[med-svn] r20753 - in trunk/packages/acedb/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Sun Dec 13 18:08:59 UTC 2015
Author: tille
Date: 2015-12-13 18:08:58 +0000 (Sun, 13 Dec 2015)
New Revision: 20753
Added:
trunk/packages/acedb/trunk/debian/patches/mayhem.patch
trunk/packages/acedb/trunk/debian/patches/spelling.patch
Modified:
trunk/packages/acedb/trunk/debian/changelog
trunk/packages/acedb/trunk/debian/patches/series
Log:
Fix Mayhem issues, spelling, upload to unstable
Modified: trunk/packages/acedb/trunk/debian/changelog
===================================================================
--- trunk/packages/acedb/trunk/debian/changelog 2015-12-12 21:58:48 UTC (rev 20752)
+++ trunk/packages/acedb/trunk/debian/changelog 2015-12-13 18:08:58 UTC (rev 20753)
@@ -1,4 +1,4 @@
-acedb (4.9.39+dfsg.01-6) UNRELEASED; urgency=low
+acedb (4.9.39+dfsg.01-6) unstable; urgency=low
[ Charles Plessy ]
* Renamed debian/upstream-metadata.yaml to debian/upstream/metadata
@@ -19,8 +19,10 @@
since not all needed functions that are used in the test suite are
available
* Propagate hardening options
+ * Fix Mayhem bugs
+ Closes: #715832, #715860
- -- Andreas Tille <tille at debian.org> Thu, 10 Dec 2015 15:24:16 +0100
+ -- Andreas Tille <tille at debian.org> Sun, 13 Dec 2015 19:01:45 +0100
acedb (4.9.39+dfsg.01-5) unstable; urgency=low
Added: trunk/packages/acedb/trunk/debian/patches/mayhem.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/mayhem.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/mayhem.patch 2015-12-13 18:08:58 UTC (rev 20753)
@@ -0,0 +1,107 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 13 Dec 2015 18:53:59 +0100
+Bug-Debian: https://bugs.debian.org/715832
+ https://bugs.debian.org/715860
+Description: Fix crashes reported by Mayhem
+
+--- a/w9/dotterMain.c
++++ b/w9/dotterMain.c
+@@ -271,6 +271,11 @@ int main(int argc, char **argv)
+ case 'r': revcompq = 1; break;
+ case 's': soffset = atoi(optarg); break;
+ case 'S':
++ if ( optind+4 >= argc ) {
++ fprintf(stderr,"Illegal number of command line arguments for option -S");
++ fprintf(stderr,"%s\n",usage);
++ exit(1);
++ }
+ selfcall = 1;
+ qname = messalloc(strlen(argv[optind])+1); strcpy(qname, argv[optind]);
+ qlen = atoi(argv[optind+1]);
+--- a/w9/efetch.c
++++ b/w9/efetch.c
+@@ -37,8 +37,9 @@
+
+ #include "dbidx.h"
+
++#define MAXFILE 128
+ extern char dbsource[32];
+-char *env, dbdir[128]="", *seqName;
++char *env, dbdir[MAXFILE]="", *seqName;
+ int wormpep2swiss = 0;
+
+ void swissprot(void)
+@@ -89,9 +90,9 @@ void prosite(void)
+ void main(int argc, char *argv[])
+ {
+ FILE *idx, *db, *actrg, *achit;
+- static char idxfile[128]="", dbfile[128]="", divfile[128]="",
+- actrgfile[128]="", achitfile[128]="", dbprefix[32]="";
+- static char *file, customName[128]="";
++ static char idxfile[MAXFILE]="", dbfile[MAXFILE]="", divfile[MAXFILE]="",
++ actrgfile[MAXFILE]="", achitfile[MAXFILE]="", dbprefix[32]="";
++ static char *file, customName[MAXFILE]="";
+ char query[32], *tmpstr, *cp, fetchstr[256];
+ int optc, pos, i;
+ int Startseq = -1, Endseq = -1;
+@@ -216,14 +217,29 @@ void main(int argc, char *argv[])
+ case 'f':
+ fasta = 1; break;
+ case 'i':
+- strcpy(idxfile, optarg); break;
++ if ( !optarg ) {
++ fprintf(stderr,"Missing idxfile for option -i.\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(1);
++ }
++ strncpy(idxfile, optarg, MAXFILE); break;
+ case 'q':
+ fasta = 1;
+ seqonly = 1; break;
+ case 'D':
+- strcpy(dbdir, optarg); break;
++ if ( !optarg ) {
++ fprintf(stderr,"Missing dir for option -D.\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(1);
++ }
++ strncpy(dbdir, optarg, MAXFILE); break;
+ case 'd':
+- strcpy(dbfile, optarg); break;
++ if ( !optarg ) {
++ fprintf(stderr,"Missing dbfile for option -d.\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(1);
++ }
++ strncpy(dbfile, optarg, MAXFILE); break;
+ case 'H':
+ display_head=1; break;
+ case 'h':
+@@ -240,7 +256,12 @@ void main(int argc, char *argv[])
+ case 'p':
+ search = 1; break;
+ case 'l':
+- strcpy(divfile, optarg); break;
++ if ( !optarg ) {
++ fprintf(stderr,"Missing divfile for option -l.\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(1);
++ }
++ strncpy(divfile, optarg, MAXFILE); break;
+ case 's':
+ case 'S':
