[med-svn] r19655 - trunk/packages/beast-mcmc/trunk/debian/patches

Andreas Tille tille at moszumanska.debian.org
Sat Jul 18 16:15:34 UTC 2015 

Author: tille
Date: 2015-07-18 16:15:33 +0000 (Sat, 18 Jul 2015)
New Revision: 19655

Modified:
   trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
   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_xml.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Log:
Adapt patches


Modified: trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/create_soname.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -2,8 +2,8 @@
 Author: Andreas Tille <tille at debian.org>
 Created: Mon, 17 Dec 2012 16:43:17 +0100
 
---- beast-mcmc-1.8.0.orig/native/Makefile.linux
-+++ beast-mcmc-1.8.0/native/Makefile.linux
+--- a/native/Makefile.linux
++++ b/native/Makefile.linux
 @@ -1,11 +1,11 @@
  CC=gcc
 -CFLAGS += -O2 -funroll-loops 

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/enable_hardening.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -2,8 +2,8 @@
 Author: Andreas Tille <tille at debian.org>
 Date: Tue, 05 Jun 2012 14:38:11 +0200
 
---- beast-mcmc-1.8.0.orig/native/Makefile.linux
-+++ beast-mcmc-1.8.0/native/Makefile.linux
+--- a/native/Makefile.linux
++++ b/native/Makefile.linux
 @@ -1,11 +1,11 @@
  CC=gcc
 -CFLAGS=-O2 -funroll-loops

Modified: 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	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -2,8 +2,8 @@
 Date: Tue, 10 Jan 2012 22:29:24 +0100
 Description: Make sure also tracer is builded with Debian packages JARs
 
---- beast-mcmc-1.8.0.orig/build_tracer.xml
-+++ beast-mcmc-1.8.0/build_tracer.xml
+--- a/build_tracer.xml
++++ b/build_tracer.xml
 @@ -32,6 +32,7 @@
      <property name="src" location="src"/>
      <property name="build" location="build"/>
@@ -15,9 +15,9 @@
 @@ -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="${build}"
+         <javac source="1.6" target="1.6" srcdir="${src}" destdir="${build}"
 -               classpath="${lib}/colt.jar:${lib}/commons-math-2.2.jar:${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="${deblib}/colt.jar:${deblib}/commons-math-2.2.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext-1.4.5.jar:${deblib}/jdom.jar:${deblib}/mtj.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar:${deblib}/mpj.jar">
++               classpath="${deblib}/colt.jar:${deblib}/commons-math-2.2.jar:${deblib}/jebl.jar:${deblib}/jam.jar:${deblib}/itext-1.4.5.jar:${deblib}/jdom.jar:${deblib}/mtj.jar:${deblib}/JRI.jar:${deblib}/mpj.jar">
              <include name="dr/app/tracer/**"/>
              <include name="dr/app/util/**"/>
              <include name="dr/app/gui/**"/>
@@ -28,7 +28,7 @@
 -            <zipgroupfileset dir="${lib}" includes="jebl.jar"/>
 -            <zipgroupfileset dir="${lib}" includes="jam.jar"/>
 -            <zipgroupfileset dir="${lib}" includes="itext-1.4.5.jar"/>
--            <zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar"/>
+-            <zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar"/>
 +            <zipgroupfileset dir="${deblib}" includes="jebl.jar"/>
 +            <zipgroupfileset dir="${deblib}" includes="jam.jar"/>
 +            <zipgroupfileset dir="${deblib}" includes="itext-1.4.5.jar"/>
@@ -83,12 +83,11 @@
  
      <target name="linux" description="release Linux/Unix version of Tracer">
          <delete dir="${Linux_package_dir}" />
-@@ -200,55 +167,4 @@
+@@ -202,54 +169,4 @@
          <echo message="Linux/Unix version release is finished." />
      </target>
  
--    <target name="mac"
--                                   description="release Mac version of Tracer">
+-    <target name="mac" description="release Mac version of Tracer">
 -        <delete dir="${Mac_package_dir}" />
 -        <!-- Create the release directory -->
 -        <mkdir dir="${Mac_package_dir}" />
@@ -106,7 +105,7 @@
 -                        vmoptions="-Xmx1024M"
 -                        arguments=""
 -                        version="${version}"
--                        infostring="${name} v${version}, Copyright 2003-2009, Andrew Rambaut & Alexei J. Drummond"
+-                        infostring="${name} v${version}, Copyright 2003-2013, Andrew Rambaut, Marc Suchard & Alexei J. Drummond"
 -                        bundleid="tracer" >
 -            <javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
 -            <jarfileset dir="${dist}">

