[Collab-qa-commits] r2212 - in packages-metadata: a d h k m n o p
Charles Plessy
plessy at alioth.debian.org
Thu Apr 5 00:55:27 UTC 2012
Author: plessy
Date: 2012-04-05 00:55:27 +0000 (Thu, 05 Apr 2012)
New Revision: 2212
Modified:
packages-metadata/a/almanah.copyright
packages-metadata/d/distro-info-data.copyright
packages-metadata/d/distro-info.copyright
packages-metadata/h/hhsuite.upstream
packages-metadata/h/hmmer.copyright
packages-metadata/h/hmmer.upstream
packages-metadata/k/kalign.copyright
packages-metadata/k/kalign.upstream
packages-metadata/m/melting.copyright
packages-metadata/m/melting.upstream
packages-metadata/m/mrbayes.copyright
packages-metadata/m/mustang.copyright
packages-metadata/m/mustang.upstream
packages-metadata/n/nodejs.copyright
packages-metadata/o/octave-nan.copyright
packages-metadata/p/probcons.upstream
packages-metadata/p/psycopg2.copyright
Log:
Pushing upload-driven updates, still by hand.
Modified: packages-metadata/a/almanah.copyright
===================================================================
--- packages-metadata/a/almanah.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/a/almanah.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -4,11 +4,11 @@
Source: http://live.gnome.org/Almanah_Diary
Files: *
-Copyright: Copyright 2008-2011, Philip Withnall <philip at tecnocode.co.uk>
+Copyright: Copyright 2008-2012, Philip Withnall <philip at tecnocode.co.uk>
License: GPL-3
Files: data/icons/*
-Copyright: Copyright 2008-2011, Jakub Szypulka <cube at szypulka.com>
+Copyright: Copyright 2008-2012, Jakub Szypulka <cube at szypulka.com>
License: GPL-3
Files: debian/*
Modified: packages-metadata/d/distro-info-data.copyright
===================================================================
--- packages-metadata/d/distro-info-data.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/d/distro-info-data.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -6,6 +6,12 @@
Copyright: 2009-2012, Benjamin Drung <bdrung at debian.org>
2010-2011, Stefano Rivera <stefanor at debian.org>
License: ISC
+
+Files: shell/*-distro-info.in shell/distro-info-util.sh
+Copyright: 2012 Canonical Ltd.
+License: ISC
+
+License: ISC
Permission to use, copy, modify, and/or distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
Modified: packages-metadata/d/distro-info.copyright
===================================================================
--- packages-metadata/d/distro-info.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/d/distro-info.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -7,7 +7,7 @@
2010-2011, Stefano Rivera <stefanor at debian.org>
License: ISC
-Files: *-distro-info.in distro-info-util.sh
+Files: shell/*-distro-info.in shell/distro-info-util.sh
Copyright: 2012 Canonical Ltd.
License: ISC
Modified: packages-metadata/h/hhsuite.upstream
===================================================================
--- packages-metadata/h/hhsuite.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/h/hhsuite.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -2,18 +2,24 @@
Contact: Andreas Hauser <hauser at genzentrum.lmu.de>
Homepage: http://toolkit.genzentrum.lmu.de/hhblits
Reference:
- Author: Remmert M., Biegert A., Hauser A., and Soding J.
+ - Author: Remmert M., Biegert A., Hauser A., and Soding J.
Title: 'HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.'
Journal: Nat. Methods
- DOI: 10.1038/NMETH.1818.
- year: 2011
- URL: http://www.ncbi.nlm.nih.gov/pubmed/22198341
+ DOI: 10.1038/NMETH.1818
+ Year: 2011
+ Volume: 9
+ Number: 2
+ Pages: 173-175
+ URL: http://www.nature.com/nmeth/journal/v9/n2/full/nmeth.1818.html
PMID: 22198341
-# Author: Soding J.
-# Title: Protein homology detection by HMM-HMM comparison.
-# Journal: Bioinformatics
-# Volume: 21
-# Pages: 951-960
-# Year: 2005
-# URL: http://www.ncbi.nlm.nih.gov/pubmed/15531603
-# PMID: 15531603
+ - Author: Söding J.
+ Title: Protein homology detection by HMM-HMM comparison.
