[med-svn] r9245 - in trunk/packages/beast-mcmc/trunk/debian: . patches

Andreas Tille tille at alioth.debian.org
Tue Jan 10 21:34:27 UTC 2012 

Author: tille
Date: 2012-01-10 21:34:27 +0000 (Tue, 10 Jan 2012)
New Revision: 9245

Added:
   trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch
Modified:
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
   trunk/packages/beast-mcmc/trunk/debian/changelog
   trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
   trunk/packages/beast-mcmc/trunk/debian/patches/series
   trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Set explicit CLASSPATH in some scripts to make them run successfully


Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install	2012-01-10 19:48:40 UTC (rev 9244)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.install	2012-01-10 21:34:27 UTC (rev 9245)
@@ -1,4 +1,4 @@
 release/Linux/scripts/* 	usr/bin
 debian/*.xpm			usr/share/pixmaps
-lib/*.jar			usr/share/beast-mcmc/lib
-build/dist/*.jar		usr/share/beast-mcmc/lib
+lib/*.jar			usr/share/beast-mcmc
+build/dist/*.jar		usr/share/beast-mcmc

Modified: trunk/packages/beast-mcmc/trunk/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/changelog	2012-01-10 19:48:40 UTC (rev 9244)
+++ trunk/packages/beast-mcmc/trunk/debian/changelog	2012-01-10 21:34:27 UTC (rev 9245)
@@ -2,5 +2,4 @@
 
   * Initial release. (Closes: #552101)
 
- -- Andreas Tille <tille at debian.org>  Fri, 04 Feb 2011 19:39:04 +0100
-
+ -- Andreas Tille <tille at debian.org>  Tue, 10 Jan 2012 22:29:24 +0100

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch	2012-01-10 19:48:40 UTC (rev 9244)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/beast.patch	2012-01-10 21:34:27 UTC (rev 9245)
@@ -27,8 +27,8 @@
 -
 -BEAST_LIB="$BEAST/lib"
 -java -Xms64m -Xmx1024m -Djava.library.path="$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 $*
++BEAST_LIB="/usr/share/beast-mcmc"
++java -Xms64m -Xmx2048m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp "$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
 --- beast-mcmc-1.6.2.orig/release/Linux/scripts/beauti
 +++ beast-mcmc-1.6.2/release/Linux/scripts/beauti
 @@ -1,27 +1,5 @@
@@ -57,7 +57,7 @@
 -fi
 -
 -BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc/lib"
++BEAST_LIB="/usr/share/beast-mcmc"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -jar "$BEAST_LIB/beauti.jar" $*
  
 --- beast-mcmc-1.6.2.orig/release/Linux/scripts/loganalyser
@@ -88,7 +88,7 @@
 -fi
 -
 -BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc/lib"
++BEAST_LIB="/usr/share/beast-mcmc"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogAnalyser $*
  
 --- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner
@@ -119,7 +119,7 @@
 -fi
 -
 -BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc/lib"
++BEAST_LIB="/usr/share/beast-mcmc"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
  
 --- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator
@@ -150,7 +150,7 @@
 -fi
 -
 -BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc/lib"
++BEAST_LIB="/usr/share/beast-mcmc"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
  
 --- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat
@@ -181,6 +181,6 @@
 -fi
 -
 -BEAST_LIB="$BEAST/lib"
-+BEAST_LIB="/usr/share/beast-mcmc/lib"
++BEAST_LIB="/usr/share/beast-mcmc"
  java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
  

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series	2012-01-10 19:48:40 UTC (rev 9244)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series	2012-01-10 21:34:27 UTC (rev 9245)
@@ -3,3 +3,4 @@
 fix_classpath_in_build_xml.patch
 patch_tex_docs.patch
 fix_classpath_in_build_tracer_xml.patch
+some_bins_need_explicit_classpath.patch

Added: trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/some_bins_need_explicit_classpath.patch	2012-01-10 21:34:27 UTC (rev 9245)
@@ -0,0 +1,42 @@
+Author: Andreas Tille <tille at debian.org>
+Description: The scripts logcombiner, treeannotator and treestat
+ did not run without explicite CLASSPATH setting.  This is done
+ in this patch
+
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/logcombiner
++++ beast-mcmc-1.6.2/release/Linux/scripts/logcombiner
+@@ -1,5 +1,7 @@
+ #!/bin/sh
+ 
+ BEAST_LIB="/usr/share/beast-mcmc"
+-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.LogCombiner $*
+-
++DEBJAR="/usr/share/java"
++java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
++  -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
++  dr.app.tools.LogCombiner $*
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/treeannotator
++++ beast-mcmc-1.6.2/release/Linux/scripts/treeannotator
+@@ -1,5 +1,9 @@
+ #!/bin/sh
+ 
+ BEAST_LIB="/usr/share/beast-mcmc"
+-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.tools.TreeAnnotator $*
++DEBJAR="/usr/share/java"
++java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
++  -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar \
++  dr.app.tools.TreeAnnotator $*
++
+ 
+--- beast-mcmc-1.6.2.orig/release/Linux/scripts/treestat
++++ beast-mcmc-1.6.2/release/Linux/scripts/treestat
+@@ -1,5 +1,8 @@
+ #!/bin/sh
+ 
+ BEAST_LIB="/usr/share/beast-mcmc"
+-java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" -cp "$BEAST_LIB/beast.jar" dr.app.treestat.TreeStatApp $*
++DEBJAR="/usr/share/java"
++java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB" \
++  -classpath ${CLASSPATH}:${BEAST_LIB}/beast.jar:${DEBJAR}/jebl.jar:${DEBJAR}/jam.jar:${DEBJAR}/treeview.jar:${DEBJAR}/jdom1.jar \
++  dr.app.treestat.TreeStatApp $*
+ 

Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules	2012-01-10 19:48:40 UTC (rev 9244)
+++ trunk/packages/beast-mcmc/trunk/debian/rules	2012-01-10 21:34:27 UTC (rev 9245)
@@ -9,7 +9,7 @@
 PACKAGE = beast-mcmc
 
 DEBJAR    := /usr/share/java
-export CLASSPATH := $(DEBJAR)/itext.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk//lib/tools.jar:lib/itext-1.4.5.jar:lib/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
 
 # to run the test suite
 JAVA       := /usr/lib/jvm/java-6-openjdk/bin/java
@@ -35,6 +35,7 @@
 	ant clean
 
 override_dh_auto_build:
+	# CLASSPATH=$(CLASS_PATH)
 	ant build ; \
 	ant -buildfile build_tracer.xml all ; \
 	cd native && /bin/sh compileNativeLinux.sh

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