Author: plessy
Date: 2010-08-23 12:13:11 +0000 (Mon, 23 Aug 2010)
New Revision: 5182
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/control
trunk/packages/seaview/trunk/debian/copyright
trunk/packages/seaview/trunk/debian/upstream-metadata.yaml
Log:
New upstream version and minor packaging changes.
* Incremented Standards-Version to reflect conformance with Policy 3.9.1
(debian/control, no changes needed).
* Refreshed debian/copyright according to latest DEP-5 discussions.
* Moved debian/upstream-metadata.yaml's PMID and DOI keys in the
Reference namespace.
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2010-08-23 09:56:30 UTC
(rev 5181)
+++ trunk/packages/seaview/trunk/debian/changelog 2010-08-23 12:13:11 UTC
(rev 5182)
@@ -1,3 +1,14 @@
+seaview (1:4.2.6-1) unstable; urgency=low
+
+ * New upstream version.
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.1
+ (debian/control, no changes needed).
+ * Refreshed debian/copyright according to latest DEP-5 discussions.
+ * Moved debian/upstream-metadata.yaml's PMID and DOI keys in the
+ Reference namespace.
+
+ -- Charles Plessy <[email protected]> Mon, 23 Aug 2010 14:30:30 +0900
+
seaview (1:4.2.5-1) unstable; urgency=low
* New upstrem version
Modified: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control 2010-08-23 09:56:30 UTC (rev
5181)
+++ trunk/packages/seaview/trunk/debian/control 2010-08-23 12:13:11 UTC (rev
5182)
@@ -6,7 +6,7 @@
Uploaders: Charles Plessy <[email protected]>,
Andreas Tille <[email protected]>
Build-Depends: debhelper ( >= 7 ), libfltk1.1-dev, libjpeg-dev, libpng12-dev,
libxft-dev, libxext-dev, zlib1g-dev
-Standards-Version: 3.8.4
+Standards-Version: 3.9.1
Vcs-Browser:
http://svn.debian.org/wsvn/debian-med/trunk/packages/seaview/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/seaview/trunk/
Homepage: http://pbil.univ-lyon1.fr/software/seaview.html
Modified: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright 2010-08-23 09:56:30 UTC
(rev 5181)
+++ trunk/packages/seaview/trunk/debian/copyright 2010-08-23 12:13:11 UTC
(rev 5182)
@@ -1,10 +1,6 @@
-Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-Name : SeaView
-Contact : Manolo Gouy <[email protected]>
-Source :
ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_4.2.1.tar.gz
-
-Disclamer : This package is not part of the Debian operating system.
+Format: http://dep.debian.net/deps/dep5/ (beta)
+Source: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive
+Disclamer: This package is not part of the Debian operating system.
The seaview 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
@@ -14,115 +10,111 @@
autobuilders to create binary packages.
Copyright: 1996-2010 Manolo Gouy <[email protected]>
-License: GPL-3+ with PHYLIP exemption.
-
- This program, except where indicated, is free software; you can
redistribute it and/or
- modify it under the terms of the GNU General Public
- License as published by the Free Software Foundation;
- either version 3 of the License, or (at your option) any later version..
-
- Two files (dnapars.c and protpars.c) have a distinct license
- which authorizes distribution that does not generate revenue.
-
- Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered
by the
- GNU General Public License but are copyright Stephane Guindon.
-
- 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
- General Public License for more details.
-
- Additional permission under GNU GPL version 3 section 7
-
- If you modify this Program, or any covered work, by linking or
combining it with PHYLIP
- (or a modified version of that library), containing parts covered by
the terms of
- the University of Washington license, the licensor of this Program
grants you additional
- permission to convey the resulting work.
-
- A copy of the GNU General Public License is available
- from http://www.gnu.org/licenses/gpl.txt .
+License: GPL-3+ with PHYLIP exemption
+ This program, except where indicated, is free software; you can redistribute
it and/or
+ modify it under the terms of the GNU General Public
+ License as published by the Free Software Foundation;
+ either version 3 of the License, or (at your option) any later version..
+ .
+ Two files (dnapars.c and protpars.c) have a distinct license
+ which authorizes distribution that does not generate revenue.
+ .
+ Three files (bionj.c, phyml_util.c and phyml_util.h) are also covered by the
+ GNU General Public License but are copyright Stephane Guindon.
+ .
