[med-svn] r5629 - trunk/packages/clustalw/trunk/debian

Charles Plessy plessy at alioth.debian.org
Tue Dec 28 18:06:12 UTC 2010


Author: plessy
Date: 2010-12-28 18:05:43 +0000 (Tue, 28 Dec 2010)
New Revision: 5629

Modified:
   trunk/packages/clustalw/trunk/debian/changelog
   trunk/packages/clustalw/trunk/debian/clustalw.1
   trunk/packages/clustalw/trunk/debian/clustalw.1.xml
   trunk/packages/clustalw/trunk/debian/control
   trunk/packages/clustalw/trunk/debian/copyright
Log:
Clustal W is free !

Not uplodading yet due to lack of time and chroot.


Modified: trunk/packages/clustalw/trunk/debian/changelog
===================================================================
--- trunk/packages/clustalw/trunk/debian/changelog	2010-12-27 16:54:19 UTC (rev 5628)
+++ trunk/packages/clustalw/trunk/debian/changelog	2010-12-28 18:05:43 UTC (rev 5629)
@@ -1,3 +1,11 @@
+clustalw (1:2.1-2) UNRELEASED; urgency=low
+
+  * New upstream archive, that makes clear the relicensing to LGPL-3+.
+  * Changed archive area in debian/control.
+  * Updated license in debian/copyright and debian/clustalw.1*
+
+ -- Charles Plessy <plessy at debian.org>  Tue, 28 Dec 2010 18:53:12 +0100
+
 clustalw (2.1-1) unstable; urgency=low
 
   * New upstream version

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1	2010-12-27 16:54:19 UTC (rev 5628)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1	2010-12-28 18:05:43 UTC (rev 5629)
@@ -2,13 +2,22 @@
 .\"     Title: CLUSTALW
 .\"    Author: Des Higgins
 .\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\"      Date: 10/14/2009
+.\"      Date: 12/28/2010
 .\"    Manual: Clustal Manual
-.\"    Source: Clustal 2.0.12
+.\"    Source: Clustal 2.1
 .\"  Language: English
 .\"
-.TH "CLUSTALW" "1" "10/14/2009" "Clustal 2.0.12" "Clustal Manual"
+.TH "CLUSTALW" "1" "12/28/2010" "Clustal 2.1" "Clustal Manual"
 .\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el       .ds Aq '
+.\" -----------------------------------------------------------------
 .\" * set default formatting
 .\" -----------------------------------------------------------------
 .\" disable hyphenation
@@ -504,7 +513,7 @@
 .PP
 \fB\-kimura\fR
 .RS 4
-Use Kimura\'s correction\&.
+Use Kimura\*(Aqs correction\&.
 .RE
 .PP
 \fB\-tossgaps\fR
@@ -682,49 +691,18 @@
 .RE
 .SH "COPYRIGHT"
 .br
-Copyright \(co 1988\(en2009 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
+Copyright \(co 1988\(en2010 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
 .br
-Copyright \(co 2008\(en2009 Charles Plessy (This manpage)
+Copyright \(co 2008\(en2010 Charles Plessy (This manpage)
 .br
 .PP
-The binaries and source code are made available and can be distributed subject to the following conditions:
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Users are free to redistribute Clustal\ \&W or Clustal\ \&X in it\'s unmodified form as long as it is not for commercial gain\&.
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at
-gibson at embl\&.de
-.RE
-.sp
-.RS 4
-.ie n \{\
-\h'-04'\(bu\h'+03'\c
-.\}
-.el \{\
-.sp -1
-.IP \(bu 2.3
-.\}
-If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at
-clustalw at ucd\&.ie
-where they will be considered for inclusion in future releases\&.
-.RE
+This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version\&.
 .PP
+This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE\&. See the GNU Lesser General Public License for more details\&.
+.PP
+You should have received a copy of the GNU Lesser General Public License along with this program\&. If not, see http://www\&.gnu\&.org/licenses/, or on Debian systems,
+/usr/share/common\-licenses/LGPL\-3\&.
+.PP
 This manual page and its XML source can be used, modified, and redistributed as if it were in public domain\&.
 .sp
 .SH "NOTES"

