Package: mothur / 1.38.1.1-1

0002-Add-hardening-flags.patch Patch series | download
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From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Date: Sun, 12 Jun 2016 19:59:04 +0200
Subject: Add hardening flags.

---
 source/uchime_src/mk | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/source/uchime_src/mk b/source/uchime_src/mk
index 8cd6282..8ac4acf 100755
--- a/source/uchime_src/mk
+++ b/source/uchime_src/mk
@@ -1,4 +1,7 @@
 #!/bin/bash
+
+set -eux
+
 CPPNames='addtargets2 alignchime alignchimel alnparams alpha alpha2 fractid getparents globalalign2 make3way mx myutils path searchchime seqdb setnucmx sfasta tracebackbit uchime_main usort viterbifast writechhit'
 ObjNames='addtargets2.o alignchime.o alignchimel.o alnparams.o alpha.o alpha2.o fractid.o getparents.o globalalign2.o make3way.o mx.o myutils.o path.o searchchime.o seqdb.o setnucmx.o sfasta.o tracebackbit.o uchime_main.o usort.o viterbifast.o writechhit.o'
 
@@ -7,7 +10,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr
 for CPPName in $CPPNames
 do
   echo $CPPName >&2
-  g++ $ENV_GCC_OPTS -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o  >> mk.stdout 2>> tmp.stderr
+  g++ $CPPFLAGS $CXXFLAGS ${ENV_GCC_OPTS:-} -c -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o  >> mk.stdout 2>> tmp.stderr
   cat tmp.stderr
 	cat tmp.stderr >> mk.stderr
 	rm -f tmp.stderr
@@ -17,7 +20,7 @@ LINK_OPTS=
 #if [ `uname -s` == Linux ] ; then
 #    LINK_OPTS=-static
 #fi
-g++ $LINK_OPTS $ENV_LINK_OPTS -g -o uchime $ObjNames >> mk.stdout 2>> tmp.stderr
+g++ $LINK_OPTS ${ENV_LINK_OPTS:-} -g -o uchime $ObjNames $LDFLAGS >> mk.stdout 2>> tmp.stderr
 cat tmp.stderr
 cat tmp.stderr >> mk.stderr
 rm -f tmp.stderr