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/[email protected]) 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/[email protected]’. + See http://lists.debian.org/msgid-search/[email protected] 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
