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biology/recombine: Remove expired port

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2024-01-17 biology/recombine: Upstream advises to use biology/lamarc
This commit is contained in:
Rene Ladan 2024-01-18 22:22:35 +01:00
parent 3071b6e5ec
commit 2f8680e1b8
7 changed files with 1 additions and 268 deletions
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1
MOVED
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@ -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

1
biology/Makefile
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@ -202,7 +202,6 @@
SUBDIR += rainbow
SUBDIR += rampler
SUBDIR += readseq
SUBDIR += recombine
SUBDIR += rna-seq
SUBDIR += ruby-bio
SUBDIR += rubygem-bio

36
biology/recombine/Makefile
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@ -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>

2
biology/recombine/distinfo
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@ -1,2 +0,0 @@
SHA256 (recombine1.41.src.doc.tar.gz) = e247810ef31414f500f9c118b6462b549c761562140519f7c57f305fcb284643
SIZE (recombine1.41.src.doc.tar.gz) = 149129

53
biology/recombine/files/patch-Makefile
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@ -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)

168
biology/recombine/files/patch-recombine.c
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@ -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) {

8
biology/recombine/pkg-descr
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@ -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