuild, +biopython-1.30.ebuild: - Moved from app-sci/biopython to sci-biology/biopython. - - 13 Dec 2004; Jason Wever <weeve@gentoo.org> biopython-1.24.ebuild: - Stable on sparc. - -*biopython-1.30 (07 Oct 2004) - - 07 Oct 2004; George Shapovalvo <george@gentoo.org> biopython-1.30.ebuild : - new version (#51833) - amd64 has problems with KDTree, will try to look into this more later - - 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> biopython-1.24.ebuild: - Stable on alpha. - - 03 Apr 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild: - Marked stable on x86 - -*biopython-1.24 (29 Feb 2004) - - 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild : - version bump - -*biopython-1.23 (30 Dec 2003) - - 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.23.ebuild : - marked stable on x86 - - 30 Dec 2003; George Shapovalvo <george@gentoo.org> biopython-1.23.ebuild : - new version, reworked to use distutils. Thanks to - Peter Bienstman <Peter.Bienstman@rug.ac.be> for an update (#35727) - - 02 Sep 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild, - biopython-1.21.ebuild: - moved dev-python/Numeric to dev-python/numeric - -*biopython-1.21 (08 Aug 2003) - - 08 Aug 2003; George Shapovalov <george@gentoo.org> biopython-1.21.ebuild : - new version, added few docs (#25428) - thanks to Daniel Jaeggi <daniel@jaeggi.co.uk> for notification - - 04 Jul 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild: - renamed reportlab dep - -*biopython-1.10 (18 Feb 2003) - - 18 Feb 2003; George Shapovalov <george@gentoo.org> ChangeLog, biopython-1.10.ebuild, files/digest-biopython-1.10 : - initial release (#11617) - Biopython - python module for Computational Moelcular Biology - ebuild submitted by Daniel Jaeggi <daniel@jaeggi.co.uk> diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest deleted file mode 100644 index 0ac23ecd9..000000000 --- a/sci-biology/biopython/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST biopython-1.62.tar.gz 11389349 SHA256 b056414028c8cc0eea3de20d740f7a12ad0813b705de7dd454deec8f9ede52c6 SHA512 0178fd2c2e7b5e9a6cf05e8b8567bb0c1a93e9b05d5faa9802e0e2b0d59fc5e2ce9786c38cbbd00be5b35e4e4a3b41869e774a50cbbcdf6b34788c873cf0f3f2 WHIRLPOOL 63f61243581afee07cd9295989cb90b2221588e066eb1d5695da4b75fcd0abc95a9341ce07a8ffdfc3e85afdc6002582c589ac39e36e98ca4c8a257e63826351 diff --git a/sci-biology/biopython/biopython-1.62-r1.ebuild b/sci-biology/biopython/biopython-1.62-r1.ebuild deleted file mode 100644 index d3e61a264..000000000 --- a/sci-biology/biopython/biopython-1.62-r1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python{2_6,2_7} ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="mysql postgres" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/reportlab[${PYTHON_USEDEP}] - media-gfx/pydot[${PYTHON_USEDEP}] - mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) - postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" -DEPEND="${RDEPEND} - sys-devel/flex" - -DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) - -src_prepare() { - distutils-r1_src_prepare - epatch "${FILESDIR}/${PN}-1.62-SffIO.patch" -} - -python_test() { - cd Tests || die - ${PYTHON} run_tests.py || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${PN} - cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die -} diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch deleted file mode 100644 index 7f2208ef6..000000000 --- a/sci-biology/biopython/files/biopython-1.62-SffIO.patch +++ /dev/null @@ -1,36 +0,0 @@ ---- Bio/SeqIO/SffIO.py.ori 2013-09-25 13:28:51.000000000 +0200 -+++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200 -@@ -383,7 +383,14 @@ - if padding: - padding = 8 - padding - if handle.read(padding).count(_null) != padding: -- raise ValueError("Post quality %i byte padding region contained data" -+ import warnings -+ from Bio import BiopythonParserWarning -+ warnings.warn("Your SFF file is valid but post quality %i byte " -+ "padding region contains UNUSED data. Was the " -+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " -+ "It did not clear some internal buffer while writing " -+ "out new data so that previous values remained in the" -+ "output unless overwritten by new real values." - % padding) - #print read, name, record_offset - yield name, record_offset ---- Bio/SeqIO/SffIO.py.ori 2013-09-25 14:07:14.000000000 +0200 -+++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200 -@@ -596,7 +596,14 @@ - if padding: - padding = 8 - padding - if handle.read(padding).count(_null) != padding: -- raise ValueError("Post quality %i byte padding region contained data" -+ import warnings -+ from Bio import BiopythonParserWarning -+ warnings.warn("Your SFF file is valid but post quality %i byte " -+ "padding region contains UNUSED data. Was the " -+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? " -+ "It did not clear some internal buffer while writing " -+ "out new data so that previous values remained in the" -+ "output unless overwritten by new real values." - % padding) - #Follow Roche and apply most aggressive of qual and adapter clipping. - #Note Roche seems to ignore adapter clip fields when writing SFF, diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml deleted file mode 100644 index f17a827e3..000000000 --- a/sci-biology/biopython/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <herd>sci-biology</herd> -</pkgmetadata> diff --git a/sci-mathematics/polymake/ChangeLog b/sci-mathematics/polymake/ChangeLog deleted file mode 100644 index 91e35b682..000000000 --- a/sci-mathematics/polymake/ChangeLog +++ /dev/null @@ -1,8 +0,0 @@ -# ChangeLog for sci-mathematics/polymake -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 03 Mar 2013; Justin Lecher <jlec@gentoo.org> polymake-2.11-r1.ebuild, - metadata.xml: - Add missing multilib.eclass - diff --git a/sci-mathematics/polymake/Manifest b/sci-mathematics/polymake/Manifest deleted file mode 100644 index 19f4c38fa..000000000 --- a/sci-mathematics/polymake/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST polymake-2.11.tar.bz2 13249691 SHA256 232dd41f39ad7f67508c513ced2642f84f9e116b3613a790b57900a3dfce286d SHA512 2af0baa07b130fabc194367774a09cbf8714ba08b73b094c5562eb5132101553b1e1ff6378bed004591cd67b73341691ae9ba11945ca4f2036324603661f4958 WHIRLPOOL fe66d72ce84a7ec5f491658988d257ecf106e55bb100f5935a5fe5f2d8a802294f68f68c7d9c4038906d5712929eb8355158ffa121e4c151ac8f14c5263767bb diff --git a/sci-mathematics/polymake/files/2.10-soname.patch b/sci-mathematics/polymake/files/2.10-soname.patch deleted file mode 100644 index 14e66eaeb..000000000 --- a/sci-mathematics/polymake/files/2.10-soname.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- polymake-2.10.fixed/support/corelib.make 2011-06-20 08:30:06.000000000 +0100 -+++ polymake-2.10/support/corelib.make 2011-08-20 23:42:29.000000000 +0100 -@@ -89,7 +89,7 @@ - ifneq (${LDcallableFlags},none) - # no explicit dependence on XSObjects here because they are built in compile-xs using the Makefile generated by xsubpp - ${CallableLib} : ${SharedObjects} ${CallableSharedObjects} ${GlueObjects} ${CallableGlueObjects} ${XXSObjects} $(patsubst %,${SourceDir}/perl/%.xs,${XSModules}) -- ${CXX} ${LDcallableFlags} -o $@ ${SharedObjects} ${CallableSharedObjects} ${GlueObjects} ${CallableGlueObjects} ${XXSObjects} ${XSObjects} ${LDFLAGS} ${PERLccdlflags} -lmpfr -lgmp ${LIBS} -L${PERLarchlib}/CORE -lperl -+ ${CXX} ${LDcallableFlags} -Wl,-soname,libpolymake.so.0 -o $@ ${SharedObjects} ${CallableSharedObjects} ${GlueObjects} ${CallableGlueObjects} ${XXSObjects} ${XSObjects} ${LDFLAGS} ${PERLccdlflags} -lmpfr -lgmp ${LIBS} -L${PERLarchlib}/CORE -lperl - else - ${CallableLib} : ${XXSObjects} $(patsubst %,${SourceDir}/perl/%.xs,${XSModules}) - endif diff --git a/sci-mathematics/polymake/files/polymake-2.11-drop-jreality.patch b/sci-mathematics/polymake/files/polymake-2.11-drop-jreality.patch deleted file mode 100644 index 0eefe58ac..000000000 --- a/sci-mathematics/polymake/files/polymake-2.11-drop-jreality.patch +++ /dev/null @@ -1,25 +0,0 @@ -diff -U 3 -dHrN polymake-2.11.orig/Makefile polymake-2.11/Makefile ---- polymake-2.11.orig/Makefile 2011-12-23 15:51:41.762207359 +0100 -+++ polymake-2.11/Makefile 2011-12-23 15:52:13.889973019 +0100 -@@ -134,11 +134,11 @@ - @case "$$(uname -s)" in \ - *linux*|*Linux*) \ - for d in linux32 linux64; do \ -- ${PERL} ${INSTALL_PL} -m ${DirMask} -U external/jreality/jni/$$d ${InstallArch}/lib/jreality/jni/$$d; \ -+ true; \ - done; \ - ;; \ - Darwin*|darwin*) \ -- ${PERL} ${INSTALL_PL} -m ${DirMask} -U external/jreality/jni/macosx ${InstallArch}/lib/jreality/jni/macosx; \ -+ true; \ - ;; \ - esac - [ -d ${InstallBin} ] || $(call _CreateDir,${InstallBin}) -@@ -166,7 +166,6 @@ - @+$(call _MakeApps, install-src) - $(if ${.svn},${CallPolymake} --no-config --script filter_rules -m ${InstallTop} ${Apps}) - [ ! -d java_build ] || $(call _InstallSubdir,java_build,-X de) -- [ ! -d java_build ] || $(call _InstallSubdirRenamed,external/jreality/lib,java_build/jreality/lib) - $(call _InstallSubdir,povray) - $(call _InstallSubdir,scripts) - $(call _InstallSubdir,xml) diff --git a/sci-mathematics/polymake/metadata.xml b/sci-mathematics/polymake/metadata.xml deleted file mode 100644 index 86e481e52..000000000 --- a/sci-mathematics/polymake/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer> - <email>tomka@gentoo.org</email> - <name>Thomas Kahle</name> - </maintainer> - <herd>sci-mathematics</herd> - <use> - <flag name="libpolymake">Build the polymake library to build applications using the C++ interface.</flag> - </use> - <longdescription lang="en"> -Polymake started out as a tool for the algorithmic treatment of convex -polyhedra. By now it also deals with finite simplicial complexes, -tight spans of finite metric spaces, and other objects. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/polymake/polymake-2.11-r1.ebuild b/sci-mathematics/polymake/polymake-2.11-r1.ebuild deleted file mode 100644 index e75f91f40..000000000 --- a/sci-mathematics/polymake/polymake-2.11-r1.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: $ - -EAPI=2 - -inherit eutils flag-o-matic multilib - -MY_PV=${PV} - -DESCRIPTION="research tool for polyhedral geometry and combinatorics" -SRC_URI="http://polymake.org/lib/exe/fetch.php/download/${PN}-${MY_PV}.tar.bz2" -HOMEPAGE="http://polymake.org" - -IUSE="libpolymake" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="dev-libs/gmp - dev-libs/boost - dev-libs/libxml2:2 - dev-perl/XML-LibXML - dev-libs/libxslt - dev-perl/XML-LibXSLT - dev-perl/XML-Writer - dev-perl/Term-ReadLine-Gnu" -RDEPEND="${DEPEND}" - -src_prepare() { - # embedded jreality is a precompiled desaster (bug #346073) - epatch "${FILESDIR}/${P}"-drop-jreality.patch - # Assign a soname - epatch "${FILESDIR}/2.10"-soname.patch - rm -rf java_build/jreality - - # Don't strip - sed -i '/system "strip $to"/d' support/install.pl || die - - einfo "During compile this package uses up to" - einfo "750MB of RAM per process. Use MAKEOPTS=\"-j1\" if" - einfo "you run into trouble." -} - -src_configure () { - export CXXOPT=$(get-flag -O) - local myconf - if use libpolymake ; then - # WTF: If we leave myconf as the empty string here - # then configure will fail. - myconf="--without-prereq" - else - # --with-callable is not supported :( - myconf="--without-callable" - fi - echo ${myconf} - # Configure does not accept --host, therefore econf cannot be used - ./configure --prefix="${EPREFIX}/usr" \ - --without-java \ - --without-prereq \ - --libdir="${EPREFIX}/usr/$(get_libdir)" \ - --libexecdir="${EPREFIX}/usr/$(get_libdir)/polymake" \ - "${myconf}" || die -} - -src_install(){ - emake -j1 DESTDIR="${D}" install || die "install failed" -} - -pkg_postinst(){ - elog "Polymake uses Perl Modules compiled during install." - elog "You have to reinstall polymake after an upgrade of Perl." - elog " " - elog "This version of polymake does not ship docs. Sorry." - elog "Help can be found on http://www.opt.tu-darmstadt.de/polymake_doku/ " - elog " " - elog "Visualization in polymake is via jreality which ships pre-compiled" - elog "binary libraries. Until this situation is resolved, support for" - elog "jreality has been dropped. Please contribute to Bug #346073 to " - elog "make jreality available in Gentoo." -} diff --git a/sci-physics/lammps/ChangeLog b/sci-physics/lammps/ChangeLog deleted file mode 100644 index 76ef3a916..000000000 --- a/sci-physics/lammps/ChangeLog +++ /dev/null @@ -1,77 +0,0 @@ -# ChangeLog for sci-physics/lammps -# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 -# $Header: $ - - 22 Dec 2013; Christoph Junghans <ottxor@gentoo.org> lammps-20130816.ebuild, - lammps-20130830.ebuild, lammps-20130917.ebuild, lammps-20130923.ebuild, - lammps-20130930.ebuild, lammps-20131111.ebuild, lammps-20131123.ebuild, - lammps-20131201.ebuild: - remove elog message - - 13 Dec 2013; Nicolas Bock <nicolasbock@gentoo.org> metadata.xml: - sci-physics/lammps: updated maintainer email to gentoo.org - -*lammps-20131201 (04 Dec 2013) - - 04 Dec 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20131201.ebuild: - sci-physics/lammps: Version bump to 20121201. - -*lammps-20131123 (22 Nov 2013) - - 22 