[med-svn] [SCM] tophat branch, master, updated. debian/1.4.1-1-5-g8de8d3a

[Andreas Tille]

The following commit has been merged in the master branch:
commit 95d39c52a9200a736b3924ed2fc2f787eb2e2940
Author: Andreas Tille <tille at debian.org>
Date:   Sat Feb 18 08:22:09 2012 +0100

    Add patch for #660309 provided by Peter Green

diff --git a/debian/patches/remove_cflag_handling_in_configure.patch b/debian/patches/remove_cflag_handling_in_configure.patch
new file mode 100644
index 0000000..7e5a377
--- /dev/null
+++ b/debian/patches/remove_cflag_handling_in_configure.patch
@@ -0,0 +1,40 @@
+Description: Remove crazy cflag determination code
+ This code was broken (for example the test for -m64 plain doesn't work)
+ and does the wrong thing (uses -m686 on x86) for debian. Strip it out 
+ completely
+Author: Peter Michael Green <plugwash at p10link.net)
+Origin: http://lists.alioth.debian.org/pipermail/debian-med-packaging/2012-February/014089.html
+Bug-Debian: http://bugs.debian.org/660309
+Forwarded: no
+Reviewed-By: <name and email of someone who approved the patch>
+Last-Update: Sat, 18 Feb 2012 03:37:47 +0000
+
+--- tophat-1.4.1.orig/configure.ac
++++ tophat-1.4.1/configure.ac
+@@ -75,26 +75,6 @@ generic_CFLAGS="-Wall -Wno-strict-aliasi
+ ext_CFLAGS=""
+ debug_CFLAGS="-g"
+ #echo "${host_cpu}-${host_os}"
+-case "${host_cpu}-${host_os}" in
+-   i*86-*linux*)
+-    ext_CFLAGS="-march=i686";;
+-   i*86-darwin*)
+-    AC_ARG_ENABLE(universal, [  --enable-universal      enable universal binary (Intel Apple only)],
+-				  [is_uni=1], [is_uni=0])
+-	case $is_uni in
+-	  1) CFLAGS="-m64"
+-	     AC_COMPILE_IFELSE([AC_LANG_PROGRAM],
+-						   [ext_CFLAGS="-arch x86_64 -arch i386 -arch ppc64 -arch ppc"],
+-						   [ext_CFLAGS="-arch i386 -arch ppc"]);;
+-	  0) CFLAGS="-m64"
+-	  	 AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-arch x86_64"], []);;
+-	esac;;
+-  *)
+-    AC_MSG_CHECKING([if gcc accepts -m64])
+-    CFLAGS="-m64"
+-    AC_COMPILE_IFELSE([AC_LANG_PROGRAM], [ext_CFLAGS="-m64"; AC_MSG_RESULT([yes])],
+-					  [ext_CFLAGS="-D_FILE_OFFSET_BITS=64"; AC_MSG_RESULT([no])]);;
+-esac
+ 
+ AC_ARG_ENABLE(intel64,      [  --enable-intel64        optimize for Intel64 CPU such as Xeon and Core2],
+ 			  [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])

-- 
A spliced read mapper for RNA-Seq