Date: Thu, 18 Jan 2024 21:23:23 GMT From: Rene Ladan <rene@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 2f8680e1b808 - main - biology/recombine: Remove expired port Message-ID: <202401182123.40ILNNWS085735@gitrepo.freebsd.org>
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The branch main has been updated by rene: URL: https://cgit.FreeBSD.org/ports/commit/?id=2f8680e1b80827df5127b2d653f4dcf8433a1fb5 commit 2f8680e1b80827df5127b2d653f4dcf8433a1fb5 Author: Rene Ladan <rene@FreeBSD.org> AuthorDate: 2024-01-18 21:22:35 +0000 Commit: Rene Ladan <rene@FreeBSD.org> CommitDate: 2024-01-18 21:23:16 +0000 biology/recombine: Remove expired port 2024-01-17 biology/recombine: Upstream advises to use biology/lamarc --- MOVED | 1 + biology/Makefile | 1 - biology/recombine/Makefile | 36 ------- biology/recombine/distinfo | 2 - biology/recombine/files/patch-Makefile | 53 ---------- biology/recombine/files/patch-recombine.c | 168 ------------------------------ biology/recombine/pkg-descr | 8 -- 7 files changed, 1 insertion(+), 268 deletions(-) diff --git a/MOVED b/MOVED index ac4bbae4b4a9..d68eab257514 100644 --- a/MOVED +++ b/MOVED @@ -2956,3 +2956,4 @@ 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 x11-wm/tvtwm||2024-01-18|Has expired: Upstream last release was in 2001 reconsider using vtwm x11-wm/treewm||2024-01-18|Has expired: Last upstream release was in 2003 +biology/recombine|biology/lamarc|2024-01-18|Has expired: Upstream advises to use biology/lamarc diff --git a/biology/Makefile b/biology/Makefile index 05251e1264c7..d6c0b3985e4a 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -202,7 +202,6 @@ SUBDIR += rainbow SUBDIR += rampler SUBDIR += readseq - SUBDIR += recombine SUBDIR += rna-seq SUBDIR += ruby-bio SUBDIR += rubygem-bio diff --git a/biology/recombine/Makefile b/biology/recombine/Makefile deleted file mode 100644 index abaa7dbf8217..000000000000 --- a/biology/recombine/Makefile +++ /dev/null @@ -1,36 +0,0 @@ -PORTNAME= recombine -PORTVERSION= 1.41 -PORTREVISION= 2 -CATEGORIES= biology -MASTER_SITES= https://lamarcweb.github.io/lamarcweb/recombine/ -DISTNAME= ${PORTNAME}${PORTVERSION}.src.doc - -MAINTAINER= ports@FreeBSD.org -COMMENT= Program to fit population models across sites -WWW= https://lamarcweb.github.io/lamarcweb/recombine/ - -DEPRECATED= Upstream advises to use biology/lamarc -EXPIRATION_DATE= 2024-01-17 - -USES= shebangfix - -SHEBANG_FILES= filetran - -ALL_TARGET= ${PORTNAME} - -WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} - -PLIST_FILES+= bin/filetran bin/recombine -PORTDOCS= recombine.txt - -OPTIONS_DEFINE= DOCS - -do-install: - ${INSTALL_PROGRAM} ${WRKSRC}/${PORTNAME} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_SCRIPT} ${WRKSRC}/filetran ${STAGEDIR}${PREFIX}/bin - -post-install-DOCS-on: - @${MKDIR} ${STAGEDIR}${DOCSDIR} - ${INSTALL_DATA} ${WRKSRC}/recombine.txt ${STAGEDIR}${DOCSDIR} - -.include <bsd.port.mk> diff --git a/biology/recombine/distinfo b/biology/recombine/distinfo deleted file mode 100644 index 86e57ab91e32..000000000000 --- a/biology/recombine/distinfo +++ /dev/null @@ -1,2 +0,0 @@ -SHA256 (recombine1.41.src.doc.tar.gz) = e247810ef31414f500f9c118b6462b549c761562140519f7c57f305fcb284643 -SIZE (recombine1.41.src.doc.tar.gz) = 149129 diff --git a/biology/recombine/files/patch-Makefile b/biology/recombine/files/patch-Makefile deleted file mode 100644 index 338b70873c8c..000000000000 --- a/biology/recombine/files/patch-Makefile +++ /dev/null @@ -1,53 +0,0 @@ ---- Makefile.orig Thu Jan 25 13:59:21 2007 -+++ Makefile Thu Jan 25 14:02:58 2007 -@@ -1,11 +1,6 @@ - LIBS = -lm - BINDIR = ./bin --#CFLAGS = -Wall -Wshadow -g --CFLAGS = -O -Wall -Wshadow -g --#CFLAGS = -fast -inline speed --#CFLAGS = -O3 -arch host -fast --CC = gcc $(CFLAGS) --#CC = cc $(CFLAGS) -+CFLAGS += -g - DCC = gcc -g -Wall -DDMALLOC_FUNC_CHECK -ansi -pedantic - PLUSCC = g++ $(CFLAGS) - LIBS = -lm -L/usr/local/lib -@@ -18,29 +13,29 @@ - # The big banana - recombine : recombine.o jdrop.o rec_modellike.o jworld.o getdata.o \ - traitlike.o getmsatdata.o -- $(CC) -o recombine recombine.o jdrop.o rec_modellike.o \ -+ $(CC) $(CFLAGS) -o recombine recombine.o jdrop.o rec_modellike.o \ - jworld.o getdata.o traitlike.o getmsatdata.o $(LIBS) - - jworld.o : jworld.c -- $(CC) -c jworld.c -+ $(CC) $(CFLAGS) -c jworld.c - - jdrop.o : jdrop.c -- $(CC) -c jdrop.c -+ $(CC) $(CFLAGS) -c jdrop.c - - rec_modellike.o : rec_modellike.c -- $(CC) -c rec_modellike.c -+ $(CC) $(CFLAGS) -c rec_modellike.c - - recombine.o : recombine.c -- $(CC) -c recombine.c -+ $(CC) $(CFLAGS) -c recombine.c - - getdata.o : getdata.c -- $(CC) -c getdata.c -+ $(CC) $(CFLAGS) -c getdata.c - - getmsatdata.o : getmsatdata.c -- $(CC) -c getmsatdata.c -+ $(CC) $(CFLAGS) -c getmsatdata.c - - traitlike.o : traitlike.c -- $(CC) -c traitlike.c -+ $(CC) $(CFLAGS) -c traitlike.c - - rectreedna : rectreedna.c - $(CC) -o rectreedna rectreedna.c $(LIBS) diff --git a/biology/recombine/files/patch-recombine.c b/biology/recombine/files/patch-recombine.c deleted file mode 100644 index bfaa37f653ca..000000000000 --- a/biology/recombine/files/patch-recombine.c +++ /dev/null @@ -1,168 +0,0 @@ ---- recombine.c.orig 2019-08-03 09:14:33 UTC -+++ recombine.c -@@ -169,7 +169,7 @@ void openfile(FILE **fp, char *filename, - file[0] = '\0'; - while (file[0] =='\0'){ - fprintf(stdout,"Please enter a new filename>"); -- gets(file); -+ fgets(file,100,stdin); - } - break; - case 'w': -@@ -177,7 +177,7 @@ void openfile(FILE **fp, char *filename, - file[0] = '\0'; - while (file[0] =='\0'){ - fprintf(stdout,"Please enter a new filename>"); -- gets(file); -+ fgets(file,100,stdin); - } - break; - } -@@ -1864,28 +1864,28 @@ if (strchr("#FLAHONESPGUMVRTD",ch) != NU - case 'R': - do { - printf("Relative mutation rate of trait?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->mutrait = atof(input); - } while (op->mutrait <= 0.0); - break; - case 'T': - do { - printf("Ratio of forward to back trait mutation?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->traitratio = atof(input); - } while (op->traitratio <= 0.0); - break; - case 'D': - do { - printf("Frequency of trait?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->pd = atof(input); - } while (op->pd <= 0.0 || op->pd >= 1.0); - break; - case 'A': - do { - printf("Number of drops while resimulating (0-2)?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->hapdrop = atol(input); - } while (op->hapdrop != 0 && op->hapdrop != 1 && op->hapdrop != 2); - default: -@@ -1972,7 +1972,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - case 'T': - do { - printf("Transition/transversion ratio?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - locus_ttratio = atof(input); - if (locus_ttratio < 0.5) - printf("TTratio cannot be less than 0.5\n"); -@@ -1991,13 +1991,13 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - op->panel = !op->panel; - if (op->panel) { - printf("Number of populations?\n"); -- gets(input); -+ ; - *numpop = atol(input); - op->numpanel = (long *)calloc(*numpop,sizeof(long)); - for(i = 0; i < *numpop; i++) { - printf("Number of panel haplotypes for population"); - printf(" %ld?