4 files changed, 25 insertions, 43 deletions

diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile
index 1b10af986ab1..7114588ea85d 100644
--- a/biology/phyml/Makefile
+++ b/biology/phyml/Makefile
@@ -1,31 +1,33 @@
-# New ports collection makefile for:   phyml 3.0 20090706
-# Date created:        July 17, 2009
-# Whom:                ballen
-#
+# Created by: ballen
 # $FreeBSD$
-#
 
 PORTNAME=	phyml
-PORTVERSION=	20090706
+PORTVERSION=	20121109
 CATEGORIES=	biology
 MASTER_SITES=	GOOGLE_CODE
-DISTNAME=	phyml_20090706
+DISTNAME=	${PORTNAME}-20120412
+DIST_SUBDIR=	${PORTNAME}
+
+PATCH_SITES=	${MASTER_SITES}
+PATCHFILES=	${PORTVERSION}.patch
+PATCH_DIST_STRIP=	-p4
 
 MAINTAINER=	ports@FreeBSD.org
-COMMENT=	A simple, fast, and accurate algorithm to estimate large phylogenies
+COMMENT=	Simple, fast, and accurate algorithm to estimate large phylogenies
 
-WRKSRC=		${WRKDIR}/${PORTNAME}/src
-GNU_CONFIGURE=	yes
-PLIST_FILES=	bin/phyml
-USE_AUTOTOOLS=	automake aclocal
-AUTOMAKE_ARGS=	--add-missing
+LICENSE=	GPLv2
 
-.include <bsd.port.pre.mk>
+PATCH_WRKSRC=	${WRKSRC}/src
 
-pre-configure:
-	${RM} ${WRKSRC}/missing
+USE_AUTOTOOLS=	aclocal autoheader automake autoconf
+AUTOMAKE_ARGS=	--add-missing
+MAKE_JOBS_SAFE=	yes
+
+PLIST_FILES=	bin/phyml
 
-pre-install:
-	${CHMOD} a+x ${WRKSRC}/install-sh
+post-patch:
+	@${REINPLACE_CMD} -e \
+		'/^AC_INIT/s|,esyscmd.*,|,[${PORTVERSION}],| ; \
+		 s|-O2 -msse|$${CFLAGS}|' ${WRKSRC}/configure.ac
 
-.include <bsd.port.post.mk>
+.include <bsd.port.mk>
diff --git a/biology/phyml/distinfo b/biology/phyml/distinfo
index f0cee8c7e8a3..c588175155a7 100644
--- a/biology/phyml/distinfo
+++ b/biology/phyml/distinfo
@@ -1,2 +1,4 @@
-SHA256 (phyml_20090706.tar.gz) = b39fa8ba2bc3a6566f3463c77db0d8992f71a71af353be539d0916173785d4bd
-SIZE (phyml_20090706.tar.gz) = 818229
+SHA256 (phyml/phyml-20120412.tar.gz) = a43e51534a1ae2d1ee4c94ced3a1855813ff4872a6c9c2b83b369ddb71198417
+SIZE (phyml/phyml-20120412.tar.gz) = 4089133
+SHA256 (phyml/20121109.patch) = 3aa8bebd0ff78a553795ddda512ef1c7542d1e3c90c1da61c7125c304f6caa2c
+SIZE (phyml/20121109.patch) = 11016
diff --git a/biology/phyml/files/patch-src-configure b/biology/phyml/files/patch-src-configure
deleted file mode 100644
index dbd05af4a45a..000000000000
--- a/biology/phyml/files/patch-src-configure
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.orig	2009-07-20 16:01:12.000000000 -0400
-+++ configure	2009-07-20 16:02:03.000000000 -0400
-@@ -5491,8 +5491,6 @@
- esac
- # End of cross-compilation macros
- 
--CFLAGS+=" -O3 -fomit-frame-pointer -funroll-loops -Wall"
--
- ac_config_files="$ac_config_files Makefile"
- 
- cat >confcache <<\_ACEOF
diff --git a/biology/phyml/files/patch-src-configure.ac b/biology/phyml/files/patch-src-configure.ac
deleted file mode 100644
index da1f2449db83..000000000000
--- a/biology/phyml/files/patch-src-configure.ac
+++ /dev/null
@@ -1,11 +0,0 @@
---- configure.ac.orig	2009-07-17 14:57:39.000000000 -0600
-+++ configure.ac	2009-07-17 14:57:55.000000000 -0600
-@@ -58,8 +58,6 @@
- esac
- # End of cross-compilation macros
- 
--CFLAGS+=" -O3 -fomit-frame-pointer -funroll-loops -Wall"
--
- AC_CONFIG_FILES([Makefile])
- AC_OUTPUT
-