commit: 57b9f13f0c8719e04a011b071e0096f660ed706e Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> AuthorDate: Sun Apr 15 10:33:19 2018 +0000 Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> CommitDate: Sun Apr 15 10:33:19 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=57b9f13f
sci-biology/beast-mcmc: remove last rited package Closes: https://bugs.gentoo.org/514432 sci-biology/beast-mcmc/Manifest | 1 - sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild | 85 ----------------------- sci-biology/beast-mcmc/beast-mcmc-9999.ebuild | 80 --------------------- sci-biology/beast-mcmc/metadata.xml | 11 --- 4 files changed, 177 deletions(-) diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest deleted file mode 100644 index 4aad90dfeaa..00000000000 --- a/sci-biology/beast-mcmc/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST beast-mcmc-1.7.5.tar.xz 40516312 BLAKE2B 9a1a374fef33dcce6e3fe9f842848366b66dbe35a42d3cc0e095b1944fbe0f3a58a59334a9c555595456db0874f8a456a844592cdd8516e746ffe57423b274d6 SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild deleted file mode 100644 index 7bbc7e087de..00000000000 --- a/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"; - -WANT_ANT_TASKS="ant-junit4" -EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" -JAVA_ANT_REWRITE_CLASSPATH="true" -JAVA_ANT_ENCODING="latin1" -JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" - -#inherit java-pkg-2 java-ant-2 eutils subversion -inherit java-pkg-2 java-ant-2 eutils - -MY_P=BEASTv${PV} - -DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" -HOMEPAGE="https://github.com/beast-dev/beast-mcmc"; -#SRC_URI="" -SRC_URI="https://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz"; - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -# TODO: sys-cluster/mpijava -COMMON_DEPS=" - dev-java/colt:0 - dev-java/jdom:0 - dev-java/itext:0 - dev-java/junit:4 - dev-java/jebl:0 - dev-java/matrix-toolkits-java - dev-java/commons-math:2 - dev-java/jdom-jaxen:1.0" -DEPEND=">=virtual/jdk-1.5 - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.5 - ${COMMON_DEPS}" - -S="${WORKDIR}/beast_release_${PV//./_}" - -src_prepare() { - sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/release/Linux/scripts/* || die - cd lib - rm -v colt.jar junit-*.jar itext-*.jar jdom.jar mtj.jar commons-math-*.jar || die - #rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die - java-pkg_jar-from jdom - java-pkg_jar-from colt - java-pkg_jar-from itext -# java-pkg_jar-from jebl - java-pkg_jar-from matrix-toolkits-java - java-pkg_jar-from commons-math-2 - java-pkg-2_src_prepare -} - -src_compile() { - eant dist_all_BEAST -f build_BEAST_MCMC.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die - eant dist -f build_pathogen.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die -} - -src_install() { - java-pkg_dojar build/dist/*.jar dist/*.jar - - java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' -# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' - - insinto /usr/share/${PN} - doins -r examples - dodoc NOTIFY doc/*.pdf -} - -src_test() { - eant junit -f build.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) -} diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild deleted file mode 100644 index 824d891c6f2..00000000000 --- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild +++ /dev/null @@ -1,80 +0,0 @@ -# Copyright 1999-2009 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="2" - -ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"; - -WANT_ANT_TASKS="ant-junit4" -EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0" -JAVA_ANT_REWRITE_CLASSPATH="true" -JAVA_ANT_ENCODING="latin1" -JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml" - -inherit java-pkg-2 java-ant-2 eutils subversion - -DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences" -HOMEPAGE="https://github.com/beast-dev/beast-mcmc"; -SRC_URI="" -#SRC_URI="mirror://gentoo/${P}.tar.bz2" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="" -IUSE="" - -# TODO: sys-cluster/mpijava -COMMON_DEPS="dev-java/colt:0 - dev-java/jdom:0 - dev-java/itext:0 - dev-java/junit:4 - dev-java/jebl:0 - dev-java/matrix-toolkits-java - dev-java/commons-math:2 - dev-java/jdom-jaxen:1.0" -DEPEND=">=virtual/jdk-1.5 - ${COMMON_DEPS}" -RDEPEND=">=virtual/jre-1.5 - ${COMMON_DEPS}" - -S="${WORKDIR}/beast_release_${PV//./_}" - -src_prepare() { - sed -i '/BEAST_LIB/ s|$BEAST|/usr/share/beast|' "${S}"/scripts/* || die - cd lib - rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die - java-pkg_jar-from jdom - java-pkg_jar-from colt - java-pkg_jar-from itext - java-pkg_jar-from jebl - java-pkg_jar-from matrix-toolkits-java - java-pkg_jar-from commons-math-1 - java-pkg-2_src_prepare -} - -src_compile() { - eant dist_all_BEAST -f build_BEAST_MCMC.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die - eant dist -f build_pathogen.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die -} - -src_install() { - java-pkg_dojar build/dist/*.jar dist/*.jar - - java-pkg_dolauncher beauti --jar beauti.jar --java_args '-Xms64m -Xmx256m' -# java-pkg_dolauncher beauti --main dr.app.beauti.BeautiApp --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher beast --main dr.app.beast.BeastMain --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher loganalyser --main dr.app.tools.LogAnalyser --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher logcombiner --main dr.app.tools.LogCombiner --java_args '-Xms64m -Xmx256m' - java-pkg_dolauncher treeannotator --main dr.app.tools.TreeAnnotator --java_args '-Xms64m -Xmx256m' - - insinto /usr/share/${PN} - doins -r examples || die - dodoc NOTIFY doc/*.pdf -} - -src_test() { - eant junit -f build_BEAST_MCMC.xml \ - -Dgentoo.classpath=$(java-pkg_getjars ${EANT_GENTOO_CLASSPATH}):$(for i in lib/*.jar; do echo -n "$i:"; done) || die -} diff --git a/sci-biology/beast-mcmc/metadata.xml b/sci-biology/beast-mcmc/metadata.xml deleted file mode 100644 index 18e746ab76f..00000000000 --- a/sci-biology/beast-mcmc/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">beast-dev/beast-mcmc</remote-id> - </upstream> -</pkgmetadata>
