Codebase list blimps / c2b9436
Try hard to build even with hardening flags switched on Andreas Tille 5 years ago
1 changed file(s) with 117 addition(s) and 25 deletion(s). Raw diff Collapse all Expand all
+117
-25
debian/patches/gets.patch less more
6565 {
6666
6767 /* open up the block file to write to */
68 @@ -255,7 +260,7 @@ void display_output()
69
70 printf("<pre>\n");
71 while (!feof(outf) && fgets(buf, LARGE_BUFF_LENGTH, outf) != NULL)
72 - printf(buf) ;
73 + printf("%s", buf) ;
74 printf("</pre>\n");
75
76 fclose(outf);
6877 @@ -264,7 +269,7 @@ void display_output()
6978
7079 /**********************************************************************/
372381 }
373382 --- a/blimps/blocks_search.c
374383 +++ b/blimps/blocks_search.c
375 @@ -104,8 +104,8 @@ char mailprog[LARGE_BUFF_LENGTH];
376 char seq_file[LARGE_BUFF_LENGTH];
377 char cs_file[LARGE_BUFF_LENGTH];
378 char csh_file[LARGE_BUFF_LENGTH];
379 -char log_dir[LARGE_BUFF_LENGTH];
380 -char log_file[LARGE_BUFF_LENGTH];
381 +const char log_dir[LARGE_BUFF_LENGTH];
382 +const char log_file[LARGE_BUFF_LENGTH];
383 char blimps_output[LARGE_BUFF_LENGTH];
384 char blksort_output[LARGE_BUFF_LENGTH];
385 char html_output[LARGE_BUFF_LENGTH];
386 @@ -118,7 +118,7 @@ char frq[LARGE_BUFF_LENGTH]; /* for am
387 char tmp_dir[LARGE_BUFF_LENGTH];
388 char mail_file[LARGE_BUFF_LENGTH];
389 char email_addr[LARGE_BUFF_LENGTH];
390 -char buf[LARGE_BUFF_LENGTH];
391 +const char buf[LARGE_BUFF_LENGTH];
392
393 int pid;
394
395384 @@ -302,8 +302,9 @@ fprintf(jgh,"Address_Ptr->val=%s\n", Add
396385 else if (!strncmp(entries[i].val, "pfam", 9))
397386 { Pfam_Flag = TRUE; }
431420 printf("<H1>Search Error</H1>\n");
432421 printf("You need to enter a sequence to search with.<P>\n");
433422 exit(0);
423 @@ -562,7 +563,7 @@ void display_output()
424
425 while (!feof(fp) &&
426 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL) {
427 - printf(buf);
428 + printf("%s", buf);
429 }
430
431 pclose(fp);
432 @@ -581,7 +582,7 @@ void display_html()
433
434 while (!feof(fp) &&
435 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL) {
436 - printf(buf);
437 + printf("%s", buf);
438 }
439
440 fclose(fp);
434441 @@ -590,7 +591,7 @@ void display_html()
435442
436443
884891 char mail_file[LARGE_BUFF_LENGTH];
885892 char email_addr[LARGE_BUFF_LENGTH];
886893 -char buf[LARGE_BUFF_LENGTH];
887 +const char buf[LARGE_BUFF_LENGTH];
894 +static char buf[LARGE_BUFF_LENGTH];
888895
889896 int pid;
890897
906913 {
907914
908915 /* open up the block file to write to */
916 @@ -535,7 +535,7 @@ void convert_LAMA_output()
917
918 while (!feof(fp) &&
919 fgets(buf, LARGE_BUFF_LENGTH, fp) != NULL)
920 - printf(buf) ;
921 + printf("%s", buf) ;
922
923 printf("</pre>\n");
924
909925 @@ -579,7 +579,7 @@ void queue_to_mail()
910926 /* mail the person the results */
911927 /* NOTE: need to echo the header lines for the LAMA output :P */
14521468 printf("\nEnter number of hits to report or ");
14531469 printf("blimps configuration file name [%d]: ", MaxHit);
14541470 - gets(ctemp);
1455 + fgets(ctemp, MAXNAME, stdin);
1471 + fgets(ctemp, FNAMELEN, stdin);
14561472 }
14571473 if (!strlen(ctemp)) strcpy(ctemp, "0");
14581474 for (i=0; i<strlen(ctemp); i++)
14851501 {
