[med-svn] r18235 - trunk/packages/snap/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-10-07 12:01:13 +0000 (Tue, 07 Oct 2014)
New Revision: 18235

Modified:
   trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch
Log:
Adapt patches to new upstream version


Modified: trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch
===================================================================
--- trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch	2014-10-07 11:41:53 UTC (rev 18234)
+++ trunk/packages/snap/trunk/debian/patches/unused-but-set-variable.patch	2014-10-07 12:01:13 UTC (rev 18235)
@@ -1,15 +1,15 @@
 Author: Andreas Tille <tille at debian.org>
-Date: Sun, 01 Apr 2012 18:40:17 +0200
+Date: Tue, 07 Oct 2014 13:31:52 +0200
 Description: When enabling hardening flags by
  using debhelper 9 unsused variables should not be assigned.
  This patch comments those variables.
 
---- snap-2010-07-28.orig/Zoe/zoeAlignment.c
-+++ snap-2010-07-28/Zoe/zoeAlignment.c
-@@ -720,15 +720,15 @@
+--- a/Zoe/zoeAlignment.c
++++ b/Zoe/zoeAlignment.c
+@@ -727,15 +727,15 @@ zoeVec zoeGroupHSPs(zoeVec HSPs, char ty
  zoeVec zoeChainHSPs (const zoeVec HSPs) {
  	int           i;
- 	zoeVec        bestHSPs = NULL; /* shush */
+ 	zoeVec        bestHSPs = NULL;
 -	zoeVec        qvec;
 -	zoeVec        svec;
 +	/* zoeVec        qvec; */
@@ -26,71 +26,3 @@
  	
  	return bestHSPs;
  }
---- snap-2010-07-28.orig/Zoe/zoeCDS.c
-+++ snap-2010-07-28/Zoe/zoeCDS.c
-@@ -396,7 +396,7 @@
- 	char text[256];
- 	struct exon_feature efstart, efstop;
- 	struct best_translation bt;	
--	int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, all_exon, split;
-+	int i, nt_length, elength, inc5, inc3, frame, idx, b1, b2, b3, b4, /* all_exon, */ split;
- 	int exstart, exend, exinc;
- 	
- 	/* assigned immediately */
-@@ -483,10 +483,10 @@
- 	}
- 	
- 	/* re-label generic exons as Einit, Eterm, Esngl only if all exons defined as Exon */
--	all_exon = 1;
-+	/* all_exon = 1; */
- 	for (i = 0; i < cds->exons->size; i++) {
- 		if (cds->exons->elem[i]->label != Exon) {
--			all_exon = 0;
-+			/* all_exon = 0; */
- 			break;
- 		}
- 	}
---- snap-2010-07-28.orig/Zoe/zoeFeature.c
-+++ snap-2010-07-28/Zoe/zoeFeature.c
-@@ -167,7 +167,7 @@
- zoeFeature zoeReadGFF (FILE * stream) {
- 	char       line[1024], Source[64], ID[64], Label[64],
- 	           Start[16], End[16], Strand[8], Score[32], Frame[8], Group[512];
--	char     * group = NULL;
-+	/* char     * group = NULL; */
- 	zoeLabel   label;
- 	coor_t     start, end;
- 	strand_t   strand;
-@@ -178,10 +178,10 @@
- 	
- 	if (sscanf(line, "%s %s %s %s %s %s %s %s %s", /* group */
- 			Source, ID, Label, Start, End, Score, Strand, Frame, Group) == 9) {
--		group = Group;
-+		/* group = Group */ ;
- 	} else if (sscanf(line, "%s %s %s %s %s %s %s %s", /* no group */
- 			Source, ID, Label, Start, End, Score, Strand, Frame) == 8) {
--		group = NULL;
-+		/* group = NULL */ ;
- 	} else {
- 		zoeWarn("zoeReadGFF format not valid");
- 		return NULL;
---- snap-2010-07-28.orig/Zoe/zoeFeatureFactory.c
-+++ snap-2010-07-28/Zoe/zoeFeatureFactory.c
-@@ -280,7 +280,7 @@
- 	int               f0, f1, f2;
- 	int             * fstop;	
- 	coor_t            i;
--	int               frame; /* should be frame_t, but screw casting */
-+	/* int               frame; *//* should be frame_t, but screw casting */
- 	zoeDNA            dna = cds_scan->dna;
- 	zoeFeatureFactory factory = zoeMalloc(sizeof(struct zoeFeatureFactory));
- 		
-@@ -334,7 +334,7 @@
- 	fstop[2] = 2;
- 	
- 	for (i = 3; i < dna->length; i++) {
--		frame = i % 3;
-+		/* frame = i % 3; */
- 		if (stop[i] != MIN_SCORE) {
- 			fstop[i] = i;
- 		} else {