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Date: Sat, 27 Sep 2008 14:13:31 GMT
From: Wen heping <wenheping@gmail.com>
To: freebsd-gnats-submit@FreeBSD.org
Subject: [Update]biology/paml:update to 4.1
X-Send-Pr-Version: www-3.1
X-GNATS-Notify:

>Number:         127683
>Category:       ports
>Synopsis:       [Update]biology/paml:update to 4.1
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    miwi
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Sat Sep 27 14:20:03 UTC 2008
>Closed-Date:    Tue Sep 30 08:55:13 UTC 2008
>Last-Modified:  Tue Sep 30 09:00:13 UTC 2008
>Originator:     Wen heping
>Release:        FreeBSD 7.0 release
>Organization:
ChangAn Middle School
>Environment:
FreeBSD tinderbox.wenjing.com 7.0-RELEASE FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008     root@logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  i386
>Description:
1 update to 4.1 from 3.15
2 take over maintainership
>How-To-Repeat:

>Fix:


Patch attached with submission follows:

--- Makefile.orig	2008-09-28 03:47:15.000000000 +0800
+++ Makefile	2008-09-28 04:42:47.000000000 +0800
@@ -6,19 +6,20 @@
 #
 
 PORTNAME=	paml
-PORTVERSION=	3.15
+PORTVERSION=	4.1
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
 DISTNAME=	${PORTNAME}${PORTVERSION}
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	wenheping@gmail.com
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
 
 USE_GMAKE=	YES
-WRKSRC=		${WRKDIR}/${DISTNAME:S/b//g}/src
+WRKSRC=		${WRKDIR}/${DISTNAME:S/.//g}/src
 MAKE_ARGS=	CC="${CC}" CFLAGS="${CFLAGS}"
 
 BINARIES=	baseml basemlg chi2 codeml evolver pamp yn00
+DOC_FILES=	MCMCtreeDoc.pdf pamlDOC.pdf pamlFAQs.pdf pamlHistory.txt
 
 do-install:
 .for f in ${BINARIES}
@@ -26,8 +27,9 @@
 .endfor
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${DOCSDIR}
-	${INSTALL_DATA} ${WRKDIR}/${DISTNAME:S/b//g}/doc/pamlDOC.pdf \
-		${DOCSDIR}
+.for f in ${DOC_FILES}
+	${INSTALL_DATA} ${WRKDIR}/${DISTNAME:S/.//g}/doc/${f} ${DOCSDIR}
+.endfor
 .endif
 
 .include <bsd.port.mk>
--- distinfo.orig	2006-05-21 02:52:19.000000000 +0800
+++ distinfo	2008-09-28 04:18:56.000000000 +0800
@@ -1,3 +1,3 @@
-MD5 (paml3.15.tar.gz) = c54ba7e15a66b57dc1140feea22e5695
-SHA256 (paml3.15.tar.gz) = f698b1d57b514e5e06e746899eae1245d098e96881e2a31c9b8fc956beb4f62a
-SIZE (paml3.15.tar.gz) = 2364043
+MD5 (paml4.1.tar.gz) = df8d8a790f5ef29e7266640d4493ec1d
+SHA256 (paml4.1.tar.gz) = 64680a56304bb3f5cd61cfc9be253fe1fe37250cb450bceaaf76b99ee08111f1
+SIZE (paml4.1.tar.gz) = 2865301
--- pkg-plist.orig	2008-09-28 03:47:17.000000000 +0800
+++ pkg-plist	2008-09-28 04:43:40.000000000 +0800
@@ -7,4 +7,7 @@
 bin/pamp
 bin/yn00
 %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
+%%PORTDOCS%%%%DOCSDIR%%/MCMCtreeDoc.pdf
+%%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
+%%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
 %%PORTDOCS%%@dirrm %%DOCSDIR%%


>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->miwi 
Responsible-Changed-By: edwin 
Responsible-Changed-When: Sat Sep 27 14:20:18 UTC 2008 
Responsible-Changed-Why:  
miwi@ wants his PRs (via the GNATS Auto Assign Tool) 

http://www.freebsd.org/cgi/query-pr.cgi?pr=127683 
State-Changed-From-To: open->closed 
State-Changed-By: miwi 
State-Changed-When: Tue Sep 30 08:55:12 UTC 2008 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=127683 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/127683: commit references a PR
Date: Tue, 30 Sep 2008 08:55:08 +0000 (UTC)

 miwi        2008-09-30 08:54:55 UTC
 
   FreeBSD ports repository
 
   Modified files:
     biology/paml         Makefile distinfo pkg-plist 
   Log:
   - Update to 4.1
   - Pass maintainership to submitter
   
   PR:             127683
   Submitted by:   Wen heping <wenheping@gmail.com>
   
   Revision  Changes    Path
   1.10      +7 -5      ports/biology/paml/Makefile
   1.10      +3 -3      ports/biology/paml/distinfo
   1.7       +4 -1      ports/biology/paml/pkg-plist
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>Unformatted:
