commit: 8c4dc835b136a9585d825da398339774c16b7c43 Author: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> AuthorDate: Sat Jan 8 10:28:27 2022 +0000 Commit: Jakov Smolić <jsmolic <AT> gentoo <DOT> org> CommitDate: Sat Jan 8 10:32:29 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8c4dc835
sci-biology/picard: treeclean Closes: https://bugs.gentoo.org/776298 Closes: https://bugs.gentoo.org/580176 Closes: https://bugs.gentoo.org/572142 Signed-off-by: Jakov Smolić <jsmolic <AT> gentoo.org> profiles/package.mask | 6 -- sci-biology/picard/Manifest | 1 - sci-biology/picard/files/1.103-gentoo.patch | 131 ---------------------------- sci-biology/picard/metadata.xml | 11 --- sci-biology/picard/picard-1.103.ebuild | 69 --------------- 5 files changed, 218 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index e798dcbe3f3b..f4e46b9e59e0 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -230,12 +230,6 @@ games-action/multimc # Package without consumers. Bug #828740. Removal in 30 days. www-apache/mod_caucho -# David Seifert <[email protected]> (2021-12-06) -# Ancient release, EAPI 5, downloads random data, -# latest version uses Gradle. -# Bug #572142, #580176, #776298, removal in 30 days. -sci-biology/picard - # Conrad Kostecki <[email protected]> (2021-12-04) # Masking newer versions for both packages, # as they cannot be compiled due upstream change. diff --git a/sci-biology/picard/Manifest b/sci-biology/picard/Manifest deleted file mode 100644 index 62dd6475dcea..000000000000 --- a/sci-biology/picard/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST picard-1.103.tar.bz2 15037887 BLAKE2B a4df3aad9242749964a997698d80634e14ce19af575de9609655483eba247d0968cbdc856dbf00d854ec7eae37da8f3d047c50e4b78843e9d08441d9ef18eff6 SHA512 f8db38a8fee278868cd2ea11f78275a5defadf36e053703133f0f90836df8e3a3ca08635fd7c02967ed99b52bc5baffa600a34b58a94288d3eede7f5c3dd79ca diff --git a/sci-biology/picard/files/1.103-gentoo.patch b/sci-biology/picard/files/1.103-gentoo.patch deleted file mode 100644 index 00e89b95056a..000000000000 --- a/sci-biology/picard/files/1.103-gentoo.patch +++ /dev/null @@ -1,131 +0,0 @@ -diff --git a/build.xml b/build.xml -index fca2271..11f4fbd 100755 ---- a/build.xml -+++ b/build.xml -@@ -52,9 +52,6 @@ - <property name="testng.verbosity" value="2"/> - <property name="test.debug.port" value="5005" /> <!-- override on the command line if desired --> - -- <property environment="env"/> -- <property name="java6.home" value="${env.JAVA6_HOME}"/> -- - <condition property="isUnix"> - <os family="unix"/> - </condition> -@@ -78,9 +75,6 @@ - <pathelement location="${classes}"/> - </path> - -- <path id="java6.lib.ref"> -- <fileset dir="${java6.home}/lib" includes="*.jar"/> -- </path> - </target> - - <!-- CLEAN --> -@@ -94,10 +88,6 @@ - </target> - - <!-- COMPILE --> -- <target name="compile" depends="compile-src, compile-tests" -- description="Compile files without cleaning"> -- </target> -- - <target name="compile-src" depends="compile-sam-jdk, compile-picard, compile-tribble, compile-variant" description="Compile files without cleaning"/> - - <target name="compile-sam-jdk" depends="init" description="Compile sam-jdk files without cleaning"> -@@ -138,7 +128,7 @@ - </target> - - <!-- TEST --> -- <target name="test" depends="compile, set_excluded_test_groups" description="Run unit tests"> -+ <target name="test" depends="compile-tests, set_excluded_test_groups" description="Run unit tests"> - <taskdef resource="testngtasks" classpathref="classpath"/> - <testng suitename="picard-tests" classpathref="classpath" outputdir="${test.output}" - failureproperty="tests.failed" excludedgroups="${excludedTestGroups}" workingDir="${basedir}" -@@ -151,6 +141,8 @@ - <classfileset dir="${classes.test}"> - <include name="**/Test*.class"/> - <include name="**/*Test.class"/> -+ <exclude name="**/ValidateSamFileTest.class" /> -+ <exclude name="**/VCFWriterUnitTest.class" /> - </classfileset> - <jvmarg value="-Xmx2G"/> - </testng> -@@ -165,7 +157,7 @@ - </target> - - <target name="single-test" -- depends="compile, compile-tests" -+ depends="compile-tests" - description="Compile and run a single test."> - <taskdef resource="testngtasks" classpathref="classpath"/> - <fail unless="name" message="Please provide input test: -Dname=..." /> -@@ -200,13 +192,12 @@ - </jar> - </target> - -- <target name="picard-jar" depends="compile" -+ <target name="picard-jar" depends="compile-src" - description="Builds picard-${picard-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/picard-${picard-version}.jar" compress="no"> - <fileset dir="${classes}" includes ="net/sf/picard/**/*.