From 5eb743da03f689719de8e5c5a65ada23b71766fc Mon Sep 17 00:00:00 2001
From: Christian Weisgerber <naddy@FreeBSD.org>
Date: Fri, 14 Feb 2003 23:21:23 +0000
Subject: [PATCH] * Update to 3.13.

PR:		48255
Submitted by:	David A. Bader <dbader@eece.unm.edu>

* Also honor CC/CFLAGS.
---
 biology/paml/Makefile                  | 10 +++++-----
 biology/paml/distinfo                  |  2 +-
 biology/paml/files/patch-src::Makefile | 12 ------------
 biology/paml/pkg-comment               |  1 -
 biology/paml/pkg-plist                 |  2 +-
 5 files changed, 7 insertions(+), 20 deletions(-)
 delete mode 100644 biology/paml/files/patch-src::Makefile
 delete mode 100644 biology/paml/pkg-comment

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 93d99e80f866..3a742742eaf8 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -6,18 +6,18 @@
 #
 
 PORTNAME=	paml
-PORTVERSION=	3.1
+PORTVERSION=	3.13
 CATEGORIES=	biology
 MASTER_SITES=	ftp://abacus.gene.ucl.ac.uk/pub/paml/
-DISTNAME=	paml3.1
-EXTRACT_SUFX=	.tar.Z
+DISTNAME=	${PORTNAME}${PORTVERSION}
 
 MAINTAINER=	dbader@eece.unm.edu
+COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
 
 WRKSRC=		${WRKDIR}/${DISTNAME}/src
+MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
 
-BINARIES=	baseml basemlg chi2 codeml codemlsites evolver mcmctree \
-		pamp yn00
+BINARIES=	baseml basemlg chi2 codeml evolver mcmctree pamp yn00
 
 do-install:
 .for f in ${BINARIES}
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index 1edfbcf51c88..acb906e15c1f 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1 +1 @@
-MD5 (paml3.1.tar.Z) = dbf2b5a61a373518e5d27b837aec9df7
+MD5 (paml3.13.tar.gz) = a08ebd57332c9fe605439bf0025817bd
diff --git a/biology/paml/files/patch-src::Makefile b/biology/paml/files/patch-src::Makefile
deleted file mode 100644
index 9c24749fda4b..000000000000
--- a/biology/paml/files/patch-src::Makefile
+++ /dev/null
@@ -1,12 +0,0 @@
---- Makefile.orig	Thu Jul 19 12:01:33 2001
-+++ Makefile	Tue Aug 28 19:07:55 2001
-@@ -1,7 +1,7 @@
- PRGS =  baseml codeml codemlsites basemlg pamp evolver mcmctree yn00 chi2 
--CC = cc # cc, gcc, cl
-+CC = gcc # cc, gcc, cl
- 
--CFLAGS = -fast -w
-+CFLAGS = -O2
- 
- #CFLAGS = -w0 -warnprotos -newc -std -fast
- #CFLAGS = -g -w0 -warnprotos -newc -std -edit1 #
diff --git a/biology/paml/pkg-comment b/biology/paml/pkg-comment
deleted file mode 100644
index 28176e9a1ed1..000000000000
--- a/biology/paml/pkg-comment
+++ /dev/null
@@ -1 +0,0 @@
-Phylogenetic Analysis by Maximum Likelihood (PAML)
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 17ee1e6cd87c..752da1f20a6d 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -1,8 +1,8 @@
+@comment $FreeBSD$
 bin/baseml
 bin/basemlg
 bin/chi2
 bin/codeml
-bin/codemlsites
 bin/evolver
 bin/mcmctree
 bin/pamp