[med-svn] r14262 - in trunk/packages/ampliconnoise/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-07-30 09:42:34 +0000 (Tue, 30 Jul 2013)
New Revision: 14262

Added:
   trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch
Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/patches/series
Log:
Patch for hardening options


Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/changelog	2013-07-30 09:41:17 UTC (rev 14261)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog	2013-07-30 09:42:34 UTC (rev 14262)
@@ -14,6 +14,7 @@
   * debian/doc-base: created
   * debian/rules:
      - do not compress pdf files
+  * debian/patches/hardening.patch: Propagate hardening options
 
  -- Andreas Tille <tille at debian.org>  Tue, 30 Jul 2013 09:49:02 +0200
 

Added: trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch	                        (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/hardening.patch	2013-07-30 09:42:34 UTC (rev 14262)
@@ -0,0 +1,167 @@
+Author: Andreas Tille <tille at debian.org>
+LastChanged: Tue, 30 Jul 2013 09:49:02 +0200
+Description: Propagate hardening options
+
+--- a/makefile
++++ b/makefile
+@@ -1,16 +1,16 @@
+ all:
+-	(cd FCluster && make)
+-	(cd FastaUnique && make)
+-	(cd NDist && make)
+-	(cd PyroDist && make)
+-	(cd PyroNoise && make)
+-	(cd SeqDist && make)
+-	(cd PyroNoiseM && make)
+-	(cd SeqNoise && make)
+-	(cd SplitClusterEven && make)
+-	(cd SplitClusterClust && make)  		
+-	(cd Perseus && make) 		
+-	(cd PerseusD && make) 		
++	(cd FCluster && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd FastaUnique && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd NDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SeqDist && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PyroNoiseM && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SeqNoise && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SplitClusterEven && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd SplitClusterClust && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd Perseus && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
++	(cd PerseusD && CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" make)
+ clean:
+ 	(cd FCluster && make clean)
+ 	(cd FastaUnique && make clean)
+--- a/FCluster/makefile
++++ b/FCluster/makefile
+@@ -1,6 +1,6 @@
+ CC     = cc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = FCluster
+ LIBS   = -lm 
+ OBJS   = FCluster.o 
+--- a/FastaUnique/makefile
++++ b/FastaUnique/makefile
+@@ -1,6 +1,6 @@
+ CC     = cc
+-CFLAGS = -O3 
+-EFLAGS =  
++CFLAGS += -O3 
++EFLAGS = $(LDFLAGS)
+ EFILE  = FastaUnique
+ LIBS   = -lm 
+ OBJS   = FastaUnique.o 
+--- a/NDist/makefile
++++ b/NDist/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = NDist
+ LIBS   = -lm  
+ OBJS   = NDist.o 
+--- a/Perseus/makefile
++++ b/Perseus/makefile
+@@ -1,6 +1,6 @@
+ CC     = cc
+-CFLAGS = -O3 
+-EFLAGS =  
++CFLAGS += -O3 
++EFLAGS = $(LDFLAGS)
+ EFILE  = Perseus
+ LIBS   = -lm -lgsl -lgslcblas
+ OBJS   = Perseus.o 
+--- a/PerseusD/makefile
++++ b/PerseusD/makefile
+@@ -1,6 +1,6 @@
+ CC     = cc
+-CFLAGS = -O3 
+-EFLAGS =  
++CFLAGS += -O3 
++EFLAGS = $(LDFLAGS)
+ EFILE  = PerseusD
+ LIBS   = -lm -lgsl -lgslcblas
+ OBJS   = PerseusD.o 
+--- a/PyroDist/makefile
++++ b/PyroDist/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = PyroDist
+ LIBS   = -lm 
+ OBJS   = PyroDist.o
+--- a/PyroNoise/makefile
++++ b/PyroNoise/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS = 
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = PyroNoise
+ LIBS   =  -lm
+ OBJS   = PyroNoise.o 
+--- a/PyroNoiseM/makefile
++++ b/PyroNoiseM/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS = 
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = PyroNoiseM
+ LIBS   =  -lm
+ OBJS   = PyroNoiseM.o 
+--- a/SeqDist/makefile
++++ b/SeqDist/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = SeqDist
+ LIBS   = -lm 
+ OBJS   = SeqDist.o
+--- a/SeqNoise/makefile
++++ b/SeqNoise/makefile
+@@ -1,6 +1,6 @@
+ CC     = mpicc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = SeqNoise
+ LIBS   = -lm 
+ OBJS   = SeqNoise.o
+--- a/SplitClusterClust/makefile
++++ b/SplitClusterClust/makefile
+@@ -1,6 +1,6 @@
+ CC     = gcc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = SplitClusterClust
+ LIBS   = -lm 
+ OBJS   = SplitClusterClust.o
+--- a/SplitClusterEven/makefile
++++ b/SplitClusterEven/makefile
+@@ -1,6 +1,6 @@
+ CC     = cc
+-CFLAGS = -O3
+-EFLAGS =  
++CFLAGS += -O3
++EFLAGS = $(LDFLAGS)
+ EFILE  = SplitClusterEven
+ LIBS   = -lm 
+ OBJS   = SplitClusterEven.o

Modified: trunk/packages/ampliconnoise/trunk/debian/patches/series
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/series	2013-07-30 09:41:17 UTC (rev 14261)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/series	2013-07-30 09:42:34 UTC (rev 14262)
@@ -1,2 +1,3 @@
 fix-path-for-data.patch
 fix-segfault-on-non-fasta-input.patch
+hardening.patch