[med-svn] r6052 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Mon Feb 21 21:10:06 UTC 2011
Author: tille
Date: 2011-02-21 21:10:06 +0000 (Mon, 21 Feb 2011)
New Revision: 6052
Added:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/patches/series
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Try also building tracer which does not work that way - any help is welcome
Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch 2011-02-21 21:10:06 UTC (rev 6052)
@@ -0,0 +1,137 @@
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/build_tracer.xml
++++ beast-mcmc-1.6.1+svnr3660.orig/build_tracer.xml
+@@ -32,6 +32,7 @@
+ <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="dist"/>
+
+ <property environment="env"/>
+@@ -56,7 +57,7 @@
+ <target name="compile-basic" depends="init">
+ <!-- Compile the java code from ${src} into ${build} -->
+ <javac source="1.5" target="1.5" srcdir="${src}" destdir="${build}"
+- classpath="${lib}/colt.jar:${lib}/commons-math-2.0.jar:${lib}/jebl.jar:${lib}/jam.jar:${lib}/itext-1.4.5.jar:${lib}/jdom.jar:${lib}/mtj.jar:${lib}/JRI.jar:${lib}/mpj.jar">
++ classpath="${lib}/colt.jar:${deblib}/commons-math.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext1.jar:${deblib}/jdom1.jar:${lib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${lib}/mpj.jar">
+ <include name="dr/app/tracer/**"/>
+ <include name="dr/app/util/**"/>
+ <include name="dr/app/gui/**"/>
+@@ -121,10 +122,10 @@
+ <include name="dr/app/tracer/**/*.tiff"/>
+ <include name="org/virion/jam/**/*.png"/>
+ </fileset>
+- <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
+- <zipgroupfileset dir="${lib}" includes="jam.jar"/>
+- <zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/>
+- <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar"/>
++ <zipgroupfileset dir="${deblib}" includes="jebl.jar"/>
++ <zipgroupfileset dir="${deblib}" includes="jam.jar"/>
++ <zipgroupfileset dir="${deblib}" includes="itext1.jar"/>
++ <zipgroupfileset dir="${deblib}" includes="commons-math.jar"/>
+ </jar>
+
+ </target>
+@@ -135,46 +136,12 @@
+
+ <property name="common_dir" value="${release_dir}/common" />
+
+- <property name="Mac_dir" value="${release_dir}/Mac" />
+ <property name="Linux_dir" value="${release_dir}/Linux" />
+- <property name="Windows_dir" value="${release_dir}/Windows" />
+
+- <property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
+ <property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
+- <property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
+
+ <!-- Need to either install Launch4j under {BEAST workspace}/${release}
+ or install it in the default directory and change the location of launch4j.dir -->
+- <target name="windows_Release" depends="dist" description="release Windows version of Tracer">
+-
+- <delete dir="${Windows_package_dir}" />
+- <!-- Create the release directory -->
+- <mkdir dir="${Windows_package_dir}" />
+-
+- <property name="launch4j.dir" location="${Windows_dir}/launch4j" />
+- <taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
+- classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
+-
+- <copy file="${dist}/tracer.jar" todir="${Windows_package_dir}/lib"/>
+- <copy todir="${Windows_package_dir}/lib">
+- <fileset dir="${Windows_dir}/lib"/>
+- </copy>
+- <copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
+-
+- <launch4j configFile="${Windows_dir}/tracer_launch4j.xml"
+- jar="${dist}/tracer.jar"
+- outfile="${Windows_package_dir}/${name} v${version}.exe"
+- fileVersion="${version}.0.0"
+- txtFileVersion="${version}"
+- productVersion="${version}.0.0"
+- txtProductVersion="${version}"/>
+-
+- <zip destfile="${release_dir}/${name} v${version}.zip">
+- <zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
+- </zip>
+-
+- <echo message="Windows version release is finished." />
+- </target>
+
+ <target name="linux_unix_Release" description="release Linux/Unix version of Tracer">
+ <delete dir="${Linux_package_dir}" />
+@@ -199,55 +166,4 @@
+ <echo message="Linux/Unix version release is finished." />
+ </target>
+
+- <target name="mac_Release"
+- description="release Mac version of Tracer">
+- <delete dir="${Mac_package_dir}" />
+- <!-- Create the release directory -->
+- <mkdir dir="${Mac_package_dir}" />
+-
+- <copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
+-
+- <taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
+-
+- <!-- create a jar bundle for the mac -->
+- <jarbundler dir="${Mac_package_dir}"
+- name="${name} v${version}"
+- mainclass="dr.app.tracer.application.TracerApp"
+- icon="${Mac_dir}/icons/Tracer.icns"
+- jvmversion="1.5+"
+- vmoptions="-Xmx1024M"
+- arguments=""
+- version="${version}"
+- infostring="${name} v${version}, Copyright 2003-2009, Andrew Rambaut & Alexei J. Drummond"
+- bundleid="tracer" >
+- <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
+- <jarfileset dir="${dist}">
+- <include name="**/tracer.jar"/>
+- </jarfileset>
+- <jarfileset dir="${Mac_dir}/lib">
+- <include name="**/quaqua.jar"/>
+- </jarfileset>
+- <jarfileset dir="${Mac_dir}/lib">
+- <include name="libquaqua*.jnilib"/>
+- </jarfileset>
+- </jarbundler>
+-
+- <echo message="Building disk image." />
+-
+- <!-- create disk image -->
+- <exec executable="/usr/bin/hdiutil">
+- <arg value="create"/>
+- <arg value="-ov"/>
+- <arg value="-srcfolder"/>
+- <arg value="${Mac_package_dir}"/>
+- <arg value="-volname"/>
+- <arg value="${name} v${version}"/>
+- <arg value="-imagekey"/>
+- <arg value="zlib-level=6"/>
+- <arg value="${release_dir}/${name} v${version}.dmg"/>
+- </exec>
+-
+- <echo message="Mac version release is finished." />
+- </target>
+-
+ </project>
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-21 20:50:30 UTC (rev 6051)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series 2011-02-21 21:10:06 UTC (rev 6052)
@@ -2,3 +2,4 @@
fix_gcc_options.patch
fix_classpath_in_build_xml.patch
patch_tex_docs.patch
+fix_classpath_in_build_tracer_xml.patch
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-21 20:50:30 UTC (rev 6051)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-21 21:10:06 UTC (rev 6052)
@@ -36,8 +36,8 @@
ant clean
override_dh_auto_build:
- # CLASSPATH=$(CLASS_PATH)
ant build ; \
+ ant -buildfile build_tracer.xml all ; \
cd native && /bin/sh compileNativeLinux.sh
#
# Build extra LaTeX documentation
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