1 Author: Simon Ruderich <simon@ruderich.org>
2 Date: Sat, 28 Apr 2012 19:09:02 UTC
3 Description: Fix build system to enable hardening flags
5 --- tabix.orig/Makefile
9 -CFLAGS= -g -Wall -O2 -fPIC #-m64 #-arch ppc
10 +# Use flags when CFLAGS is not already defined in the environment.
11 +CFLAGS?= -g -Wall -O2
12 +# But always append special flags we need.
13 +CFLAGS+= -fPIC #-m64 #-arch ppc
14 DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
15 LOBJS= bgzf.o kstring.o knetfile.o index.o bedidx.o
21 - $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
22 + $(CC) -c $(CPPFLAGS) $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
24 all-recur lib-recur clean-recur cleanlocal-recur install-recur:
25 @target=`echo $@ | sed s/-recur//`; \
29 libtabix.so.1:$(LOBJS)
30 - $(CC) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
31 + $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,-soname,libtabix.so -o $@ $(LOBJS) -lc -lz
33 libtabix.1.dylib:$(LOBJS)
34 - libtool -dynamic $(LOBJS) -o $@ -lc -lz
35 + libtool $(CFLAGS) $(LDFLAGS) -dynamic $(LOBJS) -o $@ -lc -lz
38 $(AR) -cru $@ $(LOBJS)
41 - $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
42 + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lz -L. -ltabix
44 bgzip:bgzip.o bgzf.o knetfile.o
45 - $(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
46 + $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
48 TabixReader.class:TabixReader.java
49 javac -cp .:sam.jar TabixReader.java