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jlec 14/10/02 08:01:05 |
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|
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Added: cufflinks-2.2.1-hts.patch |
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cufflinks-2.2.1-flags.patch |
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Log: |
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sci-biology/cufflinks: Drop debugging flags, fix compatibility with newer samtools, #524252 |
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|
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(Portage version: 2.2.14_rc1/cvs/Linux x86_64, signed Manifest commit with key B9D4F231BD1558AB!) |
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|
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Revision Changes Path |
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1.1 sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-hts.patch?rev=1.1&view=markup |
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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 |
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|
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Index: cufflinks-2.2.1-hts.patch |
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=================================================================== |
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ax_bam.m4 | 2 +- |
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1 file changed, 1 insertion(+), 1 deletion(-) |
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|
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diff --git a/ax_bam.m4 b/ax_bam.m4 |
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index 7d463b7..95f1bed 100644 |
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--- a/ax_bam.m4 |
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+++ b/ax_bam.m4 |
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@@ -189,7 +189,7 @@ if test "x$want_bam" = "xyes"; then |
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AC_MSG_NOTICE([Your bam libraries seem too old (version $_version).]) |
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fi |
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else |
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- BAM_LIB="-lbam" |
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+ BAM_LIB="-lbam -lhts" |
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AC_SUBST(BAM_CPPFLAGS) |
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AC_SUBST(BAM_LDFLAGS) |
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AC_SUBST(BAM_LIB) |
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|
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|
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1.1 sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch |
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|
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file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/cufflinks/files/cufflinks-2.2.1-flags.patch?rev=1.1&view=markup |
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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 |
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|
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Index: cufflinks-2.2.1-flags.patch |
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=================================================================== |
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configure.ac | 7 ++++--- |
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1 file changed, 4 insertions(+), 3 deletions(-) |
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|
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diff --git a/configure.ac b/configure.ac |
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index 96ffbac..e88b8e4 100755 |
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--- a/configure.ac |
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+++ b/configure.ac |
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@@ -61,7 +61,8 @@ AC_CANONICAL_HOST |
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|
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# set CFLAGS and CXXFLAGS |
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user_CFLAGS=${CFLAGS} |
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-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024" |
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+generic_CFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized" |
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+generic_CXXFLAGS="-Wall -Wno-strict-aliasing -Wunused -Wuninitialized -ftemplate-depth-1024" |
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ext_CFLAGS="" |
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debug_CFLAGS="" |
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#echo "${host_cpu}-${host_os}" |
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@@ -106,8 +107,8 @@ AC_ARG_ENABLE(profiling, [ --enable-profiling enable profiling with |
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[ext_LDFLAGS="-lprofiler -ltcmalloc"], []) |
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|
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CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS} ${OPENMP_CFLAGS}" |
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-CXXFLAGS="$CFLAGS" |
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-CXXFLAGS="${CXXFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" |
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+CXXFLAGS="${generic_CFLAGS} ${CXXFLAGS}" |
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+CPPFLAGS="${CPPFLAGS} ${BOOST_CPPFLAGS} ${BAM_CPPFLAGS} ${EIGEN_CPPFLAGS}" |
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user_LDFLAGS="$LDFLAGS" |
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LDFLAGS="${ext_LDFLAGS} ${user_LDFLAGS}" |
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