gets() considered harmful. What is this, 1985? Fixes the build on OpenBSD.

3 files changed, 139 insertions, 2 deletions

diff --git a/biology/coalesce/Makefile b/biology/coalesce/Makefile
index 65a021570bf..413f03c19e6 100644
--- a/biology/coalesce/Makefile
+++ b/biology/coalesce/Makefile
@@ -1,8 +1,9 @@
-# $NetBSD: Makefile,v 1.9 2012/09/11 20:32:11 asau Exp $
+# $NetBSD: Makefile,v 1.10 2015/11/07 21:06:37 dholland Exp $
 #
 
 DISTNAME=	coalesce1.5b
 PKGNAME=	coalesce-1.5.0.2
+PKGREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	http://evolution.genetics.washington.edu/lamarc/coalesce/
 
diff --git a/biology/coalesce/distinfo b/biology/coalesce/distinfo
index b67e600e130..8abd9445f63 100644
--- a/biology/coalesce/distinfo
+++ b/biology/coalesce/distinfo
@@ -1,7 +1,8 @@
-$NetBSD: distinfo,v 1.3 2015/11/02 18:42:21 agc Exp $
+$NetBSD: distinfo,v 1.4 2015/11/07 21:06:37 dholland Exp $
 
 SHA1 (coalesce1.5b.tar.gz) = ec2a13da25474440a0c57b2a2e634c94db30961e
 RMD160 (coalesce1.5b.tar.gz) = 199a0f219413ea67feea98a6864f43373d3955bc
 SHA512 (coalesce1.5b.tar.gz) = fc91001cb5f5678ff0ad095a7e1ff8a14a848db1d05c86ee8440238fff50eb5df12f4ec9e6ee2c46ec38d9f9a668294e6390ebd9386400670d50896d021afd0c
 Size (coalesce1.5b.tar.gz) = 46153 bytes
 SHA1 (patch-aa) = b4c3afcb563c54d4b16f20f8b4b9fc649b49deee
+SHA1 (patch-coalesce.c) = 6ecd1f41134c42235c2a85aa0fd2dbdaf1a0f6d2
diff --git a/biology/coalesce/patches/patch-coalesce.c b/biology/coalesce/patches/patch-coalesce.c
new file mode 100644
index 00000000000..30beb7caf53
--- /dev/null
+++ b/biology/coalesce/patches/patch-coalesce.c
@@ -0,0 +1,135 @@
+$NetBSD: patch-coalesce.c,v 1.1 2015/11/07 21:06:37 dholland Exp $
+
+gets() considered harmful.
+
+--- coalesce.c~	1996-02-29 16:00:09.000000000 +0000
++++ coalesce.c
+@@ -70,6 +70,20 @@ void readparmfile()
+ boolean		accept_slide;
+ long		slid, slacc, indecks, chaintype;
+ 
++static void dogets(char *buf, size_t max)
++{
++   size_t len;
++
++   if (!fgets(buf, max, stdin)) {
++      *buf = '\0';
++      return;
++   }
++   len = strlen(buf);
++   if (len > 0 && buf[len-1] == '\n') {
++      buf[len-1] = '\0';
++   }
++}
++
+ void openfile(FILE **fp, char *filename, char *mode, char *application,
+    char *perm)
+ {
+@@ -88,7 +102,7 @@ void openfile(FILE **fp, char *filename,
+         file[0] = '\0';
+         while (file[0] =='\0'){
+           fprintf(stdout,"Please enter a new filename>");
+-          gets(file);
++          dogets(file, sizeof(file));
+           }
+         break;
+       case 'w':
+@@ -96,7 +110,7 @@ void openfile(FILE **fp, char *filename,
+         file[0] = '\0';
+         while (file[0] =='\0'){
+           fprintf(stdout,"Please enter a new filename>");
+-          gets(file);
++          dogets(file, sizeof(file));
+           }
+         break;
+       }
+@@ -775,7 +789,7 @@ void getoptions()
+     }
+     printf("\n");
+     printf("Are these settings correct? (type Y or the letter for one to change)\n");
+-    gets(input);
++    dogets(input, sizeof(input));
+     ch = input[0];
+     ch = toupper(ch);
+     done = (ch == 'Y');
+@@ -787,7 +801,7 @@ void getoptions()
+ 	case 'S':
+ 	  do {
+ 	    printf("How many Short Chains?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             chains[0] = atoi(input);
+ 	    if (chains[0] < 0)
+ 	      printf("Must be non-negative\n");
+@@ -797,7 +811,7 @@ void getoptions()
+ 	case 'L':
+ 	  do {
+ 	    printf("How many Long Chains?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             chains[1] = atoi(input);
+ 	    if (chains[1] < 0)
+ 	      printf("Must be non-negative\n");
+@@ -811,7 +825,7 @@ void getoptions()
+ 	  if (ctgry) {
+ 	    do {
+ 	      printf("Number of categories ?");
+-              gets(input);
++              dogets(input, sizeof(input));
+               categs = atoi(input);
+ 	    } while (categs < 1);
+ 	    free(rate);
+@@ -869,7 +883,7 @@ void getoptions()
+ 	case 'T':
+ 	  do {
+ 	    printf("Transition/transversion ratio?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             locus_ttratio = atof(input);
+ 	  } while (locus_ttratio < 0.0);
+ 	  break;
+@@ -883,7 +897,7 @@ void getoptions()
+ 	  if (!watt) {
+ 	    do {
+ 	      printf("Initial theta estimate?\n");
+-              gets(input);
++              dogets(input, sizeof(input));
+               theta0 = atof(input);
+ 	    } while (theta0 <= 0.0);
+ 	  }
+@@ -909,7 +923,7 @@ void getoptions()
+ 	  done1 = false;
+ 	  while (!done1) {
+ 	    printf("How often to sample trees?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             increm[0] = atoi(input);
+ 	    if (increm[0] > 0)
+ 	      done1 = true;
+@@ -922,7 +936,7 @@ void getoptions()
+ 	  done1 = false;
+ 	  while (!done1) {
+ 	    printf("How many short steps?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             steps[0] = atoi(input);
+ 	    if (steps[0] > 0)
+ 	      done1 = true;
+@@ -935,7 +949,7 @@ void getoptions()
+ 	  done1 = false;
+ 	  while (!done1) {
+ 	    printf("How often to sample trees?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             increm[1] = atoi(input);
+ 	    if (increm[1] > 0)
+ 	      done1 = true;
+@@ -948,7 +962,7 @@ void getoptions()
+ 	  done1 = false;
+ 	  while (!done1) {
+ 	    printf("How many long steps?\n");
+-            gets(input);
++            dogets(input, sizeof(input));
+             steps[1] = atoi(input);
+ 	    if (steps[1] > 0)
+ 	      done1 = true;