[med-svn] r21829 - trunk/packages/snap/trunk/debian/patches

[Sascha Steinbiss]

Author: sascha-guest
Date: 2016-04-30 16:41:07 +0000 (Sat, 30 Apr 2016)
New Revision: 21829

Added:
   trunk/packages/snap/trunk/debian/patches/build-with-gcc-6.patch
   trunk/packages/snap/trunk/debian/patches/use-CC.patch
Modified:
   trunk/packages/snap/trunk/debian/patches/series
Log:
fix building with GCC6


Added: trunk/packages/snap/trunk/debian/patches/build-with-gcc-6.patch
===================================================================
--- trunk/packages/snap/trunk/debian/patches/build-with-gcc-6.patch	                        (rev 0)
+++ trunk/packages/snap/trunk/debian/patches/build-with-gcc-6.patch	2016-04-30 16:41:07 UTC (rev 21829)
@@ -0,0 +1,45 @@
+--- a/Zoe/zoeAlignment.c
++++ b/Zoe/zoeAlignment.c
+@@ -675,13 +675,13 @@
+ 
+ int zoeHSPCmpQuery (const zoeHSP h1, const zoeHSP h2) {
+ 	if      (h1->q_start < h2->q_start && h1->q_end < h2->q_end) return -1;
+-	else if (h1->q_start > h2->q_start && h2->q_end > h2->q_end) return  1;
++	else if (h1->q_start > h2->q_start && h1->q_end > h2->q_end) return  1;
+ 	else    return  0;
+ }
+ 
+ int zoeHSPCmpSbjct (const zoeHSP h1, const zoeHSP h2) {
+ 	if      (h1->s_start < h2->s_start && h1->s_end < h2->s_end) return -1;
+-	else if (h1->s_start > h2->s_start && h2->s_end > h2->s_end) return  1;
++	else if (h1->s_start > h2->s_start && h1->s_end > h2->s_end) return  1;
+ 	else    return  0;
+ }
+ 
+@@ -722,26 +722,6 @@
+ 	return group;
+ }
+ 
+-/*
+-
+-zoeVec zoeChainHSPs (const zoeVec HSPs) {
+-	int           i;
+-	zoeVec        bestHSPs = NULL;
+-	/* zoeVec        qvec; */
+-	/* zoeVec        svec; */
+-
+-	for (i = 0; i < HSPs->size; i++) {
+-		zoeWriteHSP(stdout, HSPs->elem[i]);
+-	}
+-	
+-	/* qvec = */ zoeGroupHSPs(HSPs, 'q');
+-	/* svec = */ zoeGroupHSPs(HSPs, 's');
+-	
+-	return bestHSPs;
+-}
+-
+-*/
+-
+ void zoeDeleteScoreSystem (zoeScoreSystem s) {
+ 	int i;
+ 	for (i = 0; i < 22; i++) zoeFree(s->score[i]);

Modified: trunk/packages/snap/trunk/debian/patches/series
===================================================================
--- trunk/packages/snap/trunk/debian/patches/series	2016-04-30 08:08:36 UTC (rev 21828)
+++ trunk/packages/snap/trunk/debian/patches/series	2016-04-30 16:41:07 UTC (rev 21829)
@@ -1,2 +1,4 @@
 unused-but-set-variable.patch
 hardening.patch
+build-with-gcc-6.patch
+use-CC.patch

Added: trunk/packages/snap/trunk/debian/patches/use-CC.patch
===================================================================
--- trunk/packages/snap/trunk/debian/patches/use-CC.patch	                        (rev 0)
+++ trunk/packages/snap/trunk/debian/patches/use-CC.patch	2016-04-30 16:41:07 UTC (rev 21829)
@@ -0,0 +1,32 @@
+--- a/Zoe/Makefile
++++ b/Zoe/Makefile
+@@ -76,7 +76,7 @@
+ 	rm -f *.o $(APP) $(APP2) $(APP3) $(APP4) $(APP5)
+ 
+ depend: $(OBJECTS:.o=.c)
+-	gcc -MM $^ > $@
++	$(CC) -MM $^ > $@
+ 
+ tar:
+ 	rm -rf /tmp/$(APP)
+@@ -92,14 +92,14 @@
+ #################
+ 
+ gcc:
+-	make $(APP)  CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP) CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+ 
+ all:
+-	make $(APP)  CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+-	make $(APP2) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+-	make $(APP3) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+-	make $(APP4) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+-	make $(APP5) CC="gcc" CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP)  CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP2) CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP3) CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP4) CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
++	make $(APP5) CFLAGS="-O2 -Wall -Werror $(CFLAGS)"
+ 
+ 
+ ###################