[med-svn] r11208 - trunk/packages/beast-mcmc/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-06-05 14:53:08 +0000 (Tue, 05 Jun 2012)
New Revision: 11208

Modified:
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
   trunk/packages/beast-mcmc/trunk/debian/compat
   trunk/packages/beast-mcmc/trunk/debian/control
   trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Debhelper 9; More adaptions to now Debian packaged JAR files


Modified: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest	2012-06-05 12:47:07 UTC (rev 11207)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc.manifest	2012-06-05 14:53:08 UTC (rev 11208)
@@ -1,7 +1,7 @@
 /usr/share/beast-mcmc/beast.jar:
  Main-Class: dr.app.beast.BeastMain
- Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/commons-math.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/jam.jar /usr/share/java/treeview.jar
 
 /usr/share/beast-mcmc/beauti.jar:
  Main-Class: dr.app.beauti.BeautiApp
- Class-Path: /usr/share/beast-mcmc/beagle.jar /usr/share/beast-mcmc/colt.jar /usr/share/java/commons-math.jar /usr/share/java/itext1-1.4.jar /usr/share/java/jam.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/junit4.jar /usr/share/beast-mcmc/mpj.jar /usr/share/beast-mcmc/mtj.jar /usr/share/java/treeview.jar
+ Class-Path: /usr/share/java/beagle.jar /usr/share/java/colt.jar /usr/share/java/commons-math.jar /usr/share/java/itext1-1.4.jar /usr/share/java/jam.jar /usr/share/java/jdom1.jar /usr/share/java/jebl.jar /usr/share/java/junit4.jar /usr/share/java/mpj.jar /usr/share/java/mtj.jar /usr/share/java/treeview.jar

Modified: trunk/packages/beast-mcmc/trunk/debian/compat
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/compat	2012-06-05 12:47:07 UTC (rev 11207)
+++ trunk/packages/beast-mcmc/trunk/debian/compat	2012-06-05 14:53:08 UTC (rev 11208)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control	2012-06-05 12:47:07 UTC (rev 11207)
+++ trunk/packages/beast-mcmc/trunk/debian/control	2012-06-05 14:53:08 UTC (rev 11208)
@@ -4,7 +4,7 @@
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), javahelper (>=0.25),
+Build-Depends: debhelper (>= 9), javahelper (>=0.25),
  ant, ant-optional, openjdk-6-jdk, default-jdk,
  libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java,
  libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2),

Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules	2012-06-05 12:47:07 UTC (rev 11207)
+++ trunk/packages/beast-mcmc/trunk/debian/rules	2012-06-05 14:53:08 UTC (rev 11208)
@@ -9,7 +9,7 @@
 PACKAGE = beast-mcmc
 
 DEBJAR    := /usr/share/java
-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/beagle.jar:lib/mpj.jar:lib/org.boehn.kmlframework_20090320.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:lib/options.jar:lib/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+CLASS_PATH := /usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:/usr/lib/jvm/java-6-openjdk/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(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
@@ -42,11 +42,11 @@
 	ant build
 	ant -buildfile build_tracer.xml all
 	# native/compileNativeLinux.sh does not create dynamic libraries
-	cd native ; \
-		gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
-		gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
-		gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
-		gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
+	cd native ; $(MAKE) -f Makefile.Linux
+#		gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o ; \
+#		gcc -shared -Wl,-soname,libNucleotideLikelihoodCore.so.0 -o libNucleotideLikelihoodCore.so.0 libNucleotideLikelihoodCore.o -lc ; \
+#		gcc $(CFLAGS) $(LDFLAGS) -Wall -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o ; \
+#		gcc -shared -Wl,-soname,libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o -lc
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