Date: Thu, 18 Jan 2024 18:29:37 GMT From: Muhammad Moinur Rahman <bofh@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: b4b8e400d39b - main - biology/seqio: Remove expired port Message-ID: <202401181829.40IITb1e083965@gitrepo.freebsd.org>
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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
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