[Collab-qa-commits] r2337 - in packages-metadata: a g l m p r s
Charles Plessy
plessy at alioth.debian.org
Wed May 16 23:50:31 UTC 2012
Author: plessy
Date: 2012-05-16 23:50:30 +0000 (Wed, 16 May 2012)
New Revision: 2337
Added:
packages-metadata/a/abyss.copyright
packages-metadata/a/abyss.upstream
packages-metadata/g/gbrowse.copyright
packages-metadata/g/gbrowse.upstream
packages-metadata/l/libhmsbeagle.copyright
packages-metadata/l/libhmsbeagle.upstream
packages-metadata/m/mlv-smile.upstream
packages-metadata/p/praat.copyright
packages-metadata/p/praat.upstream
packages-metadata/r/r-bioc-edger.copyright
packages-metadata/r/r-bioc-edger.upstream
packages-metadata/r/r-cran-genabel.copyright
packages-metadata/r/r-cran-genabel.upstream
packages-metadata/s/snap.copyright
packages-metadata/s/snap.upstream
Modified:
packages-metadata/m/mlv-smile.copyright
Log:
Manual umegaya push, see 20120516234937.GE17262 at falafel.plessy.net
Added: packages-metadata/a/abyss.copyright
===================================================================
--- packages-metadata/a/abyss.copyright (rev 0)
+++ packages-metadata/a/abyss.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,354 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ABySS
+Upstream-Contact: Shaun Jackman <sjackman at bcgsc.ca>
+Source: http://www.bcgsc.ca/platform/bioinfo/software/abyss
+ https://github.com/sjackman/abyss
+
+Files: *
+Copyright: Copyright 2012 Genome Sciences Centre
+License: BCCA-Academic
+
+Files: Common/* DistanceEst/* ParseAligns/*
+Copyright: Copyright 2012 Genome Sciences Centre
+License: BCCA-Academic or GPL-3+
+
+Files: Common/HashFunction.cpp
+Copyright: public-domain
+License: public-domain
+ You can use this free for any purpose. It's in the public domain.
+ It has no warranty.
+
+Files: dialign/*
+Copyright: Copyright 2008 Amarendran R. Subramanian
+License: LGPL-2.1+
+ On Debian systems, see `/usr/share/common-licenses/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 Street, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ Amarendran R. Subramanian, hereby disclaims all copyright interest in the
+ DIALIGN-TX (a multiple sequence alignment algorithm) written by Amarendran R. Subramanian.
+ .
+ Amarendran R. Subramanian, 2004-2008
+ .
+ DIALIGN-TX has been co-authored by Volker Menrad and Dorothea Emig.
+ .
+ Research work using DIALIGN-TX should cite:
+ .
+ DIALIGN-TX: improvement of the segment-based approach for multiple
+ sequence alignment by combining greedy and progressive alignment
+ strategies
+ Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern,
+ Algorithms for Molecular Biology 3:6, 2008
+ .
+ DIALIGN-T: An improved algorithm for segment-based multiple
+ sequence alignment
+ Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann,
+ Burkhard Morgenstern, BMC Bioinformatics 6:66, 2005
+
+Files: FMIndex/bit_array.h
+Copyright: Copyright 2010 Daisuke Okanohara
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ Redistributions of source code must retain the above Copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ Redistributions in binary form must reproduce the above Copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ Neither the name of the authors nor the names of its contributors
+ may be used to endorse or promote products derived from this
+ software without specific prior written permission.
+
+Files: FMIndex/sais.hxx
+Copyright: Copyright 2010 Yuta Mori
+License: Expat
+ Permission is hereby granted, free of charge, to any person
+ obtaining a copy of this software and associated documentation
+ files (the "Software"), to deal in the Software without
+ restriction, including without limitation the rights to use,
+ copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following
+ conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ OTHER DEALINGS IN THE SOFTWARE.
+
+License: BCCA-Academic
+ Debian may redistribute this software package.
+ .
+ BC CANCER AGENCY SOFTWARE LICENSE AGREEMENT (ACADEMIC USE)
+ CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS. This License
+ Agreement (the "Agreement") is a legal contract between you, your
+ employer, educational institution or organization (collectively, "You")
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+ 3. RESTRICTIONS: You acknowledge and agree that You shall not, and
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+ 8. LIMITATION OF LIABILITY: TO THE MAXIMUM EXTENT PERMITTED BY
+ APPLICABLE LAW, IN NO EVENT SHALL THE AGGREGATE LIABILITY OF BCCA TO
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+ relating to infringement of BCCA's intellectual property rights or
+ the intellectual property rights of any third party.
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+ 10. SUPPORT AND MAINTENANCE: You acknowledge and agree that, unless
+ and to the extent expressly agreed by BCCA in a separate written
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+ maintenance from BCCA and, for greater certainty, BCCA shall have
+ no obligation to issue any update or upgrade to any Product.
+ .
