From tkato432@yahoo.com  Mon Mar 17 18:00:45 2008
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Message-Id: <20080318030008.2a0ed919.tkato432@yahoo.com>
Date: Tue, 18 Mar 2008 03:00:08 +0900
From: KATO Tsuguru <tkato432@yahoo.com>
To: FreeBSD-gnats-submit@FreeBSD.org
Subject: Update port: biology/clustalw to 2.0.4

>Number:         121794
>Category:       ports
>Synopsis:       Update port: biology/clustalw to 2.0.4
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    jadawin
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Mon Mar 17 18:10:00 UTC 2008
>Closed-Date:    Wed Mar 19 13:40:58 UTC 2008
>Last-Modified:  Wed Mar 19 14:10:01 UTC 2008
>Originator:     KATO Tsuguru
>Release:        FreeBSD 6.3-RELEASE-p1 i386
>Organization:
>Environment:
>Description:
- Update to version 2.0.4 

>How-To-Repeat:
>Fix:

diff -urN /usr/ports/biology/clustalw/Makefile biology/clustalw/Makefile
--- /usr/ports/biology/clustalw/Makefile	2008-02-27 15:19:00.000000000 +0900
+++ biology/clustalw/Makefile	2008-03-14 01:03:59.000000000 +0900
@@ -6,18 +6,19 @@
 #
 
 PORTNAME=	clustalw
-PORTVERSION=	2.0.3
-PORTREVISION=	1
+PORTVERSION=	2.0.4
 CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
 DISTNAME=	${PORTNAME}-${PORTVERSION}-src
 
 MAINTAINER=	ports@FreeBSD.org
-COMMENT=	CLUSTAL W Multiple Sequence Alignment Program
+COMMENT=	A multiple alignment program for DNA or proteins
 
-GNU_CONFIGURE=	yes
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
 
+USE_GNOME=	gnometarget
+GNU_CONFIGURE=	yes
+
 PLIST_FILES=	bin/clustalw bin/clustalw2
 
 post-install:
diff -urN /usr/ports/biology/clustalw/distinfo biology/clustalw/distinfo
--- /usr/ports/biology/clustalw/distinfo	2008-02-26 13:36:32.000000000 +0900
+++ biology/clustalw/distinfo	2008-03-13 23:43:54.000000000 +0900
@@ -1,3 +1,3 @@
-MD5 (clustalw-2.0.3-src.tar.gz) = 77e7cf7fcea6084da22d2b19c52356c2
-SHA256 (clustalw-2.0.3-src.tar.gz) = 01a0dc2a3dc8d342367f5f7117749195a1c0d217c105d0a43e02565979cc459a
-SIZE (clustalw-2.0.3-src.tar.gz) = 287805
+MD5 (clustalw-2.0.4-src.tar.gz) = 0ee83a0e3cf8e1d2ccf406ae99621b31
+SHA256 (clustalw-2.0.4-src.tar.gz) = 2139c1edddb97b2fccf0356b3deb2d865a96db63b52aebec1a812dcd0429ad16
+SIZE (clustalw-2.0.4-src.tar.gz) = 288998
>Release-Note:
>Audit-Trail:
Responsible-Changed-From-To: freebsd-ports-bugs->jadawin 
Responsible-Changed-By: jadawin 
Responsible-Changed-When: Mon Mar 17 21:26:36 UTC 2008 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=121794 
State-Changed-From-To: open->feedback 
State-Changed-By: jadawin 
State-Changed-When: Tue Mar 18 09:17:29 UTC 2008 
State-Changed-Why:  
Ask for submitter fix. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=121794 

From: KATO Tsuguru <tkato432@yahoo.com>
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/121794: Update port: biology/clustalw to 2.0.4
Date: Tue, 18 Mar 2008 21:28:31 +0900

 Version 2.0.5 has been released.
 
 
 diff -urN /usr/ports/biology/clustalw/Makefile biology/clustalw/Makefile
 --- /usr/ports/biology/clustalw/Makefile	2008-02-27 15:19:00.000000000 +0900
 +++ biology/clustalw/Makefile	2008-03-18 19:10:29.000000000 +0900
 @@ -6,18 +6,21 @@
  #
  
  PORTNAME=	clustalw
 -PORTVERSION=	2.0.3
 -PORTREVISION=	1
 +PORTVERSION=	2.0.5
  CATEGORIES=	biology
 -MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
 +MASTER_SITES=	http://www.clustal.org/download/%SUBDIR%/ \
 +		ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
 +MASTER_SITE_SUBDIR=	${PORTVERSION}
  DISTNAME=	${PORTNAME}-${PORTVERSION}-src
  
  MAINTAINER=	ports@FreeBSD.org
 -COMMENT=	CLUSTAL W Multiple Sequence Alignment Program
 +COMMENT=	A multiple alignment program for DNA or proteins
  