+ Journal: Bioinformatics
+ Volume: 21
+ Number: 7
+ Pages: 951-960
+ Year: 2005
+ PMID: 15531603
+ DOI: 10.1093/bioinformatics/bti125
+ URL: http://bioinformatics.oxfordjournals.org/content/21/7/951.abstract
+ eprint: http://bioinformatics.oxfordjournals.org/content/21/7/951.full.pdf+html
\ No newline at end of file
Modified: packages-metadata/h/hmmer.copyright
===================================================================
--- packages-metadata/h/hmmer.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/h/hmmer.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,28 +1,74 @@
-This package was debianized by John Lapeyre <lapeyre at physics.arizona.edu> on
-Thu, 13 Aug 1998 21:48:53 -0700.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: HMMER
+Upstream-Contact: Sean R. Eddy <eddy at genetics.wustl.edu>
+Source: ftp://selab.janelia.org/pub/software/hmmer3/3.0/
-It was downloaded from ftp://selab.janelia.org/pub/software/hmmer/
+Files: *
+Copyright: 1992-2010 Sean R. Eddy <eddy at genetics.wustl.edu>
+ Howard Hughes Medical Institute
+ 1992-2004 Washington University School of Medicine
+ 1992-1994 MRC Laboratory of Molecular Biology
+License: GPL-3+
-HMMER - Biological sequence analysis with profile hidden Markov models
-Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
+Files: easel/*
+Copyright: 2004-2009 Sean R. Eddy <eddy at genetics.wustl.edu>
+ 2006-2009 Howard Hughes Medical Institute
+License: The-Janelia-Farm-Software-License
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. 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.
+ .
+ 3. Neither the name of the Howard Hughes Medical Institute 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, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
+ NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER 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;
+ REASONABLE ROYALTIES; 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.
-Upstream author: Sean Eddy <eddy at genetics.wustl.edu>
+Files: debian/*
+Copyright: 1998 John Lapeyre <lapeyre at physics.arizona.edu>
+ 1999-2001 Matthew Vernon <matthew at debian.org>
+ 2006-2007 Nelson A. de Oliveira <naoliv at gmail.com>
+ 2008-2012 Andreas Tille <tille at debian.org>
+ Charles Plessy <plessy at debian.org>
+ 2010 Eric Talevich <etal at uga.edu>,
+ Steffen Möller <moeller at debian.org>
+License: GPL-3+
-License:
-
+License: GPL-3+
This package is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License version 3 as published
by the Free Software Foundation.
-
+ .
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 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 General
+ Public License can be found in `/usr/share/common-licenses/GPL-3'.
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL-3'.
-
Modified: packages-metadata/h/hmmer.upstream
===================================================================
--- packages-metadata/h/hmmer.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/h/hmmer.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,15 +1,25 @@
Contact: http://selab.janelia.org/people/eddys/contact.html
-Reference-DOI: 10.1093/bioinformatics/14.9.755
Name: HMMER
Homepage: http://hmmer.janelia.org
-Reference-PMID: 9918945
Reference:
- Author: Eddy, SR
- Title: Profile hidden Markov models
- Journal: Bioinformatics
- Volume: 14
- Number: 9
- Pages: 755-763
- Year: 1998
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+ - Author: S. R. Eddy
+ Title: Profile hidden Markov models
+ Journal: Bioinformatics
+ Volume: 14
+ Number: 9
+ Pages: 755-763
+ Year: 1998
+ DOI: 10.1093/bioinformatics/14.9.755
+ PMID: 9918945
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/9/755
+ eprint: http://bioinformatics.oxfordjournals.org/content/14/9/755.full.pdf+html
+ - Author: S. R. Eddy
+ Title: Multiple Alignment Using Hidden Markov Models
+ Journal: Proc. Third Int. Conf. Intelligent Systems for Molecular Biology
+ Volume: 3
+ Pages: 114-120
+ Year: 1995
+ PMID: 7584426
+ URL: http://www.mendeley.com/research/multiple-alignment-using-hidden-markov-models-1/
+ Eprint: ftp://selab.janelia.org/pub/publications/Eddy95b/Eddy95b-preprint.pdf
Watch: ftp://selab.janelia.org/pub/software/hmmer/CURRENT/hmmer-([0-9\.]*)\.tar\.gz
Modified: packages-metadata/k/kalign.copyright
===================================================================
--- packages-metadata/k/kalign.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/k/kalign.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,9 +1,25 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Kalign
+Upstream-Contact: Oliver Frings <oliver.frings at sbc.su.se>
Source: http://msa.cgb.ki.se/downloads/kalign/current.tar.gz
-Files : *
+Files: *
Copyright: © 2004–2008 Timo Lassmann <timolassmann at gmail.com>
+ © 2008-2011 Timo Lassmann <timolassmann at gmail.com>,
+ Oliver Frings <oliver.frings at sbc.su.se>
License: GPL-2+
+
+Files: debian/*
+Copyright: © 2006–2011 Charles Plessy <plessy at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+ © 2008-2012 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+Files: debian/kalign.1*
+Copyright: © 2006–2009 Charles Plessy <plessy at debian.org>
+License: GPL-2+
+
+License: GPL-2+
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
@@ -17,29 +33,7 @@
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
-Comment: On Debian systems, the complete text of the GNU General Public
+ .
+ On Debian systems, the complete text of the GNU General Public
License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
-Files: COPYING
-Copyright: © 1989, 1991 Free Software Foundation, Inc.
-License: no-change
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-Files: configure
-Copyright: © 2003 Free Software Foundation, Inc.
-License: unlimited-permission
- This configure script is free software; the Free Software Foundation
- gives unlimited permission to copy, distribute and modify it.
-
-Files: debian/*
-Copyright: © 2006–2011 Charles Plessy <plessy at debian.org>
- © 2008 David Paleino <d.paleino at gmail.com>
- © 2008 Andreas Tille <tille at debian.org>
-Licence: as-public-domain.
- The packaging work is in the public domain unless stated otherwise.
-
-Files: debian/kalign.1*
-Copyright: © 2006–2009 Charles Plessy <plessy at debian.org>
-License: same-as-kalign.
- (See above)
Modified: packages-metadata/k/kalign.upstream
===================================================================
--- packages-metadata/k/kalign.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/k/kalign.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,6 +1,6 @@
Contact: Timo Lassmann <timolassmann at gmail.com>
Name: Kalign
-Homepage: http://msa.cgb.ki.se
+Homepage: http://msa.sbc.su.se/
Reference:
- Author: Lassmann, Timo and Frings, Oliver and Sonnhammer, Erik L. L.
Title: "Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features"
Modified: packages-metadata/m/melting.copyright
===================================================================
--- packages-metadata/m/melting.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/m/melting.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,35 +1,35 @@
-Format: Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
-Name: Melting
-Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
- Marine Dumousseau <marine at ebi.ac.uk>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Melting
+Upstream-Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
+ Marine Dumousseau <marine at ebi.ac.uk>
Source: http://qa.debian.org/watch/sf.php/melting/melting4_3c.tar.gz
+Files: *
Copyright: 1997–2009, Nicolas Le Novère <lenov at ebi.ac.uk>
1997–2009, Marine Dumousseau <marine at ebi.ac.uk>
License: GPL-2+
-
- Melting 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.
-
- Melting 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 complete text of the GNU General Public License version
-2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+Files: debian/*
+Copyright: 2007–2009 Charles Plessy <plessy at debian.org>
+ 2008-2012 Andreas Tille <tille at debian.org>
+ 2008 David Paleino <d.paleino at gmail.com>
+License: GPL-2+
-Files: debian/*
-Copyright: 2007–2009 Charles Plessy <plessy at debian.org>
- 2008 Andreas Tille <tille at debian.org>
- 2008 David Paleino <d.paleino at gmail.com>
-License:
- You can use, redistribute, modify
- the packaging work as if it were in the public domain.
+License: GPL-2+
+ Melting 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.
+ .
+ Melting 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 complete text of the GNU General Public License version
+ 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+
Modified: packages-metadata/m/melting.upstream
===================================================================
--- packages-metadata/m/melting.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/m/melting.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,8 +1,6 @@
Contact: Nicolas Le Novère <lenov at ebi.ac.uk>
-Reference-DOI: 10.1093/bioinformatics/17.12.1226
Homepage: http://www.ebi.ac.uk/compneur-srv/melting/
Name: MELTING
-Reference-PMID: 11751232
Reference:
author: Le Novère, Nicolas
title: MELTING, computing the melting temperature of nucleic acid duplex
@@ -11,6 +9,8 @@
number: 12
pages: 1226-1227
year: 2001
+ DOI: 10.1093/bioinformatics/17.12.1226
+ PMID: 11751232
URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/17/12/1226
eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/17/12/1226.pdf
Screenshot: http://www.ebi.ac.uk/compneur-srv/melting/melting.jpg
Modified: packages-metadata/m/mrbayes.copyright
===================================================================
--- packages-metadata/m/mrbayes.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/m/mrbayes.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,14 +1,21 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: MrBayes
Upstream-Contact: Fredrik Ronquist <ronquist at csit.fsu.edu>
Source: http://mrbayes.sourceforge.net/
Files: *
-Copyright: © 2002-2005 Fredrik Ronquist <ronquist at csit.fsu.edu>,
- John Huelsenbeck <johnh at biomail.ucsd.edu>,
- Paul van der Mark <paulvdm at csit.fsu.edu>,
- Bred Larget, Donald Simon
-License: GPL
+Copyright: © 2002-2012 Fredrik Ronquist <ronquist at csit.fsu.edu>,
+ John Huelsenbeck <johnh at biomail.ucsd.edu>,
+ Paul van der Mark <paulvdm at csit.fsu.edu>,
+ Bred Larget, Donald Simon.