14861502 printf("\nEnter Block accession number: ");
14871503 - gets(BlockFam);
1488 + fgets(BlockFam, MAXNAME, stdin);
1504 + fgets(BlockFam, FNAMELEN, stdin);
14891505 }
14901506 }
14911507 /* Chop off any A-Z block designator at the end */
16201636
16211637
16221638 -extern char ErrorBuffer[LARGE_BUFF_LENGTH];
1623 +extern const char ErrorBuffer[LARGE_BUFF_LENGTH+SMALL_BUFF_LENGTH];
1639 +extern char ErrorBuffer[LARGE_BUFF_LENGTH+SMALL_BUFF_LENGTH];
16241640 extern int ErrorLevelReport;
16251641
16261642
16311647 */
16321648
16331649 -char ErrorBuffer[LARGE_BUFF_LENGTH];
1634 +const char ErrorBuffer[LARGE_BUFF_LENGTH+SMALL_BUFF_LENGTH];
1650 +char ErrorBuffer[LARGE_BUFF_LENGTH+SMALL_BUFF_LENGTH];
16351651 int ErrorLevelReport;
16361652
16371653
1654 @@ -113,7 +113,7 @@ void ErrorReport(err_level)
1655 exit(FATAL_ERR_LVL); /* closes all the open files */
1656 }
1657
1658 - ErrorBuffer[0] = '\0'; /* clear the string incase the caller does */
1659 + ((char *)ErrorBuffer)[0] = '\0'; /* clear the string incase the caller does */
1660 /* not setup ErrorBuffer correctly for the */
1661 /* next call */
1662 if (dont_skip_error_file_report) {
1663 --- a/protomat/blosum.c
1664 +++ b/protomat/blosum.c
1665 @@ -125,7 +125,7 @@ char *argv[];
1666 else
1667 {
1668 printf("Enter name of blocks database:\n");
1669 - gets(datfile);
1670 + fgets(datfile, FNAMELEN, stdin);
1671 }
1672 if ( (fdat=fopen(datfile, "r")) == NULL)
1673 {
1674 @@ -139,7 +139,7 @@ char *argv[];
1675 {
1676 MinStr = MINSTR;
1677 printf("Enter minimum block strength [%d]: ", MinStr);
1678 - gets(ctemp);
1679 + fgets(ctemp, FNAMELEN, stdin);
1680 if (strlen(ctemp)) MinStr = atoi(ctemp);
1681 }
1682 /*-----------Arg 3, Maximum block strength----------------------*/
1683 @@ -148,7 +148,7 @@ char *argv[];
1684 {
1685 MaxStr = MAXSTR;
1686 printf("Enter maximum block strength [%d]: ", MaxStr);
1687 - gets(ctemp);
1688 + fgets(ctemp, FNAMELEN, stdin);
1689 if (strlen(ctemp)) MaxStr = atoi(ctemp);
1690 }
1691 printf("Minimum block strength=%d, Maximum block strength=%d\n",
1692 @@ -165,7 +165,7 @@ char *argv[];
1693 printf(" or w for existing sequence weights\n");
1694 printf(" or pn for position-based weights, PB weight = 1/n\n");
1695 printf("Enter clustering identity percentage or n/e/w/pn [e]: ");
1696 - gets(ctemp);
1697 + fgets(ctemp, FNAMELEN, stdin);
1698 }
1699 /* e => -1, n=> -2, w=> -3 p=> -4 */
1700 Cluster = -1;
1701 @@ -208,7 +208,7 @@ char *argv[];
1702 {
1703 iscale = 0;
1704 printf("Enter scale n for 1/n bits [%d]: ", iscale);
1705 - gets(ctemp);
1706 + fgets(ctemp, FNAMELEN, stdin);
1707 if (strlen(ctemp)) iscale = atoi(ctemp);
1708 }
1709 if (iscale < 0) iscale = 0;
1710 --- a/protomat/uextract.c
1711 +++ b/protomat/uextract.c
1712 @@ -130,7 +130,7 @@ char *argv[];
1713 else
1714 {
1715 printf("\nEnter name of file containing list of entries to extract: ");
1716 - gets(lisfile);
1717 + fgets(lisfile, FNAMELEN, stdin);
1718 }
1719 if ( (flis=fopen(lisfile, "r")) == NULL)
1720 {
1721 @@ -144,7 +144,7 @@ char *argv[];
1722 else
1723 {
1724 printf("\nEnter name of database file to extract entries from: ");
1725 - gets(infile);
1726 + fgets(infile, FNAMELEN, stdin);
1727 }
1728 if ( (fin=fopen(infile, "r")) == NULL)
1729 {