[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>1988–2009</year>
+ <year>1988–2010</year>
<holder>Des Higgins, Julie Thompson & 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 W or Clustal 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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