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+ terminate this Agreement at any time by ceasing use of the Product
+ and destroying or deleting any copies of the Product. This
+ Agreement will terminate immediately without notice from BCCA if
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+ determines, in its sole discretion, that any continued use of the
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+ following: Title 48 CFR 2.101, 52.227-19, 227.7201 through
+ 227.7202-4, FAR 52.227-14, and FAR 52.227-19(c)(1-2) and (6/87),
+ and where applicable, the customary software license, as described
+ in Title 48 CFR 227-7202 with respect to commercial software and
+ commercial software documentation including DFAR 252.227-7013,
+ DFAR 252,227-7014, DFAR 252.227-7015 and DFAR 252.7018, all as
+ applicable.
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+ (f) The provisions of this Agreement are severable in that if any
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+ its sole discretion may assign this Agreement without notice to You.
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+License: GPL-3+
+ 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 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 General Public License for more
+ details.
+ .
+ You should have received a copy of the GNU 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 full text of the GNU General Public
+ License version 3 can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
+
Added: packages-metadata/a/abyss.upstream
===================================================================
--- packages-metadata/a/abyss.upstream (rev 0)
+++ packages-metadata/a/abyss.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,13 @@
+Name: ABySS
+Reference:
+ Author: Jared T. Simpson and Kim Wong and Shaun D. Jackman and Jacqueline E. Schein and Steven J.M. Jones and İnanç Birol
+ Title: "ABySS: A parallel assembler for short read sequence data"
+ Journal: Genome Research
+ Year: 2009
+ Volume: 19
+ Number: 6
+ Pages: 1117-23
+ PMID: 19251739
+ DOI: 10.1101/gr.089532.108
+ URL: http://genome.cshlp.org/content/19/6/1117
+ eprint: http://genome.cshlp.org/content/19/6/1117.full.pdf+html
Added: packages-metadata/g/gbrowse.copyright
===================================================================
--- packages-metadata/g/gbrowse.copyright (rev 0)
+++ packages-metadata/g/gbrowse.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,386 @@
+Format: http://anonscm.debian.org/viewvc/dep/web/deps/dep5.mdwn?revision=174
+Source: http://search.cpan.org/dist/GBrowse/
+
+Files: *
+Copyright: © 2002 Cold Spring Harbor Laboratory and University of California, Berkeley
+ © 2008 H. Mark Okada <hmokada at hotmail.com>.
+ © 2001,2003,2005,2008 Cold Spring Harbor Laboratory
+ © 2010 Ontario Institute for Cancer Research
+License: GPL-1+ or Artistic-2.0
+ The Generic Genome Browser package versions between 1.0 and 1.8 and
+ all associated files are Copyright (c) 2002 Cold Spring Harbor
+ Laboratory and University of California, Berkeley. Versions 1.9 and
+ higher are copyright (c) 2010 Ontario Institute for Cancer Research.
+ .
+ This package and its accompanying libraries is free software; you can
+ redistribute it and/or modify it under the terms of the GPL (either
+ version 1, or at your option, any later version) or the Artistic
+ License 2.0. Refer to LICENSE for the full license text.
+ .
+ CSHL makes no representations whatsoever as to the SOFTWARE contained
+ herein. It is experimental in nature and is provided WITHOUT WARRANTY
+ OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER
+ WARRANTY, EXPRESS OR IMPLIED. CSHL MAKES NO REPRESENTATION OR
+ WARRANTY THAT THE USE OF THIS SOFTWARE WILL NOT INFRINGE ANY PATENT OR
+ OTHER PROPRIETARY RIGHT.
+ .
+ By downloading this SOFTWARE, your Institution hereby indemnifies CSHL
+ against any loss, claim, damage or liability, of whatsoever kind or
+ nature, which may arise from your Institution's respective use,
+ handling or storage of the SOFTWARE.
+ .
+ If publications result from research using this SOFTWARE, we ask that
+ CSHL, University of California, Berkeley and the Ontario Institute for
+ Cancer Research be acknowledged and/or credit be given to
+ CSHL/Berkeley/OICR scientists, as scientifically appropriate.
+
+Files: bin/auto_install_databases.pl
+ bin/bed2gff3.pl
+ bin/bp_load_gff.pl
+ bin/gtf2gff3.pl
+ bin/load_genbank.pl
+ bin/make_das_conf.pl
+ bin/process_gadfly.pl
+ bin/process_ncbi_human.pl
+ bin/process_ncbi_human.pl
+ bin/process_sgd.pl
+ bin/ucsc_genes2gff.pl
+ cgi-bin/gbrowse_img
+ conf/plugins/Aligner.pm
+ conf/plugins/AttributeHiliter.pm
+ conf/plugins/RestrictionAnnotator.pm
+ conf/plugins/SequenceDumper.pm
+ conf/plugins/SimpleTrackFinder.pm
+ conf/plugins/Spectrogram.pm
+ conf/plugins/TrackFinder.pm
+ contrib/Coverage/plugin/Coverage.pm
+ docs/pod/GBROWSE_IMG.pod
+ docs/pod/MAKE_IMAGES_HOWTO.pod
+ docs/pod/PLUGINS_HOWTO.pod
+ htdocs/gbrowse_karyotype_help.html
+ lib/Bio/DB/GFF/Aggregator/reftranscript.pm
+ lib/Bio/DB/GFF/Aggregator/waba_alignment.pm
+ lib/Bio/DB/GFF/Aggregator/wormbase_gene.pm
+ lib/Bio/Graphics/Browser2/CAlign.pm
+ lib/Bio/Graphics/Browser2/Markup.pm
+ lib/Bio/Graphics/Browser2/OptionPick.pm
+ lib/Bio/Graphics/Browser2/PadAlignment.pm
+ lib/Bio/Graphics/Browser2/Realign.pm
+ lib/CGI/Toggle.pm
+ libalign/CAlign.pm
+Copyright: © 2001–4 Cold Spring Harbor Laboratory
+ © Jason Stajich and Cold Spring Harbor Laboratories 2002
+ © 2009 Ontario Institute for Cancer Research
+ © 2007, University of Utah
+ © 2002 Regional Blood Center of Ribeirao Preto
+ © 2002 Advanced Biomedical Computing Center, SAIC/NCI-Frederick.