Modified: trunk/packages/clustalw/trunk/debian/clustalw.1.xml
===================================================================
--- trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2010-12-27 16:54:19 UTC (rev 5628)
+++ trunk/packages/clustalw/trunk/debian/clustalw.1.xml	2010-12-28 18:05:43 UTC (rev 5629)
@@ -18,7 +18,7 @@
   <!ENTITY dhsurname   "Plessy">
   <!ENTITY dhemail     "plessy at debian.org">
   <!ENTITY dhusername  "&dhfirstname; &dhsurname;">
-  <!ENTITY dhrelease   "2.0.12">
+  <!ENTITY dhrelease   "2.1">
   <!ENTITY dhtitle     "Clustal Manual">
   <!ENTITY dhucpackage "CLUSTALW">
   <!ENTITY dhpackage   "clustalw">
@@ -60,34 +60,17 @@
 		</authorgroup>
 		<copyright>
       <!-- I am unsure of the years, please correct me if I am wrong ! Charles -->
-      <year>1988&ndash;2009</year>
+      <year>1988&ndash;2010</year>
 			<holder>Des Higgins, Julie Thompson &amp; Toby Giboson (&dhproduct;)</holder>
 		</copyright>
 		<copyright>
-			<year>2008–2009</year>
+			<year>2008–2010</year>
 			<holder>&dhusername; (This manpage)</holder>
 		</copyright>
 		<legalnotice>
-			<para>
-        The binaries and source code are made available and can be distributed subject to the following conditions:
-      </para>
-      <itemizedlist>
-        <listitem>
-          <para>
-            Users are free to redistribute Clustal&nbsp;W or Clustal&nbsp;X in it's unmodified form as long as it is not for commercial gain.
-          </para>
-        </listitem>
-        <listitem>
-          <para>
-            Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at <email>gibson at embl.de</email>
-          </para>
-        </listitem>
-        <listitem>
-          <para>
-            If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at <email>clustalw at ucd.ie</email> where they will be considered for inclusion in future releases.
-          </para>
-        </listitem>
-      </itemizedlist>
+			<para>This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.</para>
+			<para>This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public License for more details.</para>
+			<para>You should have received a copy of the GNU Lesser General Public License along with this program.  If not, see http://www.gnu.org/licenses/, or on Debian systems, <filename>/usr/share/common-licenses/LGPL-3</filename>.</para>
     </legalnotice>
     <legalnotice>
       <para>

Modified: trunk/packages/clustalw/trunk/debian/control
===================================================================
--- trunk/packages/clustalw/trunk/debian/control	2010-12-27 16:54:19 UTC (rev 5628)
+++ trunk/packages/clustalw/trunk/debian/control	2010-12-28 18:05:43 UTC (rev 5629)
@@ -1,5 +1,5 @@
 Source: clustalw
-Section: non-free/science
+Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes

Modified: trunk/packages/clustalw/trunk/debian/copyright
===================================================================
--- trunk/packages/clustalw/trunk/debian/copyright	2010-12-27 16:54:19 UTC (rev 5628)
+++ trunk/packages/clustalw/trunk/debian/copyright	2010-12-28 18:05:43 UTC (rev 5629)
@@ -1,66 +1,23 @@
-Name      : Clustal W
-Contact   : clustalw at ucd.ie
-Source    : http://www.clustal.org/download/current/clustalw-2.0.12.tar.gz
-Disclamer : 
- This package is not part of the Debian operating system. The clustalw source
- and binary Debian packages are part of the “non-free” area in our archive. The
- packages in this area are not part of the Debian system, although they have
- been configured for use with Debian. We nevertheless support the use of the
- clustalw source and binary Debian packages and provide infrastructure for
- non-free packages (such as our bug tracking system and mailing lists). The
- licence does not forbid Debian from using autobuilders to create binary
- packages.
+Source: http://www.clustal.org/download/current/clustalw-2.1.tar.gz
 
