X-Git-Url: http://woldlab.caltech.edu/gitweb/?a=blobdiff_plain;f=debian%2Fpatches%2Fuse-dpkg-buildflags.patch;h=0275175afaa8e874404d2b31a00f1d3b60ee8cd1;hb=2836b515b23a476c4c6629750971b60158208338;hp=7856be77141317edecfb3da84e7dbc08fc925fa7;hpb=14f3697a5a53fdcaca0f48d8235dffdc8a8ee07d;p=tabix.git

diff --git a/debian/patches/use-dpkg-buildflags.patch b/debian/patches/use-dpkg-buildflags.patch
index 7856be7..0275175 100644
--- a/debian/patches/use-dpkg-buildflags.patch
+++ b/debian/patches/use-dpkg-buildflags.patch
@@ -1,11 +1,49 @@
---- tabix.orig/Makefile
-+++ tabix/Makefile
-@@ -12,7 +12,7 @@
+Author: Simon Ruderich <simon@ruderich.org>
+Date: Sat, 28 Apr 2012 19:09:02 UTC
+Description: Fix build system to enable hardening flags
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,5 +1,8 @@
+ CC=			gcc
+-CFLAGS=		-g -Wall -O2 -fPIC #-m64 #-arch ppc
++# Use flags when CFLAGS is not already defined in the environment.
++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 -DBGZF_CACHE
+ LOBJS=		bgzf.o kstring.o knetfile.o index.o bedidx.o
+ AOBJS=		main.o
+@@ -12,7 +15,7 @@
  .SUFFIXES:.c .o
  
  .c.o:
 -		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+		$(CC) -c $(CPPFLAGS) $(CFLAGS) $(CXXFLAGS) $(DFLAGS) $(LDFLAGS) $(INCLUDES) $< -o $@
++		$(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
  
  all-recur lib-recur clean-recur cleanlocal-recur install-recur:
  		@target=`echo $@ | sed s/-recur//`; \
+@@ -29,19 +32,19 @@
+ lib:libtabix.a
+ 
+ libtabix.so.1:$(LOBJS)
+-		$(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
++		$(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
+ 
+ libtabix.1.dylib:$(LOBJS)
+-		libtool -dynamic $(LOBJS) -o $@ -lc -lz
++		libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
+ 
+ libtabix.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
+ 
+ tabix:lib $(AOBJS)
+-		$(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
++		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
+ 
+ TabixReader.class:TabixReader.java
+ 		javac -cp .:sam.jar TabixReader.java