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20131123.ebuild: - sci-physics/lammps-20131123: Version bump. - -*lammps-20131111 (11 Nov 2013) - - 11 Nov 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20131111.ebuild: - sci-physics/lammps-20131111: Version bump. - -*lammps-20130930 (16 Oct 2013) - - 16 Oct 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130930.ebuild: - sci-physics/lammps-20130930: Version bump. - -*lammps-20130923 (27 Sep 2013) - - 27 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130923.ebuild, - -lammps-20130701.ebuild, -lammps-20130708.ebuild, -lammps-20130711.ebuild: - sci-physics/lammps-20130923: Version bump. I also removed older versions to - clean up a bit. - -*lammps-20130917 (18 Sep 2013) - - 18 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130917.ebuild: - sci-physics/lammps-20130917: Version bump. - -*lammps-20130830 (02 Sep 2013) - - 02 Sep 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130830.ebuild: - sci-physics/lammps: Version bump to 20130830. - -*lammps-20130816 (13 Aug 2013) - - 13 Aug 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130816.ebuild: - sci-physics/lammps-20130816: Version bump. - -*lammps-20130711 (16 Jul 2013) - - 16 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130711.ebuild: - Version bump to sci-physics/lammps-20130711 - - 09 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> lammps-20130708.ebuild: - sci-physics/lammps: Fixed repoman warning. - -*lammps-20130708 (09 Jul 2013) - - 09 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130708.ebuild: - Added current version: sci-physics/lammps-20130708. * Fixed bug in lammps to - gentoo version string conversion. In bash arithmetic operations, a string - literal with a leading "0" is interpreted in base 8. * Added potentials, which - were not installed in previous versions. * Moved examples from - /usr/share/doc/${PF} to /usr/share/lammps-${PF}. - -*lammps-20130701 (03 Jul 2013) - - 03 Jul 2013; Nicolas Bock <nicolasbock@gmail.com> +lammps-20130701.ebuild, - +metadata.xml: - Version bump to 1-Jul-2013. diff --git a/sci-physics/lammps/Manifest b/sci-physics/lammps/Manifest deleted file mode 100644 index 78879459e..000000000 --- a/sci-physics/lammps/Manifest +++ /dev/null @@ -1,8 +0,0 @@ -DIST lammps-11Nov13.tar.gz 57121119 SHA256 911035f4a428b4abfe744239fd54660a8caefcf70bc5abea820ff6c4baec9ad9 SHA512 7fa1d20834c2b58277c54ec36b286099eb29728f73a28c596285eed37c7ca0f1dfe22460eb49000d3586c88c00a0051cf73c35f718b1cd9fd1bb41aabe710021 WHIRLPOOL c79b4be1cc7dd8d038d9b4e523ec71229122de9b9d0f98d93e6255896f8f5b68dd38f5264146f22d206dee32ed5a972a881b9160f0a3b52b053613582aecf38b -DIST lammps-16Aug13.tar.gz 48337879 SHA256 740d35046961df7ea2dd39e2b7a28e5ff1414f283ac9f568986bd1f2b8b036d9 SHA512 1e56751b94e2af8487c77066846cad7e3a98b7f990a90db9b57e32dc8e3c0a4b9be3431a92f393962fb703ce4957c1d2580545e27549e47a3207e88ec158aa8d WHIRLPOOL d3d442d1d7e9e0267de2a637fd44c87df6dc8eaad61de28cc1aa75d93b49b7877c1de21df251fc8d812e36391f2c5d5e7a75b4b349e6749e9efb9b5266edeb77 -DIST lammps-17Sep13.tar.gz 49985563 SHA256 607f6bfadd644bfa8403af1f38d28b4b36bc8d2fe50f09514c7fa13c2d180cbb SHA512 fb303d26846ea3cf42cd6fae2a641989b1debd5c3c4482f006293cb9ace91040faf7bfdc9fbb7c99934414fbeb8b85899c7ff8ce7239a0c3d698a0e1187ae3c6 WHIRLPOOL bd1e308845880831d404447b88784a769c18c472cd22463b949e22a6444de0ffe7826ed2ffc238d909429e2b58c024d368f2c7ee870bda41172958cff840b394 -DIST lammps-1Dec13.tar.gz 57750078 SHA256 44ef69f31f2066fec31a6b7c9511395c21ead00030d3a5e00efa7eb27e6314d9 SHA512 1c5b0f5e9e2e09243f6ec3ac045021f8506626f8311082fb57314246f25f7ea6bd90dacd3d89db6561d5f0039f6476fd1d9e6d09c57c1bcc63be53ac519aec07 WHIRLPOOL ea3796dbca79f97eb7f9fc5f72972a882357108792f7bb96a8a5e7f3f1614917b452e129143b4e12964e51aeaa80dde6e414ec3f4a89220a3d36d012a829f2d7 -DIST lammps-23Nov13.tar.gz 57113682 SHA256 2291e26b7bc3e640f1fbd9ffebbaa2173b665fa9d3757b1eb2aa73bc7837876c SHA512 68758c58f6b8f3b554cad18e610da06875e4abfd0ddb9d85da079ccc52f8d1fce5b3447d9b7c7c607a2e887b2d71af04f221bbe96e13d4276702054338537a2a WHIRLPOOL b9aab585fd735e31beb59c5f1ce1187da8d4235aefbc1a83e89b410f79299c39f37d9157cc3549a139f9746d7b22cf2b2277609c0d675fee6cc35e67ca0c026e -DIST lammps-23Sep13.tar.gz 50063308 SHA256 0d8c575dc137a67865bbfc408f60dd7d3c74371c48d5f64f884dcfa02501a6d4 SHA512 0ffa44fe9e2ad3d16b0c23699e3a9c114c7731f49b5b7b561fda2f811c57bc273ad236cb9a091eb9bcf98324ee6451689c769cfc418046af0024862f99f81e17 WHIRLPOOL aa3c23c95071594453d585596d8cac0ecd5909a342143fdee78f9d97e205c32faa0705b6341028529bf8347c55f5f5f8e74f408010545e1154e6375e4566c7f6 -DIST lammps-30Aug13.tar.gz 48632345 SHA256 8d20ab00412feda5c9869de0188c52fb77f1faa51b317f09706eff35e651d961 SHA512 9722a3a4a7adc3387014650bd5a3ed18f3081065791507d0c39227a394f375f10a8ffbb5510fac24fcc6e84a40b98c0ad21d576969824284e65be94c445e5a24 WHIRLPOOL 50c6f4aed0ef21aa9078eb16ea15f6d6a89bc24316a40183ac993fbf3fecca2c55a5bcf1715cfbecff24ea07e96c55ba082679b11926c50f6ac2da2ec17547e4 -DIST lammps-30Sep13.tar.gz 50062591 SHA256 a39df3b158e1cc587e5f25e2aba6c3dd4696d90a30e1067b17bf64a9ebcc5795 SHA512 f6caf05d19bff3b2bf39cda55ca85966b09cf2f0a6bdbe60c4c9daa8caf13e409270db9a37e6d28267b35b5f262cdb8ae2e36095f9c942515368d9e6d8c5020b WHIRLPOOL 60236db937618d15e9b61f7aeeeecfe8273b17ff9798c91790d9a31a7578c17bb6dfcd72bbaed861f16d7df07a18348adfadf4ac5fcb8ebe32c9fa966b6c73b1 diff --git a/sci-physics/lammps/lammps-20130816.ebuild b/sci-physics/lammps/lammps-20130816.ebuild deleted file mode 100644 index 93a69ed1f..000000000 --- a/sci-physics/lammps/lammps-20130816.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20130830.ebuild b/sci-physics/lammps/lammps-20130830.ebuild deleted file mode 100644 index 93a69ed1f..000000000 --- a/sci-physics/lammps/lammps-20130830.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20130917.ebuild b/sci-physics/lammps/lammps-20130917.ebuild deleted file mode 100644 index 93a69ed1f..000000000 --- a/sci-physics/lammps/lammps-20130917.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20130923.ebuild b/sci-physics/lammps/lammps-20130923.ebuild deleted file mode 100644 index 93a69ed1f..000000000 --- a/sci-physics/lammps/lammps-20130923.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20130930.ebuild b/sci-physics/lammps/lammps-20130930.ebuild deleted file mode 100644 index fe4c7ad49..000000000 --- a/sci-physics/lammps/lammps-20130930.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20131111.ebuild b/sci-physics/lammps/lammps-20131111.ebuild deleted file mode 100644 index fe4c7ad49..000000000 --- a/sci-physics/lammps/lammps-20131111.