Index: head/biology/recombine/Makefile =================================================================== --- head/biology/recombine/Makefile (revision 510706) +++ head/biology/recombine/Makefile (revision 510707) @@ -1,33 +1,34 @@ # Created by: Johann Visagie # $FreeBSD$ PORTNAME= recombine PORTVERSION= 1.41 +PORTREVISION= 1 CATEGORIES= biology MASTER_SITES= http://evolution.gs.washington.edu/lamarc/recombine/ DISTNAME= ${PORTNAME}${PORTVERSION}.src.doc MAINTAINER= ports@FreeBSD.org COMMENT= Program to fit population models across sites USES= shebangfix WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION} ALL_TARGET= ${PORTNAME} PLIST_FILES+= bin/filetran bin/recombine PORTDOCS= recombine.txt SHEBANG_FILES= filetran 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 Index: head/biology/recombine/files/patch-recombine.c =================================================================== --- head/biology/recombine/files/patch-recombine.c (nonexistent) +++ head/biology/recombine/files/patch-recombine.c (revision 510707) @@ -0,0 +1,168 @@ +--- 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) { Property changes on: head/biology/recombine/files/patch-recombine.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property