sci-biology/beast-mcmc: remove last rited package

Closes: https://bugs.gentoo.org/514432

diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
deleted file mode 100644 (file)
index 4aad90d..0000000
--- 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 (file)
index 7bbc7e0..0000000
--- 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 (file)
index 824d891..0000000
--- 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 (file)
index 18e746a..0000000
--- 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-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-  <upstream>
-    <remote-id type="github">beast-dev/beast-mcmc</remote-id>
-  </upstream>
-</pkgmetadata>