[med-svn] [blat] 01/01: Another test in utils; propagate hardening options for utils

[Andreas Tille]

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commit 0f730dcb2fddc578728d2f12a785e3a3f2b1831c
Author: Andreas Tille <tille at debian.org>
Date:   Mon Mar 3 10:02:06 2014 +0100

    Another test in utils; propagate hardening options for utils
---
 debian/patches/avoid_external_tool_in_test.patch |  2 +-
 debian/patches/hardening.patch                   | 92 ++++++++++++++++++++++++
 debian/patches/series                            |  1 +
 debian/rules                                     |  2 +
 4 files changed, 96 insertions(+), 1 deletion(-)

diff --git a/debian/patches/avoid_external_tool_in_test.patch b/debian/patches/avoid_external_tool_in_test.patch
index 0aef1ec..ef4dc25 100644
--- a/debian/patches/avoid_external_tool_in_test.patch
+++ b/debian/patches/avoid_external_tool_in_test.patch
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Last_update: Wed, 26 Feb 2014 13:52:17 +0100
+Last-Update: Wed, 26 Feb 2014 13:52:17 +0100
 Description: The tool pslCheck is not part of the BLAT source
  If you really want to run this test fully you either need to obtain
  the full jksrc source tree
diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
new file mode 100644
index 0000000..6babe02
--- /dev/null
+++ b/debian/patches/hardening.patch
@@ -0,0 +1,92 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 26 Feb 2014 13:52:17 +0100
+Description: Propagate hardening options
+
+--- a/utils/faToNib/makefile
++++ b/utils/faToNib/makefile
+@@ -9,7 +9,7 @@ O = faToNib.o
+ 
+ faToNib: ${O}
+ 	@${MKDIR} "${DESTDIR}${BINDIR}"
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L} $(LDFLAGS)
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ clean::
+--- a/utils/faToTwoBit/makefile
++++ b/utils/faToTwoBit/makefile
+@@ -9,7 +9,7 @@ O = faToTwoBit.o
+ 
+ faToTwoBit: ${O} ${MYLIBS}
+ 	@${MKDIR} "${DESTDIR}${BINDIR}"
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L} $(LDFLAGS)
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ clean::
+--- a/utils/nibFrag/makefile
++++ b/utils/nibFrag/makefile
+@@ -8,7 +8,7 @@ O = nibFrag.o
+ 
+ nibFrag: ${O}
+ 	@${MKDIR} "${DESTDIR}${BINDIR}"
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L} $(LDFLAGS)
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ clean::
+--- a/utils/twoBitInfo/makefile
++++ b/utils/twoBitInfo/makefile
+@@ -9,7 +9,7 @@ O = twoBitInfo.o
+ 
+ twoBitInfo: ${O} ${MYLIBS}
+ 	@${MKDIR} "${DESTDIR}${BINDIR}"
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L} $(LDFLAGS)
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ clean::
+--- a/utils/twoBitToFa/makefile
++++ b/utils/twoBitToFa/makefile
+@@ -9,7 +9,7 @@ O = twoBitToFa.o
+ 
+ twoBitToFa: ${O}
+ 	@${MKDIR} "${DESTDIR}${BINDIR}"
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L}
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/${A}${EXE} $O ${MYLIBS} ${L} $(LDFLAGS)
+ 	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
+ 
+ clean::
+--- a/hg/pslPretty/makefile
++++ b/hg/pslPretty/makefile
+@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+ O = pslPretty.o
+ 
+ pslPretty: $O $(MYLIBS)
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslPretty $O $(MYLIBS) $L
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslPretty $O $(MYLIBS) $L $(LDFLAGS)
+ 
+ test:: testRna testDnax
+ 
+--- a/hg/pslReps/makefile
++++ b/hg/pslReps/makefile
+@@ -9,7 +9,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+ O = pslReps.o 
+ 
+ pslReps: $O $(MYLIBS)
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslReps${EXE} $O $(MYLIBS) $L $(LDFLAGS)
+ 
+ lib:
+ 	cd ../../lib && ${MAKE}
+--- a/hg/pslSort/makefile
++++ b/hg/pslSort/makefile
+@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+ O = pslSort.o
+ 
+ pslSort: $O $(MYLIBS)
+-	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslSort $O $(MYLIBS) $L
++	${CC} ${COPT} ${CFLAGS} -o ${DESTDIR}${BINDIR}/pslSort $O $(MYLIBS) $L $(LDFLAGS)
+ 
+ 
+ lib:
diff --git a/debian/patches/series b/debian/patches/series
index a6f10a2..14a3fbf 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 avoid_external_tool_in_test.patch
+hardening.patch
diff --git a/debian/rules b/debian/rules
index bb32241..ec94a7c 100755
--- a/debian/rules
+++ b/debian/rules
@@ -42,6 +42,8 @@ override_dh_auto_install:
 	PATH=$(DESTDIR)/bin:$${PATH} make test
 	cd utils/twoBitInfo; \
 	PATH=$(DESTDIR)/bin:$${PATH} make test
+	cd utils/twoBitToFa; \
+	PATH=$(DESTDIR)/bin:$${PATH} make test
 
 override_dh_auto_test:
 	echo "Test suite is running after dh_auto_install"

-- 
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