update to 3.03

PR:		26094
Submitted by:	    maintainer

biology/paml/Makefile

@@ -6,15 +6,15 @@
 #
 
 PORTNAME=	paml
-PORTVERSION=	3.01
+PORTVERSION=	3.03
 CATEGORIES=	biology
 MASTER_SITES=	ftp://abacus.gene.ucl.ac.uk/pub/paml/
-DISTNAME=	paml3.0a
+DISTNAME=	paml3.0c
 EXTRACT_SUFX=	.tar.Z
 
 MAINTAINER=	dbader@eece.unm.edu
 
-NO_WRKSUBDIR=	yes
+WRKSRC=		${WRKDIR}/${DISTNAME}/src
 
 BINARIES=	baseml basemlg chi2 codeml codemlsites evolver mcmctree \
 		pamp yn00
@@ -25,7 +25,7 @@ do-install:
 .endfor
 .if !defined(NOPORTDOCS)
 		${MKDIR} ${PREFIX}/share/doc/${PORTNAME}
-		${INSTALL_DATA} ${WRKSRC}/pamlDOC.pdf \
+		${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/pamlDOC.pdf \
 			${PREFIX}/share/doc/${PORTNAME}
 .endif
 

biology/paml/distinfo

@@ -1 +1 @@
-MD5 (paml3.0a.tar.Z) = 53ce654a8173407a3db278d106deb115
+MD5 (paml3.0c.tar.Z) = cfff48036c3e2520967f32c7626e21f3

biology/paml/files/patch-aa

@@ -1,11 +0,0 @@
---- Makefile.orig	Sun Mar 12 20:49:36 2000
-+++ Makefile	Fri Jul  7 06:32:33 2000
-@@ -1,7 +1,7 @@
- PRGS =  baseml codeml codemlsites basemlg pamp evolver mcmctree yn00 chi2 
- CC = cc # cc, gcc, cl
- 
--CFLAGS = -fast
-+CFLAGS += -O3
- 
- #CFLAGS = -w0 -warnprotos -newc -std -fast
- #CFLAGS = -g -w0 -warnprotos -newc -std -edit1 #

biology/paml/files/patch-ab

@@ -1,11 +0,0 @@
---- evolver.c-orig	Thu Jun 15 14:42:52 2000
-+++ evolver.c	Fri Jul  7 06:40:09 2000
-@@ -63,7 +63,7 @@
- static double Qfactor=-1, Qrates[5];  /* Qrates[] hold kappa's for nucleotides */
- 
- 
--void main(int argc, char*argv[])
-+main(int argc, char*argv[])
- {
-    char *MCctlf=NULL, outf[]="evolver.out";
-    int i, option=6, ntree=1,rooted, BD=0;