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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:
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