[med-svn] r5897 - trunk/packages/beast-mcmc/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2011-02-04 18:58:03 +0000 (Fri, 04 Feb 2011)
New Revision: 5897

Added:
   trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
Modified:
   trunk/packages/beast-mcmc/trunk/debian/patches/series
Log:
Make sure gcc will be called with valid options and correct include path


Added: trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	                        (rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_gcc_options.patch	2011-02-04 18:58:03 UTC (rev 5897)
@@ -0,0 +1,14 @@
+Author: Andreas Tille <tille at debian.org>
+Date:  Fri, 04 Feb 2011 19:39:04 +0100
+Description: Remove outdated gcc options and fix include dir to openjdk
+
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/native/compileNativeLinux.sh
++++ 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 
+ 
+-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 

Modified: trunk/packages/beast-mcmc/trunk/debian/patches/series
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/series	2011-02-04 18:40:54 UTC (rev 5896)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/series	2011-02-04 18:58:03 UTC (rev 5897)
@@ -1 +1,2 @@
 beast.patch
+fix_gcc_options.patch