[med-svn] [SCM] tabix branch, master, updated. debian/0.2.5-1-24-g185665e

[Charles Plessy]

The following commit has been merged in the master branch:
commit 2836b515b23a476c4c6629750971b60158208338
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Jun 22 13:00:10 2012 +0900

    Refreshed hardening patch.

diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index 7ece66b..0275175 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -2,8 +2,8 @@ Author: Simon Ruderich <simon at ruderich.org>
 Date: Sat, 28 Apr 2012 19:09:02 UTC
 Description: Fix build system to enable hardening flags
 
---- tabix.orig/Makefile
-+++ tabix/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -1,5 +1,8 @@
  CC=			gcc
 -CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
@@ -11,7 +11,7 @@ Description: Fix build system to enable hardening flags
 +CFLAGS?=		-g -Wall -O2
 +# But always append special flags we need.
 +CFLAGS+= -fPIC #-m64 #-arch ppc
- DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE
  LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
  AOBJS=		main.o
 @@ -12,7 +15,7 @@
@@ -35,11 +35,11 @@ Description: Fix build system to enable hardening flags
 +		libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
  
  libtabix.a:$(LOBJS)
- 		$(AR) -cru $@ $(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
  
  tabix:lib $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
+-		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -ltabix -lm $(LIBPATH) -lz
  
  bgzip:bgzip.o bgzf.o knetfile.o
 -		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz

-- 
Generic indexer for TAB-delimited genome position files.