*"/> - <fileset dir="${src.scripts}" includes="**/*.R"/> -- <zipfileset src="${lib}/apache-ant-1.8.2-bzip2.jar"/> - <manifest> - <attribute name="Implementation-Version" value="${picard-version}(${repository.revision})"/> - <attribute name="Implementation-Vendor" value="Broad Institute"/> -@@ -214,7 +205,7 @@ - </jar> - </target> - -- <target name="tribble-jar" depends="compile" -+ <target name="tribble-jar" depends="compile-src" - description="Builds tribble-${tribble-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/tribble-${tribble-version}.jar" compress="no"> -@@ -225,7 +216,7 @@ - </copy> - </target> - -- <target name="variant-jar" depends="compile" -+ <target name="variant-jar" depends="compile-src" - description="Builds variant-${variant-version}.jar for inclusion in other projects"> - <mkdir dir="${dist}"/> - <jar destfile="${dist}/variant-${variant-version}.jar" compress="no"> -@@ -262,7 +253,7 @@ - </javadoc> - </target> - -- <target name="package-commands" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar"> -+ <target name="package-commands" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar"> - <delete dir="${command_tmp}"/> - - <mkdir dir="${command_tmp}"/> -@@ -344,7 +335,7 @@ - </target> - - <!-- ALL --> -- <target name="all" depends="compile, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> -+ <target name="all" depends="compile-src, sam-jar, picard-jar, tribble-jar, variant-jar, package-commands, document-standard-options" description="Default build target"> - <zip zipfile="${dist}/picard-tools-${picard-version}.zip"> - <zipfileset dir="${dist}" includes="*.jar" prefix="picard-tools-${picard-version}"/> - <zipfileset dir="${lib}" includes="snappy*.jar"/> -@@ -468,8 +459,6 @@ - target="${javac.target}"> - <classpath refid="@{compile.classpath}"/> - <compilerarg line="@{compiler.args}" /> -- <!-- ensure that Java 6 bootclasspath is used --> -- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> - </javac> - </sequential> - </macrodef> -@@ -494,8 +483,6 @@ - <pathelement location="${classes}"/> - </classpath> - <compilerarg line="@{compiler.args}"/> -- <!-- ensure that Java 6 bootclasspath is used --> -- <compilerarg value="-Xbootclasspath/p:${toString:java6.lib.ref}"/> - </javac> - </sequential> - </macrodef> diff --git a/sci-biology/picard/metadata.xml b/sci-biology/picard/metadata.xml deleted file mode 100644 index 22fd62cbaa79..000000000000 --- a/sci-biology/picard/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">picard</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/picard/picard-1.103.ebuild b/sci-biology/picard/picard-1.103.ebuild deleted file mode 100644 index 7a6111c87746..000000000000 --- a/sci-biology/picard/picard-1.103.ebuild +++ /dev/null @@ -1,69 +0,0 @@ -# Copyright 1999-2013 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI="5" - -JAVA_PKG_IUSE="doc source test" -WANT_ANT_TASKS="ant-apache-bcel dev-java/testng:0 ant-junit4" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java-based command-line utilities that manipulate SAM files" -HOMEPAGE="http://picard.sourceforge.net/"; -SRC_URI="https://dev.gentoo.org/~ercpe/distfiles/${CATEGORY}/${PN}/${P}.tar.bz2"; - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -CDEPEND="dev-java/snappy:1.0 - dev-java/cofoja:0 - dev-java/commons-jexl:2 - dev-java/ant-core:0" - -DEPEND=">=virtual/jdk-1.6 - dev-java/ant-apache-bcel:0 - test? ( - dev-java/testng:0 - dev-lang/R - ) - ${CDEPEND}" -RDEPEND=">=virtual/jre-1.6 - ${CDEPEND}" - -EANT_BUILD_TARGET="all" -EANT_TEST_TARGET="test" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="snappy-1.0,cofoja,commons-jexl-2,ant-core" -EANT_TEST_GENTOO_CLASSPATH="${EANT_GENTOO_CLASSPATH},testng" - -java_prepare() { - mkdir "${S}"/lib || die - - epatch "${FILESDIR}"/${PV}-gentoo.patch - - mv "${S}"/src/java/net/sf/samtools/SAMTestUtil.java "${S}"/src/tests/java/net/sf/samtools || die -} - -src_install() { - cd dist || die - - for i in *-${PV}.jar; do - java-pkg_newjar $i ${i/-${PV}/} - rm $i || die - done - - java-pkg_dojar *.jar - for i in *.jar; do - java-pkg_dolauncher ${i/.jar/} --jar $i; - done - - use source && java-pkg_dosrc "${S}"/src/java/* - use doc && java-pkg_dojavadoc "${S}"/javadoc -} - -src_test() { - java-pkg-2_src_test -}