+License: GPL-2+
+
+Files: debian/*
+Copyright: © 2006 Fernando Ribeiro <fernando at staff.nerdgroup.org>
+ © 2011-2012 Andreas Tille <tille at debian.org>
+License: GPL-2+
+
+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
@@ -28,10 +35,5 @@
.
On Debian systems, the full text of the GNU General Public
License version 2 can be found in the file
- `/usr/share/common-licenses/GPL'.
+ `/usr/share/common-licenses/GPL-2'.
-Files: debian/*
-Copyright: © 2006 Fernando Ribeiro <fernando at staff.nerdgroup.org>
- © 2011 Andreas Tille <tille at debian.org>
-License: The packaging is licensed under the same conditions as the
- software itself.
Modified: packages-metadata/m/mustang.copyright
===================================================================
--- packages-metadata/m/mustang.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/m/mustang.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,43 +1,23 @@
-This package was downloaded from http://www.cs.mu.oz.au/~arun/mustang/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MUSTANG
+Upstream-Contact: Arun S Konagurthu <arun at bx.psu.edu>
+Source: http://www.csse.monash.edu.au/~karun/Site/mustang.html
-Files: Makefile, src/*, data/test/test_zf-CCHH
-Copyright: (C) 2005, Arun S Konagurthu <arun at bx.psu.edu> and The University
- of Melbourne.
+Files: Makefile src/* data/test/test_zf-CCHH
+Copyright: 2005-2009 Arun S Konagurthu <arun at bx.psu.edu>
+ The University of Melbourne.
License: BSD-like
- 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 University of Melbourne 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 COPYRIGHT OWNER 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: debian/*
-Copyright: of the Debian packaging is assigned to the copyright holder and
- condition to the above license.
+Copyright: 2007-2009 Morten Kjeldgaard <mok at bioxray.dk>
+ 2008 Steffen Möller <moeller at debian.org>
+ 2010 Charles Plessy <plessy at debian.org>
+ 2008-2012 Andreas Tille <tille at debian.org>
License: BSD-like
Files: data/test/pdbs:
Copyright: PD
-License:
+License: PD
ADVISORY NOTICE FOR USE OF THE PDB ARCHIVE
.
By using the materials available in this archive, the user agrees to abide
@@ -76,3 +56,31 @@
fitness for a particular purpose. The institutions managing this site make
no representation that these resources will not infringe any patent or other
proprietary right.
+
+License: BSD-like
+ 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 University of Melbourne 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 COPYRIGHT OWNER 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.
+
Modified: packages-metadata/m/mustang.upstream
===================================================================
--- packages-metadata/m/mustang.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/m/mustang.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,8 +1,6 @@
Contact: Arun S. Konagurthu (http://www.csse.unimelb.edu.au/~arun)
-Reference-DOI: 10.1002/prot.20921
Homepage: http://www.cs.mu.oz.au/~arun/mustang/
Name: MUSTANG
-Reference-PMID: 16736488
Reference:
Author: Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey and Arthur M. Lesk
Title: >
@@ -13,5 +11,6 @@
Number: 3
Pages: 559-574
Year: 2006
+ DOI: 10.1002/prot.20921
+ PMID: 16736488
URL: http://www3.interscience.wiley.com/journal/112638073/abstract
-Watch: http://www.cs.mu.oz.au/~arun/mustang/ ./mustang_v([.\d]*)\.tgz
Modified: packages-metadata/n/nodejs.copyright
===================================================================
--- packages-metadata/n/nodejs.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/n/nodejs.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,7 +1,7 @@
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Node
Source: http://nodejs.org/
-Upstream-Contact: Isaac Schlueter <i at izs.me>
+Upstream-Contact: https://github.com/joyent/node/issues
Files: *
Copyright: Joyent, Inc. and other Node contributors.