+ 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
+ General Public License for more details.
+ .
+ Additional permission under GNU GPL version 3 section 7
+ .
+ If you modify this Program, or any covered work, by linking or combining it
with PHYLIP
+ (or a modified version of that library), containing parts covered by the
terms of
+ the University of Washington license, the licensor of this Program grants you
additional
+ permission to convey the resulting work.
+ .
+ A copy of the GNU General Public License is available
+ from http://www.gnu.org/licenses/gpl.txt .
+Comment:
+ On Debian systems, the complete text of the GNU General Public License version
+ 3 can be found in ‘/usr/share/common-licenses/GPL-3’.
-On Debian systems, the complete text of the GNU General Public License version
-3 can be found in ‘/usr/share/common-licenses/GPL-3’.
-
-Files: csrc/bionj.c, csrc/phyml_util.h
+Files: csrc/bionj.c csrc/phyml_util.h
Copyright: © Stephane Guindon. Oct 2003 onward
License: GPL-2+ with PHYLIP exemption.
-
- This program is free software; you can redistribute it and/or modify it
under the terms of the
- GNU General Public License as published by the Free Software
Foundation; either version 2 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
- General Public License for more details.
-
- You should have received a copy of the GNU General Public License along
with this program; if not,
- see <http://www.gnu.org/licenses>.
-
- Linking PHYML statically or dynamically with other modules is making a
combined work based on PHYML.
- Thus, the terms and conditions of the GNU General Public License cover
the whole combination.
-
- In addition, as a special exception, the copyright holders of PHYML
give you permission to combine
- PHYML with free software programs or libraries that are released under
the GNU LGPL and with code
- included in the standard release of PHYLIP under the University of
Washington license (or modified
- versions of such code, with unchanged license). You may copy and
distribute such a system following
- the terms of the GNU GPL for PHYML and the licenses of the other code
concerned.
-
- Note that people who make modified versions of PHYML are not obligated
to grant this special exception
- for their modified versions; it is their choice whether to do so. The
GNU General Public License gives
- permission to release a modified version without this exception; this
exception also makes it possible
- to release a modified version which carries forward this exception.
+ This program is free software; you can redistribute it and/or modify it under
the terms of the
+ GNU General Public License as published by the Free Software Foundation;
either version 2 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
+ General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License along with
this program; if not,
+ see <http://www.gnu.org/licenses>.
+ .
+ Linking PHYML statically or dynamically with other modules is making a
combined work based on PHYML.
+ Thus, the terms and conditions of the GNU General Public License cover the
whole combination.
+ .
+ In addition, as a special exception, the copyright holders of PHYML give you
permission to combine
+ PHYML with free software programs or libraries that are released under the
GNU LGPL and with code
+ included in the standard release of PHYLIP under the University of Washington
license (or modified
+ versions of such code, with unchanged license). You may copy and distribute
such a system following
+ the terms of the GNU GPL for PHYML and the licenses of the other code
concerned.
+ .
+ Note that people who make modified versions of PHYML are not obligated to
grant this special exception
+ for their modified versions; it is their choice whether to do so. The GNU
General Public License gives
+ permission to release a modified version without this exception; this
exception also makes it possible
+ to release a modified version which carries forward this exception.
-Files: csrc/dnapars.c, csrc/protpars.c
+Files: csrc/dnapars.c csrc/protpars.c
License:
-
- (c) Copyright 1980-2008. University of Washington. All rights reserved.
Permission is
- granted to reproduce, perform, and modify these programs and
documentation files.
- Permission is granted to distribute or provide access to these programs
provided
- that this copyright notice is not removed, the programs are not
integrated with or
- called by any product or service that generates revenue, and that your
distribution
- of these documentation files and programs are free. Any modified
versions of these
- materials that are distributed or accessible shall indicate that they
are based on
- these programs. Institutions of higher education are granted permission
to
- distribute this material to their students and staff for a fee to
recover
- distribution costs. Permission requests for any other distribution of
these
- program should be directed to license (at) u.washington.edu .
+ (c) Copyright 1980-2008. University of Washington. All rights reserved.
Permission is
+ granted to reproduce, perform, and modify these programs and documentation
files.
