Author: tille Date: 2011-02-15 15:01:56 +0000 (Tue, 15 Feb 2011) New Revision: 5990
Added: trunk/packages/beast-mcmc/trunk/debian/get-orig-source trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch Modified: trunk/packages/beast-mcmc/trunk/debian/control trunk/packages/beast-mcmc/trunk/debian/patches/series trunk/packages/beast-mcmc/trunk/debian/rules Log: Remove some binarie jars which are just packaged for Debian, adapt CLASSPATH, use separate shell script get-orig-source (which might be usable for watch later) Modified: trunk/packages/beast-mcmc/trunk/debian/control =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/control 2011-02-15 13:13:09 UTC (rev 5989) +++ trunk/packages/beast-mcmc/trunk/debian/control 2011-02-15 15:01:56 UTC (rev 5990) @@ -5,7 +5,9 @@ DM-Upload-Allowed: yes Uploaders: Felix Feyertag <[email protected]>, Andreas Tille <[email protected]> -Build-Depends: debhelper (>= 7.1), cdbs, quilt, openjdk-6-jdk, ant, ant-optional, libgcj10-dev +Build-Depends: debhelper (>= 7.1), javahelper (>=0.25), quilt (>= 0.47), + ant, ant-optional, openjdk-6-jdk, libgcj10-dev, + libjebl2-java, libjam-java, r-cran-rjava, libcommons-math-java, libjdom1-java Standards-Version: 3.9.1 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/beast-mcmc/trunk/?rev=0&sc=0 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/beast-mcmc/trunk/ Added: trunk/packages/beast-mcmc/trunk/debian/get-orig-source =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/get-orig-source (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-15 15:01:56 UTC (rev 5990) @@ -0,0 +1,28 @@ +#!/bin/sh +PACKAGE=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +SRC_VERSION=`dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p'` +SVN_REVISION=`echo ${SRC_VERSION} | sed 's/^[0-9\.]\++svn//'` +TARBALL=${PACKAGE}_${SRC_VERSION}.orig.tar.gz + +cd .. +## rm -f download.html +mkdir -p tarballs +cd tarballs + +TARDIR=${PACKAGE}-${SRC_VERSION}.orig +rm -rf ${TARBALL} ${TARDIR} +svn export -r ${SVN_REVISION} http://beast-mcmc.googlecode.com/svn/trunk/ ${TARDIR} + +# remove jars which are provided as binaries but are not directly needed to build FigTree +for jar in \ + JRI.jar \ + commons-math-2.0.jar \ + jam.jar \ + jdom.jar \ + jebl.jar \ + ; do + rm -rf ${TARDIR}/lib/$jar +done + +GZIP="--best --no-name" tar czf ${TARBALL} ${TARDIR} + Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch (rev 0) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2011-02-15 15:01:56 UTC (rev 5990) @@ -0,0 +1,65 @@ +--- beast-mcmc-1.6.1+svnr3660.orig.orig/build.xml ++++ beast-mcmc-1.6.1+svnr3660.orig/build.xml +@@ -9,6 +9,7 @@ + <property name="src" location="src" /> + <property name="build" location="build" /> + <property name="lib" location="lib" /> ++ <property name="deblib" location="/usr/share/java" /> + <property name="dist" location="${build}/dist" /> + + <property name="main_class_BEAST" value="dr.app.beast.BeastMain" /> +@@ -20,6 +21,11 @@ + + <path id="classpath"> + <fileset dir="${lib}" includes="**/*.jar"/> ++ <fileset dir="${deblib}" includes="commons-math.jar"/> ++ <fileset dir="${deblib}" includes="jam.jar"/> ++ <fileset dir="${deblib}" includes="jdom1.jar"/> ++ <fileset dir="${deblib}" includes="jebl.jar"/> ++ <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/> + </path> + + <!-- start --> +@@ -130,12 +136,8 @@ + <include name="org/virion/jam/**/*.png" /> + <include name="dr/**/*.properties" /> + </fileset> +- <zipgroupfileset dir="${lib}" includes="jebl.jar" /> +- <zipgroupfileset dir="${lib}" includes="jam.jar" /> + <zipgroupfileset dir="${lib}" includes="jdom.jar" /> +- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" /> + <zipgroupfileset dir="${lib}" includes="mtj.jar" /> +- <zipgroupfileset dir="${lib}" includes="JRI.jar" /> + <zipgroupfileset dir="${lib}" includes="colt.jar" /> + <zipgroupfileset dir="${lib}" includes="beagle.jar" /> + </jar> +@@ -193,8 +195,6 @@ + <fileset dir="${src}"> + <include name="dr/**/*.png" /> + </fileset> +- <zipgroupfileset dir="${lib}" includes="jam.jar" /> +- <zipgroupfileset dir="${lib}" includes="jebl.jar" /> + <zipgroupfileset dir="${lib}" includes="jdom.jar" /> + <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" /> + <zipgroupfileset dir="${lib}" includes="mtj.jar" /> +--- beast-mcmc-1.6.1+svnr3660.orig.orig/.classpath ++++ beast-mcmc-1.6.1+svnr3660.orig/.classpath +@@ -3,13 +3,13 @@ + <classpathentry kind="src" path="src"/> + <classpathentry kind="lib" path="lib/beagle.jar"/> + <classpathentry kind="lib" path="lib/colt.jar"/> +- <classpathentry kind="lib" path="lib/commons-math-1.2.