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commit ec035c09b74a33760116b6d4a4022f790e61e8b6 Author: Andreas Tille <[email protected]> Date: Sat Jul 25 08:37:12 2015 +0200 Hardening --- debian/patches/hardening.patch | 51 +++++++++++++++++++++++ debian/patches/{makefile_patch => makefile.patch} | 0 debian/patches/series | 3 +- debian/rules | 22 +--------- 4 files changed, 55 insertions(+), 21 deletions(-) diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch new file mode 100644 index 0000000..bd42682 --- /dev/null +++ b/debian/patches/hardening.patch @@ -0,0 +1,51 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 25 Jul 2015 07:51:46 +0200 +Description: Propagate hardening options + +--- a/Makefile ++++ b/Makefile +@@ -64,21 +64,21 @@ $(PKG).${VER}-${REL}.tar.gz: $(PKG).tar. + cp $< $@ + + %: %.c fastq-lib.cpp fastq-lib.h +- $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< ++ $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) + + %: %.cpp fastq-lib.cpp fastq-lib.h +- $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< ++ $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS) + + + %: %.c gcModel.c gcModel.h +- $(CC) $(CFLAGS) gcModel.c -o $@ $< ++ $(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS) + + %: %.cpp gcModel.c gcModel.h +- $(CC) $(CFLAGS) gcModel.c -o $@ $< ++ $(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS) + + # why the libbam.a doesn't work? not sure... *.o works + sam-stats: sam-stats.cpp fastq-lib.h +- $(CC) $(CFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ ++ $(CC) $(CFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@ $(LDFLAGS) + + samtools/libbam.a: samtools/*.c samtools/*.h + cd samtools && make libbam.a +@@ -87,14 +87,14 @@ varcall: varcall.cpp fastq-lib.cpp tidx/ + ifeq ($(OS),Windows_NT) + echo varcall: not supported yet + else +- $(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas ++ $(CC) $(CFLAGS) fastq-lib.cpp tidx/tidx-lib.cpp -o $@ $< -lgsl -lgslcblas $(LDFLAGS) + endif + + fastq-stats: fastq-stats.cpp fastq-lib.cpp gcModel.c +- $(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $< ++ $(CC) $(CFLAGS) fastq-lib.cpp gcModel.c -o $@ $< $(LDFLAGS) + + bam-filter: bam-filter.cpp +- $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< -lbamtools ++ $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< -lbamtools $(LDFLAGS) + + clean: + rm -f *.o $(BIN) diff --git a/debian/patches/makefile_patch b/debian/patches/makefile.patch similarity index 100% rename from debian/patches/makefile_patch rename to debian/patches/makefile.patch diff --git a/debian/patches/series b/debian/patches/series index 6a0d9f3..0ccdd2a 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ -makefile_patch +makefile.patch +hardening.patch diff --git a/debian/rules b/debian/rules index 88913a2..5db379d 100755 --- a/debian/rules +++ b/debian/rules @@ -2,18 +2,8 @@ # DH_VERBOSE := 1 -# some helpful variables - uncomment them if needed -# shamelessly stolen from http://jmtd.net/log/awk/ -#DEBVERS := $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}') -#VERSION := $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 's/-.*//') -#DEBFLAVOR := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print $$2}') -#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') -#DEBIAN_BRANCH := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' debian/gbp.conf) -#GIT_TAG := $(subst ~,_,$(VERSION)) - -# To build with packages sparsehash change this to -I/usr/include/google -export CFLAGS:=$(CFLAGS) -I/usr/include/google -export CPPFLAGS:=$(CPPFLAGS) -I/usr/include/google +export CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) -I/usr/include/google +export CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) -I/usr/include/google %: dh $@ @@ -21,11 +11,3 @@ export CPPFLAGS:=$(CPPFLAGS) -I/usr/include/google override_dh_auto_install: dh_auto_install -- PREFIX='$${DESTDIR}/usr' -override_dh_auto_clean: - dh_auto_clean - -override_dh_clean: - dh_clean - #Kill convenience copies of code - rm -rf samtools - rm -rf google sparsehash -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ea-utils.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
