biology/seqio: Remove expired port

2024-01-17 biology/seqio: Upstream last release was in 2000

9 files changed, 1 insertions, 354 deletions

diff --git a/MOVED b/MOVED
index 955f1023c284..114a98ac9b58 100644
--- a/MOVED
+++ b/MOVED
@@ -2953,3 +2953,4 @@ editors/jove||2024-01-18|Has expired: No upstream update in last 23 years
 editors/impress||2024-01-18|Has expired: Upstream last release was in 2000
 biology/sim4||2024-01-18|Has expired: Upstream last update was in 2005
 x11-wm/w9wm||2024-01-18|Has expired: Last upstream release was in 2002
+biology/seqio||2024-01-18|Has expired: Upstream last release was in 2000
diff --git a/biology/Makefile b/biology/Makefile
index 447996cf7556..05251e1264c7 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -218,7 +218,6 @@
     SUBDIR += seqan-apps
     SUBDIR += seqan1
     SUBDIR += seqan3
-    SUBDIR += seqio
     SUBDIR += seqkit
     SUBDIR += seqtk
     SUBDIR += seqwish
diff --git a/biology/seqio/Makefile b/biology/seqio/Makefile
deleted file mode 100644
index a4684dcc41c9..000000000000
--- a/biology/seqio/Makefile
+++ /dev/null
@@ -1,40 +0,0 @@
-PORTNAME=	seqio
-PORTVERSION=	1.2.2
-PORTREVISION=	1
-CATEGORIES=	biology
-MASTER_SITES=	http://www.cs.ucdavis.edu/~gusfield/
-DISTNAME=	${PORTNAME}
-
-MAINTAINER=	ports@FreeBSD.org
-COMMENT=	Set of C functions which can read/write biological sequence files
-WWW=		https://www.cs.ucdavis.edu/~gusfield/seqio.html
-
-DEPRECATED=	Upstream last release was in 2000
-EXPIRATION_DATE=	2024-01-17
-
-WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
-
-PLIST_FILES=	${PROGRAMS:S,^,bin/,}
-PORTDOCS=	*
-PORTEXAMPLES=	*
-
-EXAMPLES=	example1.c example2.c example3.c example4.c seqio.c \
-		seqio.h Makefile
-PROGRAMS=	fmtseq grepseq idxseq typeseq wcseq
-
-OPTIONS_DEFINE=	DOCS EXAMPLES
-
-do-install:
-	${INSTALL_PROGRAM} ${PROGRAMS:S,^,${WRKSRC}/,} ${STAGEDIR}${PREFIX}/bin
-
-do-install-DOCS-on:
-	@${MKDIR} ${STAGEDIR}${DOCSDIR}/html
-	${INSTALL_DATA} ${WRKSRC}/bioseq.txt ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/doc/*.doc ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/html/*.html ${STAGEDIR}${DOCSDIR}/html
-
-do-install-EXAMPLES-on:
-	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
-	${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/,} ${STAGEDIR}${EXAMPLESDIR}
-
-.include <bsd.port.mk>
diff --git a/biology/seqio/distinfo b/biology/seqio/distinfo
deleted file mode 100644
index 61533e1ee08a..000000000000
--- a/biology/seqio/distinfo
+++ /dev/null
@@ -1,2 +0,0 @@
-SHA256 (seqio.tar.gz) = 0c1f8a55adeb900c749d1412aaa86b85ff3043b2db2dda3b884c101ea5e5d1fb
-SIZE (seqio.tar.gz) = 360714
diff --git a/biology/seqio/files/patch-Makefile b/biology/seqio/files/patch-Makefile
deleted file mode 100644
index 865b0c0f884c..000000000000
--- a/biology/seqio/files/patch-Makefile
+++ /dev/null
@@ -1,17 +0,0 @@
---- Makefile.orig	Tue Jul  9 20:20:42 1996
-+++ Makefile	Wed Oct 22 16:43:02 2003
-@@ -8,11 +8,10 @@
- # just set the CC value to your compiler and make sure optimization
- # is turned on (it significantly affects the running time).
- #
--CC=gcc
--CFLAGS= -g -O2 -Wall -Wshadow
-+CC?=cc
-+CFLAGS?=-O -pipe
- 
--
--all: grepseq fmtseq idxseq typeseq wcseq examples
-+all: grepseq fmtseq idxseq typeseq wcseq
- 
- grepseq: grepseq.o seqio.o
- 	$(CC) $(CFLAGS) -o grepseq grepseq.o seqio.o
diff --git a/biology/seqio/files/patch-fmtseq b/biology/seqio/files/patch-fmtseq
deleted file mode 100644
index a11d0218d513..000000000000
--- a/biology/seqio/files/patch-fmtseq
+++ /dev/null
@@ -1,117 +0,0 @@
---- fmtseq.c.orig	Wed Jul 10 12:58:39 1996
-+++ fmtseq.c	Tue Aug 21 13:17:23 2001
-@@ -37,7 +37,6 @@
- #include <sys/stat.h>
- #include "seqio.h"
- 
--extern char *sys_errlist[];
- 
- 
- #ifdef WIN32
-@@ -70,6 +69,7 @@
- #define ASK 2
- #define ITEMLIST 3
- 
-+#define	MAXLINE	128
- 
- int pretty_flag, pretty_count;
- FILE *fpout;
-@@ -81,7 +81,7 @@
- } pretty;
- 
- 
--char dna_complement[128], rna_complement[128];
-+char dna_complement[MAXLINE], rna_complement[MAXLINE];
- 
- 
- /*
-@@ -222,7 +222,7 @@
- void print_options(int flag)
- {
-   int i, j;
--  char line[128];
-+  char line[MAXLINE];
- 
-   printf("Program Options (text in [...] is optional):\n");
-   printf("  -al[l]            select all sequences\n");
-@@ -249,7 +249,7 @@
- 
-   if (flag) {
-     printf("More? ");
--    gets(line);
-+    fgets(line,MAXLINE-1,stdin);
-     if (line[0] == 'q' || line[0] == 'Q')
-       return;
-   }
-@@ -264,7 +264,7 @@
- 
-   if (flag) {
-     printf("More? ");
--    gets(line);
-+    fgets(line,MAXLINE-1,stdin);
-     if (line[0] == 'q' || line[0] == 'Q')
-       return;
-   }
-@@ -1646,7 +1646,7 @@
-     s = line;
-     while (*s == '\0') {
-       printf("Enter: ");
--      gets(line);
-+      fgets(line,MAXLINE-1,stdin);
-       for (s=line; *s && isspace(*s); s++) ;
-     }
-     printf("----------------------\n\n");
-@@ -1701,7 +1701,7 @@
- {
-   static char defch = 'y';
-   int init_print, count;
--  char *s, *entry, *eptr, line[128];
-+  char *s, *entry, *eptr, line[MAXLINE];
- 
-   putchar('\n');
-   if (seqcount == 1) {
-@@ -1717,7 +1717,7 @@
-   eptr = entry = NULL;
-   while (1) {
-     printf("Select? [%c] ", defch);
--    gets(line);
-+    fgets(line,MAXLINE-1,stdin);
- 
-     if (line[0] == '\0')
-       line[0] = defch;
-@@ -1771,7 +1771,7 @@
-                    SEQINFO *info, int mode)
- {
-   int len;
--  char *temp, tempbuffer[128];
-+  char *temp, tempbuffer[MAXLINE];
- 
-   if (buf != NULL)
-     temp = buf;
-@@ -1803,7 +1803,7 @@
- 
- int pretty_store(char *seq, int seqlen, SEQINFO *info)
- {
--  char buffer[128];
-+  char buffer[MAXLINE];
- 
-   if (pretty_count == psize) {
-     if (psize == 0) {
-@@ -2582,7 +2582,7 @@
- 
- void blastout_store(SEQFILE *sfp, char *seq, int seqlen, SEQINFO *info)
- {
--  static otherstrand = 0;
-+  static int otherstrand = 0;
-   int pos, al_start, ingap, len;
-   char *s, *t1, *entry, *end, *line1, *line2;
-   ALIGN newalign;
-@@ -3017,7 +3017,7 @@
- {
-   int i;
- 
--  for (i=0; i < 128; i++)
-+  for (i=0; i < MAXLINE; i++)
-     dna_complement[i] = dna_complement[i] = i;
- 
-   dna_complement['a'] = 't';  dna_complement['A'] = 'T';
