diff options
author | wjv <wjv@FreeBSD.org> | 2002-03-22 08:23:22 +0000 |
---|---|---|
committer | wjv <wjv@FreeBSD.org> | 2002-03-22 08:23:22 +0000 |
commit | 7542d349081472430a1443d418b049b6a1924b4f (patch) | |
tree | 914d072ea4270724cae0adcc36df013b2797b5a0 /biology/clustalw | |
parent | 13c9d007a603e99e77d2d94c6813bab97443c21f (diff) | |
download | FreeBSD-ports-7542d349081472430a1443d418b049b6a1924b4f.zip FreeBSD-ports-7542d349081472430a1443d418b049b6a1924b4f.tar.gz |
- Fix certain mistakes in FreeBSD patches
- Bump PORTREVISION
- Poroblem originally reported by Fernan Aguero <fernan@iib.unsam.edu.ar> on
FreeBSD-bio list
PR: 36169
Submitted by: David A. Bader <dbader@eece.unm.edu> (MAINTAINER)
Diffstat (limited to 'biology/clustalw')
-rw-r--r-- | biology/clustalw/Makefile | 1 | ||||
-rw-r--r-- | biology/clustalw/files/patch-ac | 63 | ||||
-rw-r--r-- | biology/clustalw/files/patch-ae | 138 | ||||
-rw-r--r-- | biology/clustalw/files/patch-af | 11 | ||||
-rw-r--r-- | biology/clustalw/files/patch-ag | 128 | ||||
-rw-r--r-- | biology/clustalw/files/patch-ah | 11 | ||||
-rw-r--r-- | biology/clustalw/files/patch-ai | 11 | ||||
-rw-r--r-- | biology/clustalw/files/patch-aj (renamed from biology/clustalw/files/patch-ad) | 27 |
8 files changed, 320 insertions, 70 deletions
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index 384f124..3645df9 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -7,6 +7,7 @@ PORTNAME= clustalw PORTVERSION= 1.82 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ DISTNAME= ${PORTNAME}${PORTVERSION}.UNIX diff --git a/biology/clustalw/files/patch-ac b/biology/clustalw/files/patch-ac index 9ac14ac..fc4431f 100644 --- a/biology/clustalw/files/patch-ac +++ b/biology/clustalw/files/patch-ac @@ -9,66 +9,3 @@ lf=(sint)strlen(fname); deb=path1; -@@ -2121,7 +2121,7 @@ - strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != EOS) strcpy(file_name,temp); - } - } -@@ -2129,7 +2129,7 @@ - strcpy(local_prompt,prompt); - strcat(local_prompt," [%s]: "); - fprintf(stdout,local_prompt,file_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != EOS) strcpy(file_name,temp); - } - -@@ -2335,7 +2335,7 @@ - if (usemenu) - fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(phylip_name,tree_name); - use_tree = TRUE; -@@ -2567,7 +2567,7 @@ - - fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", - phylip_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != EOS) - strcpy(phylip_name,temp); - } -@@ -2676,7 +2676,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(p1_tree_name,tree_name); - use_tree1 = TRUE; -@@ -2702,7 +2702,7 @@ - #endif - fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", - tree_name); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != