[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta6-30-gde0c32f

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit de0c32fc6c3d0e92ce98eaafa09ed863df34b488
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Tue Jul 3 10:23:06 2012 +0200

    hardening.patch to inject hardening CPPFLAGS

diff --git a/debian/changelog b/debian/changelog
index f53825c..344b17e 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,10 @@
 bowtie2 (2.0.0-beta6-4) UNRELEASED; urgency=low
 
-  * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and hurd-i386
-    SSE is not availbale on others. Closes: #668123 
+  * debian/control force architcures to i386/amd64 kfreebsd-i386/amd64 and 
+    hurd-i386 SSE is not availbale on others. Closes: #668123 
   * debhelper version 9
   * debian/rules forced hardening flags
+  * hardening.patch to inject hardening CPPFLAGS
 
  -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Mon, 02 Jul 2012 16:27:10 +0200
 
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..8e1a8b9
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,14 @@
+Subject: Patch injects hardening CPPFLAGS
+Origin: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+--- bowtie2.orig/Makefile
++++ bowtie2/Makefile
+@@ -189,7 +189,8 @@
+      $(PTHREAD_DEF) \
+      $(PREF_DEF) \
+      $(MM_DEF) \
+-     $(SHMEM_DEF)
++     $(SHMEM_DEF)\
++     $(CPPFLAGS)
+ 
+ #
+ # bowtie2-build targets
diff --git a/debian/patches/series b/debian/patches/series
index feb5f36..121e6fa 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
+hardening.patch
 bowtie2_gcc4.7.patch
 fix_makefile_machine_detection.patch
diff --git a/debian/rules b/debian/rules
index 8cb722c..bbfc29a 100755
--- a/debian/rules
+++ b/debian/rules
@@ -20,7 +20,7 @@ endif
 	dh $@
 
 override_dh_auto_build:
-	dh_auto_build -- ENABLE_SSE=$(ENABLE_SSE) EXTRA_FLAGS=$(EXTRA_FLAGS) GCC_SUFFIX=$(CPPFLAGS)
+	dh_auto_build -- ENABLE_SSE=$(ENABLE_SSE) EXTRA_FLAGS=$(EXTRA_FLAGS) CPPFLAGS=$(CPPFLAGS)
 
 override_dh_auto_install:
 	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/

-- 
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