more hardening tweaks

                deps/fastahack

                deps/libVCFH

                deps/vcflib/libVCFH

                deps/vcflib/tabixpp/htslib

                deps/sublinear-Li-Stephens/deps/htslib

Files: *

Copyright: © 2014 Erik Garrison

 $(LIB_DIR)/libsdsl.a: $(SDSL_DIR)/lib/*.cpp $(SDSL_DIR)/include/sdsl/*.hpp

 ifeq ($(shell uname -s),Darwin)

@@ -316,10 +316,10 @@

@@ -316,17 +316,17 @@

 $(LIB_DIR)/libvgio.a: $(LIB_DIR)/libhts.a $(LIB_DIR)/pkgconfig/htslib.pc $(LIBVGIO_DIR)/CMakeLists.txt $(LIBVGIO_DIR)/src/*.cpp $(LIBVGIO_DIR)/include/vg/io/*.hpp

 	+rm -f $(CWD)/$(INC_DIR)/vg.pb.h $(CWD)/$(INC_DIR)/vg/vg.pb.h

 	+rm -Rf $(CWD)/$(INC_DIR)/vg/io/

 # We also have to have the shared libdeflate or we will get complaints that the static one is not position independent.

 # If we need either the library or the pkg-config file (which we didn't used to ship), run the whole build.

 # We use a wildcard match to make sure make understands that both files come from one command run.

 # See https://stackoverflow.com/a/3077254

 $(LIB_DIR)/libhts%a $(LIB_DIR)/pkgconfig/htslib%pc: $(HTSLIB_DIR)/*.c $(HTSLIB_DIR)/*.h $(HTSLIB_DIR)/htslib/*.h $(HTSLIB_DIR)/cram/*.c $(HTSLIB_DIR)/cram/*.h

-	+. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR)" LDFLAGS="-L$(CWD)/$(LIB_DIR)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install

+	+. ./source_me.sh && cd $(HTSLIB_DIR) && rm -Rf $(CWD)/$(INC_DIR)/htslib $(CWD)/$(LIB_DIR)/libhts* && autoheader && autoconf && CFLAGS="-I$(CWD)/$(INC_DIR) $(CFLAGS)" LDFLAGS="-L$(CWD)/$(LIB_DIR) $(LDFLAGS)" ./configure --with-libdeflate --disable-s3 --disable-gcs --disable-libcurl --disable-plugins --prefix=$(CWD) $(FILTER) && $(MAKE) clean && $(MAKE) $(FILTER) && $(MAKE) install

 # We tell the vcflib build to use our own htslib.

 # We link it and libdeflate statically (on Linux) because our lib directory won't

@@ -392,7 +392,7 @@

 	+mkdir -p $(CWD)/$(INC_DIR)/dozeu && cp $(DOZEU_DIR)/*.h $(CWD)/$(INC_DIR)/dozeu/

 multichoose: pre

 	cd multichoose && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

@@ -174,7 +174,7 @@

 	cd intervaltree && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

 $(TABIX): pre

-	cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

+	cd tabixpp && INCLUDES="$(HTS_INCLUDES)" LIBPATH="-L. $(HTS_LDFLAGS)" HTSLIB="$(HTS_LIB)" HTS_HEADERS="" $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/

 $(SMITHWATERMAN): pre

 	cd smithwaterman && $(MAKE) && cp *.h* $(VCF_LIB_LOCAL)/$(INC_DIR)/ && cp *.o $(VCF_LIB_LOCAL)/$(OBJ_DIR)/

@@ -197,7 +197,7 @@

 	$(MAKE) bin/$@

 install: all

 	${MKDIR} -p ${DESTDIR}${PREFIX}/bin

--- vg.orig/deps/vcflib/tabixpp/Makefile

+++ vg/deps/vcflib/tabixpp/Makefile

@@ -44,6 +44,5 @@

 cleanlocal:

 	rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log \

 		tabix.pdf *.class libtabix.*.dylib libtabix.so*

-	cd htslib && $(MAKE) clean

 clean:cleanlocal-recur

export DEB_BUILD_MAINT_OPTIONS=hardening=+all

export CFLAGS=$(shell dpkg-buildflags --get CFLAGS)

export CPPFLAGS=$(shell dpkg-buildflags --get CPPFLAGS)

export LFFLAGS=$(shell dpkg-buildflags --get LDFLAGS)

export LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)

export CXXFLAGS=$(shell dpkg-buildflags --get CXXFLAGS)

%: