[med-svn] r9355 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Fri Jan 20 23:00:00 UTC 2012
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 <tille at debian.org>
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"/>
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