+License: GPL-1+ or Artistic
+ This library is free software; you can redistribute it and/or modify
+ it under the same terms as Perl itself. See DISCLAIMER.txt for
+ disclaimers of warranty.
+
+Files: t/Test.pm
+Copyright: © 1998-1999 Joshua Nathaniel Pritikin. All rights reserved.
+License: Artistic
+ This package is free software and is provided "as is" without express
+ or implied warranty. It may be used, redistributed and/or modified
+ under the terms of the Perl Artistic License (see
+ http://www.perl.com/perl/misc/Artistic.html)
+
+Files: htdocs/css/dropdown/default_theme.css htdocs/css/dropdown/dropdown.css
+Copyright: © 2008 Live Web Institute. All Rights Reserved.
+License: GPL-3+
+Comment: Checked on http://lwis.net/free-css-drop-down-menu/: “This CSS Drop-Down Menu
+ is free for commercial or personal use and is licensed under the GNU General
+ Public License.”
+
+Files: docs/pod/INSTALL.MacOSX.pod
+Copyright: © 2003 Cold Spring Harbor Laboratory
+License: missing-most-probably-same-as-Perl
+ Material in this document is copyright 2001-2003 by the Cold Spring
+ Harbor Laboratory. This information is provided "AS-IS" without any
+ warranty, expressed or implied.
+
+Files: htdocs/js/*.js
+Copyright: © 2005-2010 Thomas Fuchs (http://script.aculo.us, http://mir.aculo.us)
+ © 2005-2010 Ivan Krstic (http://blogs.law.harvard.edu/ivan)
+ © 2005-2010 Jon Tirsen (http://www.tirsen.com)
+ © 2007,2008 Sheldon McKay, Cold Spring Harbor Laboratory
+License: MIT
+
+Files: htdocs/js/prototype.js
+Copyright: © 2005-2010 Sam Stephenson
+ © 2009, The Dojo Foundation
+License: Dojo
+ Released under the MIT, BSD, and GPL Licenses.
+ More information: http://sizzlejs.com/
+
+Files: htdocs/js/x_cook.js
+Copyright: © 2004 Michael Foster
+License: LGPL-2.1+
+
+Files: htdocs/subtracktable.js
+Copyright: © 2005-2009 Matt Kruse (javascripttoolbox.com)
+License: MIT or GPL
+ Dual licensed under the MIT and GPL licenses.
+ This basically means you can use this code however you want for
+ free, but don't claim to have written it yourself!
+ Donations always accepted: http://www.JavascriptToolbox.com/donate/
+ .
+ Please do not link to the .js files on javascripttoolbox.com from
+ your site. Copy the files locally to your server instead.
+
+Files: debian/*
+Copyright: 2011, Olivier Sallou <olivier.sallou at irisa.fr>
+License: Artistic-2.0 or GPL-1+
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+License: GPL-1+
+ 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 1, 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, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston MA 02110-1301 USA
+ .
+ On Debian GNU/Linux systems, the complete text of version 1 of the
+ General Public License can be found in `/usr/share/common-licenses/GPL-1'.
+
+License: GPL-3+
+ 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 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 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/>
+ or </usr/share/common-licenses/GPL-3>.
+
+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 Street, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian GNU/Linux systems, the complete text of version 2.1 of the
+ Lesser General Public License can be found in `/usr/share/common-licenses/LGPL-2.1'.
+
+License: Artistic
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the Artistic License, which comes with Perl.
+ .
+ On Debian GNU/Linux systems, the complete text of the Artistic License
+ can be found in `/usr/share/common-licenses/Artistic'.
+
+License: Artistic-2.0
+ Copyright (c) 2000-2006, The Perl Foundation.
+ .
+ Everyone is permitted to copy and distribute verbatim copies of this license
+ document, but changing it is not allowed.
+ .
+ .
+ Preamble
+ This license establishes the terms under which a given free software Package may
+ be copied, modified, distributed, and/or redistributed. The intent is that the
+ Copyright Holder maintains some artistic control over the development of that
+ Package while still keeping the Package available as open source and free
+ software.
