Étienne Mollier pushed to branch master at Debian Med / biosquid
Commits: 27b99bcb by Étienne Mollier at 2026-01-12T22:54:33+01:00 buildflags.patch: new: propagate more build flags. - - - - - 95b9dfce by Étienne Mollier at 2026-01-12T22:54:59+01:00 d/changelog: initialise the changelog. - - - - - 3 changed files: - debian/changelog - + debian/patches/buildflags.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +biosquid (1.9g+cvs20050121-17) UNRELEASED; urgency=medium + + * buildflags.patch: new: propagate more build flags. + + -- Étienne Mollier <[email protected]> Mon, 12 Jan 2026 22:54:46 +0100 + biosquid (1.9g+cvs20050121-16) unstable; urgency=medium * Team upload. ===================================== debian/patches/buildflags.patch ===================================== @@ -0,0 +1,75 @@ +Description: propagate all build flags. + The upstream code misses propagation of CPPFLAGS and LDFLAGS. This + change helps propagating those to the main makefile and tests'. +Author: Étienne Mollier <[email protected]> +Forwarded: no +Last-Update: 2026-01-12 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- biosquid.orig/Testsuite/Makefile.in ++++ biosquid/Testsuite/Makefile.in +@@ -34,13 +34,13 @@ + all: sqdconfig $(TESTPROGS) + + $(TESTPROGS): @EXEC_DEPENDENCY@ +- $(CC) $(CFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) + + sqdconfig: @EXEC_DEPENDENCY@ +- $(CC) $(CFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -L../ -I../ $(DEFS) -o $@ $@_main.o $(LIBS) + + .c.o: +- $(CC) $(CFLAGS) $(DEFS) -L../ -I../ -c $< ++ $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) $(DEFS) -L../ -I../ -c $< + + ################################################################ + +--- biosquid.orig/Makefile.in ++++ biosquid/Makefile.in +@@ -166,22 +166,22 @@ + all: $(PROGS) libsquid.a + + $(PROGS): @EXEC_DEPENDENCY@ ${OBJS} ${MAINS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o afetch afetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o alistat aligneval.o cluster.o sre_math.o sre_stack.o alistat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compalign aligneval.o compalign_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compstruct sre_math.o sre_stack.o wuss.o compstruct_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o revcomp revcomp.o shuffle.o revcomp_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqsplit seqsplit_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqstat seqstat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sfetch revcomp.o shuffle.o sfetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o shuffle iupac.o shuffle.o shuffle_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sindex sindex_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sreformat eps.o shuffle.o sre_stack.o wuss.o sreformat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o translate iupac.o revcomp.o shuffle.o sre_stack.o translate.o translate_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} +- ${CC} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o weight aligneval.o cluster.o iupac.o sre_math.o sre_stack.o weight.o weight_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o afetch afetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o alistat aligneval.o cluster.o sre_math.o sre_stack.o alistat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compalign aligneval.o compalign_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o compstruct sre_math.o sre_stack.o wuss.o compstruct_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o revcomp revcomp.o shuffle.o revcomp_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqsplit seqsplit_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o seqstat seqstat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sfetch revcomp.o shuffle.o sfetch_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o shuffle iupac.o shuffle.o shuffle_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sindex sindex_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o sreformat eps.o shuffle.o sre_stack.o wuss.o sreformat_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o translate iupac.o revcomp.o shuffle.o sre_stack.o translate.o translate_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${LDFLAGS} ${PVMLIBDIR} ${DEFS} -o weight aligneval.o cluster.o iupac.o sre_math.o sre_stack.o weight.o weight_main.o ${COMMON_OBJS} ${PVMLIBS} ${LIBS} + + .c.o: +- ${CC} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $< ++ ${CC} ${CPPFLAGS} ${CFLAGS} ${CPPFLAGS} ${PVMINCDIR} ${DEFS} -c $< + + ################################################################ + +@@ -232,7 +232,7 @@ + done + + check: libsquid.a +- (cd Testsuite; make CC="$(CC)" CFLAGS="$(CFLAGS)") ++ (cd Testsuite; make CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="${LDFLAGS}") + (cd Testsuite; make check) + + distclean: ===================================== debian/patches/series ===================================== @@ -12,3 +12,4 @@ reproducible.patch perl-testsuite-inc.patch automake.patch pkg-config.patch +buildflags.patch View it on GitLab: https://salsa.debian.org/med-team/biosquid/-/compare/f23a0d90c744463da975a971a88730243902668c...95b9dfcec97a13a71097ccd4af129cb42a43926c -- View it on GitLab: https://salsa.debian.org/med-team/biosquid/-/compare/f23a0d90c744463da975a971a88730243902668c...95b9dfcec97a13a71097ccd4af129cb42a43926c You're receiving this email because of your account on salsa.debian.org.
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