@@ -80,6 +80,11 @@
Copyright: 2011 Mathias Bynens <http://mathiasbynens.be/>
License: Expat
+Files: tools/doc/node_modules/marked
+ tools/doc/node_modules/.bin/marked
+Copyright: 2011-2012, Christopher Jeffrey (https://github.com/chjj/)
+License: Expat
+
Files: tools/waf-light
tools/wafadmin/*
Copyright: © 2005-2009, Thomas Nagy <tnagy1024 at gmail.com>
Modified: packages-metadata/o/octave-nan.copyright
===================================================================
--- packages-metadata/o/octave-nan.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/o/octave-nan.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: NaN package for Octave
Upstream-Contact: Alois Schloegl <alois.schloegl at gmail.com>
Source: http://octave.sourceforge.net/nan/
@@ -10,10 +10,10 @@
Files: inst/mahal.m inst/kurtosis.m inst/center.m inst/trimean.m inst/cov.m
inst/cor.m inst/rankcorr.m inst/tinv.m inst/mad.m inst/norminv.m
inst/nantest.m inst/normcdf.m inst/coefficient_of_variation.m
- inst/meansq.m inst/median.m inst/nanconv2.m inst/percentile.m
+ inst/meansq.m inst/median.m inst/percentile.m
inst/tpdf.m inst/zscore.m inst/hist2res.m inst/meandev.m inst/rms.m
inst/sumsq.m inst/normpdf.m inst/harmmean.m inst/prctile.m
-Copyright: 1996-2010 Alois Schloegl <alois.schloegl at gmail.com>
+Copyright: 1996-2011 Alois Schloegl <alois.schloegl at gmail.com>
License: GPL-2+
Files: src/predict.c src/linear.cpp src/linear.h src/tron.h src/tron.cpp
@@ -24,7 +24,7 @@
Files: src/svmtrain_mex.cpp src/svmpredict_mex.cpp src/svm.cpp
Copyright: 2000-2009 Chih-Chung Chang and Chih-Jen Lin
- 2010 Alois Schloegl <alois.schloegl at gmail.com>
+ 2010-2011 Alois Schloegl <alois.schloegl at gmail.com>
License: GPL-3+
Files: src/svm.h src/svm_model_matlab.h
@@ -52,45 +52,11 @@
License: GPL-3+
Files: debian/*
-Copyright: 2008 Rafael Laboissiere
+Copyright: 2008-2009 Rafael Laboissiere <rafael at laboissiere.net>
+ 2008-2011 Thomas Weber <tweber at debian.org>
+ 2011-2012 Sébastien Villemot <sebastien.villemot at ens.fr>
License: GPL-3+
-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: 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: BSD-3-clause
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
@@ -118,3 +84,40 @@
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.
+
+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'.
+
Modified: packages-metadata/p/probcons.upstream
===================================================================
--- packages-metadata/p/probcons.upstream 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/p/probcons.upstream 2012-04-05 00:55:27 UTC (rev 2212)
@@ -1,8 +1,6 @@
Contact: Chuong Do <chuongdo at cs.stanford.edu>
-Reference-DOI: 10.1101/gr.2821705
Homepage: http://probcons.stanford.edu/
Name: ProbCons
-Reference-PMID: 15687296
Reference:
author: Do, Chuong B. and Mahabhashyam, Mahathi S.P. and Brudno, Michael and Batzoglou, Serafim
title: >
@@ -12,6 +10,8 @@
number: 2
pages: 330-340
year: 2005
+ DOI: 10.1101/gr.2821705
+ PMID: 15687296
URL: http://genome.cshlp.org/content/15/2/330.abstract
eprint: http://genome.cshlp.org/content/15/2/330.full.pdf+html
Watch: http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz
Modified: packages-metadata/p/psycopg2.copyright
===================================================================
--- packages-metadata/p/psycopg2.copyright 2012-04-04 19:28:01 UTC (rev 2211)
+++ packages-metadata/p/psycopg2.copyright 2012-04-05 00:55:27 UTC (rev 2212)
@@ -109,13 +109,13 @@
License and copyright for doc/html/_static/jquery.js:
- * Copyright 2010, John Resig
+ * Copyright 2010,2011 John Resig
* Dual licensed under the MIT or GPL Version 2 licenses.
* http://jquery.org/license
*
* Includes Sizzle.js
* http://sizzlejs.com/
- * Copyright 2010, The Dojo Foundation
+ * Copyright 2010,2011 The Dojo Foundation
* Released under the MIT, BSD, and GPL Licenses.
Copyright (c) The Regents of the University of California.
@@ -153,7 +153,17 @@
See above for full BSD license text
+License and copyright for doc/html/_static/underscore.js
+// Underscore.js 1.3.1
+// (c) 2009-2012 Jeremy Ashkenas, DocumentCloud Inc.
+// Underscore is freely distributable under the MIT license.
+// Portions of Underscore are inspired or borrowed from Prototype,
+// Oliver Steele's Functional, and John Resig's Micro-Templating.
+// For all details and documentation:
+// http://documentcloud.github.com/underscore
+See above for full BSD license text
+
Proprietary licenses:
A non-exclusive license is available for companies that want to include
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