[med-svn] r4050 - in trunk/packages/mafft/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2009-09-28 09:08:39 +0000 (Mon, 28 Sep 2009)
New Revision: 4050

Removed:
   trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch
Modified:
   trunk/packages/mafft/trunk/debian/changelog
   trunk/packages/mafft/trunk/debian/patches/series
Log:
Removed patch which was applied upstream


Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog	2009-09-28 08:00:45 UTC (rev 4049)
+++ trunk/packages/mafft/trunk/debian/changelog	2009-09-28 09:08:39 UTC (rev 4050)
@@ -3,8 +3,6 @@
   [ David Paleino ]
   * debian/control:
     - removed myself from Uploaders
-  * debian/patches/:
-    - fix-undefined-sprintf-usage.patch added
 
   [ Andreas Tille ]
   * New upstream version

Deleted: trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch
===================================================================
--- trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch	2009-09-28 08:00:45 UTC (rev 4049)
+++ trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch	2009-09-28 09:08:39 UTC (rev 4050)
@@ -1,126 +0,0 @@
-Author: David Paleino <d.paleino at gmail.com>,
- following instructions given by Kees Cook <kees at outflux.net> in
-   <http://lists.debian.org/debian-devel/2008/12/msg01079.html>
- (#include's added for strlen())
-License: same as MAFFT itself
-Forwarded: Kazutaka Katoh <katoh at bioreg.kyushu-u.ac.jp>
-
---- mafft-6.240.orig/src/splitfromaln.c.bk
-+++ mafft-6.240/src/splitfromaln.c.bk
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1164,7 +1165,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast.c
-+++ mafft-6.240/src/splittbfast.c
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1289,7 +1290,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast.c.bk
-+++ mafft-6.240/src/splittbfast.c.bk
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1289,7 +1290,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast.c.diana
-+++ mafft-6.240/src/splittbfast.c.diana
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1381,7 +1382,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast.c.equi
-+++ mafft-6.240/src/splittbfast.c.equi
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1248,7 +1249,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast.c.yugo
-+++ mafft-6.240/src/splittbfast.c.yugo
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1244,7 +1245,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );
---- mafft-6.240.orig/src/splittbfast2.c
-+++ mafft-6.240/src/splittbfast2.c
-@@ -1,4 +1,5 @@
- #include "mltaln.h"
-+#include <string.h>
- 
- #define TREE 1
- #define PICKSIZE 50 // must be >= 3
-@@ -1259,7 +1260,7 @@
- 		outputfile = AllocateCharVec( strlen( inputfile ) + 100 );
- 		sprintf( outputfile, "%s-%d", inputfile, branchid );
- 		if( uniform > 0 )
--			sprintf( outputfile, "%su%d", outputfile, uniform );
-+			sprintf( outputfile + strlen(outputfile), "u%d", uniform );
- 		fprintf( stderr, "GROUP %d: %d member(s) (%d) %s\n", branchid, nin, scores[0].numinseq, outputfile );
- 		outfp = fopen( outputfile, "w" );
- 		free( outputfile );

Modified: trunk/packages/mafft/trunk/debian/patches/series
===================================================================
--- trunk/packages/mafft/trunk/debian/patches/series	2009-09-28 08:00:45 UTC (rev 4049)
+++ trunk/packages/mafft/trunk/debian/patches/series	2009-09-28 09:08:39 UTC (rev 4050)
@@ -1,2 +1 @@
 Securisation-by-mktemp-usage.patch
-fix-undefined-sprintf-usage.patch