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Index: head/biology/fasttree/Makefile
===================================================================
--- head/biology/fasttree/Makefile
+++ head/biology/fasttree/Makefile
@@ -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>
Index: head/biology/fasttree/distinfo
===================================================================
--- head/biology/fasttree/distinfo
+++ head/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: head/biology/fasttree/files/Makefile
===================================================================
--- head/biology/fasttree/files/Makefile
+++ head/biology/fasttree/files/Makefile
@@ -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}
Index: head/biology/fasttree/files/patch-FastTree-2.1.10.c
===================================================================
--- head/biology/fasttree/files/patch-FastTree-2.1.10.c
+++ head/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);

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