git: b4b8e400d39b - main - biology/seqio: Remove expired port
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Date: Thu, 18 Jan 2024 18:29:37 UTC
The branch main has been updated by bofh:
URL: https://cgit.FreeBSD.org/ports/commit/?id=b4b8e400d39bb1f67fc6c70400e6536b9f34e940
commit b4b8e400d39bb1f67fc6c70400e6536b9f34e940
Author: Muhammad Moinur Rahman <bofh@FreeBSD.org>
AuthorDate: 2024-01-18 18:28:10 +0000
Commit: Muhammad Moinur Rahman <bofh@FreeBSD.org>
CommitDate: 2024-01-18 18:29:14 +0000
biology/seqio: Remove expired port
2024-01-17 biology/seqio: Upstream last release was in 2000
---
MOVED | 1 +
biology/Makefile | 1 -
biology/seqio/Makefile | 40 ----------
biology/seqio/distinfo | 2 -
biology/seqio/files/patch-Makefile | 17 ----
biology/seqio/files/patch-fmtseq | 117 ----------------------------
biology/seqio/files/patch-grepseq | 155 -------------------------------------
biology/seqio/files/patch-seqio | 18 -----
biology/seqio/pkg-descr | 4 -
9 files changed, 1 insertion(+), 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