+ .
+ You are always permitted to make arrangements wholly outside of this license
+ directly with the Copyright Holder of a given Package. If the terms of this
+ license do not permit the full use that you propose to make of the Package, you
+ should contact the Copyright Holder and seek a different licensing arrangement.
+ .
+ .
+ Definitions
+ "Copyright Holder" means the individual(s) or organization(s) named in the
+ copyright notice for the entire Package.
+ .
+ "Contributor" means any party that has contributed code or other material to the
+ Package, in accordance with the Copyright Holder's procedures.
+ .
+ "You" and "your" means any person who would like to copy, distribute, or modify
+ the Package.
+ .
+ "Package" means the collection of files distributed by the Copyright Holder, and
+ derivatives of that collection and/or of those files. A given Package may
+ consist of either the Standard Version, or a Modified Version.
+ .
+ "Distribute" means providing a copy of the Package or making it accessible to
+ anyone else, or in the case of a company or organization, to others outside of
+ your company or organization.
+ .
+ "Distributor Fee" means any fee that you charge for Distributing this Package or
+ providing support for this Package to another party. It does not mean licensing
+ fees.
+ .
+ "Standard Version" refers to the Package if it has not been modified, or has
+ been modified only in ways explicitly requested by the Copyright Holder.
+ .
+ "Modified Version" means the Package, if it has been changed, and such changes
+ were not explicitly requested by the Copyright Holder.
+ .
+ "Original License" means this Artistic License as Distributed with the Standard
+ Version of the Package, in its current version or as it may be modified by The
+ Perl Foundation in the future.
+ .
+ "Source" form means the source code, documentation source, and configuration
+ files for the Package.
+ .
+ "Compiled" form means the compiled bytecode, object code, binary, or any other
+ form resulting from mechanical transformation or translation of the Source form.
+ .
+ .
+ Permission for Use and Modification Without Distribution
+ (1) You are permitted to use the Standard Version and create and use Modified
+ Versions for any purpose without restriction, provided that you do not
+ Distribute the Modified Version.
+ .
+ .
+ Permissions for Redistribution of the Standard Version
+ (2) You may Distribute verbatim copies of the Source form of the Standard
+ Version of this Package in any medium without restriction, either gratis or for
+ a Distributor Fee, provided that you duplicate all of the original copyright
+ notices and associated disclaimers. At your discretion, such verbatim copies may
+ or may not include a Compiled form of the Package.
+ .
+ (3) You may apply any bug fixes, portability changes, and other modifications
+ made available from the Copyright Holder. The resulting Package will still be
+ considered the Standard Version, and as such will be subject to the Original
+ License.
+ .
+ .
+ Distribution of Modified Versions of the Package as Source
+ (4) You may Distribute your Modified Version as Source (either gratis or for a
+ Distributor Fee, and with or without a Compiled form of the Modified Version)
+ provided that you clearly document how it differs from the Standard Version,
+ including, but not limited to, documenting any non-standard features,
+ executables, or modules, and provided that you do at least ONE of the
+ following:
+ .
+ (a) make the Modified Version available to the Copyright Holder of the Standard
+ Version, under the Original License, so that the Copyright Holder may include
+ your modifications in the Standard Version.
+ .
+ (b) ensure that installation of your Modified Version does not prevent the user
+ installing or running the Standard Version. In addition, the Modified Version
+ must bear a name that is different from the name of the Standard Version.
+ .
+ (c) allow anyone who receives a copy of the Modified Version to make the Source
+ form of the Modified Version available to others under
+ .
+ (i) the Original License or
+ .
+ (ii) a license that permits the licensee to freely copy, modify and redistribute
+ the Modified Version using the same licensing terms that apply to the copy that
+ the licensee received, and requires that the Source form of the Modified
+ Version, and of any works derived from it, be made freely available in that
+ license fees are prohibited but Distributor Fees are allowed.
+ .
+ Distribution of Compiled Forms of the Standard Version or Modified Versions without the Source
+ .
+ (5) You may Distribute Compiled forms of the Standard Version without the
+ Source, provided that you include complete instructions on how to get the
+ Source of the Standard Version. Such instructions must be valid at the time of
+ your distribution. If these instructions, at any time while you are carrying out
+ such distribution, become invalid, you must provide new instructions on demand
+ or cease further distribution. If you provide valid instructions or cease
+ distribution within thirty days after you become aware that the instructions are
+ invalid, then you do not forfeit any of your rights under this license.
+ .
+ (6) You may Distribute a Modified Version in Compiled form without the Source,
+ provided that you comply with Section 4 with respect to the Source of the
+ Modified Version.
+ .
+ .
+ Aggregating or Linking the Package
+ (7) You may aggregate the Package (either the Standard Version or Modified
+ Version) with other packages and Distribute the resulting aggregation provided
+ that you do not charge a licensing fee for the Package. Distributor Fees are
+ permitted, and licensing fees for other components in the aggregation are
+ permitted. The terms of this license apply to the use and Distribution of the
+ Standard or Modified Versions as included in the aggregation.
