Shruti Sridhar pushed to branch master at Debian Med / ea-utils
Commits:
29cf1378 by Shruti Sridhar at 2021-08-04T19:36:59+05:30
Update hardening options
- - - - -
1 changed file:
- debian/patches/hardening.patch
Changes:
=====================================
debian/patches/hardening.patch
=====================================
@@ -9,25 +9,25 @@ Description: Propagate hardening options
%: %.c fastq-lib.cpp fastq-lib.h
- $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $<
-+ $(CC) $(CFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) 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)
++ $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< $(LDFLAGS)
%: %.c gcModel.c gcModel.h
- $(CC) $(CFLAGS) gcModel.c -o $@ $<
-+ $(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) gcModel.c -o $@ $< $(LDFLAGS)
%: %.cpp gcModel.c gcModel.h
- $(CC) $(CFLAGS) gcModel.c -o $@ $<
-+ $(CC) $(CFLAGS) gcModel.c -o $@ $< $(LDFLAGS)
++ $(CC) $(CFLAGS) $(CPPFLAGS) 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)
++ $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp $< -lbam -lz -lpthread -o $@
$(LDFLAGS)
samtools/libbam.a: samtools/*.c samtools/*.h
cd samtools && make libbam.a
@@ -36,16 +36,16 @@ Description: Propagate hardening options
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)
++ $(CC) $(CFLAGS) $(CPPFLAGS) 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)
++ $(CC) $(CFLAGS) $(CPPFLAGS) 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)
++ $(CC) $(CFLAGS) $(CPPFLAGS) fastq-lib.cpp -o $@ $< -lbamtools
$(LDFLAGS)
clean:
rm -f *.o $(BIN)
View it on GitLab:
https://salsa.debian.org/med-team/ea-utils/-/commit/29cf1378fea6f2b5e8c452c5f45bae2ebd2f709a
--
View it on GitLab:
https://salsa.debian.org/med-team/ea-utils/-/commit/29cf1378fea6f2b5e8c452c5f45bae2ebd2f709a
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