- Update to version 3.1

PR:		30176
Submitted by:	David A. Bader <dbader@eece.unm.edu> (MAINTAINER)

biology/paml/Makefile

@@ -6,10 +6,10 @@
 #
 
 PORTNAME=	paml
-PORTVERSION=	3.04
+PORTVERSION=	3.1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://abacus.gene.ucl.ac.uk/pub/paml/
-DISTNAME=	paml3.0d
+DISTNAME=	paml3.1
 EXTRACT_SUFX=	.tar.Z
 
 MAINTAINER=	dbader@eece.unm.edu
@@ -24,9 +24,9 @@ do-install:
 		${INSTALL_PROGRAM} ${WRKSRC}/${f} ${PREFIX}/bin
 .endfor
 .if !defined(NOPORTDOCS)
-		${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
+		${MKDIR} ${DOCSDIR}
 		${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/pamlDOC.pdf \
-			${PREFIX}/share/doc/${PORTNAME}
+			${DOCSDIR}
 .endif
 
 .include <bsd.port.mk>

biology/paml/distinfo

@@ -1 +1 @@
-MD5 (paml3.0d.tar.Z) = a4c7b9d6dc2137ff080b5da816412936
+MD5 (paml3.1.tar.Z) = dbf2b5a61a373518e5d27b837aec9df7

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

@@ -0,0 +1,12 @@
+--- 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-plist

@@ -1,6 +1,6 @@
 bin/baseml
 bin/basemlg
-bin/chi2 
+bin/chi2
 bin/codeml
 bin/codemlsites
 bin/evolver