Author: tille Date: 2012-01-20 23:00:00 +0000 (Fri, 20 Jan 2012) New Revision: 9355
Modified: trunk/packages/beast-mcmc/trunk/debian/control trunk/packages/beast-mcmc/trunk/debian/get-orig-source trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch Log: Use now available Debian packaged libraries Modified: trunk/packages/beast-mcmc/trunk/debian/control =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/control 2012-01-20 21:02:42 UTC (rev 9354) +++ trunk/packages/beast-mcmc/trunk/debian/control 2012-01-20 23:00:00 UTC (rev 9355) @@ -7,7 +7,7 @@ Andreas Tille <[email protected]> Build-Depends: debhelper (>= 8), javahelper (>=0.25), ant, ant-optional, openjdk-6-jdk, default-jdk, - libjebl2-java, libjam-java, figtree, + libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java, r-cran-rjava, libcommons-math-java, libjdom1-java, junit4, libitext1-java, texlive-latex-base Standards-Version: 3.9.2 @@ -88,4 +88,3 @@ analyses and a suit of programs for analysing the results. . This package contains the documentation. - Modified: trunk/packages/beast-mcmc/trunk/debian/get-orig-source =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2012-01-20 21:02:42 UTC (rev 9354) +++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2012-01-20 23:00:00 UTC (rev 9355) @@ -3,11 +3,12 @@ set -e NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` +ORIGNAME=beast if ! echo $@ | grep -q upstream-version ; then VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` else - VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*beast_release.*?\1?'` + VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${ORIGNAME}_release.*?\1?"` if echo "$VERSION" | grep -q "upstream-version" ; then echo "Unable to parse version number" exit @@ -15,8 +16,8 @@ fi SVNTAG=`echo ${VERSION} | sed 's/\./_/g'` -rm -f ../beast_release_${SVNTAG} -RELEASE=beast_release_${SVNTAG} +rm -f ../${ORIGNAME}_release_${SVNTAG} +RELEASE=${ORIGNAME}_release_${SVNTAG} TARDIR=${NAME}-${VERSION} mkdir -p ../tarballs @@ -27,6 +28,7 @@ # remove jars which are provided as binaries but are not directly needed to build FigTree for jar in \ JRI.jar \ + beagle.jar \ commons-math-2.0.jar \ figtreepanel.jar \ itext-1.4.5.jar \ @@ -35,6 +37,8 @@ jebl.jar \ junit-4.4.jar \ libjri.jnilib \ + options.jar \ + org.boehn.kmlframework_20090320.jar \ ; do rm -rf ${TARDIR}/lib/$jar done @@ -54,5 +58,5 @@ rm -rf ${TARDIR}/$pdf done -GZIP="--best --no-name" tar -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}" -rm -rf "${NAME}" +GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -czf "$NAME"_"$VERSION".orig.tar.gz "${TARDIR}" +rm -rf "${NAME}"-"$VERSION" Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch =================================================================== --- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-01-20 21:02:42 UTC (rev 9354) +++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch 2012-01-20 23:00:00 UTC (rev 9355) @@ -8,10 +8,11 @@ <property name="dist" location="${build}/dist" /> <property name="main_class_BEAST" value="dr.app.beast.BeastMain" /> -@@ -20,6 +21,14 @@ +@@ -20,6 +21,16 @@ <path id="classpath"> <fileset dir="${lib}" includes="**/*.jar"/> ++ <fileset dir="${deblib}" includes="beagle.jar"/> + <fileset dir="${deblib}" includes="commons-math.jar"/> + <fileset dir="${deblib}" includes="figtree.jar"/> + <fileset dir="${deblib}" includes="itext1.jar"/> @@ -20,10 +21,11 @@ + <fileset dir="${deblib}" includes="jebl.jar"/> + <fileset dir="/usr/lib/R/site-library/rJava/jri/" includes="JRI.jar"/> + <fileset dir="${deblib}" includes="junit4.jar"/> ++ <fileset dir="${deblib}" includes="options.jar"/> </path> <!-- start --> -@@ -130,12 +139,7 @@ +@@ -130,14 +141,8 @@ <include name="org/virion/jam/**/*.png" /> <include name="dr/**/*.properties" /> </fileset> @@ -34,9 +36,11 @@ <zipgroupfileset dir="${lib}" includes="mtj.jar" /> - <zipgroupfileset dir="${lib}" includes="JRI.jar" /> <zipgroupfileset dir="${lib}" includes="colt.jar" /> - <zipgroupfileset dir="${lib}" includes="beagle.jar" /> +- <zipgroupfileset dir="${lib}" includes="beagle.jar" /> </jar> -@@ -193,9 +197,6 @@ + + <!-- Put everything in ${build} into the beauti.jar file --> +@@ -193,9 +198,6 @@ <fileset dir="${src}"> <include name="dr/**/*.png" /> </fileset> @@ -48,9 +52,12 @@ </jar> --- beast-mcmc-1.6.2.orig/.classpath +++ beast-mcmc-1.6.2/.classpath -@@ -3,18 +3,18 @@ +@@ -1,20 +1,20 @@ + <?xml version="1.0" encoding="UTF-8"?> + <classpath> <classpathentry kind="src" path="src"/> - <classpathentry kind="lib" path="lib/beagle.jar"/> +- <classpathentry kind="lib" path="lib/beagle.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/beagle.jar"/> <classpathentry kind="lib" path="lib/colt.jar"/> - <classpathentry kind="lib" path="lib/figtreepanel.jar"/> - <classpathentry kind="lib" path="lib/itext-1.4.5.jar"/> @@ -68,7 +75,8 @@ + <classpathentry kind="lib" path="/usr/share/java/junit4.jar"/> <classpathentry kind="lib" path="lib/mpj.jar"/> <classpathentry kind="lib" path="lib/mtj.jar"/> - <classpathentry kind="lib" path="lib/options.jar"/> +- <classpathentry kind="lib" path="lib/options.jar"/> ++ <classpathentry kind="lib" path="/usr/share/java/options.jar"/> <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> - <classpathentry kind="lib" path="lib/commons-math-2.0.jar"/> + <classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/> _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
