[med-svn] [beast-mcmc] 05/06: Adapt patches

[Andreas Tille]

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tille pushed a commit to branch master
in repository beast-mcmc.

commit a5a6b1cbcac851830b38a0d0e8df9e4fd3840d0e
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jan 29 16:03:19 2016 +0100

    Adapt patches
---
 .../patches/fix_classpath_in_build_tracer_xml.patch  | 11 ++++++-----
 debian/patches/fix_classpath_in_build_xml.patch      | 20 +++++++++-----------
 2 files changed, 15 insertions(+), 16 deletions(-)

diff --git a/debian/patches/fix_classpath_in_build_tracer_xml.patch b/debian/patches/fix_classpath_in_build_tracer_xml.patch
index c3d6426..84f2c91 100644
--- a/debian/patches/fix_classpath_in_build_tracer_xml.patch
+++ b/debian/patches/fix_classpath_in_build_tracer_xml.patch
@@ -36,8 +36,8 @@ Description: Make sure also tracer is builded with Debian packages JARs
          </jar>
  
      </target>
-@@ -136,46 +137,12 @@
- 
+@@ -137,46 +138,12 @@
+     <property name="packaging_tools" value="packaging_tools" />
      <property name="common_dir" value="${release_dir}/common" />
  
 -    <property name="Mac_dir" value="${release_dir}/Mac" />
@@ -83,7 +83,7 @@ Description: Make sure also tracer is builded with Debian packages JARs
  
      <target name="linux" description="release Linux/Unix version of Tracer">
          <delete dir="${Linux_package_dir}" />
-@@ -202,54 +169,4 @@
+@@ -203,55 +170,4 @@
          <echo message="Linux/Unix version release is finished." />
      </target>
  
@@ -100,12 +100,13 @@ Description: Make sure also tracer is builded with Debian packages JARs
 -        <jarbundler dir="${Mac_package_dir}"
 -                        name="${name} v${version}"
 -                        mainclass="dr.app.tracer.application.TracerApp"
+-                        stubfile="${packaging_tools}/mac/universalJavaApplicationStub"
 -                        icon="${Mac_dir}/icons/Tracer.icns"
--                        jvmversion="1.5+"
+-                        jvmversion="1.6+"
 -                        vmoptions="-Xmx1024M"
 -                        arguments=""
 -                        version="${version}"
--                        infostring="${name} v${version}, Copyright 2003-2013, Andrew Rambaut, Marc Suchard & Alexei J. Drummond"
+-                        copyright="${name} v${version}, Copyright 2003-2015, Andrew Rambaut, Marc Suchard & Alexei J. Drummond"
 -                        bundleid="tracer" >
 -            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
 -            <jarfileset dir="${dist}">
diff --git a/debian/patches/fix_classpath_in_build_xml.patch b/debian/patches/fix_classpath_in_build_xml.patch
index bfc77b3..6383a1c 100644
--- a/debian/patches/fix_classpath_in_build_xml.patch
+++ b/debian/patches/fix_classpath_in_build_xml.patch
@@ -62,7 +62,7 @@ Forwarded: no
      </target>
 --- a/.classpath
 +++ b/.classpath
-@@ -1,20 +1,20 @@
+@@ -1,20 +1,16 @@
  <?xml version="1.0" encoding="UTF-8"?>
  <classpath>
  	<classpathentry kind="src" path="src"/>
@@ -78,21 +78,19 @@ Forwarded: no
 -	<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/figtreepanel.jar"/>
-+	<classpathentry kind="lib" path="/usr/share/java/itext-1.4.5.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/jdom.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/JRI.jar"/>
-+	<classpathentry kind="lib" path="/usr/share/java/junit-4.4.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/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="/usr/share/java/commons-math-2.2.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
  	<classpathentry kind="output" path="bin"/>
  </classpath>
- 

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