[med-svn] r1649 - trunk/packages/bioperl/trunk/debian
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sat Mar 22 05:16:55 UTC 2008
Author: charles-guest
Date: 2008-03-22 05:16:54 +0000 (Sat, 22 Mar 2008)
New Revision: 1649
Modified:
trunk/packages/bioperl/trunk/debian/README.Debian
trunk/packages/bioperl/trunk/debian/changelog
trunk/packages/bioperl/trunk/debian/control
trunk/packages/bioperl/trunk/debian/copyright
Log:
Downgraded most recommended package to the lower priority, and converted debian/copyright to a machine-readable format.
Modified: trunk/packages/bioperl/trunk/debian/README.Debian
===================================================================
--- trunk/packages/bioperl/trunk/debian/README.Debian 2008-03-22 04:17:37 UTC (rev 1648)
+++ trunk/packages/bioperl/trunk/debian/README.Debian 2008-03-22 05:16:54 UTC (rev 1649)
@@ -1,20 +1,23 @@
bioperl for DEBIAN
----------------------
-BioPerl on Debian has been configured to use the readseq program
-(see Bio::Parse and Bio::Seq) and so depends on readseq.
+* BioPerl on Debian has been configured to use the readseq program
+ (see Bio::Parse and Bio::Seq) and so depends on readseq.
-Stephane Bortzmeyer <bortzmeyer at debian.org>, Wed, 19 May 1999 11:35:30 +0200
+ Stephane Bortzmeyer <bortzmeyer at debian.org>, Wed, 19 May 1999 11:35:30 +0200
-Adopted by a new maintainer
- Matt Hope <dopey at debian.org> Tue, 6 Nov 2001 17:17:30 +1100
+* The Debian package for bioperl suggests the installation of all the perl
+ modules that are 'recommended' in the Build.PL file. As an exception to this,
+ libio-string-perl, libwww-perl, liburi-perl and libxml-writer-perl will be
+ installed by default, as they are more frequently used (see
+ http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html for the
+ discussion).
-and now by
+ To install bioperl and all the suggested Debian package, you can use the
+ option ~Rsuggests:^package$ of the `aptitude' package manager.
- Charles Plessy <charles-debian-nospam at plessy.org>
- assisted by the Debian-Med community.
+* Please cite:
-Please cite
@article{bioperl:2002,
author={J.E. Stajich and D. Block and K. Boulez and S.E. Brenner
and S.A. Chervitz and C. Dagdigian and G. Fuellen and J.G. Gilbert
Modified: trunk/packages/bioperl/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog 2008-03-22 04:17:37 UTC (rev 1648)
+++ trunk/packages/bioperl/trunk/debian/changelog 2008-03-22 05:16:54 UTC (rev 1649)
@@ -3,6 +3,11 @@
* debian/control:
- Removed MIA Matt Hope (dopey) from the Uploaders field.
Thank you for your work, Matt. I hope you are doing well.
+ - Downgraded some recommended package to the 'Suggests' priority,
+ according to the followingdiscussion on Upstream's mail list.
+ http://bioperl.org/pipermail/bioperl-l/2008-March/027379.html
+ (Closes: #448890)
+ * debian/copyright converted to machine-readable format.
-- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 18 Mar 2008 14:44:57 +0900
Modified: trunk/packages/bioperl/trunk/debian/control
===================================================================
--- trunk/packages/bioperl/trunk/debian/control 2008-03-22 04:17:37 UTC (rev 1648)
+++ trunk/packages/bioperl/trunk/debian/control 2008-03-22 05:16:54 UTC (rev 1649)
@@ -16,15 +16,16 @@
Package: bioperl
Architecture: all
Depends: libio-string-perl, ${perl:Depends}
-Recommends: libace-perl, libbio-asn1-entrezgene-perl, libclass-autoclass-perl,
+Recommends: libio-string-perl, libwww-perl, liburi-perl, libxml-writer-perl
+Suggests: libace-perl, libbio-asn1-entrezgene-perl, libclass-autoclass-perl,
libclone-perl, libconvert-binary-c-perl, libdata-stag-xmlwriter-perl,
libgd-gd2-perl, libgraph-perl, libhtml-parser-perl, libwww-perl,
libpostscript-perl, libset-scalar-perl, libsoap-lite-perl,
libspreadsheet-parseexcel-perl, libsvg-perl, libsvg-graph-perl,
libtext-shellwords-perl, liburi-perl, libxml-parser-perl, libxml-perl,
libxml-sax-perl, libxml-sax-writer-perl, libxml-twig-perl, libxml-writer-perl,
- libdbd-mysql-perl
-Suggests: blast2, clustalw, emboss, primer3, repeatmasker, glimmer, hmmer,
+ libdbd-mysql-perl,
+ blast2, clustalw, emboss, primer3, repeatmasker, glimmer, hmmer,
molphy, phylip, sim4 | sibsim4, wise, exonerate, spidey
Description: Perl tools for computational molecular biology
The Bioperl project is a coordinated effort to collect computational methods
Modified: trunk/packages/bioperl/trunk/debian/copyright
===================================================================
--- trunk/packages/bioperl/trunk/debian/copyright 2008-03-22 04:17:37 UTC (rev 1648)
+++ trunk/packages/bioperl/trunk/debian/copyright 2008-03-22 05:16:54 UTC (rev 1649)
@@ -1,59 +1,208 @@
-This package was debianized by Stephane Bortzmeyer bortzmeyer at debian.org on
-Wed, 19 May 1999 11:35:30 +0200.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Stephane Bortzmeyer bortzmeyer at debian.org
+X-Debinized-Date: Wed, 19 May 1999 11:35:30 +0200.
