This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository picard-tools.
commit 9679a96cc91d8409d258bc452a4f5589f0e2d4db Author: Andreas Tille <[email protected]> Date: Sun Mar 13 12:16:34 2016 +0100 Take over patches from previous version --- debian/patches/10-build.xml | 84 ++++++++++++++++----------------------------- 1 file changed, 29 insertions(+), 55 deletions(-) diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml index a7cc494..e84a9b4 100644 --- a/debian/patches/10-build.xml +++ b/debian/patches/10-build.xml @@ -4,17 +4,15 @@ Description: Modifies the upstream build system. and get htsjdk version from system jar. Origin: vendor Forwarded: no -Index: picard-tools/build.xml -=================================================================== ---- picard-tools.orig/build.xml -+++ picard-tools/build.xml +--- a/build.xml ++++ b/build.xml @@ -42,17 +42,16 @@ <property name="htsjdk_git_url" value="[email protected]:samtools/htsjdk.git"/> <!-- TODO: get this from the build.xml in htsjdk --> <property name="htsjdk-classes" value="htsjdk/classes"/> + <property name="htsjdk-jar" value="/usr/share/java/htsjdk.jar"/> - <property name="javac.target" value="1.6"/> + <property name="javac.target" value="1.8"/> <property name="javac.debug" value="true"/> <!-- Get GIT hash, if available, otherwise leave it blank. --> @@ -28,10 +26,10 @@ Index: picard-tools/build.xml + packaging repo), but use the "dfsg" string as sources are + repacked --> + <property name="repository.revision" value="dfsg"/> - <property name="picard-version" value="1.138"/> + <property name="picard-version" value="2.1.1"/> <property name="command-line-html-dir" value="${dist}/html"/> <property name="testng.verbosity" value="2"/> -@@ -77,23 +76,17 @@ +@@ -83,23 +82,17 @@ <!-- INIT --> <target name="init"> <path id="classpath"> @@ -45,8 +43,8 @@ Index: picard-tools/build.xml - <include name="**/*.jar"/> - </fileset> - <fileset dir="${lib}"> -- <include name="**/*.jar"/> -- </fileset> +- <include name="**/*.jar"/> +- </fileset> + <!-- for the HTSJDK library JAR --> + <pathelement path="/usr/share/java/htsjdk.jar"/> + <!-- other system required installed JARs --> @@ -62,7 +60,7 @@ Index: picard-tools/build.xml </path> </target> -@@ -107,23 +100,13 @@ +@@ -113,23 +106,13 @@ <delete dir="javadoc"/> </target> @@ -89,7 +87,7 @@ Index: picard-tools/build.xml </target> <target name="clone-htsjdk" description="Clone HTS-JDK sources from Sourceforge"> -@@ -165,13 +148,13 @@ +@@ -171,13 +154,13 @@ description="Compile files without cleaning"> </target> @@ -105,46 +103,41 @@ Index: picard-tools/build.xml <target name="compile-picard-tests" depends="init" description="Compile picard test files without cleaning"> <compile-tests includes="picard/**/*.*"/> -@@ -199,6 +182,7 @@ +@@ -260,6 +243,8 @@ <pathelement path="${classes}"/> <pathelement path="${classes.test}"/> <pathelement path="${scripts}"/> + <pathelement path="/usr/share/java/jcommander.jar"/> - </classpath> - <classfileset dir="${classes.test}"> - <include name="**/Test*.class"/> -@@ -234,6 +218,7 @@ - <pathelement path="${classes}"/> - <pathelement path="${classes.test}"/> - <pathelement path="${scripts}"/> + <pathelement path="/usr/share/java/jcommander.jar"/> </classpath> <classfileset dir="${classes.test}"> <include name="**/${name}.class"/> -@@ -258,21 +243,17 @@ - </unzip> +@@ -284,7 +269,7 @@ + </unzip> </target> - + - <target name="picard-jar" depends="compile, process-external-jars" + <target name="picard-jar" depends="compile, process-external-jars, set-htsjdk-version" - description="Builds the main executable picard.jar"> - <mkdir dir="${dist}"/> - <mkdir dir="${dist.tmp}"/> - <unjar dest="${dist.tmp}"> - <fileset dir="${lib}" /> -- <fileset dir="${htsjdk_lib_dir}"> -- <include name="*.jar"/> -- </fileset> - </unjar> + description="Builds the main executable picard.jar"> + <mkdir dir="${dist}"/> + <mkdir dir="${dist.tmp}"/> +@@ -292,15 +277,11 @@ + <fileset dir="${lib}"> + <exclude name="**/jacocoant.jar"/> <!-- must exclude this jar from packing into picard - this is only used for testing --> + </fileset> +- <fileset dir="${htsjdk_lib_dir}"> +- <include name="*.jar"/> +- </fileset> + </unjar> <jar destfile="${dist}/picard.jar" compress="no"> <fileset dir="${classes}" includes="picard/**/*.*, META-INF/**/*"/> <fileset dir="${src.scripts}" includes="**/*.R"/> - <fileset dir="${htsjdk-classes}" includes ="${htsjdk}/*/**/*.*"/> <fileset dir="${dist.tmp}" includes="**/*"/> - <fileset dir="${jar_opt}" includes="**/*"/> + <fileset dir="${jar_opt}" includes="**/*"/> -@@ -319,43 +300,17 @@ +@@ -348,44 +329,17 @@ <fileset dir="${lib}"> <include name="**/*.jar"/> </fileset> @@ -175,6 +168,7 @@ Index: picard-tools/build.xml - protected="true" - use="true" - version="true" +- additionalparam="-Xdoclint:none -notimestamp" - failonerror="true" - excludepackagenames="picard*"> - <classpath> @@ -194,7 +188,7 @@ Index: picard-tools/build.xml <mkdir dir="${command-line-html-dir}"/> <javadoc doclet="picard.util.MetricsDoclet" docletpathref="metrics.classpath" -@@ -366,13 +321,12 @@ +@@ -396,13 +350,12 @@ <fileset dir="${lib}"> <include name="**/*.jar"/> </fileset> @@ -211,27 +205,7 @@ Index: picard-tools/build.xml </fileset> <arg line="-f ${command-line-html-dir}/picard-metric-definitions.html"/> </javadoc> -@@ -477,6 +431,9 @@ - failonerror="true"> - <classpath> - <pathelement location="${dist}/picard.jar"/> -+ <pathelement path="/usr/share/java/htsjdk.jar"/> -+ <pathelement path="/usr/share/java/guava.jar"/> -+ <pathelement path="/usr/share/java/testng.jar"/> - </classpath> - </java> - </sequential> -@@ -498,6 +455,9 @@ - failonerror="true"> - <classpath> - <pathelement location="${dist}/picard.jar"/> -+ <pathelement path="/usr/share/java/htsjdk.jar"/> -+ <pathelement path="/usr/share/java/guava.jar"/> -+ <pathelement path="/usr/share/java/testng.jar"/> - </classpath> - <arg value="@{main-class}"/> - </java> -@@ -561,4 +521,25 @@ +@@ -617,4 +570,25 @@ </javac> </sequential> </macrodef> -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
