Subject: Add hardening
Description: makefiles do not import default CFLAGS,...
this patch add debian cflags for hardening
Forwarded: no
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2014-02-01
--- a/kissnp2/makefile
+++ b/kissnp2/makefile
@@ -33,7 +33,10 @@
 #knowledge of the CeCILL license and that you accept its terms.
 
 CC=g++
-CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
+
 #CFLAGS=  -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -DDONTMARK
 SRC=../minia/Pool.cpp ../minia/Bank.cpp ../minia/Bloom.cpp ../minia/Hash16.cpp ../minia/Terminator.cpp ../minia/Kmer.cpp ../minia/Traversal.cpp ../minia/LinearCounter.cpp ../minia/Set.cpp ../minia/Utils.cpp ../minia/SortingCount.cpp ../minia/Debloom.cpp ../minia/OAHash.cpp Kmer_for_kissnp2.cpp SNP.cpp filter.cpp IterativeExtensions.cpp commons.cpp
 EXEC=kissnp2
@@ -41,7 +44,7 @@
 all: $(EXEC)
 
 ifeq ($(prof),1)
- CFLAGS=-O3 -pg -lz
+ CFLAGS= $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O3 -pg -lz
 endif
 ifeq ($(deb),1)
  CFLAGS+=-O0 -DASSERTS -g -lz 
@@ -79,7 +82,7 @@
 all: $(EXEC)
 
 kissnp2:  $(OBJ) kissnp2.cpp
-	$(CC) -o $@ $^ $(CFLAGS) 
+	$(CC) -o $@ $^ $(CFLAGS) $(LDFLAGS)
 
 %.o: %.cpp %.h
 	$(CC) -o $@ -c $< $(CFLAGS)
--- a/minia/makefile
+++ b/minia/makefile
@@ -1,4 +1,7 @@
-CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
+#CFLAGS+= -O4 -D_FILE_OFFSET_BITS=64 # needed to handle files > 2 GB on 32 bits systems
+CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS)
+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -O4 -D_FILE_OFFSET_BITS=64
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS)
 SRC=Pool.cpp Bank.cpp Bloom.cpp Hash16.cpp LargeInt.cpp Kmer.cpp Terminator.cpp Traversal.cpp LinearCounter.cpp Set.cpp Utils.cpp SortingCount.cpp Debloom.cpp OAHash.cpp
 EXEC=minia
 OBJ= $(SRC:.cpp=.o)
@@ -60,7 +63,7 @@
 	$(MAKE) $(EXEC)
 
 minia: $(OBJ) Minia.cpp
-	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) -lz
+	$(CXX) -o $@ $(OBJ) Minia.cpp $(CFLAGS) $(LDFLAGS) -lz
 
 %.o: %.cpp %.h
 	$(CXX) -o $@ -c $< $(CFLAGS)
--- a/kissreads/Makefile
+++ b/kissreads/Makefile
@@ -20,10 +20,10 @@
 # optimized flags
 
 #CFLAGS=-Wall -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!§
-CFLAGS= -O3 -lz -fopenmp -DOMP #openmp is incompatiblre with clang #@!
+CFLAGS = $(shell dpkg-buildflags --get CFLAGS) $(CPPFLAGS) -Wall -O3 -lz
 CFLAGS+=$(MYFLAGS)
 #LDFLAGS+=-Wall -lm -O3 -lz -DOMP -fopenmp#-fopenmp
-LDFLAGS+= -lm -O3 -lz -DOMP -fopenmp#-fopenmp
+LDFLAGS:=$(shell dpkg-buildflags --get LDFLAGS) -Wall -lm -O3 -lz
 
 ## debug flags
 
@@ -51,7 +51,7 @@
 	@echo "#################"
 
 kissreads: $(OBJ) 
-	$(CC)  -o $@ $^ $(LDFLAGS)
+	$(CC)  -o $@ $^ $(CFLAGS) $(LDFLAGS)
 
 
 kissReads.o: $(INCLDIR)coherence_algorithm.h  $(INCLDIR)couple.h $(INCLDIR)extension_algorithm.h $(INCLDIR)fragment_info.h  $(INCLDIR)libchash.h  $(INCLDIR)outputs.h $(INCLDIR)commons.h $(INCLDIR)extending_fragment.h $(INCLDIR)fragment_index.h $(INCLDIR)hash.h $(INCLDIR)list.h 
