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 <[email protected]>
+ Closes: #683509
+
+ -- Andreas Tille <[email protected]> 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 <[email protected]> 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 <[email protected]> Fri, 29 Jun 2012 11:24:51 +0200
+
+beast-mcmc (1.6.2-1) unstable; urgency=low
+
* Initial release. (Closes: #552101)
-- Andreas Tille <[email protected]> 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 <[email protected]>
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 ; \
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