[med-svn] [trnascan-se] 01/08: Add patch to use LDFLAGS so that hardening flags are applied

[Afif Elghraoui]

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afif-guest pushed a commit to branch master
in repository trnascan-se.

commit 74fba966b50ca242b2da834ad15942476d805dd7
Author: Afif Elghraoui <afif at ghraoui.name>
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 <afif at ghraoui.name>
+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

-- 
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