[med-svn] [Git][med-team/biosquid][master] 2 commits: buildflags.patch: new: propagate more build flags.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Jan 12 21:55:24 GMT 2026
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 <emollier at debian.org> 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 <emollier at debian.org>
+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
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