 -GNU_CONFIGURE=	yes
  WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
  
 +USE_GNOME=	gnometarget
 +GNU_CONFIGURE=	yes
 +
  PLIST_FILES=	bin/clustalw bin/clustalw2
  
  post-install:
 diff -urN /usr/ports/biology/clustalw/distinfo biology/clustalw/distinfo
 --- /usr/ports/biology/clustalw/distinfo	2008-02-26 13:36:32.000000000 +0900
 +++ biology/clustalw/distinfo	2008-03-18 18:45:16.000000000 +0900
 @@ -1,3 +1,3 @@
 -MD5 (clustalw-2.0.3-src.tar.gz) = 77e7cf7fcea6084da22d2b19c52356c2
 -SHA256 (clustalw-2.0.3-src.tar.gz) = 01a0dc2a3dc8d342367f5f7117749195a1c0d217c105d0a43e02565979cc459a
 -SIZE (clustalw-2.0.3-src.tar.gz) = 287805
 +MD5 (clustalw-2.0.5-src.tar.gz) = f18a332a61f9cd90fc7c88e122ef7487
 +SHA256 (clustalw-2.0.5-src.tar.gz) = 6a21bb7d389cc145c4175ae99f227eda356415731952bb2e58b6c951a205046a
 +SIZE (clustalw-2.0.5-src.tar.gz) = 289291
 diff -urN /usr/ports/biology/clustalw/pkg-descr biology/clustalw/pkg-descr
 --- /usr/ports/biology/clustalw/pkg-descr	2007-12-16 14:55:00.000000000 +0900
 +++ biology/clustalw/pkg-descr	2008-03-18 19:07:00.000000000 +0900
 @@ -1,19 +1,8 @@
 -               CLUSTAL W Multiple Sequence Alignment Program
 +ClustalW2 is a general purpose multiple sequence alignment program for
 +DNA or proteins. It produces biologically meaningful multiple sequence
 +alignments of divergent sequences. It calculates the best match for the
 +selected sequences, and lines them up so that the identities,
 +similarities and differences can be seen. Evolutionary relationships
 +can be seen via viewing Cladograms or Phylograms. 
  
 -Clustal W is a multiple alignment program for DNA or proteins.
 -Clustal W was written by Des Higgins (des@chah.ucc.ie), Julie Thompson
 -(julie@IGBMC.u-strasbg.fr), and Toby Gibson (Gibson@EMBL-Heidelberg.DE).
 -Version 2.0 has been completely rewritten in C++.
 -
 -Original Paper:
 -    Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W:
 -improving the sensitivity of progressive multiple sequence alignment
 -through sequence weighting, positions-specific gap penalties and
 -weight matrix choice. Nucleic Acids Research 22: 4673-4680.
 -    
 -Tips:
 -    Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using
 -CLUSTAL for multiple sequence alignments. Methods in Enzymology 266:
 -383-402.
 -
 -WWW: http://bips.u-strasbg.fr/fr/Documentation/ClustalX/
 +WWW: http://www.clustal.org/

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/121794: commit references a PR
Date: Wed, 19 Mar 2008 13:31:56 +0000 (UTC)

 jadawin     2008-03-19 13:31:52 UTC
 
   FreeBSD ports repository
 
   Modified files:
     biology/clustalw     distinfo pkg-descr 
   Log:
   - Update to version 2.0.5
   - Add RESTRICTED due to a non-commercial use licence.
   
   PR:             ports/121794
   Submitted by:   KATO Tsuguru <tkato432@yahoo.com>
   Approved by:    thierry and tabthorpe (mentors)
   
   Revision  Changes    Path
   1.7       +3 -3      ports/biology/clustalw/distinfo
   1.4       +7 -18     ports/biology/clustalw/pkg-descr
 _______________________________________________
 cvs-all@freebsd.org mailing list
 http://lists.freebsd.org/mailman/listinfo/cvs-all
 To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
 
State-Changed-From-To: feedback->closed 
State-Changed-By: jadawin 
State-Changed-When: Wed Mar 19 13:40:57 UTC 2008 
State-Changed-Why:  
Committed, with minor changes. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=121794 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/121794: commit references a PR
Date: Wed, 19 Mar 2008 14:01:22 +0000 (UTC)

 jadawin     2008-03-19 14:01:13 UTC
 
   FreeBSD ports repository
 
   Modified files:
     biology/clustalw     Makefile 
   Log:
   - Update to 2.0.5
   - Add RESTRICTED due to non-commercial use licence.
   
   PR:             ports/121794
   Submitted by:   KATO Tsuguru <tkato432@yahoo.com>
   Approved by:    thierry and tabthorpe (mentors)
   
   Revision  Changes    Path
   1.12      +10 -5     ports/biology/clustalw/Makefile
 _______________________________________________
 cvs-all@freebsd.org mailing list
 http://lists.freebsd.org/mailman/listinfo/cvs-all
 To unsubscribe, send any mail to "cvs-all-unsubscribe@freebsd.org"
 
>Unformatted:
