[med-svn] r3720 - in trunk/packages/mummer/trunk/debian: . patches

[Charles Plessy]

Author: plessy
Date: 2009-08-02 03:13:51 +0000 (Sun, 02 Aug 2009)
New Revision: 3720

Modified:
   trunk/packages/mummer/trunk/debian/changelog
   trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
   trunk/packages/mummer/trunk/debian/patches/series
Log:
Updated patch from Boyd Stephen Smith Jr.

(see http://lists.debian.org/msgid-search/200907281349.35052.bss@iguanasuicide.net)


Modified: trunk/packages/mummer/trunk/debian/changelog
===================================================================
--- trunk/packages/mummer/trunk/debian/changelog	2009-07-31 14:12:12 UTC (rev 3719)
+++ trunk/packages/mummer/trunk/debian/changelog	2009-08-02 03:13:51 UTC (rev 3720)
@@ -15,9 +15,9 @@
     - replaces some Makefile patches by environment variables in debian/rules.
     - replaced 02at_scripts.diff by separate files in sh-replacement-scripts.
     - added a series file to use Quilt.
-    - Ignore for the moment the patch ‘01sm_src_tigr.diff’ that allows to use
-      MUMmer on computers with less that 512 Mo of memory, because it is not
-      accepted upstream.
+    - refreshed the patch ‘01sm_src_tigr.diff’ that allows to use MUMmer on
+      computers with less that 512 Mo of memory, with the great help of
+      Boyd Stephen Smith Jr.
   * debian/rules converted to debhelper (the build system is too odd to be
     handled gently by CDBS without patches).
   * Mangled ‘~dfsg’ from the Debian version number in debian/watch.

Modified: trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff	2009-07-31 14:12:12 UTC (rev 3719)
+++ trunk/packages/mummer/trunk/debian/patches/01sm_src_tigr.diff	2009-08-02 03:13:51 UTC (rev 3720)
@@ -1,11 +1,11 @@
 Description: Dynamically allocates space for the strings, instead allocating a predefined size.
- This is not applied as its implementation appears to be buggy.
- See ‘http://lists.debian.org/msgid-search/200907061138.56896.bss@iguanasuicide.net’.
+ See http://lists.debian.org/msgid-search/20090704120642.GH6047@kunpuu.plessy.org and its replies.
 Origin: vendor : Debian
-Bug: https://sourceforge.net/tracker/?func=detail&aid=1215086&group_id=133157&atid=726404
-diff -urbN src/tigr.orig/annotate.cc src/tigr/annotate.cc
---- ./src/tigr.orig/annotate.cc	2007-07-13 19:06:58.000000000 +0200
-+++ ./src/tigr/annotate.cc	2007-11-07 21:47:03.000000000 +0100
+Bug: https://sourceforge.net/support/tracker.php?aid=1215086
+Index: ./src/tigr/annotate.cc
+===================================================================
+--- ./src/tigr/annotate.cc
++++ ./src/tigr.orig/annotate.cc
 @@ -10,6 +10,7 @@
  */
  
@@ -14,7 +14,7 @@
  
  #define  FIELD_LEN  20
  #define  MAX_ALIGN  10000
-@@ -138,19 +139,19 @@
+@@ -138,19 +139,26 @@ void  Show_Alignment (char A [], long in
  //  Print the alignment between strings  A [1 .. M]  and  B [1 .. N] .
  
    {
@@ -35,16 +35,23 @@
 -        fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
 -        return;
 -       }
-+   assert ( D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
++   assert ( SIZE_MAX / (M+1) >= (N+1) ) ;
++   D_buf  = (int  *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
++   assert ( D_buf ) ;
 +   D  = &D_buf ;
-+   assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
++   Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ;
++   assert ( Op_buf ) ;
 +   Op = &Op_buf ;
-+   assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
-+   assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
++
++   assert ( SIZE_MAX >> 1 >= (M+1) ) ;
++   Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
++   assert ( Show_A ) ;
++   Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
++   assert ( Show_B ) ;
  
     D [0] [0] = 0;
     Op [0] [0] = 'a';
-@@ -229,5 +230,10 @@
+@@ -229,5 +237,10 @@ void  Show_Alignment (char A [], long in
        putchar ('\n');
        Ct -= WIDTH;
       }  while  (Ct > 0);

Modified: trunk/packages/mummer/trunk/debian/patches/series
===================================================================
--- trunk/packages/mummer/trunk/debian/patches/series	2009-07-31 14:12:12 UTC (rev 3719)
+++ trunk/packages/mummer/trunk/debian/patches/series	2009-08-02 03:13:51 UTC (rev 3720)
@@ -1,2 +1,2 @@
-#01sm_src_tigr.diff
+01sm_src_tigr.diff
 02at_docs_web.diff