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Code Issues Releases Activity

- Fix certain mistakes in FreeBSD patches

Browse Source 
- 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)
This commit is contained in:
Johann Visagie 2002-03-22 08:23:22 +00:00
parent cbde27d2e2
commit 5e52a21fed
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=56444
8 changed files with 320 additions and 70 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
biology/clustalw/Makefile
View File

@ -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

63
biology/clustalw/files/patch-ac
View File

@ -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);
}

138
biology/clustalw/files/patch-ae Normal file
View File

@ -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

11
biology/clustalw/files/patch-af Normal file
View File

@ -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);

128
biology/clustalw/files/patch-ag Normal file
View File

@ -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);
}

11
biology/clustalw/files/patch-ah Normal file
View File

@ -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;

11
biology/clustalw/files/patch-ai Normal file
View File

@ -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);
}

27
biology/clustalw/files/patch-ad → biology/clustalw/files/patch-aj
View File

@ -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");