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 <[email protected]> DM-Upload-Allowed: yes Uploaders: Andreas Tille <[email protected]> -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 # # Build extra LaTeX documentation # _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
