[gentoo-commits] gentoo-x86 commit in sci-biology/cufflinks/files: cufflinks-2.2.1-hts.patch cufflinks-2.2.1-flags.patch

[Justin Lecher (jlec)]

jlec        14/10/02 08:01:05

  Added:                cufflinks-2.2.1-hts.patch
                        cufflinks-2.2.1-flags.patch
  Log:
  sci-biology/cufflinks: Drop debugging flags, fix compatibility with newer 
samtools, #524252
  
  (Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with 
key B9D4F231BD1558AB!)

Revision  Changes    Path
1.1                  sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch

file : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch?rev=1.1&view=markup
plain: 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch?rev=1.1&content-type=text/plain

Index: cufflinks-2.2.1-hts.patch
===================================================================
 ax_bam.m4 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ax_bam.m4 b/ax_bam.m4
index 7d463b7..95f1bed 100644
--- a/ax_bam.m4
+++ b/ax_bam.m4
@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then
                        AC_MSG_NOTICE([Your bam libraries seem too old (version 
$_version).])
                fi
        else
-               BAM_LIB="-lbam"
+               BAM_LIB="-lbam -lhts"
                AC_SUBST(BAM_CPPFLAGS)
                AC_SUBST(BAM_LDFLAGS)
                AC_SUBST(BAM_LIB)



1.1                  sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch

file : 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch?rev=1.1&view=markup
plain: 
http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch?rev=1.1&content-type=text/plain

Index: cufflinks-2.2.1-flags.patch
===================================================================
 configure.ac | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/configure.ac b/configure.ac
index 96ffbac..e88b8e4 100755
--- a/configure.ac
+++ b/configure.ac
@@ -61,7 +61,8 @@ AC_CANONICAL_HOST
 
 # set CFLAGS and CXXFLAGS
 user_CFLAGS=${CFLAGS}
-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused 
-Wuninitialized -ftemplate-depth-1024"
+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized"
+generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized 
-ftemplate-depth-1024"
 ext_CFLAGS=""
 debug_CFLAGS=""
 #echo "${host_cpu}-${host_os}"
@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling,      [  --enable-profiling        
enable profiling with
          [ext_LDFLAGS="-lprofiler -ltcmalloc"], [])
          
 CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} 
${OPENMP_CFLAGS}"
-CXXFLAGS="$CFLAGS"
-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
+CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}"
+CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}"
 user_LDFLAGS="$LDFLAGS"
 LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}"