\n",i+1); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->numpanel[i] = atol(input); - } - } else -@@ -2012,7 +2012,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - if (op->ctgry) { - do { - printf("Number of categories ?"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->categs = atoi(input); - } while (op->categs < 1); - free(op->rate); -@@ -2091,7 +2091,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - if (!op->watt) { - do { - printf("Initial theta estimate?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - theta0 = atof(input); - } while (theta0 <= 0.0); - } -@@ -2099,7 +2099,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - case 'Z': - printf("What recombination rate?\n"); - do { -- gets(input); -+ fgets(input,LINESIZE,stdin); - rec0 = atof(input); - if (rec0 < 0.0) - printf("recombination rate must be non-negative\n"); -@@ -2108,7 +2108,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - case 'S': - do { - printf("How many Short Chains?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->numchains[0] = atoi(input); - if (op->numchains[0] < 0) - printf("Must be non-negative\n"); -@@ -2118,7 +2118,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - done = FALSE; - while (!done) { - printf("How often to sample trees?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->increm[0] = atoi(input); - if (op->increm[0] > 0) done = TRUE; - else printf("Must be a positive integer\n"); -@@ -2128,7 +2128,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - done = FALSE; - while (!done) { - printf("How many short steps?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->steps[0] = atoi(input); - if (op->steps[0] > 0) done = TRUE; - else printf("Must be a positive integer\n"); -@@ -2137,7 +2137,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - case 'L': - do { - printf("How many Long Chains?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->numchains[1] = atoi(input); - if (op->numchains[1] < 1) - printf("Must be a positive integer\n"); -@@ -2147,7 +2147,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - done = FALSE; - while (!done) { - printf("How often to sample trees?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->increm[1] = atoi(input); - if (op->increm[1] > 0) done = TRUE; - else printf("Must be a positive integer\n"); -@@ -2157,7 +2157,7 @@ if(strchr("#NQPDITFCRVHWZS12L34AB",ch) ! - done = FALSE; - while (!done) { - printf("How many long steps?\n"); -- gets(input); -+ fgets(input,LINESIZE,stdin); - op->steps[1] = atoi(input); - if (op->steps[1] > 0) done = TRUE; - else printf("Must be a positive integer\n"); -@@ -2239,7 +2239,7 @@ do { - if (menu1) print_startmenu(op,writeout); - else {print_datamenu(op); print_searchmenu(op);} - print_menuend(); -- gets(input); -+ fgets(input,LINESIZE,stdin); - ch = toupper((int)input[0]); - done = (ch == 'Y'); - if (!done) { diff --git a/biology/recombine/pkg-descr b/biology/recombine/pkg-descr deleted file mode 100644 index 1db8a11e46fb..000000000000 --- a/biology/recombine/pkg-descr +++ /dev/null @@ -1,8 +0,0 @@ -Recombine fits a model which has a single population of constant size with a -single recombination rate across all sites. It can accomodate either plain -DNA or RNA data or SNP (single nucleotide polymorphism) data. - -Recombine forms part of the Lamarc (Likelihood Analysis with Metropolis -Algorithm using Random Coalescence) suite. See: - - http://evolution.genetics.washington.edu/lamarc.html
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