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	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -3,8 +3,8 @@
 Subject: use Debian jars
 Description: Make sure package builds with Debian packages JARs
 Forwarded: no
---- beast-mcmc-1.8.0.orig/build.xml
-+++ beast-mcmc-1.8.0/build.xml
+--- a/build.xml
++++ b/build.xml
 @@ -36,6 +36,7 @@
      <property name="src" location="src"/>
      <property name="build" location="build"/>
@@ -60,8 +60,8 @@
          </jar>
  
      </target>
---- beast-mcmc-1.8.0.orig/.classpath
-+++ beast-mcmc-1.8.0/.classpath
+--- a/.classpath
++++ b/.classpath
 @@ -1,20 +1,20 @@
  <?xml version="1.0" encoding="UTF-8"?>
  <classpath>

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_encoding.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -1,15 +1,22 @@
 Author: Andreas Tille <tille at debian.org>
-Last-Update: Tue, 30 Sep 2014 18:15:36 +0200
+Last-Update: Sat, 18 Jul 2015 18:14:37 +0200
 Description: Fix encoding issue
 
---- beast-mcmc-1.8.0.orig/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
-+++ beast-mcmc-1.8.0/src/dr/app/beauti/siteModelsPanel/PartitionModelPanel.java
-@@ -243,7 +243,7 @@
-         PanelUtils.setupComponent(setYang96Button);
-         setYang96Button
-                 .setToolTipText("<html>Sets a 3 codon-position model with independent GTR and Gamma as described in<br>"
--                        + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587–596. This model is named 3' in this paper.</html>");
-+                        + "Yang (1996) <i>J Mol Evol</i> <b>42</b>: 587-596. This model is named 3' in this paper.</html>");
+--- a/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java
++++ b/src/dr/app/beauti/components/discrete/DiscreteTraitsComponentGenerator.java
+@@ -263,7 +263,7 @@ public class DiscreteTraitsComponentGene
  
-         setSRD06Button = new JButton("Use SRD06 model");
-         setSRD06Button.addActionListener(new ActionListener() {
+         }
+ 
+-        if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not b§e there.
++        if (model.isActivateBSSVS()) // If "BSSVS" is not activated, rateIndicator should not be there.
+             writeStatisticModel(model, writer);
+     }
+ 
+@@ -520,4 +520,4 @@ public class DiscreteTraitsComponentGene
+         }
+     }
+ 
+-}
+\ No newline at end of file
++}

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch	2015-07-18 15:36:40 UTC (rev 19654)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch	2015-07-18 16:15:33 UTC (rev 19655)
@@ -3,8 +3,8 @@
 Date: Tue, 05 Jun 2012 14:38:11 +0200
 LastUpdated: Mon, 17 Dec 2012 16:43:17 +0100
 
---- beast-mcmc-1.8.0.orig/doc/Yule.tex
-+++ beast-mcmc-1.8.0/doc/Yule.tex
+--- a/doc/Yule.tex
++++ b/doc/Yule.tex
 @@ -35,6 +35,7 @@
  \begin{document}
  
@@ -13,8 +13,8 @@
  
  \author{\textsc{Alexei J. Drummond}}
  
---- beast-mcmc-1.8.0.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.8.0/doc/BookSection/BookSection.tex
+--- a/doc/BookSection/BookSection.tex
++++ b/doc/BookSection/BookSection.tex
 @@ -1,7 +1,7 @@
  
  \NeedsTeXFormat{LaTeX2e}[1996/06/01]
@@ -32,8 +32,8 @@
  
  \makeatother
  \begin{document}
---- beast-mcmc-1.8.0.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.8.0/doc/SerialSampleCoalescent.tex
+--- a/doc/SerialSampleCoalescent.tex
++++ b/doc/SerialSampleCoalescent.tex
 @@ -33,7 +33,7 @@
  \begin{document}
  
@@ -43,8 +43,8 @@
  \author{\textsc{Alexei J. Drummond}}
  
  \maketitle
---- beast-mcmc-1.8.0.orig/doc/BEAST14_Manual.tex
-+++ beast-mcmc-1.8.0/doc/BEAST14_Manual.tex
+--- a/doc/BEAST14_Manual.tex
++++ b/doc/BEAST14_Manual.tex
 @@ -35,7 +35,7 @@
  \begin{document}
  
@@ -54,9 +54,9 @@
  
  \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
   \textsc{Nic Rawlence}  and \textsc{Andrew Rambaut}$^{2}$\\
---- beast-mcmc-1.8.0.orig/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
-+++ beast-mcmc-1.8.0/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
-@@ -789,7 +789,7 @@
+--- a/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
++++ b/doc/tutorial/Virus_Practical_1_6_1/Practical_BEAST.tex
+@@ -789,7 +789,7 @@ Define the prior not specified (marked a
  
  \medskip{}

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