Author: osallou-guest
Date: 2013-02-26 09:05:48 +0000 (Tue, 26 Feb 2013)
New Revision: 13111
Modified:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
Log:
adapt patch to new release
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
2013-02-25 14:25:53 UTC (rev 13110)
+++
trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch
2013-02-26 09:05:48 UTC (rev 13111)
@@ -1,64 +1,65 @@
Author: Andreas Tille <[email protected]>
-Date: Tue, 10 Jan 2012 22:29:24 +0100
+Last-Updated: 2012-02-26
+Subject: use Debian jars
Description: Make sure package builds with Debian packages JARs
-
---- beast-mcmc-1.6.2.orig/build.xml
-+++ beast-mcmc-1.6.2/build.xml
+Forwarded: no
+--- a/build.xml
++++ b/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="${build}/dist" />
+ <property name="src" location="src"/>
+ <property name="build" location="build"/>
+ <property name="lib" location="lib"/>
++ <property name="deblib" location="/usr/share/java" />
+ <property name="dist" location="${build}/dist"/>
- <property name="main_class_BEAST" value="dr.app.beast.BeastMain" />
-@@ -20,6 +21,19 @@
+ <property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
+@@ -21,6 +22,19 @@
- <path id="classpath">
- <fileset dir="${lib}" includes="**/*.jar"/>
-+ <fileset dir="${deblib}" includes="beagle.jar"/>
-+ <fileset dir="${deblib}" includes="colt.jar"/>
-+ <fileset dir="${deblib}" includes="commons-math.jar"/>
-+ <fileset dir="${deblib}" includes="figtree.jar"/>
-+ <fileset dir="${deblib}" includes="itext1.jar"/>
-+ <fileset dir="${deblib}" includes="jam.jar"/>
-+ <fileset dir="${deblib}" includes="jdom1.jar"/>
-+ <fileset dir="${deblib}" includes="jebl.jar"/>
-+ <fileset dir="/usr/lib/R/site-library/rJava/jri/"
includes="JRI.jar"/>
-+ <fileset dir="${deblib}" includes="junit4.jar"/>
-+ <fileset dir="${deblib}" includes="mpj.jar"/>
-+ <fileset dir="${deblib}" includes="mtj.jar"/>
-+ <fileset dir="${deblib}" includes="options.jar"/>
- </path>
+ <path id="classpath">
+ <fileset dir="${lib}" includes="**/*.jar"/>
++ <fileset dir="${deblib}" includes="beagle.jar"/>
++ <fileset dir="${deblib}" includes="colt.jar"/>
++ <fileset dir="${deblib}" includes="commons-math.jar"/>
++ <fileset dir="${deblib}" includes="figtree.jar"/>
++ <fileset dir="${deblib}" includes="itext1.jar"/>
++ <fileset dir="${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"/>
++ <fileset dir="${deblib}" includes="junit4.jar"/>
++ <fileset dir="${deblib}" includes="mpj.jar"/>
++ <fileset dir="${deblib}" includes="mtj.jar"/>
++ <fileset dir="${deblib}" includes="options.jar"/>
+ </path>
- <!-- start -->
-@@ -130,14 +144,6 @@
- <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>
+ <!-- start -->
+@@ -132,14 +146,6 @@
+ <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-2.2.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>
- <!-- Put everything in ${build} into the beauti.jar file -->
-@@ -193,11 +199,6 @@
- <fileset dir="${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="${lib}" includes="mtj.jar" />
- </jar>
-
- <!-- <jar jarfile="${dist}/treestat.jar">
+ <!-- Put everything in ${build} into the beauti.jar file -->
+@@ -195,11 +201,6 @@
+ <fileset dir="${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-2.2.jar"/>
+- <zipgroupfileset dir="${lib}" includes="mtj.jar"/>
+ </jar>
+
+ </target>
--- beast-mcmc-1.6.2.orig/.classpath
+++ beast-mcmc-1.6.2/.classpath
@@ -1,20 +1,20 @@
@@ -74,24 +75,25 @@
- <classpathentry kind="lib" path="lib/jebl.jar"/>
- <classpathentry kind="lib" path="lib/JRI.jar"/>
- <classpathentry kind="lib" path="lib/junit-4.4.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="/usr/share/java/beagle.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/colt.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/figtree.jar"/>
-+ <classpathentry kind="lib" path="/usr/share/java/itext1.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/figtreepanel.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.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/jdom.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="/usr/share/java/junit4.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/JRI.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/junit-4.4.jar"/>
+ <classpathentry kind="lib" path="lib/libjri.jnilib"/>
+- <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="/usr/share/java/mpj.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/mtj.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"/>
- <classpathentry kind="lib" path="lib/libjri.jnilib"/>
+- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
++ <classpathentry kind="lib" path="/usr/share/java/commons-math-2.2.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
+
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