From: William L. Thomson Jr <wlt@o-sinc.com>
Date: Fri, 18 Sep 2015 00:14:54 +0000 (-0400)
Subject: sci-biology/beast-mcmc: Updated dev-java/jdom slot from 1.0 -> 0 for v1
X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=e0e9910db038c8293a0c817be7300ef6be338ffa;p=gentoo.git

sci-biology/beast-mcmc: Updated dev-java/jdom slot from 1.0 -> 0 for v1

Also removed old version.
---

diff --git a/sci-biology/beast-mcmc/Manifest b/sci-biology/beast-mcmc/Manifest
index 7fd843d7d423..56293f2fdd27 100644
--- a/sci-biology/beast-mcmc/Manifest
+++ b/sci-biology/beast-mcmc/Manifest
@@ -1,2 +1 @@
-DIST beast-mcmc-1.5.2.tar.bz2 38834702 SHA256 f7312c6a7a14f6b32e9701a6386ff87728574460b7861880aa2cb87290756ea1 SHA512 8549db6cb49d64eb3a97fa6478bdbabfecd44ccc6236c474a1961ec5d6fc8326072fb961035df70982a9f1c08a36572529a07b88e2d33a43fa0fd5c07df3a414 WHIRLPOOL 595f606640daa32c79373c9003ddbc1f80dcbbf01e9e9c18191328b80eb50b45ac70032027dd1efb0e256d78b88bfe1742151a16f6f333938099943a7b2cd16a
 DIST beast-mcmc-1.7.5.tar.xz 40516312 SHA256 905248cbf07513a0d11375656391d86e310d28f07b6fe78de6b9768eb2548f4f SHA512 9b2ab98fdc5a173e8d9fc74d27cdfd8105e9685fdcbe69a373666e77b6865b74fdd87dfa404fc4ab5bea927728d5b6b35fabd5e376a66e5f014e978952797937 WHIRLPOOL 2daded22cfd59b3b44908ce27f4ef61178f5d174de02080a7e94ba311462f482e381556d4b81bc053e33e1c4bb193d172f2c23f331659b3548f7900d3fc297d5
diff --git a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
deleted file mode 100644
index e3566919c375..000000000000
--- a/sci-biology/beast-mcmc/beast-mcmc-1.5.2.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2009 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
-
-WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,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
-
-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="~amd64 ~x86"
-IUSE=""
-
-# TODO: sys-cluster/mpijava
-COMMON_DEPS="dev-java/colt:0
-	dev-java/jdom:1.0
-	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|' "${S}"/scripts/* || die
-	cd lib
-	rm -v colt.jar junit-*.jar itext-*.jar jdom.jar jebl.jar mtj.jar commons-math-*.jar || die
-	java-pkg_jar-from jdom-1.0
-	java-pkg_jar-from colt
-	java-pkg_jar-from itext
-	java-pkg_jar-from jebl
-	java-pkg_jar-from matrix-toolkits-java
-	java-pkg_jar-from commons-math-1
-	java-pkg-2_src_prepare
-}
-
-src_compile() {
-	eant dist_all_BEAST -f build_BEAST_MCMC.xml \
-		-Dgentoo.classpath=$(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/beast-mcmc-1.7.5.ebuild b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
similarity index 94%
rename from sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
rename to sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
index 5a66f595593c..8e59912e7175 100644
--- a/sci-biology/beast-mcmc/beast-mcmc-1.7.5.ebuild
+++ b/sci-biology/beast-mcmc/beast-mcmc-1.7.5-r1.ebuild
@@ -7,7 +7,7 @@ EAPI=5
 ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
 
 WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+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"
@@ -30,7 +30,7 @@ IUSE=""
 # TODO: sys-cluster/mpijava
 COMMON_DEPS="
 	dev-java/colt:0
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/itext:0
 	dev-java/junit:4
 	dev-java/jebl:0
@@ -49,7 +49,7 @@ src_prepare() {
 	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-1.0
+	java-pkg_jar-from jdom
 	java-pkg_jar-from colt
 	java-pkg_jar-from itext
 #	java-pkg_jar-from jebl
diff --git a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
index 768799ce2195..7bb1f0faa1b3 100644
--- a/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
+++ b/sci-biology/beast-mcmc/beast-mcmc-9999.ebuild
@@ -7,7 +7,7 @@ EAPI="2"
 ESVN_REPO_URI="https://beast-mcmc.googlecode.com/svn/trunk/"
 
 WANT_ANT_TASKS="ant-junit4"
-EANT_GENTOO_CLASSPATH="colt,jdom-1.0,itext,junit-4,jebl,matrix-toolkits-java,commons-math-2,jdom-jaxen-1.0"
+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"
@@ -26,7 +26,7 @@ IUSE=""
 
 # TODO: sys-cluster/mpijava
 COMMON_DEPS="dev-java/colt:0
-	dev-java/jdom:1.0
+	dev-java/jdom:0
 	dev-java/itext:0
 	dev-java/junit:4
 	dev-java/jebl:0
@@ -44,7 +44,7 @@ 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-1.0
+	java-pkg_jar-from jdom
 	java-pkg_jar-from colt
 	java-pkg_jar-from itext
 	java-pkg_jar-from jebl