Attachment #130982 for bug #175014

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# Created by: ballen
# Date created:        July 17, 2009
# Whom:                ballen
#
# $FreeBSD: head/biology/phyml/Makefile 308268 2012-12-04 20:28:16Z zi $
#

PORTNAME=	phyml
PORTVERSION=	20121109
CATEGORIES=	biology
MASTER_SITES=	GOOGLE_CODE
DISTNAME=	${PORTNAME}-20120412
DIST_SUBDIR=	${PORTNAME}

PATCH_SITES=	${MASTER_SITES}
PATCHFILES=	${PORTVERSION}.patch
PATCH_DIST_STRIP=	-p4

MAINTAINER=	ports@FreeBSD.org
COMMENT=	Simple, fast, and accurate algorithm to estimate large phylogenies

LICENSE=	GPLv2
GNU_CONFIGURE=	yes
PLIST_FILES=	bin/phyml
USE_AUTOTOOLS=	automake aclocal
AUTOMAKE_ARGS=	--add-missing

PATCH_WRKSRC=	${WRKSRC}/src

USE_AUTOTOOLS=	aclocal autoheader automake autoconf
AUTOMAKE_ARGS=	--add-missing
MAKE_JOBS_SAFE=	yes

PLIST_FILES=	bin/phyml

post-patch:
	@${REINPLACE_CMD} -e \
		'/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \
		 s|-O2 -msse|$${CFLAGS}|' ${WRKSRC}/configure.ac

.include <bsd.port.mk>

Lines 1-2 Link Here

(-)biology/phyml/distinfo (-2 / +4 lines)
1	SHA256 (phyml_20090706.tar.gz) = b39fa8ba2bc3a6566f3463c77db0d8992f71a71af353be539d0916173785d4bd	1	SHA256 (phyml/phyml-20120412.tar.gz) = a43e51534a1ae2d1ee4c94ced3a1855813ff4872a6c9c2b83b369ddb71198417
2	SIZE (phyml_20090706.tar.gz) = 818229	2	SIZE (phyml/phyml-20120412.tar.gz) = 4089133
		3	SHA256 (phyml/20121109.patch) = 3aa8bebd0ff78a553795ddda512ef1c7542d1e3c90c1da61c7125c304f6caa2c
		4	SIZE (phyml/20121109.patch) = 11016

Lines 1-11 Link Here

(-)biology/phyml/files/patch-src-configure (-11 lines)
1	--- configure.orig 2009-07-20 16:01:12.000000000 -0400
2	+++ configure 2009-07-20 16:02:03.000000000 -0400
3	@@ -5491,8 +5491,6 @@
4	esac
5	# End of cross-compilation macros
6
7	-CFLAGS+=" -O3 -fomit-frame-pointer -funroll-loops -Wall"
8	-
9	ac_config_files="$ac_config_files Makefile"
10
11	cat >confcache <<\_ACEOF

Lines 1-11 Link Here

(-)biology/phyml/files/patch-src-configure.ac (-11 lines)
1	--- configure.ac.orig 2009-07-17 14:57:39.000000000 -0600
2	+++ configure.ac 2009-07-17 14:57:55.000000000 -0600
3	@@ -58,8 +58,6 @@
4	esac
5	# End of cross-compilation macros
6
7	-CFLAGS+=" -O3 -fomit-frame-pointer -funroll-loops -Wall"
8	-
9	AC_CONFIG_FILES([Makefile])
10	AC_OUTPUT
11

Return to bug 175014

Lines 1-31 Link Here

(-)biology/phyml/Makefile (-19 / +21 lines)
1	# New ports collection makefile for: phyml 3.0 20090706	1	# Created by: ballen
2	# Date created: July 17, 2009
3	# Whom: ballen
4	#
5	# $FreeBSD: head/biology/phyml/Makefile 308268 2012-12-04 20:28:16Z zi $	2	# $FreeBSD: head/biology/phyml/Makefile 308268 2012-12-04 20:28:16Z zi $
6	#
7		3
8	PORTNAME= phyml	4	PORTNAME= phyml
9	PORTVERSION= 20090706	5	PORTVERSION= 20121109
10	CATEGORIES= biology	6	CATEGORIES= biology
11	MASTER_SITES= GOOGLE_CODE	7	MASTER_SITES= GOOGLE_CODE
12	DISTNAME= phyml_20090706	8	DISTNAME= ${PORTNAME}-20120412
		9	DIST_SUBDIR= ${PORTNAME}
		10
		11	PATCH_SITES= ${MASTER_SITES}
		12	PATCHFILES= ${PORTVERSION}.patch
		13	PATCH_DIST_STRIP= -p4
13		14
14	MAINTAINER= ports@FreeBSD.org	15	MAINTAINER= ports@FreeBSD.org
15	COMMENT= A simple, fast, and accurate algorithm to estimate large phylogenies	16	COMMENT= Simple, fast, and accurate algorithm to estimate large phylogenies
16		17
17	WRKSRC= ${WRKDIR}/${PORTNAME}/src	18	LICENSE= GPLv2
18	GNU_CONFIGURE= yes
19	PLIST_FILES= bin/phyml
20	USE_AUTOTOOLS= automake aclocal
21	AUTOMAKE_ARGS= --add-missing
22		19
23	.include <bsd.port.pre.mk>	20	PATCH_WRKSRC= ${WRKSRC}/src
24		21
25	pre-configure:	22	USE_AUTOTOOLS= aclocal autoheader automake autoconf
26	${RM} ${WRKSRC}/missing	23	AUTOMAKE_ARGS= --add-missing
		24	MAKE_JOBS_SAFE= yes
		25
		26	PLIST_FILES= bin/phyml
27		27
28	pre-install:	28	post-patch:
29	${CHMOD} a+x ${WRKSRC}/install-sh	29	@${REINPLACE_CMD} -e \
		30	'/^AC_INIT/s\|,esyscmd.*,\|,[${PORTVERSION}],\| ; \
		31	s\|-O2 -msse\|$${CFLAGS}\|' ${WRKSRC}/configure.ac
30		32
31	.include <bsd.port.post.mk>	33	.include <bsd.port.mk>