+ Startseq = atoi(optarg);
+@@ -259,7 +280,12 @@ void main(int argc, char *argv[])
+ Mini = 1; /* Mini output format */
+ fasta = 1; break;
+ case 'n':
+- strcpy(customName, optarg); break;
++ if ( !optarg ) {
++ fprintf(stderr,"Missing name for option -n.\n");
++ fprintf(stderr,"%s\n",helpText);
++ exit(1);
++ }
++ strncpy(customName, optarg, MAXFILE); break;
+ case 'w':
+ wormpep2swiss = 1; break;
+ case '-':
Modified: trunk/packages/acedb/trunk/debian/patches/series
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/series 2015-12-12 21:58:48 UTC (rev 20752)
+++ trunk/packages/acedb/trunk/debian/patches/series 2015-12-13 18:08:58 UTC (rev 20753)
@@ -6,3 +6,5 @@
no-curses.patch
hardening.patch
fix_hardening_errors.patch
+mayhem.patch
+spelling.patch
Added: trunk/packages/acedb/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/acedb/trunk/debian/patches/spelling.patch (rev 0)
+++ trunk/packages/acedb/trunk/debian/patches/spelling.patch 2015-12-13 18:08:58 UTC (rev 20753)
@@ -0,0 +1,93 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sun, 13 Dec 2015 18:53:59 +0100
+Description: Silence lintians spelling nitpicking
+
+--- a/w1/helpsubs.c
++++ b/w1/helpsubs.c
+@@ -1708,7 +1708,7 @@ static BOOL parseSection (char **cp, Htm
+ else if (strncasecmp (*cp, "</pre>", 6) == 0)
+ {
+ if (!MODE_PREFORMAT)
+- fprintf (stderr, "Help warning : found </PRE> without preceeding <PRE>\n") ;
++ fprintf (stderr, "Help warning : found </PRE> without preceding <PRE>\n") ;
+ MODE_PREFORMAT = FALSE ;
+
+ leftnode = makeNode (HTML_ENDPREFORMAT, handle) ;
+@@ -1738,7 +1738,7 @@ static BOOL parseSection (char **cp, Htm
+ }
+ else
+ fprintf (stderr, "Help warning : found </BLOCKQUOTE> "
+- "without preceeding <BLOCKQUOTE>\n") ;
++ "without preceding <BLOCKQUOTE>\n") ;
+
+ *cp += 13 ;
+ skipSpaces (cp) ;
+--- a/w7/dendrogram.c
++++ b/w7/dendrogram.c
+@@ -3746,7 +3746,7 @@ static BOOL parseMember (FILE *ttfil, ch
+ {
+ blankAtom (ttfil) ;
+ /* Substitute blank to ensure that subsequent empty names
+- preceeding the next ',' or ')' are scanned */
++ preceding the next ',' or ')' are scanned */
+ **cp = ' ' ;
+ return TRUE ;
+ }
+@@ -3773,7 +3773,7 @@ static BOOL parseMember (FILE *ttfil, ch
+ if( **cp == ',' )
+ {
+ /* Substitute blank to ensure that subsequent empty names
+- preceeding the next ',' or ')' are scanned */
++ preceding the next ',' or ')' are scanned */
+ **cp = ' ' ;
+ return TRUE ;
+ }
+@@ -3819,7 +3819,7 @@ static BOOL parseMember (FILE *ttfil, ch
+ if( **cp == ',' )
+ {
+ /* Substitute blank to ensure that subsequent empty names
+- preceeding the next ',' or ')' are scanned */
++ preceding the next ',' or ')' are scanned */
+ **cp = ' ' ;
+ return TRUE ;
+ }
+@@ -3879,7 +3879,7 @@ static BOOL parseMember (FILE *ttfil, ch
+ if( **cp == ',' )
+ {
+ /* Substitute blank to ensure that subsequent empty names
+- preceeding the next ',' or ')' are scanned */
++ preceding the next ',' or ')' are scanned */
+ **cp = ' ' ;
+ return TRUE ;
+ }
+--- a/wdemo/wspec/help.wrm
++++ b/wdemo/wspec/help.wrm
+@@ -1196,7 +1196,7 @@ corresponding number, in this case a pos
+ may use this column of number to draw a multiple map.
+
+ You may also edit the tag field manually, following the Query-syntax
+-explained in the preceeding page, but this will not edit the Class
++explained in the preceding page, but this will not edit the Class
+ field of the definition which must be set either by editing the .def
+ file manually or by using first the tag button and choosing the same
+ sort of field.
+@@ -2450,7 +2450,7 @@ Intrinsic tree:
+ button:
+
+ Refine tree:
+- This should better the results of the preceeding button but
++ This should better the results of the preceding button but
+ is not yet available.
+
+ Map:
+--- a/whelp/Interval_Mapping.html
++++ b/whelp/Interval_Mapping.html
+@@ -61,7 +61,7 @@ innacurate algorithm to reorder the gene
+ the next button:<p>
+
+ <li><strong>Refine tree</strong>: This should better the results of
+-the preceeding button but is not yet available.<p>
++the preceding button but is not yet available.<p>
+
+ <li><strong>Map</strong>: Creates a new window with a useful graphic
+ presentation of the data. It is interesting even on the standard data,
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