+X-Source-Downloaded-From: http://www.bioperl.org/DIST/
+Upstream Authors: Bioperl core developpers and many other contributors <bioperl-l at bioperl.org>
-It was downloaded from http://www.bioperl.org/
+Files: debian/*
+Copyright: © 1999 Stéphane Bortzmeyer <bortzmeyer at debian.org>
+ © 2001 Dr. Guenter Bechly <gbechly at debian.org>
+ © 2001 Adrian Bunk <bunk at fs.tum.de>
+ © 2001—2004 Matt Hope <dopey at debian.org>
+ © 2007—2008 Charles Plessy <charles-debian-nospam at plessy.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+ © 2008 Nelson A. de Oliveira <naoliv at debian.org>
+License: unclear
+ The license under which is placed the work of the earlier contributors is
+ unknown. The work of Charles Plessy can be treated as if it were public
+ domain.
-Upstream Authors: Bioperl Team <bioperl-l at bioperl.org>
-
-License:
-
- This program is free software; you can redistribute it and/or modify it
- under the terms of the "Artistic License" which comes with Debian.
-
- THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
- WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
- OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-
-On Debian systems, the complete text of the Artistic License
-can be found in `/usr/share/common-licenses/Artistic'.
-
-Bio/SeqIO/bsml.pm:
-
- Copyright (C) 2001 Charles Tilford <tilfordc at bms.com>
-
- This library 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 2.1 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
- Lesser General Public License for more details.
-
- You should have received a copy of the GNU Lesser General Public
- License along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
-On Debian systems, the complete text of the GNU Lesser General
+Files: Bio/SeqIO/bsml.pm
+Copyright: © 2001 Charles Tilford <tilfordc at bms.com>
+License: LGPL-2.1+
+ This library 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 2.1 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
+ Lesser General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+X-Comment: On Debian systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL'.
-t/lib/Error.pm:
-
- Copyright (C) 1997-8 Graham Barr <gbarr at ti.com>
-
+Files: t/lib/Error.pm
+Copyright: © 1997-8 Graham Barr <gbarr at ti.com>
+License: Artistic | GPL-1+
This program is free software; you can redistribute it and/or
modify it under the same terms as Perl itself.
+X-Comment: See below for the terms of the Perl license.
-t/lib/Test/Builder/Tester/Color.pm
-
- Copyright (C) 2002 Mark Fowler <mark at twoshortplanks.com>
-
+Files: t/lib/Test/Builder/Tester/Color.pm
+Copyright: © 2002 Mark Fowler <mark at twoshortplanks.com>
This program is free software; you can redistribute it
and/or modify it under the same terms as Perl itself.
+X-Comment: See below for the terms of the Perl license.
-Perl is distributed under your choice of the GNU General Public License or
-the Artistic License.
-
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Files: *
+Copyright: The Bioperl developers.
+ PRIMARY AUTHORS AND MAJOR CONTRIBUTORS TO BIOPERL
+ Releases co-ordinated and submitted by bioperl core devs.
+ .
+ .
+ * Ewan Birney <birney at ebi.ac.uk>
+ * Chris Dagdigian <dag at sonsorol.org>
+ * Hilmar Lapp <hlapp at gmx.net>
+ * Heikki Lehväslaiho <heikki at ebi.ac.uk>
+ * Jason Stajich <jason at bioperl.org>
+ * Lincoln Stein <lstein at cshl.org>
+ .
+ Previous Bioperl Coordinators:
+ .
+ .
+ * Steven Brenner <brenner at compbio.berkely.edu>
+ * Georg Fuellen <fuellen at alum.mit.edu>
+ * Steve Chervitz <sac at bioperl.org>
+ .
+ Major Contributors
+ .
+ * Richard Adams <Richard.Adams at ed.ac.uk>
+ * Shuly Avraham <avraham at cshl.org> - Bio::Graphics::Glyph
+ * Sendu Bala <bix at sendu.me.uk>
+ * Peter Blaiklock <pblaiklo at restrictionmapper.org>
+ * Benjamin Berman <benb at fruitfly.berkeley.edu>
+ * Matthew Betts <Matthew.Betts at ii.uib.no>
+ * David Block <dblock at gnf.org>
+ * Kris Boulez <kris.boulez at algonomics.com>
+ * Tim Bunce <Tim.Bunce at pobox.com> - code optimizations
+ * Scott Cain <cain at cshl.org> - Bio::Graphics::Glyph
+ * Yee Man Chan <ymc at yahoo.com> - Bio::Tools::dpAlign
+ * Brad Chapman <chapmanb at arches.uga.edu>
+ * Michele Clamp <michele at sanger.ac.uk>
+ * Tony Cox <avc at sanger.ac.uk>
+ * James Cuff <james at sanger.ac.uk>
+ * Andrew Dalke <dalke at acm.org>
+ * Allen Day <allenday at ucla.edu>
+ * Jared Fox <jaredfox at ucla.edu> - Bio::SeqIO::interpro
+ * Brian O’Connor <boconnor at ucla.edu> - Bio::TreeIO::svggraph
+ * James Diggans <JDiggans at genelogic.com>
+ * Peter Dimitrov <dimitrov at gnf.org> - Bio::Ontology
+ * Rich Dobson <r.j.dobson at qmul.ac.uk> - Bio::Pop‐Gen::IO::hapmap,phase
+ * Paul Edlefsen <pedlefsen at systemsbiology.org>
+ * Rob Edwards <redwards at utmem.edu> - Bio::Restriction
+ * Arne Elofsson <arne at sbc.su.se>
+ * David Evans <David.Evans at vir.gla.ac.uk>
+ * Christopher Fields <cjfields at uiuc.edu>
+ * Mark Fiers <M.W.E.J.Fiers at plant.wag-ur.nl>
+ * The Fugu Team <fuguteam at fugu-sg.org>
+ * Luc Gauthier <lgauthie at hotmail.com>
+ * James Gilbert <jgrg at sanger.ac.uk>
+ * Nat Goodman
+ * Ed Green <ed at compbio.berkeley.edu>
+ * Matthew Hahn <matthew.hahn at duke.edu>
+ * Roger Hall <roger at iosea.com>
+ * Todd Harris <harris at cshl.org> - SVG support in Bio::Graphics
+ * Mauricio Herrera Cuadra <arareko at campus.iztacala.unam.mx>
+ * Ian Holmes <ihn at fruitfly.org>
+ * Shawn Hoon <shawnh at fugu-sg.org>
+ * Robert Hubley <rhubley at systemsbiology.org>
+ * Joseph Insana <insana at ebi.ac.uk> - Bio::LiveSeq
+ * Donald Jackson <donald.jackson at bms.com> - SiRNA
+ * Keith James <kdj at sanger.ac.uk> - Bio::Tools::Geneid
+ * Nicolas Joly <njoly at pasteur.fr>
+ * Ian Korf <ikorf at sapiens.wustl.edu>
+ * Dan Kortschak <kortschak at rsbs.anu.edu.au>
+ * Arek Kasprzyk <arek at ebi.ac.uk>
+ * Andreas Kähäri <andreas.kahari at ebi.ac.uk>
+ * Charles C. Kim <cckim at stanford.edu>
+ * Stefan Kirov <skirov at utk.edu> - Bio::Matrix::PSM
+ * Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
+ * Josh Lauricha <laurichj at cs.ucr.edu> - Bio::SeqIO::tigr
+ * Eckhard Lehmann <ecky at e-lehmann.de>
+ * Catherine Letondal <letondal at pasteur.fr>
+ * Philip Lijnzaad <p.lijnzaad at med.uu.nl>
+ * Aaron Mackey <amackey at pcbi.upenn.edu>
+ * Brad Marshall <bradmars at yahoo.com>
+ * Chad Matsalla <chad at dieselwurks.com>
+ * Andrew Macgregor <andrew at anatomy.otago.ac.nz>
+ * Sheldon McKay <mckays at cshl.edu>
+ * Juha Muilu <muilu at ebi.ac.uk>
+ * Chris Mungall <cjm at fruitfly.org>
+ * Giri Narasimhan <giri at cs.fiu.edu>
+ * Brian Osborne <bosborne at alum.mit.edu>
+ * Xiaokang Pan <pan at cshl.org> - Bio::Graphics::Glyph
+ * Jong Park
+ * Matthew Pocock <matthew_pocock at yahoo.co.uk>
+ * Lorenz Pollack <lorenz at ist.org> -- BPlite porting