+ .
+ (8) You are permitted to link Modified and Standard Versions with other works,
+ to embed the Package in a larger work of your own, or to build stand-alone
+ binary or bytecode versions of applications that include the Package, and
+ Distribute the result without restriction, provided the result does not expose a
+ direct interface to the Package.
+ .
+ .
+ Items That are Not Considered Part of a Modified Version
+ (9) Works (including, but not limited to, modules and scripts) that merely
+ extend or make use of the Package, do not, by themselves, cause the Package to
+ be a Modified Version. In addition, such works are not considered parts of the
+ Package itself, and are not subject to the terms of this license.
+ .
+ .
+ General Provisions
+ (10) Any use, modification, and distribution of the Standard or Modified
+ Versions is governed by this Artistic License. By using, modifying or
+ distributing the Package, you accept this license. Do not use, modify, or
+ distribute the Package, if you do not accept this license.
+ .
+ (11) If your Modified Version has been derived from a Modified Version made by
+ someone other than you, you are nevertheless required to ensure that your
+ Modified Version complies with the requirements of this license.
+ .
+ (12) This license does not grant you the right to use any trademark, service
+ mark, tradename, or logo of the Copyright Holder.
+ .
+ (13) This license includes the non-exclusive, worldwide, free-of-charge patent
+ license to make, have made, use, offer to sell, sell, import and otherwise
+ transfer the Package with respect to any patent claims licensable by the
+ Copyright Holder that are necessarily infringed by the Package. If you institute
+ patent litigation (including a cross-claim or counterclaim) against any party
+ alleging that the Package constitutes direct or contributory patent
+ infringement, then this Artistic License to you shall terminate on the date that
+ such litigation is filed.
+ .
+ (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT HOLDER AND
+ CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES. THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR
+ NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT PERMITTED BY YOUR LOCAL LAW.
+ UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY
+ OUT OF THE USE OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
Added: packages-metadata/g/gbrowse.upstream
===================================================================
--- packages-metadata/g/gbrowse.upstream (rev 0)
+++ packages-metadata/g/gbrowse.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,8 @@
+Reference:
+ Author: Maureen J. Donlin
+ Title: "Using the Generic Genome Browser (GBrowse)"
+ Journal: Department of Biochemistry and Molecular Biology and Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine
+ Year: 2009
+ DOI: 10.1002/0471250953.bi0909s28
+ URL: http://www.currentprotocols.com/WileyCDA/CPUnit/refId-bi0909.html
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0909s28/pdf
Added: packages-metadata/l/libhmsbeagle.copyright
===================================================================
--- packages-metadata/l/libhmsbeagle.copyright (rev 0)
+++ packages-metadata/l/libhmsbeagle.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: beagle-lib
+Upstream-Contact: Aaron Darling <aarondarling at ucdavis.edu>
+Source: http://code.google.com/p/beagle-lib/source/browse/#svn%2Ftags
+
+Files: *
+Copyright: © 2009-2011 The BEAGLE Developer group
+License: 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/>.
+ .
+ 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: © 2011 Tim Booth <tbooth at ceh.ac.uk>
+ © 2012 Andreas Tille <tille at debian.org>
+License: LGPL-3+
+ Same license as the software itself
+
Added: packages-metadata/l/libhmsbeagle.upstream
===================================================================
--- packages-metadata/l/libhmsbeagle.upstream (rev 0)
+++ packages-metadata/l/libhmsbeagle.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,16 @@
+Contact: Andrew Rambaut <rambaut at gmail.com>
+Homepage: http://code.google.com/p/beagle-lib
+Name: beagle-lib
+Reference:
+ author: Daniel L. Ayres and Aaron Darling and Derrick J. Zwickl and Peter Beerli and Mark T. Holder and Paul O. Lewis and John P. Huelsenbeck and Fredrik Ronquist and David L. Swofford and Michael P. Cummings and Andrew Rambaut and Marc A. Suchard
+ title: >
+ BEAGLE: an Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics
+ journal: Systematic Biology
+ year: 2012
+ volume: 61
+ number: 1
+ pages: 170-3
+ DOI: 10.1093/sysbio/syr100
+ PMID: 21963610
+ URL: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.abstract
+ eprint: http://sysbio.oxfordjournals.org/content/early/2011/09/29/sysbio.syr100.full.pdf+html
Modified: packages-metadata/m/mlv-smile.copyright
===================================================================
--- packages-metadata/m/mlv-smile.copyright 2012-05-16 23:12:57 UTC (rev 2336)
+++ packages-metadata/m/mlv-smile.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -1,8 +1,9 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Contact: Alain.Viari at inrialpes.fr
Source: http://www-igm.univ-mlv.fr/~marsan/smile_english.html
Files: *
-Copyright: © 2004 L.Marsan (lama -AT- prism.uvsq.fr)
+Copyright: © 2004 L.Marsan (lama at prism.uvsq.fr)
License: GPL-2+
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
@@ -25,7 +26,6 @@
P_BLOCS/include/libsysk.h
P_BLOCS/src/libfasta.c
Copyright: © Atelier de BioInformatique
-Contact: Alain.Viari at inrialpes.fr
License: LGPL-2+
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
@@ -44,3 +44,4 @@
Comment: On Debian systems, the complete text of the GNU LGPL version 2 can be
found in ‘/usr/share/common-licenses/LGPL-2.1’. The mismatch between licence
name and license version is verbatim from the source file headers.
