This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository trnascan-se.
commit 74fba966b50ca242b2da834ad15942476d805dd7 Author: Afif Elghraoui <[email protected]> Date: Fri Oct 30 01:34:00 2015 -0700 Add patch to use LDFLAGS so that hardening flags are applied --- debian/patches/ldflags.patch | 107 +++++++++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 108 insertions(+) diff --git a/debian/patches/ldflags.patch b/debian/patches/ldflags.patch new file mode 100644 index 0000000..2b97c1c --- /dev/null +++ b/debian/patches/ldflags.patch @@ -0,0 +1,107 @@ +Description: Honor LDFLAGS in calls to CC +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2015-10-30 +--- trnascan-se.orig/Makefile ++++ trnascan-se/Makefile +@@ -107,17 +107,17 @@ + all: $(PROGS) tRNAscan-SE setpaths + + covels-SE: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o covels-SE scan_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + coves-SE: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o coves-SE score_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + eufindtRNA: $(SQUIDOBJ) pavesi.o eufind_main.o + $(CC) $(CFLAGS) -o eufindtRNA eufind_main.o \ +- pavesi.o $(SQUIDOBJ) $(LIBS) ++ pavesi.o $(SQUIDOBJ) $(LIBS) $(LDFLAGS) + + trnascan-1.4: trnascan.o +- $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c ++ $(CC) $(CFLAGS) -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4 trnascan.c $(LDFLAGS) + + tRNAscan-SE: + $(PERLDIR)/$(PERLBIN) checkversion.pl +@@ -199,12 +199,12 @@ + noambig: trnascan-1.4-NA eufindtRNA-NA + + trnascan-1.4-NA: trnascan.o +- $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c ++ $(CC) $(CFLAGS) -DNO_AMBIG -DTSCANDIR=\"$(LIBDIR)\" -o trnascan-1.4-NA trnascan.c $(LDFLAGS) + + eufindtRNA-NA: $(SQUIDOBJ) eufind_main.o +- $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c ++ $(CC) $(CFLAGS) -DNO_AMBIG -c -o pavesi-NA.o pavesi.c $(LDFLAGS) + $(CC) $(CFLAGS) -o eufindtRNA-NA eufind_main.o \ +- pavesi-NA.o $(SQUIDOBJ) $(LIBS) ++ pavesi-NA.o $(SQUIDOBJ) $(LIBS) $(LDFLAGS) + + + clean: +@@ -219,7 +219,7 @@ + rmdir -ps $(MANDIR) + + .c.o: +- $(CC) $(CFLAGS) $(MDEFS) -c $< ++ $(CC) $(CFLAGS) $(MDEFS) -c $< $(LDFLAGS) + + ## programs from Sean Eddy's sequence i/o function library not + ## needed for tRNAscan-SE but included for their utility +@@ -232,16 +232,16 @@ + cp $(UTILS) $(BINDIR)/. + + reformat: $(SQUIDOBJ) reformat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(MDEFS) -o reformat $(SQUIDOBJ) reformat_main.o $(LIBS) $(LDFLAGS) + + revcomp: $(SQUIDOBJ) revcomp_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(MDEFS) -o revcomp $(SQUIDOBJ) revcomp_main.o $(LIBS) $(LDFLAGS) + + seqstat: $(SQUIDOBJ) seqstat_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(MDEFS) -o seqstat $(SQUIDOBJ) seqstat_main.o $(LIBS) $(LDFLAGS) + + shuffle: $(SQUIDOBJ) shuffle_main.o +- $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) ++ $(CC) $(CFLAGS) $(MDEFS) -o shuffle $(SQUIDOBJ) shuffle_main.o $(LIBS) $(LDFLAGS) + + ## other programs in Cove package (below) not needed for + ## tRNAscan-SE, but are included for users who wish to apply +@@ -254,25 +254,25 @@ + cp $(COVE_SUITE) $(BINDIR)/. + + covea: $(OBJ) align_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o covea align_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + coveb: $(OBJ) build_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o coveb build_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + covee: $(OBJ) emit_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o covee emit_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + covet: $(OBJ) train_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o covet train_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + covels: $(OBJ) scan_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o covels scan_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + coves: $(OBJ) score_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o coves score_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + structcheck: $(OBJ) structcheck_main.o +- $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(RFLAGS) -o structcheck structcheck_main.o $(OBJ) $(LIBS) $(LDFLAGS) + + + ## Maspar memory limits diff --git a/debian/patches/series b/debian/patches/series index 8ac56d0..b6f7156 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ install-location.patch perl5dir.patch cflags.patch +ldflags.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/trnascan-se.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
