From nobody@FreeBSD.org  Mon Jan 23 04:57:47 2006
Return-Path: <nobody@FreeBSD.org>
Received: from mx1.FreeBSD.org (mx1.freebsd.org [216.136.204.125])
	by hub.freebsd.org (Postfix) with ESMTP id 21A6516A41F
	for <freebsd-gnats-submit@FreeBSD.org>; Mon, 23 Jan 2006 04:57:47 +0000 (GMT)
	(envelope-from nobody@FreeBSD.org)
Received: from www.freebsd.org (www.freebsd.org [216.136.204.117])
	by mx1.FreeBSD.org (Postfix) with ESMTP id D64D443D45
	for <freebsd-gnats-submit@FreeBSD.org>; Mon, 23 Jan 2006 04:57:46 +0000 (GMT)
	(envelope-from nobody@FreeBSD.org)
Received: from www.freebsd.org (localhost [127.0.0.1])
	by www.freebsd.org (8.13.1/8.13.1) with ESMTP id k0N4vkNr062485
	for <freebsd-gnats-submit@FreeBSD.org>; Mon, 23 Jan 2006 04:57:46 GMT
	(envelope-from nobody@www.freebsd.org)
Received: (from nobody@localhost)
	by www.freebsd.org (8.13.1/8.13.1/Submit) id k0N4vkjo062484;
	Mon, 23 Jan 2006 04:57:46 GMT
	(envelope-from nobody)
Message-Id: <200601230457.k0N4vkjo062484@www.freebsd.org>
Date: Mon, 23 Jan 2006 04:57:46 GMT
From: "Choe, Cheng-Dae" <whitekid@gmail.com>
To: freebsd-gnats-submit@FreeBSD.org
Subject: update biology/phylip to 3.65
X-Send-Pr-Version: www-2.3

>Number:         92182
>Category:       ports
>Synopsis:       update biology/phylip to 3.65
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    lawrance
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Jan 23 05:00:19 GMT 2006
>Closed-Date:    Wed Feb 08 14:47:30 GMT 2006
>Last-Modified:  Wed Feb 08 14:47:30 GMT 2006
>Originator:     "Choe, Cheng-Dae"
>Release:        FreeBSD 6.0-STABLE i386
>Organization:
>Environment:
System: FreeBSD w.comdongin.com 6.0-STABLE FreeBSD 6.0-STABLE #1: Sat Jan 21 00:34:59 KST 2006 root@w.comdongin.com:/usr/obj/data/src/sys/CDI i386
>Description:
- update phylip to 3.65
- use Makefile's PORTDOCS variables
- install documents in post-install target
- installed files are not listed in Makefile(more flexible), find and installed with ${FIND} command
>How-To-Repeat:
              N/A
>Fix:
diff -ruN phylip.orig/Makefile phylip/Makefile
--- phylip.orig/Makefile	Fri Apr 22 21:08:12 2005
+++ phylip/Makefile	Mon Jan 23 11:19:33 2006
@@ -6,8 +6,7 @@
 #
 
 PORTNAME=	phylip
-PORTVERSION=	3.6
-PORTEPOCH=	1
+PORTVERSION=	3.65
 CATEGORIES=	biology
 MASTER_SITES=	ftp://evolution.genetics.washington.edu/pub/phylip/ \
 		http://bioinformatics.weizmann.ac.il/software/linkage_and_mapping/phylip/ \
@@ -17,6 +16,7 @@
 MAINTAINER=	dbader@ece.unm.edu
 COMMENT=	A Phylogeny Inference Package
 
+WRKSRC=		${WRKDIR}/${PORTNAME}${PORTVERSION}
 USE_XLIB=	yes
 BUILD_WRKSRC=	${WRKSRC}/src
 
@@ -24,36 +24,23 @@
 		DC="${CC} -DX -I${X11BASE}/include ${CFLAGS}" \
 		GLIBS="-L${X11BASE}/lib -lX11 -lm"
 
