[med-svn] r20821 - in trunk/packages/ampliconnoise/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-12-18 15:04:55 +0000 (Fri, 18 Dec 2015)
New Revision: 20821

Added:
   trunk/packages/ampliconnoise/trunk/debian/patches/mayhem.patch
Modified:
   trunk/packages/ampliconnoise/trunk/debian/changelog
   trunk/packages/ampliconnoise/trunk/debian/patches/series
Log:
Fix Mayhem issues by making reading fasta files more robust



Modified: trunk/packages/ampliconnoise/trunk/debian/changelog
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/changelog	2015-12-18 15:04:15 UTC (rev 20820)
+++ trunk/packages/ampliconnoise/trunk/debian/changelog	2015-12-18 15:04:55 UTC (rev 20821)
@@ -1,3 +1,11 @@
+ampliconnoise (1.29-5) UNRELEASED; urgency=medium
+
+  * Fix Mayhem issues
+    Closes: #715593, #715594
+  * Fix remaining hardening issue
+
+ -- Andreas Tille <tille at debian.org>  Fri, 18 Dec 2015 12:14:54 +0100
+
 ampliconnoise (1.29-4) unstable; urgency=medium
 
   [ Bas Couwenberg ]

Added: trunk/packages/ampliconnoise/trunk/debian/patches/mayhem.patch
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/mayhem.patch	                        (rev 0)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/mayhem.patch	2015-12-18 15:04:55 UTC (rev 20821)
@@ -0,0 +1,73 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 18 Dec 2015 12:14:54 +0100
+Bug-Debian: https://bugs.debian.org/715593
+            https://bugs.debian.org/715594
+Description: Fix Mayhem issues by 
+ making reading fasta files more robust
+
+--- a/Perseus/Perseus.c
++++ b/Perseus/Perseus.c
+@@ -839,6 +839,11 @@ void readData(char* szInputFile, t_Data
+ 	}
+ 
+ 	szBrk = strpbrk(szLine, " \n");
++        if(! szBrk)
++        {
++            fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
++            exit(EXIT_FAILURE);
++        }
+ 	(*szBrk) = '\0';
+ 	ptData->aszID[nSequences] = strdup(szLine + 1);
+ 	ptData->adFreq[nSequences] = getWeight(ptData->aszID[nSequences]);
+--- a/PerseusD/PerseusD.c
++++ b/PerseusD/PerseusD.c
+@@ -891,6 +891,11 @@ void readData(char* szInputFile, t_Data
+ 	}
+ 
+ 	szBrk = strpbrk(szLine, " \n");
++        if(! szBrk)
++        {
++            fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
++            exit(EXIT_FAILURE);
++        }
+ 	(*szBrk) = '\0';
+ 	ptData->aszID[nSequences] = strdup(szLine + 1);
+ 	ptData->anFreq[nSequences] = getWeight(ptData->aszID[nSequences]);
+--- a/SeqNoise/SeqNoise.c
++++ b/SeqNoise/SeqNoise.c
+@@ -634,6 +634,11 @@ void readData(t_Data *ptData, t_Params *
+ 	}
+ 
+ 	szBrk = strpbrk(szLine, " \n");
++        if(! szBrk)
++        {
++            fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
++            exit(EXIT_FAILURE);
++        }
+ 	(*szBrk) = '\0';
+ 	ptData->aszID[nSequences] = strdup(szLine + 1);
+ 	ptData->adW[nSequences]   = getWeight(ptData->aszID[nSequences]);
+@@ -2454,6 +2459,11 @@ void readDistanceMatrix(char *szDistFile
+     
+     szBrk = strpbrk(szLine, "\n");
+ 
++    if(! szBrk)
++    {
++        fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
++        exit(EXIT_FAILURE);
++    }
+     (*szBrk) = '\0';
+ 
+     nTest = strtol(szLine, &pcError, 10);
+@@ -2478,6 +2488,11 @@ void readDistanceMatrix(char *szDistFile
+ 	fgets(szLine, MAX_LINE_LENGTH, ifp);
+     
+ 	szBrk = strpbrk(szLine, "\n");
++        if(! szBrk)
++        {
++            fprintf(stderr, "File %s does not appear to be in FASTA format.\n", szInputFile);
++            exit(EXIT_FAILURE);
++        }
+ 	(*szBrk) = '\0';
+ 
+ 	afDist[i*nN + j] = (float) strtod(szLine, &pcError);

Modified: trunk/packages/ampliconnoise/trunk/debian/patches/series
===================================================================
--- trunk/packages/ampliconnoise/trunk/debian/patches/series	2015-12-18 15:04:15 UTC (rev 20820)
+++ trunk/packages/ampliconnoise/trunk/debian/patches/series	2015-12-18 15:04:55 UTC (rev 20821)
@@ -2,3 +2,4 @@
 fix-segfault-on-non-fasta-input.patch
 hardening.patch
 clang-ftbfs.patch
+mayhem.patch