[med-svn] r12655 - trunk/packages/beast-mcmc/branches/1.7.4/debian

[Andreas Tille]

Author: tille
Date: 2012-12-17 14:27:59 +0000 (Mon, 17 Dec 2012)
New Revision: 12655

Modified:
   trunk/packages/beast-mcmc/branches/1.7.4/debian/changelog
   trunk/packages/beast-mcmc/branches/1.7.4/debian/control
   trunk/packages/beast-mcmc/branches/1.7.4/debian/rules
Log:
use default java implementation (closes #683509)


Modified: trunk/packages/beast-mcmc/branches/1.7.4/debian/changelog
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/changelog	2012-12-17 14:27:16 UTC (rev 12654)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/changelog	2012-12-17 14:27:59 UTC (rev 12655)
@@ -1,5 +1,30 @@
 beast-mcmc (1.7.4-1) UNRELEASED; urgency=low
 
+  * New upstream version (adapted patches)
+  * debian/{control,rules}: use default java implementation
+    thanks for the patch to James Page <james.page at ubuntu.com>
+    Closes: #683509
+
+ -- Andreas Tille <tille at debian.org>  Tue, 05 Jun 2012 14:38:11 +0200
+
+beast-mcmc (1.6.2-3) unstable; urgency=low
+
+  * rename pixmap for menu to avoid name space conflict
+    Closes: #680483
+
+ -- Andreas Tille <tille at debian.org>  Fri, 06 Jul 2012 11:30:19 +0200
+
+beast-mcmc (1.6.2-2) unstable; urgency=low
+
+  * debian/control: rename beast-doc to beast-mcmc-doc
+    Closes: #679394
+    For consistency reasons also rename beast-examples to
+    beast-mcmc-examples
+
+ -- Andreas Tille <tille at debian.org>  Fri, 29 Jun 2012 11:24:51 +0200
+
+beast-mcmc (1.6.2-1) unstable; urgency=low
+
   * Initial release. (Closes: #552101)
 
  -- Andreas Tille <tille at debian.org>  Tue, 05 Jun 2012 14:38:11 +0200

Modified: trunk/packages/beast-mcmc/branches/1.7.4/debian/control
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/control	2012-12-17 14:27:16 UTC (rev 12654)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/control	2012-12-17 14:27:59 UTC (rev 12655)
@@ -5,7 +5,7 @@
 DM-Upload-Allowed: yes
 Uploaders: Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 9), javahelper (>=0.25),
- ant, ant-optional, openjdk-6-jdk, default-jdk,
+ ant, ant-optional, default-jdk,
  libjebl2-java, libjam-java, figtree, liboptions-java, libhmsbeagle-java (>= 1.1r1092),
  libcolt-java, libmpj-java, r-cran-rjava, libcommons-math-java (>= 2.2),
  libjdom1-java, junit4, libmtj-java, libitext1-java, texlive-latex-base

Modified: trunk/packages/beast-mcmc/branches/1.7.4/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/branches/1.7.4/debian/rules	2012-12-17 14:27:16 UTC (rev 12654)
+++ trunk/packages/beast-mcmc/branches/1.7.4/debian/rules	2012-12-17 14:27:59 UTC (rev 12655)
@@ -8,11 +8,13 @@
 
 PACKAGE = beast-mcmc
 
+JAVA_HOME  := /usr/lib/jvm/default-java
+
 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:$(DEBJAR)/beagle.jar:$(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
+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:$(JAVA_HOME)/lib/tools.jar:$(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
+JAVA       := $(JAVA_HOME)/bin/java
 ANT_HOME   := /usr/share/ant
 ANT_BIN    := $(ANT_HOME)/bin/ant
 ANT_ARGS   := -Dcompile.debug=true -Dcompile.optimize=true
@@ -42,7 +44,7 @@
 	ant build
 	ant -buildfile build_tracer.xml all
 	# native/compileNativeLinux.sh does not create dynamic libraries
-	cd native ; $(MAKE) -f Makefile.Linux
+	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 ; \