-BINARIES=	clique consense contml contrast dnacomp dnadist dnainvar \
-		dnaml dnamlk dnamove dnapars dnapenny dollop dolmove \
-		dolpenny drawgram drawtree factor fitch gendist kitsch \
-		mix move neighbor pars penny proml promlk protdist \
-		protpars restdist restml retree seqboot treedist
-DOCFILES=	clique.html consense.html contchar.html contml.html \
-		contrast.html discrete.html distance.html dnacomp.html \
-		dnadist.html dnainvar.html dnaml.html dnamlk.html \
-		dnamove.html dnapars.html dnapenny.html dollop.html \
-		dolmove.html dolpenny.html draw.html drawgram.html \
-		drawtree.html factor.html fitch.html gendist.html \
-		kitsch.html main.html mix.html move.html neighbor.html \
-		pars.html penny.html phylip.gif proml.html promlk.html \
-		protdist.html protpars.html restdist.html restml.html \
-		retree.html seqboot.html sequence.html treedist.html
-FONTFILES=	font1 font2 font3 font4 font5 font6
+PORTDOCS=	*
 
 do-install:
-.for f in ${BINARIES}
-	${INSTALL_PROGRAM} ${BUILD_WRKSRC}/${f} ${PREFIX}/bin
-.endfor
+	@cd ${BUILD_WRKSRC} && ${MAKE} install
+
+	@cd ${WRKSRC}/exe && \
+		${FIND} . -not -type d -not -name 'font*' -exec ${INSTALL_PROGRAM} "{}" "${PREFIX}/bin/{}" \;
+
 	${MKDIR} ${DATADIR}
-.for font in ${FONTFILES}
-	${INSTALL_DATA} ${BUILD_WRKSRC}/${font} ${DATADIR}
-.endfor
+	@cd ${WRKSRC}/exe && \
+		${FIND} . -not -type d -name 'font*' -exec ${INSTALL_DATA} "{}" "${DATADIR}/{}" \;
+
+post-install:
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-.for f in ${DOCFILES}
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/doc/${f} ${DOCSDIR}
-.endfor
+	@cd ${WRKSRC}/doc && \
+		${FIND} . -not -type d -exec ${INSTALL_DATA} "{}" "${DOCSDIR}/{}" \;
 .endif
 