+ Permission is granted to distribute or provide access to these programs
provided
+ that this copyright notice is not removed, the programs are not integrated
with or
+ called by any product or service that generates revenue, and that your
distribution
+ of these documentation files and programs are free. Any modified versions of
these
+ materials that are distributed or accessible shall indicate that they are
based on
+ these programs. Institutions of higher education are granted permission to
+ distribute this material to their students and staff for a fee to recover
+ distribution costs. Permission requests for any other distribution of these
+ program should be directed to license (at) u.washington.edu .
Files: FL/*
-Copyright: © 2004 Greg Ercolano
- © 2005 Nathan Vander Wilt
+Copyright:
+ © 2004 Greg Ercolano
+ © 2005 Nathan Vander Wilt
License: LGPL-2+
-
- This library is free software; you can redistribute it and/or
- modify it under the terms of the GNU Library General Public
- License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
-
- This library 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
- Library General Public License for more details.
-
- You should have received a copy of the GNU Library General Public
- License along with this library; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA
02110-1301 USA
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Library General Public
+ License as published by the Free Software Foundation; either
+ version 2 of the License, or (at your option) any later version.
+ .
+ This library 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
+ Library General Public License for more details.
+ .
+ You should have received a copy of the GNU Library General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
+Comment:
+ On Debian systems, the complete text of the GNU Lesser General Public License
+ version 2 can be found in ‘/usr/share/common-licenses/LGPL-2’.
-On Debian systems, the complete text of the GNU Lesser General Public License
-version 2 can be found in ‘/usr/share/common-licenses/LGPL-2’.
-
Files: zconf.h
Copyright: © 1995-1998 Jean-loup Gailly and Mark Adler
License: zlib
-
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
-
+ .
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
-
+ .
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
@@ -130,22 +122,22 @@
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
-
+ .
Jean-loup Gailly Mark Adler
[email protected] [email protected]
-
Files: debian/*
-Copyright: © 1999 Stephane Bortzmeyer <[email protected]>
- © 2001 Dr. Guenter Bechly <[email protected]>
- © 2001 Adrian Bunk <[email protected]>
- © 2001 Doug Porter <[email protected]>
- © 2002 Matej Vela <[email protected]>
- © 2003 Colin Watson <[email protected]>
- © 2003 Aaron M. Ucko <[email protected]>
- © 2003 Brian R Furry <[email protected]>
- © 2005 Steve Langasek <[email protected]>
- © 2007 Nelson A. de Oliveira <[email protected]>
- © 2006–2010 Charles Plessy <[email protected]>
+Copyright:
+ © 1999 Stephane Bortzmeyer <[email protected]>
+ © 2001 Dr. Guenter Bechly <[email protected]>
+ © 2001 Adrian Bunk <[email protected]>
+ © 2001 Doug Porter <[email protected]>
+ © 2002 Matej Vela <[email protected]>
+ © 2003 Colin Watson <[email protected]>
+ © 2003 Aaron M. Ucko <[email protected]>
+ © 2003 Brian R Furry <[email protected]>
+ © 2005 Steve Langasek <[email protected]>
+ © 2007 Nelson A. de Oliveira <[email protected]>
+ © 2006–2010 Charles Plessy <[email protected]>
License: unknown
Please treat the contributions of Charles Plessy as if they were in the
public domain.
Modified: trunk/packages/seaview/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/seaview/trunk/debian/upstream-metadata.yaml 2010-08-23
09:56:30 UTC (rev 5181)
+++ trunk/packages/seaview/trunk/debian/upstream-metadata.yaml 2010-08-23
12:13:11 UTC (rev 5182)
@@ -1,10 +1,8 @@
Contact: Manolo Gouy <[email protected]>
Documentation: http://pbil.univ-lyon1.fr/software/seaview_data/seaview
-DOI: 10.1093/molbev/msp259
Downloads: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/
Homepage: http://pbil.univ-lyon1.fr/software/seaview
Name: SeaView
-PMID: 19854763
Reference:
author: Gouy, Manolo and Guindon, Stephane and Gascuel, Olivier
title: SeaView version 4 : a multiplatform graphical user interface for
sequence alignment and phylogenetic tree building
@@ -13,6 +11,8 @@
number: 2
pages: 221-224
year: 2010
+ PMID: 19854763
+ DOI: 10.1093/molbev/msp259
URL: http://mbe.oxfordjournals.org/cgi/content/abstract/27/2/221
eprint: http://mbe.oxfordjournals.org/cgi/reprint/27/2/221.pdf
Screenshots:
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