[med-svn] r9133 - trunk/packages/beast-mcmc/trunk/debian/patches

Andreas Tille tille at alioth.debian.org
Sat Dec 31 13:44:43 UTC 2011 

Author: tille
Date: 2011-12-31 13:44:43 +0000 (Sat, 31 Dec 2011)
New Revision: 9133

Removed:
   trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
Modified:
   trunk/packages/beast-mcmc/trunk/debian/patches/beast.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_gcc_options.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
Log:
Adapted patches to new version


Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,50 +0,0 @@
---- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
-+++ beast-mcmc-1.5.3+svnr2672/scripts/beast
-@@ -22,6 +22,6 @@
- 	cd "$saveddir"
- fi
- 
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
- 
---- trunk.orig/scripts/beauti
-+++ trunk/scripts/beauti
-@@ -22,6 +22,6 @@
- 	cd "$saveddir"
- fi
- 
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar $BEAST_LIB/beauti.jar $*
- 
---- trunk.orig/scripts/loganalyser
-+++ trunk/scripts/loganalyser
-@@ -22,6 +22,6 @@
- 	cd "$saveddir"
- fi
- 
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.LogAnalyser $*
- 
---- trunk.orig/scripts/logcombiner
-+++ trunk/scripts/logcombiner
-@@ -22,6 +22,6 @@
- 	cd "$saveddir"
- fi
- 
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx128m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.LogCombiner $*
- 
---- trunk.orig/scripts/treeannotator
-+++ trunk/scripts/treeannotator
-@@ -22,6 +22,6 @@
- 	cd "$saveddir"
- fi
- 
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar dr.app.tools.TreeAnnotator $*
- 

Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,10 +0,0 @@
---- beast-mcmc-1.5.3+svnr2672.orig/native/Makefile
-+++ beast-mcmc-1.5.3+svnr2672/native/Makefile
-@@ -36,6 +36,6 @@
- 	     -output lib$(OUTNAME).jnilib
- 
- linux :
--	gcc -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99 -DSTATE_COUNT=$(STATE_COUNT)  -o lib$(OUTNAME).o
-+	gcc -fPIC -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99 -DSTATE_COUNT=$(STATE_COUNT)  -o lib$(OUTNAME).o
- 	ld -$(LINUX_LINK) -o lib$(OUTNAME).so lib$(OUTNAME).o
- 

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,7 +1,5 @@
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beast
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beast	2011-01-24 16:39:22.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/beast	2011-01-24 16:39:41.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/beast
++++ beast-mcmc-1.6.2/release/Linux/scripts/beast
 @@ -1,26 +1,4 @@
  #!/bin/sh
  
@@ -31,10 +29,8 @@
 -java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/local/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
 +BEAST_LIB="/usr/share/beast-mcmc/lib"
 +java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beauti
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/beauti	2011-01-24 16:39:49.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/beauti	2011-01-24 16:40:13.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/beauti
++++ beast-mcmc-1.6.2/release/Linux/scripts/beauti
 @@ -1,27 +1,5 @@
  #!/bin/sh
  
@@ -64,10 +60,8 @@
 +BEAST_LIB="/usr/share/beast-mcmc/lib"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
  
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/loganalyser
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/loganalyser	2011-01-24 16:40:19.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/loganalyser	2011-01-24 16:40:34.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/loganalyser
++++ beast-mcmc-1.6.2/release/Linux/scripts/loganalyser
 @@ -1,27 +1,5 @@
  #!/bin/sh
  
@@ -97,10 +91,8 @@
 +BEAST_LIB="/usr/share/beast-mcmc/lib"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
  
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/logcombiner
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/logcombiner	2011-01-24 16:40:52.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/logcombiner	2011-01-24 16:41:09.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner
++++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner
 @@ -1,27 +1,5 @@
  #!/bin/sh
  
@@ -130,10 +122,8 @@
 +BEAST_LIB="/usr/share/beast-mcmc/lib"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
  
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treeannotator
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treeannotator	2011-01-24 16:41:21.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/treeannotator	2011-01-24 16:41:41.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator
++++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator
 @@ -1,27 +1,5 @@
  #!/bin/sh
  
@@ -163,10 +153,8 @@
 +BEAST_LIB="/usr/share/beast-mcmc/lib"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
  
-Index: beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treestat
-===================================================================
---- beast-mcmc-1.6.1+svnr3660.orig/release/Linux/scripts/treestat	2011-01-24 16:41:53.000000000 +0000
-+++ beast-mcmc-1.6.1+svnr3660/release/Linux/scripts/treestat	2011-01-24 16:42:22.000000000 +0000
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat
++++ beast-mcmc-1.6.2/release/Linux/scripts/treestat
 @@ -1,27 +1,5 @@
  #!/bin/sh
  

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	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_tracer_xml.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.6.1+svnr3660.orig.orig/build_tracer.xml
-+++ beast-mcmc-1.6.1+svnr3660.orig/build_tracer.xml
+--- beast-mcmc-1.6.2.orig/build_tracer.xml
++++ beast-mcmc-1.6.2/build_tracer.xml
 @@ -32,6 +32,7 @@
      <property name="src" location="src"/>
      <property name="build" location="build"/>

