[med-svn] [blat] 01/01: include CPPFLAGS for better hardening

[Michael Crusoe]

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misterc-guest pushed a commit to branch master
in repository blat.

commit dfe314824b5351d19eedde785f13ebe586acecfd
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Thu Aug 27 15:40:15 2015 -0700

    include CPPFLAGS for better hardening
---
 debian/patches/hardening.patch | 75 +++++++++++++++++++++++-------------------
 debian/patches/series          |  1 +
 debian/patches/spelling        | 13 ++++++++
 3 files changed, 56 insertions(+), 33 deletions(-)

diff --git a/debian/patches/hardening.patch b/debian/patches/hardening.patch
index 94fa468..e11c97a 100644
--- a/debian/patches/hardening.patch
+++ b/debian/patches/hardening.patch
@@ -2,9 +2,9 @@ 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
+--- blat.orig/utils/faToNib/makefile
++++ blat/utils/faToNib/makefile
+@@ -9,7 +9,7 @@
  
  faToNib: ${O}
  	@${MKDIR} "${DESTDIR}${BINDIR}"
@@ -13,9 +13,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
  
  clean::
---- a/utils/faToTwoBit/makefile
-+++ b/utils/faToTwoBit/makefile
-@@ -9,7 +9,7 @@ O = faToTwoBit.o
+--- blat.orig/utils/faToTwoBit/makefile
++++ blat/utils/faToTwoBit/makefile
+@@ -9,7 +9,7 @@
  
  faToTwoBit: ${O} ${MYLIBS}
  	@${MKDIR} "${DESTDIR}${BINDIR}"
@@ -24,9 +24,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
  
  clean::
---- a/utils/nibFrag/makefile
-+++ b/utils/nibFrag/makefile
-@@ -8,7 +8,7 @@ O = nibFrag.o
+--- blat.orig/utils/nibFrag/makefile
++++ blat/utils/nibFrag/makefile
+@@ -8,7 +8,7 @@
  
  nibFrag: ${O}
  	@${MKDIR} "${DESTDIR}${BINDIR}"
@@ -35,9 +35,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
  
  clean::
---- a/utils/twoBitInfo/makefile
-+++ b/utils/twoBitInfo/makefile
-@@ -9,7 +9,7 @@ O = twoBitInfo.o
+--- blat.orig/utils/twoBitInfo/makefile
++++ blat/utils/twoBitInfo/makefile
+@@ -9,7 +9,7 @@
  
  twoBitInfo: ${O} ${MYLIBS}
  	@${MKDIR} "${DESTDIR}${BINDIR}"
@@ -46,9 +46,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
  
  clean::
---- a/utils/twoBitToFa/makefile
-+++ b/utils/twoBitToFa/makefile
-@@ -9,7 +9,7 @@ O = twoBitToFa.o
+--- blat.orig/utils/twoBitToFa/makefile
++++ blat/utils/twoBitToFa/makefile
+@@ -9,7 +9,7 @@
  
  twoBitToFa: ${O}
  	@${MKDIR} "${DESTDIR}${BINDIR}"
@@ -57,9 +57,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/${A}${EXE}
  
  clean::
---- a/hg/pslPretty/makefile
-+++ b/hg/pslPretty/makefile
-@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+--- blat.orig/hg/pslPretty/makefile
++++ blat/hg/pslPretty/makefile
+@@ -8,7 +8,7 @@
  O = pslPretty.o
  
  pslPretty: $O $(MYLIBS)
@@ -68,9 +68,9 @@ Description: Propagate hardening options
  
  test:: testRna testDnax
  
---- a/hg/pslReps/makefile
-+++ b/hg/pslReps/makefile
-@@ -9,7 +9,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+--- blat.orig/hg/pslReps/makefile
++++ blat/hg/pslReps/makefile
+@@ -9,7 +9,7 @@
  O = pslReps.o 
  
  pslReps: $O $(MYLIBS)
@@ -79,9 +79,9 @@ Description: Propagate hardening options
  
  lib:
  	cd ../../lib && ${MAKE}
---- a/hg/pslSort/makefile
-+++ b/hg/pslSort/makefile
-@@ -8,7 +8,7 @@ MYLIBS =  $(MYLIBDIR)/jkweb.a
+--- blat.orig/hg/pslSort/makefile
++++ blat/hg/pslSort/makefile
+@@ -8,7 +8,7 @@
  O = pslSort.o
  
  pslSort: $O $(MYLIBS)
@@ -90,9 +90,9 @@ Description: Propagate hardening options
  
  
  lib:
---- a/gfClient/makefile
-+++ b/gfClient/makefile
-@@ -8,7 +8,7 @@ O = gfClient.o
+--- blat.orig/gfClient/makefile
++++ blat/gfClient/makefile
+@@ -8,7 +8,7 @@
  X = gfClient
  
  gfClient: $O $(MYLIBS)
@@ -101,9 +101,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/$X${EXE}
  
  clean::
---- a/gfServer/makefile
-+++ b/gfServer/makefile
-@@ -8,7 +8,7 @@ O = gfServer.o
+--- blat.orig/gfServer/makefile
++++ blat/gfServer/makefile
+@@ -8,7 +8,7 @@
  X = gfServer
  
  gfServer: $O $(MYLIBS)
@@ -112,9 +112,9 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/$X${EXE}
  
  test:
---- a/blat/makefile
-+++ b/blat/makefile
-@@ -7,7 +7,7 @@ MYLIBS =  $(MYLIBDIR)/jkOwnLib.a $(MYLIB
+--- blat.orig/blat/makefile
++++ blat/blat/makefile
+@@ -7,7 +7,7 @@
  O = blat.o
  
  blat: $O $(MYLIBS)
@@ -123,3 +123,12 @@ Description: Propagate hardening options
  	${STRIP} ${DESTDIR}${BINDIR}/blat${EXE}
  
  all:
+--- blat.orig/inc/common.mk
++++ blat/inc/common.mk
+@@ -29,5 +29,5 @@
+ endif
+ 
+ %.o: %.c
+-	${CC} ${COPT} ${CFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
++	${CC} ${COPT} ${CFLAGS} ${CPPFLAGS} ${HG_DEFS} ${LOWELAB_DEFS} ${HG_WARN} ${HG_INC} ${XINC} -o $@ -c $<
+ 
diff --git a/debian/patches/series b/debian/patches/series
index 14a3fbf..7cf4bea 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 avoid_external_tool_in_test.patch
 hardening.patch
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 0000000..4fc0f6c
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,13 @@
+Description: fix typo
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+--- blat.orig/hg/pslSort/pslSort.c
++++ blat/hg/pslSort/pslSort.c
+@@ -26,7 +26,7 @@
+    "alignments across the diagonal.\n"
+    "\n"
+    "Adding 1 or 2 after the dirs or g2g will limit the program to\n"
+-   "only the first or second pass repectively of the sort\n"
++   "only the first or second pass respectively of the sort\n"
+    "\n"
+    "Options:\n"
+    "   -nohead - do not write psl header:\n"

-- 
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