* Update to 3.13.

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

* Also honor CC/CFLAGS.

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}

biology/paml/distinfo

@@ -1 +1 @@
-MD5 (paml3.1.tar.Z) = dbf2b5a61a373518e5d27b837aec9df7
+MD5 (paml3.13.tar.gz) = a08ebd57332c9fe605439bf0025817bd

biology/paml/files/patch-src::Makefile

@@ -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 #

biology/paml/pkg-comment

@@ -1 +0,0 @@
-Phylogenetic Analysis by Maximum Likelihood (PAML)

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