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Author: Andreas Tille <tille@debian.org>
Last-Updated: 2012-02-26
Subject: use Debian jars
Description: Make sure package builds with Debian packages JARs
Forwarded: no
--- a/build.xml
+++ b/build.xml
@@ -37,6 +37,7 @@
<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="${build}/dist"/>
<property name="main_class_BEAST" value="dr.app.beast.BeastMain"/>
@@ -48,6 +49,31 @@
<path id="classpath">
<fileset dir="${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"/>
+ <fileset dir="${deblib}" includes="EJML.jar"/>
+ <fileset dir="${deblib}" includes="ejml-all.jar"/>
+ <fileset dir="${deblib}" includes="ejml-all.jar"/>
+ <fileset dir="${deblib}" includes="ejml-cdense.jar"/>
+ <fileset dir="${deblib}" includes="ejml-core.jar"/>
+ <fileset dir="${deblib}" includes="ejml-ddense.jar"/>
+ <fileset dir="${deblib}" includes="ejml-dsparse.jar"/>
+ <fileset dir="${deblib}" includes="ejml-experimental.jar"/>
+ <fileset dir="${deblib}" includes="ejml-fdense.jar"/>
+ <fileset dir="${deblib}" includes="ejml-simple.jar"/>
+ <fileset dir="${deblib}" includes="ejml-zdense.jar"/>
+ <fileset dir="${deblib}" includes="jlapack-lapack.jar"/>
</path>
<!-- start -->
@@ -161,17 +187,6 @@
<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"/>
- <zipgroupfileset dir="${lib}" includes="beagle.jar"/>
- <zipgroupfileset dir="${lib}" includes="EJML-core-0.30.jar"/>
- <zipgroupfileset dir="${lib}" includes="EJML-dense64-0.30.jar"/>
</jar>
<!-- Put everything in ${build} into the beauti.jar file -->
@@ -228,11 +243,6 @@
<fileset dir="${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>
<!-- Put everything in ${build} into the trace.jar file -->
--- a/.classpath
+++ b/.classpath
@@ -1,20 +1,27 @@
<?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/colt.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="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="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry kind="lib" path="lib/commons-math-2.2.jar"/>
- <classpathentry kind="lib" path="lib/freemarker.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/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/share/java/junit4.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/commons-math.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/EJML.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-all.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-cdense.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-core.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-ddense.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-dsparse.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-experimental.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-fdense.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-simple.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/ejml-zdense.jar"/>
+ <classpathentry kind="lib" path="/usr/share/java/jlapack-lapack.jar"/>
<classpathentry kind="output" path="bin"/>
</classpath>
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