+
Added: packages-metadata/m/mlv-smile.upstream
===================================================================
--- packages-metadata/m/mlv-smile.upstream (rev 0)
+++ packages-metadata/m/mlv-smile.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,40 @@
+Reference:
+ - Author: L. Marsan and M.-F. Sagot
+ Title: Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification
+ Journal: J. of Comput. Biol.
+ Year: 2000
+ Volume: 7
+ Number: 3-4
+ Pages: 345-362
+ DOI: 10.1089/106652700750050826
+ PMID: 11108467
+ URL: http://online.liebertpub.com/doi/abs/10.1089/106652700750050826
+ eprint: http://online.liebertpub.com/doi/pdfplus/10.1089/106652700750050826
+ - Author: A. Vanet and L. Marsan and M.-F. Sagot
+ Title: Promoter sequences and algorithmical methods for identifying them
+ Journal: Research in Microbiology
+ Year: 1999
+ Volume: 150
+ Number: 9-10
+ Pages: 779-799
+ DOI: 10.1016/S0923-2508(99)00115-1
+ PMID: 10673015
+ URL: http://www.sciencedirect.com/science/article/pii/S0923250899001151
+ - Author: A. Vanet and L. Marsan and A. Labigne and M.-F. Sagot
+ Title: Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.
+ Journal: J. Mol. Biol.
+ Year: 2000
+ Volume: 297
+ Number: 2
+ Pages: 335-353
+ DOI: 10.1006/jmbi.2000.3576
+ PMID: 10715205
+ URL: http://www.sciencedirect.com/science/article/pii/S0022283600935769
+ - Author: D. Arquès and J.-P. Fallot and L. Marsan and C. Michel
+ Title: An evolutionary analytical model of a complementary circular code
+ Journal: Biosystems
+ Year: 1999
+ Volume: 49
+ Number: 2
+ Pages: 83-103
+ PMID: 10203190
Added: packages-metadata/p/praat.copyright
===================================================================
--- packages-metadata/p/praat.copyright (rev 0)
+++ packages-metadata/p/praat.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,224 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Program for speech analysis and synthesis
+Upstream-Contact: Paul Boersma <paul.boersma at uva.nl>
+Source: http://www.fon.hum.uva.nl/praat/download_sources.html
+
+Files: EEG/* artsynth/* fon/* gram/* kar/* num/* stat/* sys/* FFNet/* LPC/*
+ dwsys/* dwtools/*
+Copyright: 1990-2012 Paul Boersma
+ 1992-2012 David Weenink
+ 2007 Erez Volk
+ 2002 Hansjoerg Mixdorff
+License: GPL-2+
+
+Files: external/glpk/*
+Copyright: 1996-2010 Andrew Makhorin
+License: GPL-3+
+
+Files: external/flac/*
+Copyright: 2000-2007 Josh Coalson
+License: BSD (3 clause)
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ .
+ - Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ - Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in the
+ documentation and/or other materials provided with the distribution.
+ .
+ - Neither the name of the Xiph.org Foundation nor the names of its
+ contributors may be used to endorse or promote products derived from
+ this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE FOUNDATION OR
+ CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: external/flac/flac_share_alloc.h
+Copyright: 2007 Josh Coalson
+License: LGPL-2.1+
+
+Files: external/mp3/*
+Copyright: 2000-2004 Underbit Technologies, Inc
+ 2007 Erez Volk
+License: GPL-2+
+
+Files: external/portaudio/* external/espeak/portaudio*
+Copyright: 1999-2007 Ross Bencina, Phil Burk
+ 1999-2006 Robert Marsanyi
+ 1999-2004 Andrew Baldwin
+ 2002 Joshua Haberman
+ 2005-2007 Arve Knudsen
+ 2005-2006 Bjorn Roche
+License: MIT/X11 (BSD like)
+ Permission is hereby granted, free of charge, to any person obtaining
+ a copy of this software and associated documentation files
+ (the "Software"), to deal in the Software without restriction,
+ including without limitation the rights to use, copy, modify, merge,
+ publish, distribute, sublicense, and/or sell copies of the Software,
+ and to permit persons to whom the Software is furnished to do so,
+ subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be
+ included in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR
+ ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
+ CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+Files: external/glpk/amd*
+Copyright: 2007 Timothy A. Davis, Patrick R. Amestoy, and Iain S. Duff
+License: GPL-2+
+
+Files: external/glpk/colamd.c
+Copyright: 1998-2007, Timothy A. Davis
+License: LGPL-2.1+
+
+Files: external/espeak/*
+Copyright: 2005-2011 Jonathan Duddington
+ 2010 Nicolas Pitre
+ 2010 Bill Cox
+ 2007 Gilles Casse
+ 2008 Sun Microsystems, Inc.
