- 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)

8 files changed, 320 insertions, 70 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index 384f12477c37..3645df9e280f 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 9ac14ac11427..fc4431f3b68f 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 000000000000..b9e3678ea31b
--- /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 000000000000..102413fb84c6
--- /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 000000000000..9cde8d9d019d
--- /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 000000000000..e16d4f3b28d9
--- /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 000000000000..a228ed5b1eb4
--- /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 da64accff072..d5881bdb2c03 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");