[med-svn] r5906 - in trunk/packages/beast-mcmc/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2011-02-05 15:26:27 +0000 (Sat, 05 Feb 2011)
New Revision: 5906

Added:
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
   trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides
Modified:
   trunk/packages/beast-mcmc/trunk/debian/control
   trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
   trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Better clean target, add soname to libraries and proper links, more generic installation of docs, some cleanups


Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.links	2011-02-05 15:26:27 UTC (rev 5906)
@@ -0,0 +1,2 @@
+usr/lib/libNucleotideLikelihoodCore.so	usr/lib/libNucleotideLikelihoodCore.so.0
+usr/lib/libAminoAcidLikelihoodCore.so	usr/lib/libAminoAcidLikelihoodCore.so.0

Added: trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/beast-mcmc-lib.lintian-overrides	2011-02-05 15:26:27 UTC (rev 5906)
@@ -0,0 +1,5 @@
+# The libraries are rather private to beast-mcmc and naming the package differently or
+# splitting them into two packages does not make any practical sense
+# Andreas Tille <tille at debian.org>
+beast-mcmc-lib: package-name-doesnt-match-sonames libAminoAcidLikelihoodCore0 libNucleotideLikelihoodCore0
+

Modified: trunk/packages/beast-mcmc/trunk/debian/control
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/control	2011-02-05 14:07:15 UTC (rev 5905)
+++ trunk/packages/beast-mcmc/trunk/debian/control	2011-02-05 15:26:27 UTC (rev 5906)
@@ -46,11 +46,11 @@
  is a simple to use user-interface program for setting up standard 
  analyses and a suit of programs for analysing the results.
  .
- This package contains an architecture dependant library.
+ This package contains an architecture dependent library.
 
 Package: beast-doc
 Architecture: all
-Section: doc
+Section: non-free/doc
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Enhances: beast-mcmc
 Description: Bayesian MCMC phylogenetic inference - documentation

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	2011-02-05 14:07:15 UTC (rev 5905)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	2011-02-05 15:26:27 UTC (rev 5906)
@@ -6,9 +6,11 @@
 +++ beast-mcmc-1.6.1+svnr3660.orig/native/compileNativeLinux.sh
 @@ -1,5 +1,5 @@
 -gcc -O4 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/java/j2sdk1.4.1_01/include/ -I/usr/java/j2sdk1.4.1_01/include/linux NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
-+gcc -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/java-6-openjdk/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
- ld -shared -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o 
+-ld -shared -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o 
++gcc -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ NucleotideLikelihoodCore.c -o libNucleotideLikelihoodCore.o
++ld -shared -soname=libNucleotideLikelihoodCore.so.0 --export-dynamic -o libNucleotideLikelihoodCore.so libNucleotideLikelihoodCore.o 
  
 -gcc -O4 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/java/j2sdk1.4.1_01/include/ -I/usr/java/j2sdk1.4.1_01/include/linux AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
-+gcc -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/java-6-openjdk/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
- ld -shared -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o 
+-ld -shared -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o 
++gcc -O4 -funroll-loops -ffast-math -fstrict-aliasing -c -I/usr/lib/jvm/default-java/include/ AminoAcidLikelihoodCore.c -o libAminoAcidLikelihoodCore.o
++ld -shared -soname=libAminoAcidLikelihoodCore.so.0 -o libAminoAcidLikelihoodCore.so libAminoAcidLikelihoodCore.o 

Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules	2011-02-05 14:07:15 UTC (rev 5905)
+++ trunk/packages/beast-mcmc/trunk/debian/rules	2011-02-05 15:26:27 UTC (rev 5906)
@@ -21,7 +21,8 @@
 override_dh_auto_clean:
 	rm -f build-stamp configure-stamp
 	#$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml clean
-	rm -f native/*\.o
+	rm -f native/*\.o native/*\.so
+	ant clean
 
 override_dh_auto_build:
 	$(JAVA) -classpath $(CLASS_PATH) -Dant.home=$(ANT_HOME) org.apache.tools.ant.Main $(ANT_ARGS) -buildfile build.xml build
@@ -38,8 +39,6 @@
 
 override_dh_install:
 	dh_install
-	# dh_install seems to fail in moving this fail for whatever reason
-	cp -a doc/Virus\ Practical\ Tex/*.pdf $(CURDIR)/debian/$(DOCPACKAGE)/usr/share/doc/beast-mcmc
 	# rename beast to beast-mcmc
 	mv $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast $(CURDIR)/debian/$(PACKAGE)/usr/bin/beast-mcmc