 'n' && *temp != 'N') { - strcpy(p2_tree_name,tree_name); - use_tree2 = TRUE; -@@ -3730,7 +3730,7 @@ - if(usemenu) { - fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", - parname); -- gets(temp); -+ fgets(temp,sizeof(temp),stdin); - if(*temp != EOS) - strcpy(parname,temp); - } diff --git a/biology/clustalw/files/patch-ae b/biology/clustalw/files/patch-ae new file mode 100644 index 0000000..b9e3678 --- /dev/null +++ b/biology/clustalw/files/patch-ae @@ -0,0 +1,138 @@ +--- amenu.c-orig Tue Feb 6 03:15:01 2001 ++++ amenu.c Thu Mar 21 10:19:02 2002 +@@ -13,7 +13,8 @@ + static jmp_buf jmpbuf; + #ifndef VMS + #ifndef AIX +-#define BADSIG (void (*)())-1 ++/* #define BADSIG (void (*)())-1 */ ++#define BADSIG SIG_ERR + #endif + #endif + +@@ -176,7 +177,7 @@ + fprintf(stdout," H. HELP\n"); + fprintf(stdout," X. EXIT (leave program)\n\n\n"); + +- getstr("Your choice",lin1); ++ getstr("Your choice",lin1,MAXLINE); + + switch(toupper(*lin1)) { + case '1': seq_input(FALSE); +@@ -260,7 +261,7 @@ + fprintf(stdout," H. HELP\n"); + fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); + +- getstr("Your choice",lin1); ++ getstr("Your choice",lin1,MAXLINE); + if(*lin1 == EOS) return; + + switch(toupper(*lin1)) +@@ -353,7 +354,7 @@ + fprintf(stdout," H. HELP\n"); + fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); + +- getstr("Your choice",lin1); ++ getstr("Your choice",lin1,MAXLINE); + if(*lin1 == EOS) return; + + switch(toupper(*lin1)) +@@ -449,7 +450,7 @@ + fprintf(stdout,"\n\n"); + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + if( *lin2 == EOS) { + return; + } +@@ -525,7 +526,7 @@ + fprintf(stdout,"--\n"); + + +- getstr("\n\nEnter number (or [RETURN] to exit)",lin2); ++ getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE); + if(*lin2 == EOS) return(output_struct_penalties); + + switch(toupper(*lin2)) +@@ -594,7 +595,7 @@ + fprintf(stdout," H. HELP\n"); + fprintf(stdout," or press [RETURN] to go back to main menu\n\n\n"); + +- getstr("Your choice",lin1); ++ getstr("Your choice",lin1,MAXLINE); + if(*lin1 == EOS) return; + + switch(toupper(*lin1)) +@@ -669,7 +670,7 @@ + fprintf(stdout,"\n"); + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + if(*lin2 == EOS) return; + + switch(toupper(*lin2)) { +@@ -752,7 +753,7 @@ + fprintf(stdout,"\n"); + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + if(*lin2 == EOS) return; + + switch(toupper(*lin2)) { +@@ -886,7 +887,7 @@ + + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + if( *lin2 == EOS) { + if(dnaflag) { + dna_pw_go_penalty = pw_go_penalty; +@@ -1008,7 +1009,7 @@ + fprintf(stdout," 8. Protein Gap Parameters\n\n"); + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + + if(*lin2 == EOS) { + if(dnaflag) { +@@ -1101,7 +1102,7 @@ + fprintf(stdout," 5. Toggle End Gap Separation :%s\n\n",(!use_endgaps) ? "OFF" : "ON"); + fprintf(stdout," H. HELP\n\n\n"); + +- getstr("Enter number (or [RETURN] to exit)",lin2); ++ getstr("Enter number (or [RETURN] to exit)",lin2,MAXLINE); + + if(*lin2 == EOS) return; + +@@ -1115,7 +1116,7 @@ + case '3': + fprintf(stdout,"Hydrophilic Residues Currently: %s\n",hyd_residues); + +- getstr("Enter residues (or [RETURN] to quit)",lin1); ++ getstr("Enter residues (or [RETURN] to quit)",lin1,MAXLINE); + if (*lin1 != EOS) { + for (i=0;i<strlen(hyd_residues) && i<26;i++) { + c = lin1[i]; +@@ -1167,7 +1168,7 @@ + fprintf(stdout,"--\n"); + + +- getstr("\n\nEnter number (or [RETURN] to exit)",lin2); ++ getstr("\n\nEnter number (or [RETURN] to exit)",lin2,MAXLINE); + if(*lin2 == EOS) return(matn); + + i=toupper(*lin2)-'0'; +@@ -1202,7 +1203,7 @@ + fprintf(stdout,"\n%s\n",title); + strcpy(line,prompt); + strcat(line, "(y/n) ? [y]"); +- getstr(line,lin2); ++ getstr(line,lin2,80); + if ((*lin2 != 'n') && (*lin2 != 'N')) + return('y'); + else diff --git a/biology/clustalw/files/patch-af b/biology/clustalw/files/patch-af new file mode 100644 index 0000000..102413f --- /dev/null +++ b/biology/clustalw/files/patch-af @@ -0,0 +1,11 @@ +--- clustalw.h-orig Thu Mar 21 10:15:28 2002 ++++ clustalw.h Thu Mar 21 10:15:43 2002 +@@ -234,7 +234,7 @@ + char *blank_to_(char *str); + char *upstr(char *str); + char *lowstr(char *str); +-void getstr(char *instr, char *outstr); ++void getstr(char *instr, char *outstr, int len); + double getreal(char *instr, double minx, double maxx, double def); + int getint(char *instr, int minx, int maxx, int def); + void do_system(void); diff --git a/biology/clustalw/files/patch-ag b/biology/clustalw/files/patch-ag new file mode 100644 index 0000000..9cde8d9 --- /dev/null +++ b/biology/clustalw/files/patch-ag @@ -0,0 +1,128 @@ +--- interface.c-orig Thu Mar 21 10:19:26 2002 ++++ interface.c Thu Mar 21 10:22:18 2002 +@@ -1170,7 +1170,7 @@ + if(strstr(temp, help_marker)){ + if(usemenu) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + fclose(help_file); + return; +@@ -1182,7 +1182,7 @@ + if(usemenu) { + if(nlines >= PAGE_LEN) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue or X to stop",lin2); ++ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); + if(toupper(*lin2) == 'X') { + fclose(help_file); + return; +@@ -1194,7 +1194,7 @@ + } + if(usemenu) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + fclose(help_file); + } +@@ -1232,7 +1232,7 @@ + ++nlines; + if(nlines >= PAGE_LEN) { + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue or X to stop",lin2); ++ getstr("Press [RETURN] to continue or X to stop",lin2,MAXLINE); + if(toupper(*lin2) == 'X') { + fclose(file); + return; +@@ -1243,7 +1243,7 @@ + } + fclose(file); + fprintf(stdout,"\n"); +- getstr("Press [RETURN] to continue",lin2); ++ getstr("Press [RETURN] to continue",lin2,MAXLINE); + } + + +@@ -1692,7 +1692,7 @@ + FILE *infile; + + if(usemenu) +- getstr("Enter name of the matrix file",lin2); ++ getstr("Enter name of the matrix file",lin2,MAXLINE); + else + strcpy(lin2,str); + +@@ -1718,7 +1718,7 @@ + FILE *infile; + + if(usemenu) +- getstr("Enter name of the matrix file",lin2); ++ getstr("Enter name of the matrix file",lin2,MAXLINE); + else + strcpy(lin2,str); + +@@ -2121,7 +2121,7 @@ + strcpy(local_prompt,"\n\nEnter new name to avoid overwriting "); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + } +@@ -2129,7 +2129,7 @@ + strcpy(local_prompt,prompt); + strcat(local_prompt," [%s]: "); + fprintf(stdout,local_prompt,file_name); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) strcpy(file_name,temp); + } + +@@ -2335,7 +2335,7 @@ + if (usemenu) + fprintf(stdout,"\nUse the existing GUIDE TREE file, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(phylip_name,tree_name); + use_tree = TRUE; +@@ -2567,7 +2567,7 @@ + + fprintf(stdout,"\nEnter a name for the guide tree file [%s]: ", + phylip_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != EOS) + strcpy(phylip_name,temp); + } +@@ -2676,7 +2676,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 1, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p1_tree_name,tree_name); + use_tree1 = TRUE; +@@ -2702,7 +2702,7 @@ + #endif + fprintf(stdout,"\nUse the existing GUIDE TREE file for Profile 2, %s (y/n) ? [y]: ", + tree_name); +- gets(temp); ++ fgets(temp,MAXLINE,stdin); + if(*temp != 'n' && *temp != 'N') { + strcpy(p2_tree_name,tree_name); + use_tree2 = TRUE; +@@ -3730,7 +3730,7 @@ + if(usemenu) { + fprintf(stdout,"\nEnter a name for the parameter output file [%s]: ", + parname); +- gets(temp); ++ fgets(temp,FILENAMELEN+1,stdin); + if(*temp != EOS) + strcpy(parname,temp); + } diff --git a/biology/clustalw/files/patch-ah b/biology/clustalw/files/patch-ah new file mode 100644 index 0000000..e16d4f3 --- /dev/null +++ b/biology/clustalw/files/patch-ah @@ -0,0 +1,11 @@ +--- sequence.c-orig Thu Mar 21 10:22:35 2002 ++++ sequence.c Thu Mar 21 10:22:53 2002 +@@ -922,7 +922,7 @@ + static Boolean dnaflag1; + + if(usemenu) +- getstr("Enter the name of the sequence file",line); ++ getstr("Enter the name of the sequence file",line,FILENAMELEN+1); + else + strcpy(line,seqname); + if(*line == EOS) return -1; diff --git a/biology/clustalw/files/patch-ai b/biology/clustalw/files/patch-ai new file mode 100644 index 0000000..a228ed5 --- /dev/null +++ b/biology/clustalw/files/patch-ai @@ -0,0 +1,11 @@ +--- trees.c-orig Thu Mar 21 10:23:04 2002 ++++ trees.c Thu Mar 21 10:23:20 2002 +@@ -845,7 +845,7 @@ + fprintf(stdout,"\n or 3) use the PHYLIP package."); + fprintf(stdout,"\n\n"); + if (usemenu) +- getstr("Press [RETURN] to continue",dummy); ++ getstr("Press [RETURN] to continue",dummy,10); + } + + diff --git a/biology/clustalw/files/patch-ad b/biology/clustalw/files/patch-aj index da64acc..d5881bd 100644 --- a/biology/clustalw/files/patch-ad +++ b/biology/clustalw/files/patch-aj @@ -1,11 +1,15 @@ ---- util.c.orig Wed Jun 7 16:50:08 2000 -+++ util.c Tue Aug 8 02:59:43 2000 -@@ -174,7 +174,7 @@ - void getstr(char *instr,char *outstr) +--- util.c-orig Thu Mar 21 10:15:59 2002 ++++ util.c Thu Mar 21 10:17:11 2002 +@@ -171,10 +171,10 @@ + return str; + } + +-void getstr(char *instr,char *outstr) ++void getstr(char *instr,char *outstr, int len) { fprintf(stdout,"%s: ",instr); - gets(outstr); -+ fgets(outstr,sizeof(outstr),stdin); ++ fgets(outstr, len, stdin); } double getreal(char *instr,double minx,double maxx,double def) @@ -14,7 +18,7 @@ while(TRUE) { fprintf(stdout,"%s (%.1f-%.1f) [%.1f]: ",instr,minx,maxx,def); - gets(line); -+ fgets(line,sizeof(line),stdin); ++ fgets(line, MAXLINE, stdin); status=sscanf(line,"%f",&ret); if(status == EOF) return def; if(ret>maxx) { @@ -23,7 +27,16 @@ fprintf(stdout,"%s (%d..%d) [%d]: ", instr,(pint)minx,(pint)maxx,(pint)def); - gets(line); -+ fgets(line,sizeof(line),stdin); ++ fgets(line, MAXLINE, stdin); status=sscanf(line,"%d",&ret); if(status == EOF) return def; if(ret>maxx) { +@@ -230,7 +230,7 @@ + { + char line[MAXLINE]; + +- getstr("\n\nEnter system command",line); ++ getstr("\n\nEnter system command",line,MAXLINE); + if(*line != EOS) + system(line); + fprintf(stdout,"\n\n"); |