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20131123.ebuild b/sci-physics/lammps/lammps-20131123.ebuild deleted file mode 100644 index fe4c7ad49..000000000 --- a/sci-physics/lammps/lammps-20131123.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/lammps-20131201.ebuild b/sci-physics/lammps/lammps-20131201.ebuild deleted file mode 100644 index fe4c7ad49..000000000 --- a/sci-physics/lammps/lammps-20131201.ebuild +++ /dev/null @@ -1,114 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/lammps/lammps-20130526.ebuild,v 1.1 2013/06/26 23:53:11 ottxor Exp $ - -EAPI=5 - -FORTRAN_NEEDED="package-meam" - -inherit eutils fortran-2 - -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}-$((10#${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/${MY_P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="doc examples gzip lammps-memalign mpi package-dipole package-meam package-rigid" - -DEPEND="mpi? ( virtual/mpi )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -lmp_emake() { - local LAMMPS_INCLUDEFLAGS="$(usex gzip '-DLAMMPS_GZIP' '')" - LAMMPS_INCLUDEFLAGS+="$(usex lammps-memalign ' -DLAMMPS_MEMALIGN' '')" - - # Note: The lammps makefile uses CC to indicate the C++ compiler. - emake \ - ARCHIVE=$(tc-getAR) \ - CC=$(usex mpi "mpic++" "$(tc-getCXX)") \ - F90=$(usex mpi "mpif90" "$(tc-getFC)") \ - LINK=$(usex mpi "mpic++" "$(tc-getCXX)") \ - CCFLAGS="${CXXFLAGS}" \ - F90FLAGS="${FCFLAGS}" \ - LINKFLAGS="${LDFLAGS}" \ - LMP_INC="${LAMMPS_INCLUDEFLAGS}" \ - MPI_INC=$(usex mpi '' "-I../STUBS") \ - MPI_PATH=$(usex mpi '' '-L../STUBS') \ - MPI_LIB=$(usex mpi '' '-lmpi_stubs') \ - "$@" -} - -src_compile() { - # Compile stubs for serial version. - use mpi || lmp_emake -C src stubs - - # Build optional packages. - if use package-meam; then - lmp_emake -C src yes-meam - lmp_emake -j1 -C lib/meam -f Makefile.gfortran - fi - use package-dipole && emake -C src yes-dipole - use package-rigid && emake -C src yes-rigid - - # Compile. - lmp_emake -C src serial -} - -src_install() { - newbin "src/lmp_serial" "lmp" - - local LAMMPS_POTENTIALS="/usr/share/${PF}/potentials" - insinto "${LAMMPS_POTENTIALS}" - doins potentials/* - echo "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS}" > 99lammps - doenvd 99lammps - - if use examples; then - local LAMMPS_EXAMPLES="/usr/share/${PF}/examples" - insinto "${LAMMPS_EXAMPLES}" - doins -r examples/* - fi - - dodoc README - if use doc; then - dodoc doc/Manual.pdf - dohtml -r doc/* - fi -} diff --git a/sci-physics/lammps/metadata.xml b/sci-physics/lammps/metadata.xml deleted file mode 100644 index 7a1dc9492..000000000 --- a/sci-physics/lammps/metadata.xml +++ /dev/null @@ -1,31 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <longdescription lang="en"> - LAMMPS is a classical molecular dynamics code, and an acronym for - Large-scale Atomic/Molecular Massively Parallel Simulator. - - LAMMPS has potentials for soft materials (biomolecules, polymers) and - solid-state materials (metals, semiconductors) and coarse-grained or - mesoscopic systems. It can be used to model atoms or, more generically, - as a parallel particle simulator at the atomic, meso, or continuum - scale. - - LAMMPS runs on single processors or in parallel using message-passing - techniques and a spatial-decomposition of the simulation domain. The - code is designed to be easy to modify or extend with new functionality. - </longdescription> - <use> - <flag name="lammps-memalign">Enables the use of the posix_memalign() - call instead of malloc() when large chunks or memory are allocated - by LAMMPS</flag> - <flag name="package-meam">modified EAM potential</flag> - <flag name="package-dipole">point dipole particles</flag> - <flag name="package-rigid">rigid bodies</flag> - </use> - <herd>sci-physics</herd> - <maintainer> - <email>nicolasbock@gentoo.org</email> - </maintainer> -</pkgmetadata> - diff --git a/sci-physics/root/ChangeLog b/sci-physics/root/ChangeLog index 848c44667..c7010f76b 100644 --- a/sci-physics/root/ChangeLog +++ b/sci-physics/root/ChangeLog @@ -2,6 +2,10 @@ # Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2 # $Header: /var/cvsroot/gentoo-x86/sci-physics/root/ChangeLog,v 1.96 2012/03/29 18:21:49 bicatali Exp $ + 28 Dec 2013; Justin Lecher <jlec@gentoo.org> -root-5.32.03-r2.ebuild, + -root-5.34.13.ebuild, root-9999.ebuild: + Import tree changes, drop old + 22 Dec 2013; Andrew Savchenko <bircoph@gmail.com> +root-5.32.03-r2.ebuild, +files/root-5.28.00b-asneeded.patch, +files/root-5.28.00b-prop-ldflags.patch, +files/root-5.28.00b-unuran.patch, diff --git a/sci-physics/root/Manifest b/sci-physics/root/Manifest index 77af0e37a..97569049f 100644 --- a/sci-physics/root/Manifest +++ b/sci-physics/root/Manifest @@ -1,16 +1,7 @@ -DIST ROOTPrimer-5.34.13.pdf 2308794 SHA256 39cd18fac66b2de4e829aaffb819b43b11579b38ffb2e45b12e8216f8457c74f SHA512 95e5c7af8a949d842a19d71b97de6f2c6a0e866a4f786e008303cd25bbaab5d658ded299bd667788d3ba462c30b0fda321327b53a4f50352360d1cf51a39ef57 WHIRLPOOL ad534bdfbaf45a574e67b0c1ee9be5e8931dfee87963bbe4c89cd7a39a1baa5f3e72991df656513303c1553e72933bad02e41172a2c8bcad3e8a9a23f6181e22 -DIST ROOTPrimerLetter-5.34.13.pdf 2310846 SHA256 b12ae7e21a084ba847337bfb4e3fbcb784d98a67178d87c399eeea0369580b93 SHA512 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file mode 100644 index 979b7536e..000000000 --- a/sci-physics/root/root-5.32.03-r2.ebuild +++ /dev/null @@ -1,383 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.32.03-r2.ebuild,v 1.6 2013/03/02 23:27:01 hwoarang Exp $ - -EAPI=5 - -PYTHON_COMPAT=( python2_{6,7} ) - -if [[ ${PV} == "9999" ]] ; then - _SVN=subversion - ESVN_REPO_URI="https://root.cern.ch/svn/root/trunk" - ESVN_OPTIONS="--non-interactive --trust-server-cert" - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz" - KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -fi - -inherit elisp-common eutils fdo-mime fortran-2 multilib python-single-r1 toolchain-funcs user ${_SVN} - -ROOFIT_DOC_PV=2.91-33 -TMVA_DOC_PV=4.03 -PATCH_PV=5.28.00b -PATCH_PV2=5.32.00 - -DESCRIPTION="C++ data analysis framework and interpreter from CERN" -HOMEPAGE="http://root.cern.ch/" -SRC_URI="${SRC_URI} - doc? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuide.pdf - math? ( - ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf - http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf ) - htmldoc? ( - http://root.cern.ch/drupal/sites/default/files/rootdrawing-logo.png - http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/root-banner.png - http://root.cern.ch/drupal/sites/all/themes/newsflash/images/info.png ) )" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="+X afs avahi clarens doc emacs examples fits fftw graphviz htmldoc kerberos - ldap +math mpi mysql odbc +opengl openmp oracle postgres prefix pythia6 - pythia8 python qt4 +reflex ruby ssl xinetd xml xrootd" - -CDEPEND=" - app-arch/xz-utils - >=dev-lang/cfortran-4.4-r2 - dev-libs/libpcre - media-fonts/dejavu - media-libs/freetype - media-libs/giflib - media-libs/libpng:0 - media-libs/tiff:0 - sys-libs/zlib - virtual/jpeg - virtual/shadow - X? ( - media-libs/ftgl - media-libs/glew - x11-libs/libX11 - x11-libs/libXext - x11-libs/libXpm - || ( - >=media-libs/libafterimage-1.20[gif,jpeg,png,tiff] - >=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff] - ) - opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps ) - qt4? ( - dev-qt/qtgui:4 - dev-qt/qtopengl:4 - dev-qt/qt3support:4 - dev-qt/qtsvg:4 - dev-qt/qtwebkit:4 - dev-qt/qtxmlpatterns:4 ) - x11-libs/libXft - ) - afs? ( net-fs/openafs ) - avahi? ( net-dns/avahi ) - clarens? ( dev-libs/xmlrpc-c[curl] ) - emacs? ( virtual/emacs ) - fits? ( sci-libs/cfitsio ) - fftw? ( sci-libs/fftw:3.0 ) - graphviz? ( media-gfx/graphviz ) - kerberos? ( virtual/krb5 ) - ldap? ( net-nds/openldap ) - math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) ) - mysql? ( virtual/mysql ) - odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) ) - oracle? ( dev-db/oracle-instantclient-basic ) - postgres? ( dev-db/postgresql-base ) - pythia6? ( sci-physics/pythia:6 ) - pythia8? ( <sci-physics/pythia-8.1.80:8 ) - python? ( ${PYTHON_DEPS} ) - ruby? ( - dev-lang/ruby - dev-ruby/rubygems ) - ssl? ( dev-libs/openssl ) - xml? ( dev-libs/libxml2 ) - xrootd? ( <net-libs/xrootd-3.3 )" - -DEPEND="${CDEPEND} - virtual/pkgconfig" - -RDEPEND="${CDEPEND} - reflex? ( dev-cpp/gccxml ) - xinetd? ( sys-apps/xinetd )" - -PDEPEND="htmldoc? ( ~app-doc/root-docs-${PV} )" - -REQUIRED_USE=" - !X? ( !opengl !qt4 ) - mpi? ( math !openmp ) - openmp? ( math !mpi ) - python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${PN}" - -pkg_setup() { - fortran-2_pkg_setup - use python && python-single-r1_pkg_setup - echo - elog "There are extra options on packages not yet in Gentoo:" - elog "AliEn, castor, Chirp, dCache, gfal, gLite, Globus," - elog "HDFS, Monalisa, MaxDB/SapDB, SRP." - elog "You can use the env variable EXTRA_ECONF variable for this." - elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=/usr/$(get_libdir)\"" - echo - enewgroup rootd - enewuser rootd -1 -1 /var/spool/rootd rootd - - if use math; then - if use openmp; then - if [[ $(tc-getCC)$ == *gcc* ]] && ! tc-has-openmp; then - ewarn "You are using a gcc without OpenMP capabilities" - die "Need an OpenMP capable compiler" - else - export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 - fi - elif use mpi; then - export USE_MPI=1 USE_PARALLEL_MINUIT2=1 - fi - fi -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-${PATCH_PV}-prop-ldflags.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV}-asneeded.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-nobyte-compile.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV}-unuran.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-afs.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-chklib64.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-explicit-functions.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-dotfont.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-rmkdepend.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-rusage.patch - - # make sure we use system libs and headers - rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die - rm -rf graf2d/asimage/src/libAfterImage || die - rm -rf graf3d/ftgl/{inc,src} || die - rm -rf graf2d/freetype/src || die - rm -rf graf3d/glew/{inc,src} || die - rm -rf core/pcre/src || die - rm -rf math/unuran/src/unuran-*.tar.gz || die - LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | xargs -0 rm -f || die - rm -rf core/lzma/src/*.tar.gz || die - rm graf3d/gl/{inc,src}/gl2ps.* || die - sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' graf3d/gl/Module.mk || die - - # In Gentoo, libPythia6 is called libpythia6 - # libungif is called libgif, - # iodbc is in /usr/include/iodbc - # pg_config.h is checked instead of libpq-fe.h - sed -i \ - -e 's:libPythia6:libpythia6:g' \ - -e 's:ungif:gif:g' \ - -e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \ - -e 's:libpq-fe.h:pg_config.h:' \ - configure || die "adjusting configure for Gentoo failed" - - # prefixify the configure script - sed -i \ - -e 's:/usr:${EPREFIX}/usr:g' \ - configure || die "prefixify configure failed" - - # QTDIR only used for qt3 in gentoo, and configure looks for it. - unset QTDIR - - # Make html docs self-consistent for offline work (based on Fedora spec) - if use htmldoc; then - epatch "${FILESDIR}"/${PN}-${PATCH_PV2}-htmldoc.patch - # make images local - sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/!!' \ - -i etc/html/ROOT.css || die "htmldoc sed failed" - sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/!!' \ - -i etc/html/ROOT.css || die "htmldoc sed failed" - sed 's!http://root.cern.ch/drupal/sites/default/files/!!' \ - -i etc/html/header.html || die "htmldoc sed failed" - - cp "${DISTDIR}"/{rootdrawing-logo.png,root-banner.png,info.png} etc/html || - die "htmldoc preparation failed" - fi -} - -src_configure() { - # the configure script is not the standard autotools - ./configure \ - --prefix="${EPREFIX}"/usr \ - --etcdir="${EPREFIX}"/etc/root \ - --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ - --docdir="${EPREFIX}"/usr/share/doc/${PF} \ - --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ - --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ - --with-cc=$(tc-getCC) \ - --with-cxx=$(tc-getCXX) \ - --with-f77=$(tc-getFC) \ - --with-ld=$(tc-getCXX) \ - --with-afs-shared=yes \ - --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \ - --disable-builtin-afterimage \ - --disable-builtin-freetype \ - --disable-builtin-ftgl \ - --disable-builtin-glew \ - --disable-builtin-pcre \ - --disable-builtin-zlib \ - --disable-builtin-lzma \ - --disable-cling \ - --enable-astiff \ - --enable-exceptions \ - --enable-explicitlink \ - --enable-gdml \ - --enable-memstat \ - --enable-shadowpw \ - --enable-shared \ - --enable-soversion \ - --enable-table \ - --fail-on-missing \ - $(use_enable X x11) \ - $(use_enable X asimage) \ - $(use_enable afs) \ - $(use_enable avahi bonjour) \ - $(use_enable clarens) \ - $(use_enable clarens peac) \ - $(use_enable fits fitsio) \ - $(use_enable fftw fftw3) \ - $(use_enable graphviz gviz) \ - $(use_enable kerberos krb5) \ - $(use_enable ldap) \ - $(use_enable math gsl-shared) \ - $(use_enable