gentoo resync : 16.04.2018

8 files changed, 4 insertions, 223 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 625d4d8a2ee3..8f33bfdedeee 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
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>
diff --git a/sci-biology/bioruby/Manifest b/sci-biology/bioruby/Manifest
index 4783d13c149a..4d791d308887 100644
--- a/sci-biology/bioruby/Manifest
+++ b/sci-biology/bioruby/Manifest
@@ -1,6 +1,4 @@
 AUX bioruby-1.4.3.0001-fix-tests.patch 1082 BLAKE2B cd12d78630371cc453de5abb2d352b329acc98076dbafad393d56dce5c2eaa25e6bb435206bc8d09671fd086af884d2f105fa1b4ffab55cffbc2e2eb6ceba265 SHA512 0a46f8d049521d90993274b52d7bece39464999a4286ac2052a7c8cfb97fe31af7eeadfc8d42c2cbd71f80aca6ac6a778eeb1de7341368ef2ee726444b74752e
 DIST bio-1.5.1.gem 1445376 BLAKE2B 4de704293ed1c4dee7edc9c86df4ddd35f66eb4433a339fadb58c3f877206e240a8b1dfe6aa8ccd92f0edf9d0f28825cc2b58e33f817fec6bab39e3162f179cf SHA512 822ac6c3d85847193fc1992087abc868e4d1a7cfca82da6ab1830af2927a2a582c3993bc681e129a6aac224ed1cb0b33056d8cc02d3e36d68c9d6a4153c321ca
-DIST bioruby-1.4.3.0001.tar.gz 1500656 BLAKE2B 10c5a882608e33d1d9fe2cd4e07a92992a78b99ae33349d1916cd6a2fe658b553e32d1ce05edb9bfa23d7d822f6a730d6a40a098ecc05a8deb8dae49d4be7856 SHA512 77ad96388e1e8b1dccab582a3bc309b99b36cac1803f79b42707fc4dbf439de31ed491ce5e1c2e59f695643756ae0df2e275bbcd9ad6827f251b52edd677d821
-EBUILD bioruby-1.4.3.0001-r1.ebuild 720 BLAKE2B bf991823574efe9750c99173270a034a25c07bb1d10fc682796a97e923fa88113c2bced77643df8b2758dec7b194e6a38b27e356a75771e9a0d790b12554fc6c SHA512 9a929ffe9e804ce835d0399fad4afa9dd8b0d9d2acfd234d2944168826e05d77e538c1163ad5add74b62433a10319b1b492d91ddd8786ba52dabbf7b27ea2b8f
-EBUILD bioruby-1.5.1.ebuild 440 BLAKE2B c30688066c4d760ebfd6df314dda0fc85367231e01c320dfadde9664b915f5bc36416c28b7afef4ea7cb729de708045a02b1d71927d6beec0ec2e68c2c03ed11 SHA512 b6812050b69f792b268d9e06e0d72f19d4b7a01d4fcb8fd8aa335ac111359f4585de8f7a55793192c94a7291f2caf0e038668aa5a0a5171b762a3fc04f6d1e2d
+EBUILD bioruby-1.5.1.ebuild 431 BLAKE2B 187d9e6996db7e7324b2702d51620a520d822353b6cae625eef3e1b53ffc415bd5edd851676948deb4ac3ea2bd9a1f6a18a98bba52e739395896b69240fbd813 SHA512 5dea0c9996aca5536dac3ff2ec702a2cd0705321b05304ad6c10e8c6265379e35877e7f1a281ab0e6f6c6c3b506185f044f69700c19e614f34e084657c636ef1
 MISC metadata.xml 261 BLAKE2B 3768c926bca545090342a947ba83e706a8954c51b99a5e7b3476ba5198cd326fe1c3b8efb51dfd6be1800682556b8ceea065e388981463ab32f3d687951872f3 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a
diff --git a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild b/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild
deleted file mode 100644
index de7ff26eeb4b..000000000000
--- a/sci-biology/bioruby/bioruby-1.4.3.0001-r1.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-USE_RUBY="ruby21 ruby22"
-
-inherit ruby-fakegem
-
-DESCRIPTION="An integrated environment for bioinformatics using the Ruby language"
-LICENSE="Ruby"
-HOMEPAGE="http://bioruby.org/"
-SRC_URI="http://${PN}.org/archive/${P}.tar.gz"
-
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 ~ppc x86"
-
-ruby_add_rdepend "dev-ruby/libxml"
-
-PATCHES=( "${FILESDIR}"/${P}-fix-tests.patch )
-
-each_ruby_configure() {
-	${RUBY} setup.rb config || die
-}
-
-each_ruby_compile() {
-	${RUBY} setup.rb setup || die
-}
-
-each_ruby_install() {
-	${RUBY} setup.rb install --prefix="${D}" || die
-}
-
-each_ruby_test() {
-	${RUBY} -rubygems test/runner.rb || die
-}
diff --git a/sci-biology/bioruby/bioruby-1.5.1.ebuild b/sci-biology/bioruby/bioruby-1.5.1.ebuild
index f5e558c7ff33..d64585281278 100644
--- a/sci-biology/bioruby/bioruby-1.5.1.ebuild
+++ b/sci-biology/bioruby/bioruby-1.5.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-USE_RUBY="ruby21 ruby22 ruby23"
+USE_RUBY="ruby22 ruby23"
 
 RUBY_FAKEGEM_NAME="bio"
 
@@ -17,6 +17,6 @@ HOMEPAGE="http://bioruby.org/"
 
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~ppc ~x86"
+KEYWORDS="amd64 ~ppc x86"
 
 ruby_add_rdepend "dev-ruby/libxml"