The following commit has been merged in the master branch:
commit 2836b515b23a476c4c6629750971b60158208338
Author: Charles Plessy <[email protected]>
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 <[email protected]>
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.
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