git: 2f8680e1b808 - main - biology/recombine: Remove expired port
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Date: Thu, 18 Jan 2024 21:23:23 UTC
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