gentoo resync : 16.04.2018

4 files changed, 0 insertions, 180 deletions

diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
deleted file mode 100644
index cb2c28c4bdb3..000000000000
--- a/sci-biology/beast-mcmc/Manifest
+++ /dev/null
@@ -1,4 +0,0 @@
-DIST beast-mcmc-1.7.5.tar.xz 40516312 BLAKE2B 9a1a374fef33dcce6e3fe9f842848366b66dbe35a42d3cc0e095b1944fbe0f3a58a59334a9c555595456db0874f8a456a844592cdd8516e746ffe57423b274d6 SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937
-EBUILD beast-mcmc-1.7.5-r1.ebuild 2906 BLAKE2B 4fbb1cbd387f6c988c48ce77eea753d3e5b5f82b44af02c9e025c4c086fc2d0ddd48e7dbdc3e1dc3f527093d539785ebc27af9f0989279e26ce2219961f46788 SHA512 1bc83f37bd0bfd2477bcf31e7206d1d4337c24123870a407aac2b2ac69ea65d52958930dd2d5c9c961b862f3e7935356809aefbadc8938b7798125b4ebec7ac0
-EBUILD beast-mcmc-9999.ebuild 2743 BLAKE2B 69ef6c55609cae9938b2ef6f870798699e03ea7c6e6b4b01b489f39f59d5c380f91d1d8090fef895272684a7f3a49dd00377c8da0c8107c3fa8e10c3df6a7469 SHA512 d2860b91189860b027ca7f10026e99df5e5d447912445061fa09aa770d10ef33ed972107355df15d5e7c6f034baefbb8798efecca3e7132852183c2c9bcc0ed1
-MISC metadata.xml 356 BLAKE2B 57c13645d9bca2bcd9339fb11f7136cd5bd20e35b97aa1f46f67967dfb0b398758ea9f61688f4f6cdd7d5220a8b1ebad1f73ffc2e30f8cbb92c073a7b22d5d69 SHA512 fa6d4dc538ef266e20cfb717dd6c7982c9b88e7b5ab3fcd11074ab41be660ae2f8a0bf55bc5abbb1a669ad64c3e46c1dd47cc8761e7e4b5767cff7d2da661dec
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 7bbc7e087de8..000000000000
--- 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 "$i:"; done)
-}
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
deleted file mode 100644
index 824d891c6f2f..000000000000
--- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
+++ /dev/null
@@ -1,80 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI="2"
-
-ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
-
-WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
-JAVA_ANT_REWRITE_CLASSPATH="true"
-JAVA_ANT_ENCODING="latin1"
-JAVA_PKG_BSFIX_NAME="build.xml build_BEAST_MCMC.xml build_coalsim.xml build_development.xml build_pathogen.xml build_release.xml build_treestat.xml build_vcs.xml"
-
-inherit java-pkg-2 java-ant-2 eutils subversion
-
-DESCRIPTION="Bayesian MCMC of Evolution & Phylogenetics using Molecular Sequences"
-HOMEPAGE="https://github.com/beast-dev/beast-mcmc"
-SRC_URI=""
-#SRC_URI="mirror://gentoo/${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 18e746ab76ff..000000000000
--- 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>