[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna/files: vienna-rna-1.8.4-overflows.patch vienna-rna-1.8.4-implicits.patch vienna-rna-1.7.2-disable-gd.patch vienna-rna-1.7.2-gcc4.3.patch vienna-rna-1.7.2-gcc4.4.patch

[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna/files: vienna-rna-1.8.4-overflows.patch vienna-rna-1.8.4-implicits.patch vienna-rna-1.7.2-disable-gd.patch vienna-rna-1.7.2-gcc4.3.patch vienna-rna-1.7.2-gcc4.4.patch

[Kacper Kowalik (xarthisius)]

xarthisius    10/10/15 07:15:15

  Added:                vienna-rna-1.8.4-overflows.patch
                        vienna-rna-1.8.4-implicits.patch
  Removed:              vienna-rna-1.7.2-disable-gd.patch
                        vienna-rna-1.7.2-gcc4.3.patch
                        vienna-rna-1.7.2-gcc4.4.patch
  Log:
  Fix buffer overflows wrt bug 341089. Thanks to Diego for the report. Fix implicit function declarations. Drop old.
  
  (Portage version: 2.2_rc92/cvs/Linux x86_64)

Revision  Changes    Path
1.1                  sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.4-overflows.patch?rev=1.1&content-type=text/plain

Index: vienna-rna-1.8.4-overflows.patch
===================================================================
Fix buffer overflows

http://bugs.gentoo.org/show_bug.cgi?id=341089

--- Readseq/ureadseq.c
+++ Readseq/ureadseq.c
@@ -1579,7 +1579,7 @@
 
   short linesout = 0, seqtype = kNucleic;
   long  i, j, l, l1, ibase;
-  char  idword[31], endstr[10];
+  char  idword[31], endstr[15];
   char  seqnamestore[128], *seqname = seqnamestore;
   char  s[kMaxseqwidth], *cp;
   char  nameform[10], numform[10], nocountsymbols[10];
--- lib/part_func_up.c
+++ lib/part_func_up.c
@@ -1438,7 +1438,7 @@
 PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) {
   int size,s,i,len;
   double dG_u;
-  char nan[4], *time, startl[2], dg[10];;
+  char nan[4], *time, startl[3], dg[10];;
   FILE *wastl;
 
   wastl = fopen(ofile,"a");



1.1                  sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch

file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.4-implicits.patch?rev=1.1&content-type=text/plain

Index: vienna-rna-1.8.4-implicits.patch
===================================================================
Fix implicit function declarations and attempt to free non-heap obj

--- lib/subopt.c
+++ lib/subopt.c
@@ -80,12 +80,12 @@
 #include <string.h>
 #include <math.h>
 #include "fold.h"
+#include "cofold.h"
 #include "utils.h"
 #include "energy_par.h"
 #include "fold_vars.h"
 #include "pair_mat.h"
 #include "list.h"
-#include "subopt.h"
 #include "params.h"
 
 #define true	  1
--- Progs/RNAfold.c
+++ Progs/RNAfold.c
@@ -20,6 +20,7 @@
 #include "MEA.h"
 extern void  read_parameter_file(const char fname[]);
 extern plist * stackProb(double cutoff);
+extern void init_pf_circ_fold(int length);
 
 /*@unused@*/
 static char UNUSED rcsid[] = "$Id: vienna-rna-1.8.4-implicits.patch,v 1.1 2010/10/15 07:15:15 xarthisius Exp $";
--- Cluster/AS_main.c
+++ Cluster/AS_main.c
@@ -1,6 +1,7 @@
 #include <stdio.h>
 #include <string.h>
 #include <stdlib.h>
+#include <unistd.h>
 #include "distance_matrix.h"
 #include "statgeom.h"
 #include "split.h"
@@ -226,7 +227,7 @@
 	    for(j=0;j<nn[i];j++) free(ss[i][j]);
 	    free(ss[i]);
          }
-	 free(ss);
+	 // free(ss); 	//  attempt to free a non-heap object ‘ss’
       }
       else {
          printf_taxa_list();