diff --git a/biology/seqio/files/patch-grepseq b/biology/seqio/files/patch-grepseq
deleted file mode 100644
index a501901e0b47..000000000000
--- a/biology/seqio/files/patch-grepseq
+++ /dev/null
@@ -1,155 +0,0 @@
---- grepseq.c.orig	Sat Aug 18 16:19:15 2001
-+++ grepseq.c	Sat Aug 18 16:37:58 2001
-@@ -18,7 +18,6 @@
- #include <string.h>
- #include "seqio.h"
- 
--extern char *sys_errlist[];
- 
- #define ASCII 4
- 
-@@ -475,7 +474,7 @@
-         ascii_alpha_mask[num] |= mask;
-       }
-       else
--        ascii_alpha_mask[*s] |= mask;
-+        ascii_alpha_mask[(int) *s] |= mask;
-       break;
-       
-     case '.':
-@@ -518,7 +517,7 @@
-             ascii_alpha_mask[num] |= mask;
-           }
-           else
--            ascii_alpha_mask[*s] |= mask;
-+            ascii_alpha_mask[(int) *s] |= mask;
-         }
-         else {
-           if (dna_flag) {
-@@ -526,17 +525,17 @@
-               dna_flag = 0;
-             else
-               for ( ; *t; t++)
--                dna_alpha_mask[*t] |= mask;
-+                dna_alpha_mask[(int) *t] |= mask;
-           }
-           if (prt_flag) {
-             if ((t = prt_expand(*s)) == NULL)
-               prt_flag = 0;
-             else
-               for ( ; *t; t++)
--                prt_alpha_mask[*t] |= mask;
-+                prt_alpha_mask[(int) *t] |= mask;
-           }
-               
--          ascii_alpha_mask[*s] |= mask;
-+          ascii_alpha_mask[(int) *s] |= mask;
-         }
-       }
-         
-@@ -557,17 +556,17 @@
-           dna_flag = 0;
-         else
-           for ( ; *t; t++)
--            dna_alpha_mask[*t] |= mask;
-+            dna_alpha_mask[(int) *t] |= mask;
-       }
-       if (prt_flag) {
-         if ((t = prt_expand(*s)) == NULL)
-           prt_flag = 0;
-         else
-           for ( ; *t; t++)
--            prt_alpha_mask[*t] |= mask;
-+            prt_alpha_mask[(int) *t] |= mask;
-       }
-               
--      ascii_alpha_mask[*s] |= mask;
-+      ascii_alpha_mask[(int) *s] |= mask;
-     }
- 
-     /*
-@@ -677,16 +676,16 @@
-      */
-     if (num_errors == 0) {
-       score = 0;
--      while ((ch = *s) && table[ch] &&
--             !((masklist0 = ((masklist0 << 1) & alpha_mask[*s]) + 1) &
-+      while ((ch = *s) && table[(int) ch] &&
-+             !((masklist0 = ((masklist0 << 1) & alpha_mask[(int) *s]) + 1) &
-                accept_mask))
-         s++;
-     }
-     else if (num_errors == 1) {
-       score = -1;
-       if (misonly_flag) {
--        while ((ch = *s) && table[ch]) {
--          chmask = alpha_mask[ch];
-+        while ((ch = *s) && table[(int) ch]) {
-+          chmask = alpha_mask[(int) ch];
-           last_mask = masklist0;
-           masklist0 = ((masklist0 << 1) & chmask) + 1;
-           masklist1 = ((masklist1 << 1) & chmask) | (last_mask << 1);
-@@ -703,8 +702,8 @@
-         }
-       }
-       else {
--        while ((ch = *s) && table[ch]) {
--          chmask = alpha_mask[ch];
-+        while ((ch = *s) && table[(int) ch]) {
