[med-svn] [Git][med-team/ea-utils][master] Update hardening options

[Shruti Sridhar (@shruti_sridhar)]

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

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View it on GitLab: https://salsa.debian.org/med-team/ea-utils/-/commit/29cf1378fea6f2b5e8c452c5f45bae2ebd2f709a
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