The following commit has been merged in the master branch:
commit b01514b30354dccc6a7f43e6acc002aec9f5b64b
Author: Alexandre Mestiashvili <[email protected]>
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 <[email protected]>
+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.
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