+ 1993-1994 Jon Iles and Nick Ing-Simmons
+License: GPL-3+
+
+Files: external/espeak/espeakdata_FileInMemory.*
+Copyright: David Weenink 2012
+License: GPL-2+
+
+Files: contrib/ola/*
+Copyright: 2007-2009 Ola Söder
+ 2007-2011, Paul Boersma
+License: GPL-2+
+
+Files: external/gsl/*
+Copyright: 1996-2004, 2006-2007 Brian Gough
+ 1996-2006 Gerard Jungman
+ 1996-2000, 2003-2004, 2007 James Theiler
+ 1996-2001, 2007 Thomas Walter
+ 1996-2000, 2007 Jim Davies
+ 2006-2007 Patrick Alken
+ 1996-2000, 2007 Reid Priedhorsky
+ 2000 Simone Piccardi
+ 1996-2000 Fabrice Rossi
+ 2004 Ivo Alxneit
+ 2002, 2004 Jason H. Stover
+ 1996-2000 Michael Booth
+ 2000-2011, 2004 David Morrison
+ 2001 Carlo Perassi
+ 2003 Heiko Bauke
+ 2002-2003 Lowell Johnson
+ 2001 Szymon Jaroszewicz
+ 2004 Joerg Wensch
+ 2002 Przemyslaw Sliwa
+ 2002, 2004 Jason H. Stover
+ 2001 Jason Beegan
+ 1996-2000, 2004, 2007 Jorma Olavi Tähtinen
+ 1996-2000 Mark Galassi
+ 2002 Achim Gaedke
+ 2002 Atakan Gurkan
+ 2002 Gavin E. Crooks
+ 2002 Tuomo Keskitalo
+ 1996-2000, 2007 John Fisher
+ 1997 Makoto Matsumoto
+ 2006 Charles Karney
+ 2001 Dan, Ho-Jin
+ 2006 Erik Schnetter
+ 2002 Gavin E. Crooks
+ 1996-2000, 2002, 2004, 2007 David Necas
+ 2002 Gert Van den Eynde
+ 1998-2000 Theodore C. Belding
+ 2004, 2006 Giulio Bottazzi
+ 2001 Henry Sobotka
+ 2005 Jochen Voss
+ 2001-2002 Nicolas Darnis
+ 2003 Olaf Lenz
+ 2002 Przemyslaw Sliwa
+ 2001 Rodney Sparapani
+ 2000 Vladimir Kushnir
+ 1996-2000 Tim Mooney
+License: GPL-3+
+
+Files: kar/ipaSerifRegularPS.cpp
+Copyright: 2005 Rafael Laboissière
+License: GPL-2+
+
+Files: dwsys/regularExp.h
+Copyright: 1986, 2002 The NEdit Developers
+License: GPL-2+
+
+Files: debian/*
+Copyright: 2005-2009, 2012 Rafael Laboissière <rafael at laboissiere.net>
+ 2009-2011 Andreas Tille <tille at debian.org>
+License: GPL-3+
+
+License: GPL-2+
+ 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/>.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License, version 2, can be found in the file
+ `/usr/share/common-licenses/GPL-2'.
+
+License: GPL-3+
+ 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 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 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/>.
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License, version 3, can be found in the file
+ `/usr/share/common-licenses/GPL-3'.
+
+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 Street, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General Public
+ License, version 3, can be found in the file
+ `/usr/share/common-licenses/LGPL-2.1'.
Added: packages-metadata/p/praat.upstream
===================================================================
--- packages-metadata/p/praat.upstream (rev 0)
+++ packages-metadata/p/praat.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,13 @@
+Name: praat
+Homepage: http://www.fon.hum.uva.nl/praat/
+Contact: http://uk.groups.yahoo.com/group/praat-users/
+FAQ: http://www.fon.hum.uva.nl/praat/manual/FAQ__Frequently_Asked_Questions_.html
+Reference:
+ Author: Paul Boersma
+ Title: Praat, a system for doing phonetics by computer
+ Journal: Glot International
+ Year: 2001
+ Volume: 5
+ Number: 9/10
+ Pages: 341-345
+ URL: http://www.citeulike.org/user/schulman/article/4016976
Added: packages-metadata/r/r-bioc-edger.copyright
===================================================================
--- packages-metadata/r/r-bioc-edger.copyright (rev 0)
+++ packages-metadata/r/r-bioc-edger.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,27 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://www.bioconductor.org/packages/release/bioc/src/contrib/edgeR_2.6.1.tar.gz
+Comment: inst/doc/edgeRUsersGuide.pdf is not accompanied by its source.
+License: GPL-2
+ edgeR is LGPL-2+, but depend on LIMMA and R (GPL-2), so its effective license
+ is GPL-2.
+Removed: inst/doc/edgeRUsersGuide.pdf
+
+Files: *
+Copyright: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
+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
+Comment: On Debian systems, a copy of the GNU Library General Public version 2
+ is available in ‘/usr/share/common-licenses/LGPL-2’.
