Date: Tue, 5 Dec 2017 03:03:38 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r455562 - in head/biology/fasttree: . files Message-ID: <201712050303.vB533cHO052848@repo.freebsd.org>
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Author: jwb Date: Tue Dec 5 03:03:38 2017 New Revision: 455562 URL: https://svnweb.freebsd.org/changeset/ports/455562 Log: biology/fasttree: update to version 2.1.10 Approved by: jrm Differential Revision: https://reviews.freebsd.org/D8187 Added: head/biology/fasttree/files/ head/biology/fasttree/files/Makefile (contents, props changed) head/biology/fasttree/files/patch-FastTree-2.1.10.c (contents, props changed) Modified: head/biology/fasttree/Makefile head/biology/fasttree/distinfo (contents, props changed) Modified: head/biology/fasttree/Makefile ============================================================================== --- head/biology/fasttree/Makefile Tue Dec 5 02:59:01 2017 (r455561) +++ head/biology/fasttree/Makefile Tue Dec 5 03:03:38 2017 (r455562) @@ -1,34 +1,23 @@ -# Created by: Jason Bacon <bacon4000@gmail.com> # $FreeBSD$ PORTNAME= FastTree -PORTVERSION= 2.1.8 -PORTREVISION= 3 +DISTVERSION= 2.1.10 CATEGORIES= biology MASTER_SITES= http://www.microbesonline.org/fasttree/ EXTRACT_SUFX= .c -MAINTAINER= bacon4000@gmail.com +MAINTAINER= jwb@FreeBSD.org COMMENT= Approximately-maximum-likelihood phylogenetic trees from alignments -# LICENSE= unspecified open source +LICENSE= GPLv2+ USES= compiler:openmp -CFLAGS+= -DOPENMP -fopenmp -O3 -finline-functions -funroll-loops -LDFLAGS+= -lm - +NO_WRKSUBDIR= yes PLIST_FILES= bin/FastTree do-extract: - ${MKDIR} ${WRKSRC} - ${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} - -do-build: - cd ${WRKSRC} && ${CC} ${CFLAGS} -o FastTree ${DISTFILES} ${LDFLAGS} - -do-install: - ${MKDIR} ${STAGEDIR}${PREFIX}/bin - ${INSTALL_PROGRAM} ${WRKSRC}/FastTree ${STAGEDIR}${PREFIX}/bin + @${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} + @${CP} ${FILESDIR}/Makefile ${WRKSRC} .include <bsd.port.mk> Modified: head/biology/fasttree/distinfo ============================================================================== --- head/biology/fasttree/distinfo Tue Dec 5 02:59:01 2017 (r455561) +++ head/biology/fasttree/distinfo Tue Dec 5 03:03:38 2017 (r455562) @@ -1,2 +1,3 @@ -SHA256 (FastTree-2.1.8.c) = b172d160f1b12b764d21a6937c3ce01ba42fa8743d95e083e031c6947762f837 -SIZE (FastTree-2.1.8.c) = 385231 +TIMESTAMP = 1512317739 +SHA256 (FastTree-2.1.10.c) = 54cb89fc1728a974a59eae7a7ee6309cdd3cddda9a4c55b700a71219fc6e926d +SIZE (FastTree-2.1.10.c) = 390916 Added: head/biology/fasttree/files/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fasttree/files/Makefile Tue Dec 5 03:03:38 2017 (r455562) @@ -0,0 +1,25 @@ + +BIN = FastTree +SRC = FastTree*.c +CC ?= gcc +CFLAGS ?= -O3 +CFLAGS += -DOPENMP -fopenmp -finline-functions -funroll-loops + +MKDIR ?= mkdir +INSTALL ?= install +PREFIX ?= /usr/local +DESTDIR ?= . + +.PHONY: all install clean + +all: ${BIN} + +${BIN}: ${SRC} Makefile + ${CC} ${CFLAGS} ${SRC} -o ${BIN} -lm + +install: ${BIN} + ${MKDIR} -p ${DESTDIR}${PREFIX}/bin + ${INSTALL} -s -c ${BIN} ${DESTDIR}${PREFIX}/bin + +clean: + ${RM} -f ${BIN} Added: head/biology/fasttree/files/patch-FastTree-2.1.10.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/fasttree/files/patch-FastTree-2.1.10.c Tue Dec 5 03:03:38 2017 (r455562) @@ -0,0 +1,11 @@ +--- FastTree-2.1.10.c.orig 2017-12-04 15:09:11 UTC ++++ FastTree-2.1.10.c +@@ -8759,7 +8759,7 @@ double pnorm(double x) + + void *mymalloc(size_t sz) { + if (sz == 0) return(NULL); +- void *new = malloc(sz); ++ void *new = aligned_alloc(16, sz); + if (new == NULL) { + fprintf(stderr, "Out of memory\n"); + exit(1);
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