Index: biology/fasttree/Makefile =================================================================== --- biology/fasttree/Makefile +++ biology/fasttree/Makefile @@ -2,8 +2,7 @@ # $FreeBSD$ PORTNAME= FastTree -PORTVERSION= 2.1.8 -PORTREVISION= 3 +PORTVERSION= 2.1.10 CATEGORIES= biology MASTER_SITES= http://www.microbesonline.org/fasttree/ EXTRACT_SUFX= .c @@ -11,18 +10,18 @@ MAINTAINER= bacon4000@gmail.com 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 +CFLAGS+= -DOPENMP -fopenmp -finline-functions -funroll-loops LDFLAGS+= -lm +NO_WRKSUBDIR= yes PLIST_FILES= bin/FastTree do-extract: - ${MKDIR} ${WRKSRC} - ${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} + @${CP} ${DISTDIR}/${DISTFILES} ${WRKSRC} do-build: cd ${WRKSRC} && ${CC} ${CFLAGS} -o FastTree ${DISTFILES} ${LDFLAGS} Index: biology/fasttree/distinfo =================================================================== --- biology/fasttree/distinfo +++ biology/fasttree/distinfo @@ -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 Index: biology/fasttree/files/patch-FastTree-2.1.10.c =================================================================== --- /dev/null +++ biology/fasttree/files/patch-FastTree-2.1.10.c @@ -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);