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/> + <classpathentry kind="lib" path="lib/figtreepanel.jar"/> + <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/> +- <classpathentry kind="lib" path="lib/jam.jar"/> +- <classpathentry kind="lib" path="lib/jdom.jar"/> +- <classpathentry kind="lib" path="lib/jebl.jar"/> +- <classpathentry kind="lib" path="lib/JRI.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/jam.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/jdom1.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/jebl.jar"/> ++ <classpathentry kind="lib" path="/usr/lib/R/site-library/rJava/jri/JRI.jar"/> + <classpathentry kind="lib" path="lib/junit-4.4.jar"/> + <classpathentry kind="lib" path="lib/libjri.jnilib"/> + <classpathentry kind="lib" path="lib/mpj.jar"/> Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-15 13:13:09 UTC (rev 5989) +++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-15 15:01:56 UTC (rev 5990) @@ -1,2 +1,3 @@ beast.patch fix_gcc_options.patch +fix_classpath_in_build_xml.patch Modified: trunk/packages/beast-mcmc/trunk/debian/rules =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-15 13:13:09 UTC (rev 5989) +++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-15 15:01:56 UTC (rev 5990) @@ -7,25 +7,28 @@ DOCPACKAGE = beast-doc SRC_VERSION := $(shell dpkg-parsechangelog | sed -ne 's/^Version: \(\([0-9]\+\):\)\?\(.*\)-.*/\3/p') SVN_REVISION := $(shell echo $(SRC_VERSION) | awk -F"+" '{ print $$2 }' | sed 's/svn//' ) -TARBALL = $(PACKAGE)_$(SRC_VERSION).orig.tar.gz +TARBALL=$(PACKAGE)_$(SRC_VERSION).orig.tar.gz -JAVA := /usr/lib/jvm/java-6-openjdk/bin/java -CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/commons-math-2.0.jar:lib/beagle.jar:lib/jebl.jar:lib/mpj.jar:lib/jam.jar:lib/org.boehn.kmlframework_20090320.jar:lib/junit-4.4.jar:lib/JRI.jar:lib/figtreepanel.jar:lib/colt.jar:lib/jdom.jar:lib/options.jar:lib/mtj.jar -ANT_HOME := /usr/share/ant -ANT_BIN := $(ANT_HOME)/bin/ant -ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true +DEBJAR := /usr/share/java +CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:lib/junit-4.4.jar:lib/figtreepanel.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jar.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar +# to run the test suite +JAVA := /usr/lib/jvm/java-6-openjdk/bin/java +ANT_HOME := /usr/share/ant +ANT_BIN := $(ANT_HOME)/bin/ant +ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true + + %: - dh $@ + dh $@ --with javahelper override_dh_auto_clean: rm -f build-stamp configure-stamp - #$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml clean rm -f native/*\.o native/*\.so ant clean override_dh_auto_build: - $(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build + CLASSPATH=$(CLASS_PATH) ant build ; \ cd native && /bin/sh compileNativeLinux.sh # ##################################################################### @@ -46,12 +49,4 @@ dh_compress --exclude=.pdf get-orig-source: - rm -rf get-orig-source $(TARBALL) - mkdir get-orig-source - svn export -r $(SVN_REVISION) http://beast-mcmc.googlecode.com/svn/trunk/ \ - get-orig-source/$(PACKAGE)-$(SRC_VERSION).orig - GZIP="--best --no-name" tar czf $(TARBALL) -C get-orig-source $(PACKAGE)-$(SRC_VERSION).orig - rm -rf get-orig-source - rm -rf ../tarballs/ - mkdir ../tarballs/ - mv $(TARBALL) ../tarballs/ + . debian/get-orig-source _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
