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Message-Id: <201103301305.p2UD5T3M027768@red.freebsd.org>
Date: Wed, 30 Mar 2011 13:05:29 GMT
From: Gvozdikov Veniamin <g.veniamin@googlemail.com>
To: freebsd-gnats-submit@FreeBSD.org
Subject: Update port: science/massxpert up to 2.4.3
X-Send-Pr-Version: www-3.1
X-GNATS-Notify:

>Number:         156059
>Category:       ports
>Synopsis:       Update port: science/massxpert up to 2.4.3
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    culot
>State:          closed
>Quarter:        
>Keywords:       
>Date-Required:  
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Wed Mar 30 13:10:10 UTC 2011
>Closed-Date:    Thu Mar 31 06:51:57 UTC 2011
>Last-Modified:  Thu Mar 31 07:00:23 UTC 2011
>Originator:     Gvozdikov Veniamin
>Release:        FreeBSD 8.2-RELEASE
>Organization:
>Environment:
FreeBSD LSD.zlonet.ru 8.2-RELEASE FreeBSD 8.2-RELEASE #0: Fri Feb 18 02:24:46 UTC 2011 root@almeida.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC i386
>Description:
New version.
 Fixed a problem with considering that the lightest isotope was necessarily the most abundant isotope. In fact this is true for the main chemical elements in biological matter, but can be not true for other chemical elements. This fix will only matter to people using chemical elements of which the most abundant isotope is not the lightest one.
 Fixed a bug that crashed the program when the user would click (on the sequence editor) left of first monomer vignette.
 Added feature: when running the mz calculations dialog from the sequence editor window, the masses are automatically set in the dialog window. 
Added ion charge proton to the formula of the z fragmentation specification. 
Rewrote the Formula's elementalComposition() so that the order of the atoms is in the CHNO->alphabetic conventional order.
>How-To-Repeat:

>Fix:
diff -up massxpert.orig/Makefile massxpert/Makefile
--- massxpert.orig/Makefile	2011-03-30 21:00:30.000000000 +0800
+++ massxpert/Makefile	2011-03-30 16:16:38.000000000 +0800
@@ -6,14 +6,15 @@
 #
 
 PORTNAME=	massxpert
-PORTVERSION=	2.3.6
-PORTREVISION=	1
+PORTVERSION=	2.4.3
 CATEGORIES=	science
 MASTER_SITES=	http://download.tuxfamily.org/massxpert/source/
 
 MAINTAINER=	g.veniamin@googlemail.com
 COMMENT=	The massXpert software for (bio)chemists
 
+LICENSE=	GPLv3
+
 USE_QT_VER=	4
 USE_CMAKE=	yes
 QT_COMPONENTS=	gui xml rcc_build qmake_build uic_build moc_build \
diff -up massxpert.orig/distinfo massxpert/distinfo
--- massxpert.orig/distinfo	2011-03-30 21:00:30.000000000 +0800
+++ massxpert/distinfo	2011-03-30 16:15:50.000000000 +0800
@@ -1,3 +1,2 @@
-MD5 (massxpert-2.3.6.tar.gz) = e51cf36f01e78cf07a71e33a8e0f8ad7
-SHA256 (massxpert-2.3.6.tar.gz) = 9c28de0eb45c027551b52b865bae4a9cdcc874869cefadb3fe61a71e391f49e4
-SIZE (massxpert-2.3.6.tar.gz) = 14197098
+SHA256 (massxpert-2.4.3.tar.gz) = 2c8cb51b9d81c2ddf8a1f212d067d64dab066756a4b0c15e01ad6071c2741702
+SIZE (massxpert-2.4.3.tar.gz) = 14208974
Common subdirectories: massxpert.orig/files and massxpert/files
diff -up massxpert.orig/pkg-plist massxpert/pkg-plist
--- massxpert.orig/pkg-plist	2011-03-30 21:00:30.000000000 +0800
+++ massxpert/pkg-plist	2011-03-30 17:41:27.000000000 +0800
@@ -198,6 +198,8 @@ share/applications/massxpert.desktop
 %%DATADIR%%/pol-seqs/protein-3-letters.mxp
 %%DATADIR%%/pol-seqs/tev-protease-his-tag.mxp
 %%DATADIR%%/pol-seqs/yellow-fluorescent-protein.mxp
+%%DATADIR%%/pol-seqs/insulin-a-ox.mxp
+%%DATADIR%%/pol-seqs/insulin-b-ox.mxp
 %%DATADIR%%/dictionaries/codon-to-protein-1.dic
 %%DATADIR%%/dictionaries/codon-to-protein-3.dic
 %%DATADIR%%/dictionaries/pdb-protein-to-mxp.dic

>Release-Note:
>Audit-Trail:
Class-Changed-From-To: sw-bug->maintainer-update 
Class-Changed-By: linimon 
Class-Changed-When: Thu Mar 31 03:38:41 UTC 2011 
Class-Changed-Why:  
Fix up category and class. 


Responsible-Changed-From-To: freebsd-bugs->freebsd-ports-bugs 
Responsible-Changed-By: linimon 
Responsible-Changed-When: Thu Mar 31 03:38:41 UTC 2011 
Responsible-Changed-Why:  

http://www.freebsd.org/cgi/query-pr.cgi?pr=156059 
Responsible-Changed-From-To: freebsd-ports-bugs->culot 
Responsible-Changed-By: culot 
Responsible-Changed-When: Thu Mar 31 05:09:33 UTC 2011 
Responsible-Changed-Why:  
I'll take it. 

http://www.freebsd.org/cgi/query-pr.cgi?pr=156059 
State-Changed-From-To: open->closed 
State-Changed-By: culot 
State-Changed-When: Thu Mar 31 06:51:56 UTC 2011 
State-Changed-Why:  
Committed. Thanks! 

http://www.freebsd.org/cgi/query-pr.cgi?pr=156059 

From: dfilter@FreeBSD.ORG (dfilter service)
To: bug-followup@FreeBSD.org
Cc:  
Subject: Re: ports/156059: commit references a PR
Date: Thu, 31 Mar 2011 06:51:46 +0000 (UTC)

 culot       2011-03-31 06:51:37 UTC
 
   FreeBSD ports repository
 
   Modified files:
     science/massxpert    Makefile distinfo pkg-plist 
   Log:
   - Update to 2.4.3
   - LICENSE added
   
   PR:             ports/156059
   Submitted by:   Gvozdikov Veniamin <g.veniamin AT googlemail.com> (maintainer)
   
   Revision  Changes    Path
   1.3       +3 -2      ports/science/massxpert/Makefile
   1.2       +2 -3      ports/science/massxpert/distinfo
   1.3       +2 -0      ports/science/massxpert/pkg-plist
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>Unformatted:
