[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-1-gb01514b

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit b01514b30354dccc6a7f43e6acc002aec9f5b64b
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Jun 5 10:44:18 2012 +0200

    debian/patches imported 0004-fix-m64-usage-and-lfs.patch from Ubuntu

diff --git a/debian/patches/0004-fix-m64-usage-and-lfs.patch b/debian/patches/0004-fix-m64-usage-and-lfs.patch
new file mode 100644
index 0000000..ab78e2d
--- /dev/null
+++ b/debian/patches/0004-fix-m64-usage-and-lfs.patch
@@ -0,0 +1,21 @@
+Author: Ben Collins <bcollins at ubuntu.com>
+Description: Update configure.ac to not force -m64.
+Just because the compiler supports it, doesn't mean it can compile
+natively to it (e.g. on powerpc, you can compile -m64, but there are
+no headers for it plus it cannot run on 32-bit systems).
+
+--- cufflinks/configure.ac~	2012-01-02 13:34:14.000000000 +0000
++++ cufflinks/configure.ac	2012-01-18 22:13:30.000000000 +0000
+@@ -64,12 +64,7 @@
+   i*86-darwin*)
+ 	CFLAGS="-m64"
+ 	AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
+-  *)
+-    AC_MSG_CHECKING([if gcc accepts -m64])
+-    CFLAGS="-m64"
+-    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
+-					  [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
+ esac
+ 
+ AC_ARG_ENABLE(vectorize,    [  --enable-vectorize        Enable GCC auto-vectorization],
+ 			  [ext_CFLAGS="${ext_CFLAGS} -ftree-vectorize -msse3 -ffast-math -ftree-vectorizer-verbose=99"], [])
diff --git a/debian/patches/series b/debian/patches/series
index a527c3f..683174c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
+0004-fix-m64-usage-and-lfs.patch
 0001-fix_spelling.patch
 0002-bam2samtools.patch
 0003-fix_includes_path.patch

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.