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	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_classpath_in_build_xml.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,5 +1,5 @@
---- beast-mcmc-1.6.1+svnr3660.orig.orig/build.xml
-+++ beast-mcmc-1.6.1+svnr3660.orig/build.xml
+--- beast-mcmc-1.6.2.orig/build.xml
++++ beast-mcmc-1.6.2/build.xml
 @@ -9,6 +9,7 @@
  	<property name="src" location="src" />
  	<property name="build" location="build" />
@@ -46,27 +46,32 @@
  			<zipgroupfileset dir="${lib}" includes="commons-math-2.0.jar" />
  			<zipgroupfileset dir="${lib}" includes="mtj.jar" />
  		</jar>
---- beast-mcmc-1.6.1+svnr3660.orig.orig/.classpath
-+++ beast-mcmc-1.6.1+svnr3660.orig/.classpath
-@@ -3,14 +3,14 @@
- 	<classpathentry kind="src" path="src"/>
- 	<classpathentry kind="lib" path="lib/beagle.jar"/>
- 	<classpathentry kind="lib" path="lib/colt.jar"/>
--	<classpathentry kind="lib" path="lib/commons-math-1.2.jar"/>
--	<classpathentry kind="lib" path="lib/figtreepanel.jar"/>
-+	<classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
-+	<classpathentry kind="lib" path="/usr/share/java/figtree.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="/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/lib/R/site-library/rJava/jri/JRI.jar"/>
-+	<classpathentry kind="lib" path="/usr/share/java/junit4.jar"/>
- 	<classpathentry kind="lib" path="lib/libjri.jnilib"/>
- 	<classpathentry kind="lib" path="lib/mpj.jar"/>
- 	<classpathentry kind="lib" path="lib/mtj.jar"/>
+--- beast-mcmc-1.6.2.orig/.classpath
++++ beast-mcmc-1.6.2/.classpath
+@@ -3,18 +3,18 @@
+ 	<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="/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/lib/R/site-library/rJava/jri/JRI.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/junit4.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-2.0.jar"/>
++	<classpathentry kind="lib" path="/usr/share/java/commons-math.jar"/>
+ 	<classpathentry kind="lib" path="lib/libjri.jnilib"/>
+ 	<classpathentry kind="output" path="bin"/>
+ </classpath>

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -2,8 +2,8 @@
 Date:  Fri, 04 Feb 2011 19:39:04 +0100
 Description: Remove outdated gcc options and fix include dir to openjdk
 
---- beast-mcmc-1.6.1+svnr3660.orig.orig/native/compileNativeLinux.sh
-+++ beast-mcmc-1.6.1+svnr3660.orig/native/compileNativeLinux.sh
+--- beast-mcmc-1.6.2.orig/native/compileNativeLinux.sh
++++ beast-mcmc-1.6.2/native/compileNativeLinux.sh
 @@ -1,5 +1,5 @@
 -gcc -O4 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/java/j2sdk1.4.1_01/include/ -I/usr/java/j2sdk1.4.1_01/include/linux NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
 -ld -shared -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o 

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch	2011-12-30 12:34:43 UTC (rev 9132)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch	2011-12-31 13:44:43 UTC (rev 9133)
@@ -1,16 +1,5 @@
---- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/StarBEAST/STARBEAST.tex
-+++ beast-mcmc-1.6.1+svnr3660.orig/doc/StarBEAST/STARBEAST.tex
-@@ -8,7 +8,7 @@
- 
- \author{Joseph Heled, Alexei J Drummond and Walter Xie}
- 
--\date{\today{}}
-+\date{October 8, 2010}
- 
- \maketitle
- 
---- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/Yule.tex
-+++ beast-mcmc-1.6.1+svnr3660.orig/doc/Yule.tex
+--- beast-mcmc-1.6.2.orig/doc/Yule.tex
++++ beast-mcmc-1.6.2/doc/Yule.tex
 @@ -35,6 +35,7 @@
  \begin{document}
  
@@ -19,8 +8,8 @@
  
  \author{\textsc{Alexei J. Drummond}}
  
---- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/BookSection/BookSection.tex
-+++ beast-mcmc-1.6.1+svnr3660.orig/doc/BookSection/BookSection.tex
+--- beast-mcmc-1.6.2.orig/doc/BookSection/BookSection.tex
++++ beast-mcmc-1.6.2/doc/BookSection/BookSection.tex
 @@ -1,7 +1,7 @@
  
  \NeedsTeXFormat{LaTeX2e}[1996/06/01]
@@ -38,8 +27,8 @@
  
  \makeatother
  \begin{document}
---- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/SerialSampleCoalescent.tex
-+++ beast-mcmc-1.6.1+svnr3660.orig/doc/SerialSampleCoalescent.tex
+--- beast-mcmc-1.6.2.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.6.2/doc/SerialSampleCoalescent.tex
 @@ -33,7 +33,7 @@
  \begin{document}
  
@@ -49,8 +38,8 @@
  \author{\textsc{Alexei J. Drummond}}
  
  \maketitle
---- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/BEAST14_Manual.tex
-+++ beast-mcmc-1.6.1+svnr3660.orig/doc/BEAST14_Manual.tex
+--- beast-mcmc-1.6.2.orig/doc/BEAST14_Manual.tex
++++ beast-mcmc-1.6.2/doc/BEAST14_Manual.tex
 @@ -35,7 +35,7 @@
  \begin{document}

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