[med-svn] r5990 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Tue Feb 15 15:02:06 UTC 2011
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 <felix.feyertag at googlemail.com>,
Andreas Tille <tille at debian.org>
-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
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