[med-svn] r5906 - in trunk/packages/beast-mcmc/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Sat Feb 5 15:26:28 UTC 2011
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
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