biology/recombine: Remove expired port

2024-01-17 biology/recombine: Upstream advises to use biology/lamarc

7 files changed, 1 insertions, 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