+ * Richard Resnick -- original Bio::Seq
+ * Todd Richmond <todd at andrew2.stanford.edu>
+ * Peter Schattner <schattner at alum.mit.edu>
+ * Torsten Seemann <torsten.seemann at infotech.monash.edu.au> -- Bio::Tools::Run::StandaloneBlast
+ * Martin Senger <senger at ebi.ac.uk> -- Bio::Biblio
+ * Nigam Shah <nigam at psu.edu>
+ * Shengqiang Shu <sshu at bdgp.lbl.gov> - Bio::Graphics::Glyph
+ * Allen Smith <allens at cpan.org> -- Bio::Matrix and Bio::SimpleAlign fixes
+ * Marc Sohrmann <ms2 at sanger.ac.uk>
+ * Robson Francisco de Souza <rfsouza at citri.iq.usp.br> - Bio::Assem‐bly
+ * Mark Southern <mark_southern at merck.com>
+ * Will Spooner <whs at sanger.ac.uk>
+ * Arne Stabenau <stabenau at ebi.ac.uk>
+ * Elia Stupka <elia at fugu-sg.org>
+ * Gert Thijs <gert.thijs at esat.kuleuven.ac.be>
+ * James Thompson <tex at biosysadmin.com> - Bio::Matrix::PSM protein-related modules.
+ * Charles Tilford <tilfordc at bms.com>
+ * Anthony Underwood <aunderwood at phls.org.uk>
+ * Paul-Christophe Varoutas
+ * Andrew G. Walsh <paeruginosa at hotmail.com>
+ * Kai Wang <tumorimmunology at yahoo.com>
+ * Gary Williams <G.Williams at hgmp.mrc.ac.uk>
+ * Mark Wilkinson <mwilkinson at gene.pbi.nrc.ca>
+ * Helge Weissig <helgew at sdsc.edu>
+ * Juguang Xiao <juguang at tll.org.sg>
+ * Alex Zelensky <alex_zelensky at mac.com> - Bioperl-DB
+ * Peili Zhang <peili at morgan.harvard.edu>
+ * Christian M. Zmasek <czmasek at gnf.org> - Bio::Phenotype & Bio::Ontology
+License: Artistic | GPL-1+
+ Everyone can use it! We don't care if you are academic, corporate, or
+ government. BioPerl is licensed under the same terms as Perl itself, which
+ means it is dually-licensed under either the Artistic or GPL licenses. The Perl
+ Artistic License, or the GNU GPL covers all the legalese and what you can and
+ can't do with the source code.
+ .
+ We do appreciate:
+ .
+ * You letting us know you sell or use a product that uses BioPerl. This helps
+ us show people how useful our toolkit is. It also helps us if we seek funding
+ from a government source, to identify the utility of the code to many different
+ groups of users. Add your project and institution to our BioPerl Users page.
+ .
+ * If you fix bugs, please let us know about them. Because Bioperl is
+ dual-licensed under the GPL or Artistic licenses, you can choose the Artistic
+ license, which means that you are not required to submit the code fixes, but in
+ the spirit of making a better product we hope you'll contribute back to the
+ community any insight or code improvements.
+ .
+ * Please include the AUTHORS file and ascribe credit to the original BioPerl
+ toolkit where appropriate.
+ .
+ * If you are an academic and you use the software, please cite the article.
+ See the BioPerl publications for a list of papers which describe components in
+ the toolkit.
+X-Comment: see http://www.bioperl.org/wiki/Licensing_BioPerl
+X-Comment: Perl license
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of either:
+ .
+ a) the GNU General Public License as published by the Free Software
+ Foundation; either version 1, or (at your option) any later
+ version, or
+ .
+ b) the "Artistic License" which comes with Perl.
+X-Comment: On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic', and the complete text of the
+ GNU General Public License can be found in `/usr/share/common-licenses/GPL'.
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