-Copyright : © Des Higgins, Julie Thompson and Toby Gibson
-Licence   : Not for commercial use, No modification of the code.
-	
-	Date:29 November 2007
-	
-	The copyright for ClustalW and ClustalX is held by Des Higgins, Julie Thompson
-	and Toby Gibson
-	
-	The binaries and source code are made available and can be distributed subject
-	to the following conditions:
-	
-	Users are free to redistribute ClustalW or ClustalX in it's unmodified form as
-	long as it is not for commercial gain.
-	
-	Anyone wishing to redistribute Clustal commercially should contact Toby Gibson
-	at gibson at embl.de
-	
-	
-	If users make changes/have ideas that they believe would be useful to the
-	broader research community they can send their suggestions to the clustal
-	development team at clustalw at ucd.ie where they will be considered for inclusion
-	in future releases.
-	
+Files: *
+Copyright: © Des Higgins, Julie Thompson and Toby Gibson
+Licence: LGPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ GNU Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program.  If not, see <http://www.gnu.org/licenses/>.
 Comment:
- 
- Frequently asked questions about Clustal licensing?
- ---------------------------------------------------
- 
- 1. Do I have to pay to use ClustalW or ClustalX?
- No - unless you wish to redistribute Clustal for profit. In this case see question 4.
- 
- 2. Can I redistribute the Clustal binaries and source code?
- Yes. We have always wanted to see Clustal have as wide a userbase and
- distribution network as possible and are happy to see other sites host copies
- of the official Clustal code.
- 
- 3. Can I make changes to the source code?
- 
- You can make changes for your own purposes but you should not redistribute the
- changed code.
- 
- 4. I want to include ClustalW/ClustalX in a commercial application who should I contact?
- Toby Gibson at gibson at embl.de (also cc des.higgins at ucd.ie)
- 
- 5. There is no Clustal distribution for platform X. I have changed the code in
- order to compile Clustal on this platform. Can I redistribute it?
- 
- Ideally you should send us a copy of your source code changes as well as a
- binary. We will include it in our contributed binaries section on our FTP site
- along with an acknowledgement of your contribution.
+ On Debian systems, you can read the full text of the GNU Lesser General Public
+ License in ‘/usr/share/common-licenses/LGPL-3’.
 
 Files: debian/*
 Copyright: © 1998-1999 Stephane Bortzmeyer <bortzmeyer at debian.org>
@@ -70,7 +27,7 @@
 	   © 2006 Kai Hendry <hendry at iki.fi>
 	   © 2007 Nelson A. de Oliveira <naoliv at debian.org>
 	   © 2003-2008 Steffen Möller <moeller at debian.org>
-	   © 2007-2009 Charles Plessy <plessy at debian.org>
+	   © 2007-2010 Charles Plessy <plessy at debian.org>
 	   © 2008 David Paleino <d.paleino at gmail.com>
 Licence: Unclear
  The licence of the earlier works was never stated. Some works have been
@@ -78,7 +35,6 @@
  but authors are left in the list of copyright holders by courtesy. The work
  of Charles Plessy and Steffen Möller can be treated as if it were public domain.
 Comment: I have received the following message from Des Higgins. -- Charles Plessy
-  
    "We are happy to give the Debian team permission to modify
    ClustalW 2 and ClustalX 2 code and redistribute the binaries as long as
    those modifications do not alter the algorithmic core, i.e. only affect
@@ -86,7 +42,7 @@
    LICENSE file into your package."
 
 Files: debian/clustalw.1.xml, debian/clustalw.1
-Copyright: © 2008 Charles Plessy <plessy at debian.org>
+Copyright: © 2008–10 Charles Plessy <plessy at debian.org>
 Licence: Public Domain
  The manual page and its XML source can be used, modified, and
  redistributed as if it were in public domain.




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