+
Added: packages-metadata/r/r-bioc-edger.upstream
===================================================================
--- packages-metadata/r/r-bioc-edger.upstream (rev 0)
+++ packages-metadata/r/r-bioc-edger.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,24 @@
+Archive: Bioconductor
+Bioconductor: edgeR
+Contact: Mark Robinson <mrobinson at wehi.edu.au>, Davis McCarthy <dmccarthy at wehi.edu.au>, Gordon Smyth <smyth at wehi.edu.au>
+Download: http://bioconductor.org/packages/release/bioc/src/contrib/
+Homepage: http://www.bioconductor.org/packages/release/bioc/html/edgeR.html
+Name: edgeR
+Reference:
+ author: Robinson, Mark D. and Smyth, Gordon K.
+ title: Moderated statistical tests for assessing differences in tag abundance
+ journal: Bioinformatics
+ volume: 23
+ number: 21
+ pages: 2881-2887
+ doi: 10.1093/bioinformatics/btm453
+ PMID: 17881408
+ year: 2007
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/21/2881
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/23/21/2881.pdf
+Watch: |
+ version=3
+
+ # This tracks the current stable version of edgeR
+ opts="dversionmangle=s|~dfsg||,downloadurlmangle=s|\.\.|packages/release/bioc|" \
+ http://www.bioconductor.org/packages/release/bioc/html/edgeR.html .*/edgeR_(.*).tar.gz
Added: packages-metadata/r/r-cran-genabel.copyright
===================================================================
--- packages-metadata/r/r-cran-genabel.copyright (rev 0)
+++ packages-metadata/r/r-cran-genabel.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,24 @@
+Format: http://dep.debian.net/deps/dep5/
+Source: http://cran.r-project.org/src/contrib/GenABEL_1.7-0.tar.gz
+
+Files: *
+Copyright: GenABEL is copyright 2006-2008 of Yurii Aulchenko, Maksim Struchalin, with
+ contributions from Stephan Ripke, Terry Therneau and Toby Johnson and
+ released under version 2 or later of the GNU General Public License (GPL).
+License: GPL-2+
+ 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, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+Comment: On a Debian GNU/Linux system, the GPL license version 2 is included
+ in the file /usr/share/common-licenses/GPL-2.
+
Added: packages-metadata/r/r-cran-genabel.upstream
===================================================================
--- packages-metadata/r/r-cran-genabel.upstream (rev 0)
+++ packages-metadata/r/r-cran-genabel.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,22 @@
+Archive: CRAN
+Bug-Database: https://r-forge.r-project.org/tracker/?atid=2058&group_id=505
+Contact: GenABEL developers <genabel.project at gmail.com>
+Name: GenABEL
+Homepage: http://www.genabel.org/
+Reference:
+ author: Aulchenko, Yurii S. and Ripke, Stephan and Isaacs, Aaron and van Duijn, Cornelia M.
+ title: >
+ GenABEL: an R library for genome-wide association analysis
+ volume: 23
+ number: 10
+ pages: 1294-1296
+ year: 2007
+ doi: 10.1093/bioinformatics/btm108
+ URL: http://bioinformatics.oxfordjournals.org/content/23/10/1294.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/23/10/1294.full.pdf+html
+ journal: Bioinformatics
+ PMID: 17384015
+Repostiory: svn://svn.r-forge.r-project.org/svnroot/genabel
+Repository-Browse: https://r-forge.r-project.org/scm/viewvc.php/?root=genabel
+Watch: |
+ http://cran.r-project.org/src/contrib/GenABEL_(.*)\.tar\.gz
Added: packages-metadata/s/snap.copyright
===================================================================
--- packages-metadata/s/snap.copyright (rev 0)
+++ packages-metadata/s/snap.copyright 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SNAP
+Upstream-Contact: ik1 at sanger.ac.uk
+Source: http://homepage.mac.com/iankorf/snap-2010-07-28.tar.gz
+
+Files: *
+Copyright: 2002-2005 Ian Korf <ifkorf at ucdavis.edu>
+ UC Davis Genome Center, Davis, CA, USA
+License: GPL-2.0+
+
+Files: debian/*
+Copyright: 2011 Steffen Moeller <moeller at debian.org>
+License: GPL-2.0+
+
+License: GPL-2.0+
+ This package 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 package 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/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Added: packages-metadata/s/snap.upstream
===================================================================
--- packages-metadata/s/snap.upstream (rev 0)
+++ packages-metadata/s/snap.upstream 2012-05-16 23:50:30 UTC (rev 2337)
@@ -0,0 +1,12 @@
+Name: SNAP
+Reference:
+ Authors: Ian Korf
+ Title: Gene finding in novel Genomes
+ Journal: BMC Bioinformatics
+ Year: 2004
+ Volume: 5
+ Pages: 59
+ PMID: 15144565
+ DOI: 10.1186/1471-2105-5-59
+ URL: http://www.biomedcentral.com/1471-2105/5/59/abstract
+ eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-59.pdf
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