[med-svn] r21635 - trunk/packages/seer/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2016-03-31 20:41:58 +0000 (Thu, 31 Mar 2016)
New Revision: 21635

Added:
   trunk/packages/seer/trunk/debian/patches/hardening.patch
Log:
Hardening patch does not really work - no idea why (leave this for a later point in time)


Added: trunk/packages/seer/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/seer/trunk/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/seer/trunk/debian/patches/hardening.patch	2016-03-31 20:41:58 UTC (rev 21635)
@@ -0,0 +1,39 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 29 Mar 2016 19:32:29 +0200
+Description: Propagate hardening options
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -13,11 +13,11 @@ BINDIR=$(PREFIX)/bin
+ # gcc
+ CXXFLAGS+=-Wall -O3 -std=c++11
+ SEER_LDLIBS=-lhdf5 -lgzstream -lz -larmadillo -lboost_program_options -llapack -lblas $(LDFLAGS)
+-MAP_LDLIBS=-L$(PREFIX)/lib -lboost_program_options
+-COMBINE_LDLIBS=-lgzstream -lz -lboost_program_options
+-FILTER_LDLIBS=-L$(PREFIX)/lib -lboost_program_options
++MAP_LDLIBS=-lboost_program_options $(LDFLAGS)
++COMBINE_LDLIBS=-lgzstream -lz -lboost_program_options $(LDFLAGS)
++FILTER_LDLIBS=-lboost_program_options $(LDFLAGS)
+ 
+-CPPFLAGS=-I$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
++CPPFLAGS+=-I$(PREFIX)/include -I../gzstream -I../dlib -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1
+ 
+ # For static linking. To use type 'make static'
+ # Requires icpc and mkl
+@@ -56,13 +56,13 @@ kmds: $(KMDS_OBJECTS)
+ 	$(LINK.cpp) $^ $(SEER_LDLIBS) -o $@
+ 
+ map_back: $(MAP_OBJECTS)
+-	$(LINK.cpp) $^ $(MAP_LDLIBS) -o $@
++	$(LINK.cpp) $^ $(MAP_LDLIBS) $(LDFLAGS) -o $@
+ 
+ combineKmers: $(COMBINE_OBJECTS)
+-	$(LINK.cpp) $^ $(COMBINE_LDLIBS) -o $@
++	$(LINK.cpp) $^ $(COMBINE_LDLIBS) $(LDFLAGS) -o $@
+ 
+ filter_seer: $(FILTER_OBJECTS)
+-	$(LINK.cpp) $^ $(FILTER_LDLIBS) -o $@
++	$(LINK.cpp) $^ $(FILTER_LDLIBS) $(LDFLAGS) -o $@
+ 
+ seer_static: $(SEER_OBJECTS)
+ 	$(LINK.cpp) $^ $(SEER_STATIC_LDLIBS) -o $@