math genvector) \ - $(use_enable math mathmore) \ - $(use_enable math minuit2) \ - $(use_enable math roofit) \ - $(use_enable math tmva) \ - $(use_enable math unuran) \ - $(use_enable mysql) \ - $(use_enable odbc) \ - $(use_enable opengl) \ - $(use_enable postgres pgsql) \ - $(usex postgres "--with-pgsql-incdir=$(pg_config --includedir)" "") \ - $(use_enable prefix rpath) \ - $(use_enable pythia6) \ - $(use_enable pythia8) \ - $(use_enable python) \ - $(use_enable qt4 qt) \ - $(use_enable qt4 qtgsi) \ - $(use_enable reflex cintex) \ - $(use_enable reflex) \ - $(use_enable ruby) \ - $(use_enable ssl) \ - $(use_enable xml) \ - $(use_enable xrootd) \ - ${EXTRA_ECONF} \ - || die "configure failed" -} - -src_compile() { - emake OPT="${CXXFLAGS}" F77OPT="${FFLAGS}" - if use emacs; then - elisp-compile build/misc/*.el || die "elisp-compile failed" - fi -} - -doc_install() { - cd "${S}" - if use doc; then - einfo "Installing user's guides" - dodoc "${DISTDIR}"/ROOTUsersGuide.pdf - use math && dodoc \ - "${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \ - "${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf - fi - - if use examples; then - # these should really be taken care of by the root make install - insinto /usr/share/doc/${PF}/examples/tutorials/tmva - doins -r tmva/test - else - rm -rf "${ED}"/usr/share/doc/${PF}/examples || die - fi -} - -daemon_install() { - cd "${S}" - local daemons="rootd proofd" - dodir /var/spool/rootd - fowners rootd:rootd /var/spool/rootd - dodir /var/spool/rootd/{pub,tmp} - fperms 1777 /var/spool/rootd/{pub,tmp} - - for i in ${daemons}; do - newinitd "${FILESDIR}"/${i}.initd ${i} - newconfd "${FILESDIR}"/${i}.confd ${i} - done - if use xinetd; then - insinto /etc/xinetd - doins etc/daemons/{rootd,proofd}.xinetd - fi -} - -desktop_install() { - cd "${S}" - sed -e 's,@prefix@,/usr,' \ - build/package/debian/root-system-bin.desktop.in > root.desktop - domenu root.desktop - doicon "${S}"/build/package/debian/root-system-bin.png - - insinto /usr/share/icons/hicolor/48x48/mimetypes - doins build/package/debian/application-x-root.png - - insinto /usr/share/icons/hicolor/48x48/apps - doicon build/package/debian/root-system-bin.xpm -} - -src_install() { - emake DESTDIR="${D}" install - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/root" > 99root - use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root - if use python; then - echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root - python_optimize "${D}/usr/$(get_libdir)/root" - fi - use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root - doenvd 99root - - # The build system installs Emacs support unconditionally and in the wrong - # directory. Remove it and call elisp-install in case of USE=emacs. - rm -rf "${ED}"/usr/share/emacs - if use emacs; then - elisp-install ${PN} build/misc/*.{el,elc} || die "elisp-install failed" - fi - - doc_install - daemon_install - desktop_install - - # Cleanup of files either already distributed or unused on Gentoo - rm "${ED}"usr/share/doc/${PF}/{INSTALL,LICENSE,COPYING.CINT} || die - rm "${ED}"usr/share/root/fonts/LICENSE || die - pushd "${ED}"usr/$(get_libdir)/root/cint/cint/lib > /dev/null - rm -f posix/mktypes dll_stl/setup \ - G__* dll_stl/G__* dll_stl/rootcint_* posix/exten.o || die - rm -f "${ED}"usr/$(get_libdir)/root/cint/cint/include/makehpib || die - rm -f "${ED}"/etc/root/proof/*.sample || die - rm -rf "${ED}"/etc/root/daemons || die - popd > /dev/null - # these should be in PATH - mv "${ED}"etc/root/proof/utils/pq2/pq2* \ - "${ED}"usr/bin/ || die -} - -pkg_postinst() { - fdo-mime_desktop_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update -} diff --git a/sci-physics/root/root-5.34.13.ebuild b/sci-physics/root/root-5.34.13.ebuild deleted file mode 100644 index f8e0f1a4b..000000000 --- a/sci-physics/root/root-5.34.13.ebuild +++ /dev/null @@ -1,425 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.10-r2.ebuild,v 1.1 2013/10/29 17:00:37 bicatali Exp $ - -EAPI=5 - -if [[ ${PV} == "9999" ]] ; then - _GIT=git-2 - EGIT_REPO_URI="http://root.cern.ch/git/root.git" - SRC_URI="" - KEYWORDS="" -else - SRC_URI="ftp://root.cern.ch/${PN}/${PN}_v${PV}.source.tar.gz" - KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -fi - -PYTHON_COMPAT=( python2_{6,7} ) -inherit elisp-common eutils fdo-mime fortran-2 ${_GIT} multilib python-single-r1 toolchain-funcs user versionator - -ROOFIT_DOC_PV=2.91-33 -TMVA_DOC_PV=4.03 -PATCH_PV=5.28.00b -PATCH_PV2=5.32.00 -PATCH_PV3=5.34.05 -PATCH_PV4=5.34.13 - -DESCRIPTION="C++ data analysis framework and interpreter from CERN" -HOMEPAGE="http://root.cern.ch/" -SRC_URI="${SRC_URI} - !minimal? ( doc? ( - math? ( - ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf - http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf - metric? ( ftp://root.cern.ch/root/doc/spectrum/Spectrum.pdf -> Spectrum-${PV}.pdf ) - !metric? ( ftp://root.cern.ch/root/doc/spectrum/SpectrumLetter.pdf -> SpectrumLetter-${PV}.pdf ) - ) - metric? ( - ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideA4.pdf -> ROOTUsersGuideA4-${PV}.pdf - ftp://root.cern.ch/root/doc/primer/ROOTPrimer.pdf -> ROOTPrimer-${PV}.pdf ) - !metric? ( - ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideLetter.pdf -> ROOTUsersGuideLetter-${PV}.pdf - ftp://root.cern.ch/root/doc/primer/ROOTPrimerLetter.pdf -> ROOTPrimerLetter-${PV}.pdf ) - htmldoc? ( - http://root.cern.ch/drupal/sites/default/files/rootdrawing-logo.png - http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/root-banner.png - http://root.cern.ch/drupal/sites/all/themes/newsflash/images/info.png ) - ) )" - -SLOT="0" -LICENSE="LGPL-2.1" -IUSE="+X afs avahi c++0x doc emacs examples fits fftw graphviz htmldoc - kerberos ldap +math +metric minimal mpi mysql odbc +opengl openmp oracle postgres - prefix pythia6 pythia8 python qt4 +reflex ruby sqlite ssl xinetd xml xrootd" - -REQUIRED_USE=" - !X? ( !opengl !qt4 ) - htmldoc? ( doc ) - mpi? ( math !openmp ) - openmp? ( math !mpi ) - python? ( ${PYTHON_REQUIRED_USE} )" - -CDEPEND=" - app-arch/xz-utils - >=dev-lang/cfortran-4.4-r2 - dev-libs/libpcre - media-fonts/dejavu - media-libs/freetype - media-libs/giflib - media-libs/libpng:0 - media-libs/tiff:0 - sys-libs/zlib - virtual/jpeg - virtual/shadow - X? ( - media-libs/ftgl - media-libs/glew - x11-libs/libX11 - x11-libs/libXext - x11-libs/libXpm - !minimal? ( - || ( - >=media-libs/libafterimage-1.20[gif,jpeg,png,tiff] - >=x11-wm/afterstep-2.2.11[gif,jpeg,png,tiff] - ) - opengl? ( virtual/opengl virtual/glu x11-libs/gl2ps ) - qt4? ( - dev-qt/qtgui:4 - dev-qt/qtopengl:4 - dev-qt/qt3support:4 - dev-qt/qtsvg:4 - dev-qt/qtwebkit:4 - dev-qt/qtxmlpatterns:4 - ) - x11-libs/libXft - ) - ) - !minimal? ( - afs? ( net-fs/openafs ) - avahi? ( net-dns/avahi ) - emacs? ( virtual/emacs ) - fits? ( sci-libs/cfitsio ) - fftw? ( sci-libs/fftw:3.0 ) - graphviz? ( media-gfx/graphviz ) - kerberos? ( virtual/krb5 ) - ldap? ( net-nds/openldap ) - math? ( sci-libs/gsl sci-mathematics/unuran mpi? ( virtual/mpi ) ) - mysql? ( virtual/mysql ) - odbc? ( || ( dev-db/libiodbc dev-db/unixODBC ) ) - oracle? ( dev-db/oracle-instantclient-basic ) - postgres? ( dev-db/postgresql-base ) - pythia6? ( sci-physics/pythia:6 ) - pythia8? ( >=sci-physics/pythia-8.1.80:8 ) - python? ( ${PYTHON_DEPS} ) - ruby? ( - dev-lang/ruby - dev-ruby/rubygems ) - sqlite? ( dev-db/sqlite:3 ) - ssl? ( dev-libs/openssl ) - xml? ( dev-libs/libxml2 ) - xrootd? ( >=net-libs/xrootd-3.2.0 ) - )" - -DEPEND="${CDEPEND} - virtual/pkgconfig" - -RDEPEND="${CDEPEND} - reflex? ( dev-cpp/gccxml ) - xinetd? ( sys-apps/xinetd )" - -PDEPEND="htmldoc? ( ~app-doc/root-docs-${PV} )" - -S="${WORKDIR}/${PN}" - -pkg_setup() { - fortran-2_pkg_setup - use python && python-single-r1_pkg_setup - echo - elog "There are extra options on packages not yet in Gentoo:" - elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite," - elog "HDFS, Monalisa, MaxDB/SapDB, SRP." - elog "You can use the env variable EXTRA_ECONF variable for this." - elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\"" - echo - enewgroup rootd - enewuser rootd -1 -1 /var/spool/rootd rootd - use minimal && return - - if use math; then - if use openmp; then - if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then - ewarn "You are using a g++ without OpenMP capabilities" - die "Need an OpenMP capable compiler" - else - export USE_OPENMP=1 USE_PARALLEL_MINUIT2=1 - fi - elif use mpi; then - export USE_MPI=1 USE_PARALLEL_MINUIT2=1 - fi - fi - if use c++0x && [[ $(tc-getCXX) == *g++* ]] && \ - ! version_is_at_least "4.7" "$(gcc-version)"; then - eerror "You are using a g++ without C++0x capabilities" - die "Need an C++0x capable compiler" - fi -} - -src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-prop-flags.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV3}-nobyte-compile.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV}-glibc212.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV4}-unuran.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-afs.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-cfitsio.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-chklib64.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV2}-dotfont.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV4}-pythia8.patch \ - "${FILESDIR}"/${PN}-${PATCH_PV4}-desktop.patch - - # make sure we use system libs and headers - rm montecarlo/eg/inc/cfortran.h README/cfortran.doc || die - rm -r graf2d/asimage/src/libAfterImage || die - rm -r graf3d/ftgl/{inc,src} || die - rm -r graf2d/freetype/src || die - rm -r graf3d/glew/{inc,src} || die - rm -r core/pcre/src || die - rm -r math/unuran/src/unuran-*.tar.gz || die - LANG=C LC_ALL=C find core/zip -type f -name "[a-z]*" -print0 | xargs -0 rm -f || die - rm -r core/lzma/src/*.tar.gz || die - rm graf3d/gl/{inc,src}/gl2ps.* || die - sed -i -e 's/^GLLIBS *:= .* $(OPENGLLIB)/& -lgl2ps/' graf3d/gl/Module.mk || die - - # In Gentoo, libPythia6 is called libpythia6 - # libungif is called libgif, - # iodbc is in /usr/include/iodbc - # pg_config.h is checked instead of libpq-fe.h - sed -i \ - -e 's:libPythia6:libpythia6:g' \ - -e 's:ungif:gif:g' \ - -e 's:$ODBCINCDIR:$ODBCINCDIR /usr/include/iodbc:' \ - -e 's:libpq-fe.h:pg_config.h:' \ - configure || die "adjusting configure for Gentoo failed" - - # prefixify the configure script - sed -i \ - -e 's:/usr:${EPREFIX}/usr:g' \ - configure || die "prefixify configure failed" - - # QTDIR only used for qt3 in gentoo, and configure looks for it. - unset QTDIR - - # Make html docs self-consistent for offline work (based on Fedora spec) - if use htmldoc && ! use minimal; then - epatch "${FILESDIR}"/${PN}-${PATCH_PV2}-htmldoc.patch - # make images local - sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/!!' \ - -i etc/html/ROOT.css || die "htmldoc sed failed" - sed 's!http://root.cern.ch/drupal/sites/all/themes/newsflash/images/!!' \ - -i etc/html/ROOT.css || die "htmldoc sed failed" - sed 's!http://root.cern.ch/drupal/sites/default/files/!!' \ - -i etc/html/header.html || die "htmldoc sed failed" - - cp "${DISTDIR}"/{rootdrawing-logo.png,root-banner.png,info.png} etc/html || - die "htmldoc preparation failed" - fi -} - -src_configure() { - # the configure script is not the standard autotools - local mycommonconf=" - --prefix="${EPREFIX}"/usr \ - --etcdir="${EPREFIX}"/etc/root \ - --libdir="${EPREFIX}"/usr/$(get_libdir)/${PN} \ - --docdir="${EPREFIX}"/usr/share/doc/${PF} \ - --tutdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tutorials \ - --testdir="${EPREFIX}"/usr/share/doc/${PF}/examples/tests \ - --with-cc=$(tc-getCC) \ - --with-cxx=$(tc-getCXX) \ - --with-f77=$(tc-getFC) \ - --with-ld=$(tc-getCXX) \ - --nohowto - " - if use minimal; then - ./configure \ - ${mycommonconf} \ - $(usex X --gminimal --minimal) \ - || die "configure failed" - return - fi - # cling is disabled because in requires live llvm and clang - ./configure \ - ${mycommonconf} \ - --with-afs-shared=yes \ - --with-sys-iconpath="${EPREFIX}"/usr/share/pixmaps \ - --disable-builtin-afterimage \ - --disable-builtin-ftgl \ - --disable-builtin-freetype \ - --disable-builtin-glew \ - --disable-builtin-pcre \ - --disable-builtin-zlib \ - --disable-builtin-lzma \ - --disable-cling \ - --enable-astiff \ - --enable-explicitlink \ - --enable-gdml \ - --enable-memstat \ - --enable-shadowpw \ - --enable-shared \ - --enable-soversion \ - --enable-table \ - --fail-on-missing \ - $(use_enable X x11) \ - $(use_enable X asimage) \ - $(use_enable X xft) \ - $(use_enable afs) \ - $(use_enable avahi bonjour) \ - $(use_enable c++0x cxx11) \ - $(use_enable fits fitsio) \ - $(use_enable fftw fftw3) \ - $(use_enable graphviz gviz) \ - $(use_enable kerberos krb5) \ - $(use_enable ldap) \ - $(use_enable math gsl-shared) \ - $(use_enable math genvector) \ - $(use_enable math mathmore) \ - $(use_enable math minuit2) \ - $(use_enable math roofit) \ - $(use_enable math tmva) \ - $(use_enable math unuran) \ - $(use_enable mysql) \ - $(use_enable odbc) \ - $(use_enable opengl) \ - $(use_enable oracle) \ - $(use_enable postgres pgsql) \ - $(usex postgres "--with-pgsql-incdir=$(pg_config --includedir)" "") \ - $(use_enable prefix rpath) \ - $(use_enable pythia6) \ - $(use_enable pythia8) \ - $(use_enable python) \ - $(use_enable qt4 qt) \ - $(use_enable qt4 qtgsi) \ - $(use_enable reflex cintex) \ - $(use_enable reflex) \ - $(use_enable ruby) \ - $(use_enable sqlite) \ - $(use_enable ssl) \ - $(use_enable xml) \ - $(use_enable xrootd) \ - ${EXTRA_ECONF} \ - || die "configure failed" -} - -src_compile() { - emake OPT="${CXXFLAGS}" F77OPT="${FFLAGS}" ROOTSYS="${S}" LD_LIBRARY_PATH="${S}/lib" - if use emacs && ! use minimal; then - elisp-compile build/misc/*.el || die "elisp-compile failed" - fi -} - -doc_install() { - cd "${S}" - if use doc && ! use minimal; then - einfo "Installing user's guides" - if use metric; then - dodoc "${DISTDIR}"/ROOTUsersGuideA4-${PV}.pdf - dodoc "${DISTDIR}"/ROOTPrimer-${PV}.pdf - use math && dodoc "${DISTDIR}"/Spectrum-${PV}.pdf - else - dodoc "${DISTDIR}"/ROOTUsersGuideLetter-${PV}.pdf - dodoc "${DISTDIR}"/ROOTPrimerLetter-${PV}.pdf - use math && dodoc "${DISTDIR}"/SpectrumLetter-${PV}.pdf - fi - use math && dodoc \ - "${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \ - "${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf - fi - - if use examples && ! use minimal; then - # these should really be taken care of by the root make install - insinto /usr/share/doc/${PF}/examples/tutorials/tmva - doins -r tmva/test - else - rm -r "${ED}"/usr/share/doc/${PF}/examples || die - fi -} - -daemon_install() { - cd "${S}" - local daemons="rootd proofd" - dodir /var/spool/rootd - fowners rootd:rootd /var/spool/rootd - dodir /var/spool/rootd/{pub,tmp} - fperms 1777 /var/spool/rootd/{pub,tmp} - - for i in ${daemons}; do - newinitd "${FILESDIR}"/${i}.initd ${i} - newconfd "${FILESDIR}"/${i}.confd ${i} - done - if use xinetd; then - insinto /etc/xinetd - doins etc/daemons/{rootd,proofd}.xinetd - fi -} - -desktop_install() { - cd "${S}" - echo "Icon=root-system-bin" >> etc/root.desktop - domenu etc/root.desktop - doicon build/package/debian/root-system-bin.png - - insinto /usr/share/icons/hicolor/48x48/mimetypes - doins build/package/debian/application-x-root.png - - insinto /usr/share/icons/hicolor/48x48/apps - doicon build/package/debian/root-system-bin.xpm -} - -src_install() { - emake DESTDIR="${D}" install - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/root" > 99root - if ! use minimal; then - use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root - if use python; then - echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root - python_optimize "${D}/usr/$(get_libdir)/root" - fi - use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root - fi - doenvd 99root - - # The build system installs Emacs support unconditionally and in the wrong - # directory. Remove it and call elisp-install in case of USE=emacs. - rm -r "${ED}"/usr/share/emacs - if use emacs && ! use minimal; then - elisp-install ${PN} build/misc/*.{el,elc} || die "elisp-install failed" - fi - - doc_install - daemon_install - desktop_install - - # Cleanup of files either already distributed or unused on Gentoo - rm "${ED}"usr/share/doc/${PF}/{INSTALL,LICENSE,COPYING.CINT} || die - rm "${ED}"usr/share/root/fonts/LICENSE || die - pushd "${ED}"usr/$(get_libdir)/root/cint/cint/lib > /dev/null - rm posix/mktypes dll_stl/setup \ - G__* dll_stl/G__* dll_stl/rootcint_* posix/exten.o || die - rm "${ED}"usr/$(get_libdir)/root/cint/cint/include/makehpib || die - rm "${ED}"/etc/root/proof/*.sample || die - rm -r "${ED}"/etc/root/daemons || die - popd > /dev/null - # these should be in PATH - mv "${ED}"etc/root/proof/utils/pq2/pq2* \ - "${ED}"usr/bin/ || die -} - -pkg_postinst() { - fdo-mime_desktop_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update -} diff --git a/sci-physics/root/root-9999.ebuild b/sci-physics/root/root-9999.ebuild index 4c6ffdbdd..05b899c19 100644 --- a/sci-physics/root/root-9999.ebuild +++ b/sci-physics/root/root-9999.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2013 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-physics/root/root-5.34.09.ebuild,v 1.2 2013/09/05 19:44:52 mgorny Exp $ +# $Header: $ EAPI=5 @@ -32,7 +32,7 @@ SRC_URI="${SRC_URI} ftp://root.cern.ch/${PN}/doc/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf http://tmva.sourceforge.net/docu/TMVAUsersGuide.pdf -> TMVAUsersGuide-v${TMVA_DOC_PV}.pdf ) metric? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideA4.pdf -> ROOTUsersGuideA4-${PV}.pdf ) - !metric? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideLetter.pdf -> ROOTUsersGuideLetter-${PV}.pdf ) + !metric? ( ftp://root.cern.ch/${PN}/doc/ROOTUsersGuideLetter.pdf -> ROOTUsersGuideLetter-${PV}.pdf ) htmldoc? ( http://root.cern.ch/drupal/sites/default/files/rootdrawing-logo.png http://root.cern.ch/drupal/sites/all/themes/newsflash/images/blue/root-banner.png @@ -103,7 +103,7 @@ CDEPEND=" oracle? ( dev-db/oracle-instantclient-basic ) postgres? ( dev-db/postgresql-base ) pythia6? ( sci-physics/pythia:6 ) - pythia8? ( sci-physics/pythia:8 ) + pythia8? ( >=sci-physics/pythia-8.1.80:8 ) python? ( ${PYTHON_DEPS} ) ruby? ( dev-lang/ruby @@ -126,19 +126,19 @@ S="${WORKDIR}/${PN}" pkg_setup() { fortran-2_pkg_setup + use python && python-single-r1_pkg_setup echo elog "There are extra options on packages not yet in Gentoo:" elog "Afdsmgrd, AliEn, castor, Chirp, dCache, gfal, Globus, gLite," elog "HDFS, Monalisa, MaxDB/SapDB, SRP." elog "You can use the env variable EXTRA_ECONF variable for this." elog "For example, for SRP, you would set: " - elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=/usr/$(get_libdir)\"" + elog "EXTRA_ECONF=\"--enable-srp --with-srp-libdir=${EROOT%/}/usr/$(get_libdir)\"" echo enewgroup rootd enewuser rootd -1 -1 /var/spool/rootd rootd use minimal && return - use python && python-single-r1_pkg_setup if use math; then if use openmp; then if [[ $(tc-getCXX)$ == *g++* ]] && ! tc-has-openmp; then @@ -311,8 +311,11 @@ doc_install() { cd "${S}" if use doc && ! use minimal; then einfo "Installing user's guides" - use metric && dodoc "${DISTDIR}"/ROOTUsersGuideA4-${PV}.pdf || \ + if use metric; then + dodoc "${DISTDIR}"/ROOTUsersGuideA4-${PV}.pdf + else dodoc "${DISTDIR}"/ROOTUsersGuideLetter-${PV}.pdf + fi use math && dodoc \ "${DISTDIR}"/RooFit_Users_Manual_${ROOFIT_DOC_PV}.pdf \ "${DISTDIR}"/TMVAUsersGuide-v${TMVA_DOC_PV}.pdf @@ -366,7 +369,7 @@ src_install() { use pythia8 && echo "PYTHIA8=${EPREFIX}/usr" >> 99root if use python; then echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/root" >> 99root - python_optimize /usr/$(get_libdir)/root + python_optimize "${ED}/usr/$(get_libdir)/root" fi use ruby && echo "RUBYLIB=${EPREFIX}/usr/$(get_libdir)/root" >> 99root fi |