-+          chmask = alpha_mask[(int) ch];
-           last_mask = masklist0;
-           masklist0 = ((masklist0 << 1) & chmask) + 1;
-           masklist1 = ((masklist1 << 1) & chmask) |  /* match */
-@@ -727,8 +726,8 @@
-     else if (num_errors == 2) {
-       score = -1;
-       if (misonly_flag) {
--        while ((ch = *s) && table[ch]) {
--          chmask = alpha_mask[ch];
-+        while ((ch = *s) && table[(int) ch]) {
-+          chmask = alpha_mask[(int) ch];
-           last_mask = masklist0;
-           masklist0 = ((masklist0 << 1) & chmask) + 1;
-           newmask = ((masklist1 << 1) & chmask) | (last_mask << 1);
-@@ -752,8 +751,8 @@
-         }
-       }
-       else {
--        while ((ch = *s) && table[ch]) {
--          chmask = alpha_mask[ch];
-+        while ((ch = *s) && table[(int) ch]) {
-+          chmask = alpha_mask[(int) ch];
-           last_mask = masklist0;
-           masklist0 = ((masklist0 << 1) & chmask) + 1;
-           newmask = ((masklist1 << 1) & chmask) |  /* match */
-@@ -785,8 +784,8 @@
-     }
-     else if (misonly_flag) {
-       score = -1;
--      while ((ch = *s) && table[ch]) {
--        chmask = alpha_mask[ch];
-+      while ((ch = *s) && table[(int) ch]) {
-+        chmask = alpha_mask[(int) ch];
- 
-         last_mask = masklist[0];
-         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
-@@ -808,8 +807,8 @@
-     }
-     else {
-       score = -1;
--      while ((ch = *s) && table[ch]) {
--        chmask = alpha_mask[ch];
-+      while ((ch = *s) && table[(int) ch]) {
-+        chmask = alpha_mask[(int) ch];
- 
-         last_mask = masklist[0];
-         masklist[0] = ((masklist[0] << 1) & chmask) + 1;
-@@ -835,7 +834,7 @@
-       
-     if (!ch)
-       break;
--    else if (!table[ch]) {
-+    else if (!table[(int) ch]) {
-       fprintf(stderr, "%s, entry %d:  Sequence contains invalid characters.\n",
-               seqffilename(sfp, 0), seqfentryno(sfp));
-       return NULL;
diff --git a/biology/seqio/files/patch-seqio b/biology/seqio/files/patch-seqio
deleted file mode 100644
index 3e637ebacbc5..000000000000
--- a/biology/seqio/files/patch-seqio
+++ /dev/null
@@ -1,18 +0,0 @@
---- seqio.c.orig	Sat Aug 18 16:20:53 2001
-+++ seqio.c	Sat Aug 18 16:21:23 2001
-@@ -147,7 +147,6 @@
-  * files, and replacement functions for system calls that don't exist on
-  * one or more machines.
-  */
--extern char *sys_errlist[];
- 
- #if defined(__sun) && !defined(FILENAME_MAX)
- #include <sys/param.h>
-@@ -158,7 +157,6 @@
- static int ctype_initflag = 0;
- static char tubuf[384], *tuary;
- 
--#define toupper(chr) tuary[(int) (chr)]
- 
- static void init_ctype(void)
- {
diff --git a/biology/seqio/pkg-descr b/biology/seqio/pkg-descr
deleted file mode 100644
index 8e0d717f3793..000000000000
--- a/biology/seqio/pkg-descr
+++ /dev/null
@@ -1,4 +0,0 @@
-"The SEQIO package is a set of C functions which can read and write
-biological sequence files formatted using various file formats and which
-can be used to perform database searches on biological databases."
-- from the README file