 .include <bsd.port.mk>
diff -ruN phylip.orig/distinfo phylip/distinfo
--- phylip.orig/distinfo	Mon Jan 23 03:09:06 2006
+++ phylip/distinfo	Mon Jan 23 09:24:24 2006
@@ -1,3 +1,3 @@
-MD5 (phylip-3.6.tar.gz) = ff0ded7756db29d948f355ed5cc020cc
-SHA256 (phylip-3.6.tar.gz) = 2e5ccf074ae33d17302afc75dd0533a189502bb2b83ed361ccc345cad09a142b
-SIZE (phylip-3.6.tar.gz) = 855538
+MD5 (phylip-3.65.tar.gz) = c89a92c8692faaba4310b69b2d89bc33
+SHA256 (phylip-3.65.tar.gz) = 8f8ab66a58dbe1fdf0b615c13b6d358d6c49195fbaeaabc6190253e895c0d528
+SIZE (phylip-3.65.tar.gz) = 1036976
diff -ruN phylip.orig/pkg-plist phylip/pkg-plist
--- phylip.orig/pkg-plist	Tue Oct 12 07:26:34 2004
+++ phylip/pkg-plist	Mon Jan 23 13:19:21 2006
@@ -33,48 +33,6 @@
 bin/retree
 bin/seqboot
 bin/treedist
-%%PORTDOCS%%%%DOCSDIR%%/clique.html
-%%PORTDOCS%%%%DOCSDIR%%/consense.html
-%%PORTDOCS%%%%DOCSDIR%%/contchar.html
-%%PORTDOCS%%%%DOCSDIR%%/contml.html
-%%PORTDOCS%%%%DOCSDIR%%/contrast.html
-%%PORTDOCS%%%%DOCSDIR%%/discrete.html
-%%PORTDOCS%%%%DOCSDIR%%/distance.html
-%%PORTDOCS%%%%DOCSDIR%%/dnacomp.html
-%%PORTDOCS%%%%DOCSDIR%%/dnadist.html
-%%PORTDOCS%%%%DOCSDIR%%/dnainvar.html
-%%PORTDOCS%%%%DOCSDIR%%/dnaml.html
-%%PORTDOCS%%%%DOCSDIR%%/dnamlk.html
-%%PORTDOCS%%%%DOCSDIR%%/dnamove.html
-%%PORTDOCS%%%%DOCSDIR%%/dnapars.html
-%%PORTDOCS%%%%DOCSDIR%%/dnapenny.html
-%%PORTDOCS%%%%DOCSDIR%%/dollop.html
-%%PORTDOCS%%%%DOCSDIR%%/dolmove.html
-%%PORTDOCS%%%%DOCSDIR%%/dolpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/draw.html
-%%PORTDOCS%%%%DOCSDIR%%/drawgram.html
-%%PORTDOCS%%%%DOCSDIR%%/drawtree.html
-%%PORTDOCS%%%%DOCSDIR%%/factor.html
-%%PORTDOCS%%%%DOCSDIR%%/fitch.html
-%%PORTDOCS%%%%DOCSDIR%%/gendist.html
-%%PORTDOCS%%%%DOCSDIR%%/kitsch.html
-%%PORTDOCS%%%%DOCSDIR%%/main.html
-%%PORTDOCS%%%%DOCSDIR%%/mix.html
-%%PORTDOCS%%%%DOCSDIR%%/move.html
-%%PORTDOCS%%%%DOCSDIR%%/neighbor.html
-%%PORTDOCS%%%%DOCSDIR%%/pars.html
-%%PORTDOCS%%%%DOCSDIR%%/penny.html
-%%PORTDOCS%%%%DOCSDIR%%/phylip.gif
-%%PORTDOCS%%%%DOCSDIR%%/proml.html
-%%PORTDOCS%%%%DOCSDIR%%/promlk.html
-%%PORTDOCS%%%%DOCSDIR%%/protdist.html
-%%PORTDOCS%%%%DOCSDIR%%/protpars.html
-%%PORTDOCS%%%%DOCSDIR%%/restdist.html
-%%PORTDOCS%%%%DOCSDIR%%/restml.html
-%%PORTDOCS%%%%DOCSDIR%%/retree.html
-%%PORTDOCS%%%%DOCSDIR%%/seqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/sequence.html
-%%PORTDOCS%%%%DOCSDIR%%/treedist.html
 %%DATADIR%%/font1
 %%DATADIR%%/font2
 %%DATADIR%%/font3
@@ -82,4 +40,3 @@
 %%DATADIR%%/font5
 %%DATADIR%%/font6
 @dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
>Release-Note:
>Audit-Trail:
State-Changed-From-To: open->feedback 
State-Changed-By: edwin 
State-Changed-When: Mon Jan 23 05:04:11 UTC 2006 
State-Changed-Why:  
Awaiting maintainers feedback 

http://www.freebsd.org/cgi/query-pr.cgi?pr=92182 
Responsible-Changed-From-To: freebsd-ports-bugs->lawrance 
Responsible-Changed-By: lawrance 
Responsible-Changed-When: Wed Feb 8 13:45:35 UTC 2006 
Responsible-Changed-Why:  
Take it 

http://www.freebsd.org/cgi/query-pr.cgi?pr=92182 
State-Changed-From-To: feedback->closed 
State-Changed-By: lawrance 
State-Changed-When: Wed Feb 8 14:47:17 UTC 2006 
State-Changed-Why:  
Committed, thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=92182 
>Unformatted:
