Subject: add fortify flags
Description: Makefile does not load CFLAGS
 from env, add extra flags for debian fortify
Forwarded: no
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2013-02-09
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
@@ -12,7 +12,11 @@
 CFLAGS=         -O0 -g -fomit-frame-pointer -DDEBUG#-msse4.2
 else
 CFLAGS=         -O3 -fomit-frame-pointer -w #-msse4.2
+CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
+CFLAGS+=$(HARDENING_CFLAGS)
 endif
+LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+LDFLAGS+=$(HARDENING_LDFLAGS)
 DFLAGS=         
 OBJS=		arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
 		concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
@@ -77,9 +81,10 @@
 		@test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
 		@test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
 
-SOAPdenovo:	envTest $(OBJS)
+#SOAPdenovo:	envTest $(OBJS)
+SOAPdenovo:
 		@printf "Linking...                                          \r"
-		@$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+		@$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) $(LDFLAGS)
 		@printf "$(PROG) compilation done.                           \n"
 
 clean:
--- a/sparsePregraph/Makefile
+++ b/sparsePregraph/Makefile
@@ -3,7 +3,11 @@
 CFLAGS=         -O0 -g -fomit-frame-pointer -DDEBUG
 else
 CFLAGS=         -O3 -fomit-frame-pointer -w
+CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
+CFLAGS+=$(HARDENING_CFLAGS)
 endif
+LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+LDFLAGS+=$(HARDENING_LDFLAGS)
 
 DFLAGS=         
 OBJS=		build_graph.o build_edge.o multi_threads.o \
@@ -66,7 +70,7 @@
 
 pregraph_sparse: clean envTest $(OBJS)
 		@printf "Linking...                                     \r"
-		@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+		@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG)  $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) $(LDFLAGS)
 		@printf "$(PROG) compilation done.                      \n"
 
 clean:
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,11 @@
 CFLAGS=         -O0 -g -fomit-frame-pointer -DDEBUG
 else
 CFLAGS=         -O3 -fomit-frame-pointer
++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++CFLAGS+=$(HARDENING_CFLAGS)
 endif
+LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+LDFLAGS+=$(HARDENING_LDFLAGS)
 
 SUBDIRS = sparsePregraph standardPregraph fusion
 PROG=       SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion
@@ -46,20 +50,20 @@
 SOAPdenovo-63mer:
 	@cd sparsePregraph;make 63mer=1 debug=1 clean all;cd ..;
 	@cd standardPregraph;make 63mer=1 debug=1 clean all;cd ..;
-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer $(LDFLAGS)
 SOAPdenovo-127mer:
 	@cd sparsePregraph;make 127mer=1 debug=1 clean all;cd ..;
 	@cd standardPregraph;make 127mer=1 debug=1 clean all;cd ..;
-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS)
 else
 SOAPdenovo-63mer:
 	@cd sparsePregraph;make 63mer=1 clean all;cd ..;
 	@cd standardPregraph;make 63mer=1 clean all;cd ..;
-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer $(LDFLAGS)
 SOAPdenovo-127mer:
 	@cd sparsePregraph;make 127mer=1 clean all;cd ..;
 	@cd standardPregraph;make 127mer=1 clean all;cd ..;
-	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+	@$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS)
 endif
 
 clean:
