[gentoo-commits] repo/gentoo:master commit in: profiles/, sci-biology/picard/files/, sci-biology/picard/

[Jakov Smolić]

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 <soap@g.o> (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 <conikost@g.o> (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>sci-biology@g.o</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
-}