[med-svn] r2859 - in trunk/packages/mafft/trunk/debian: . patches

[hanska-guest at alioth.debian.org]

Author: hanska-guest
Date: 2008-12-28 09:53:18 +0000 (Sun, 28 Dec 2008)
New Revision: 2859

Added:
   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:
* debian/patches/:
  - fix-undefined-sprintf-usage.patch added

Modified: trunk/packages/mafft/trunk/debian/changelog
===================================================================
--- trunk/packages/mafft/trunk/debian/changelog	2008-12-28 09:24:09 UTC (rev 2858)
+++ trunk/packages/mafft/trunk/debian/changelog	2008-12-28 09:53:18 UTC (rev 2859)
@@ -1,9 +1,11 @@
-mafft (6.240-2.1) UNRELEASED; urgency=low
+mafft (6.240-3) UNRELEASED; urgency=low
 
   * debian/control:
     - removed myself from Uploaders
+  * debian/patches/:
+    - fix-undefined-sprintf-usage.patch added
 
- -- David Paleino <d.paleino at gmail.com>  Sun, 28 Dec 2008 10:23:37 +0100
+ -- David Paleino <d.paleino at gmail.com>  Sun, 28 Dec 2008 10:53:11 +0100
 
 mafft (6.240-2) unstable; urgency=high
 

Added: trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch
===================================================================
--- trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch	                        (rev 0)
+++ trunk/packages/mafft/trunk/debian/patches/fix-undefined-sprintf-usage.patch	2008-12-28 09:53:18 UTC (rev 2859)
@@ -0,0 +1,125 @@
+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
+
+--- 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	2008-12-28 09:24:09 UTC (rev 2858)
+++ trunk/packages/mafft/trunk/debian/patches/series	2008-12-28 09:53:18 UTC (rev 2859)
@@ -1 +1,2 @@
 Securisation-by-mktemp-usage.patch
+fix-undefined-sprintf-usage.patch