[Collab-qa-commits] r2173 - in packages-metadata: a b e l m p r t
Charles Plessy
plessy at alioth.debian.org
Sat Mar 17 04:30:35 UTC 2012
Author: plessy
Date: 2012-03-17 04:30:35 +0000 (Sat, 17 Mar 2012)
New Revision: 2173
Modified:
packages-metadata/a/ants.copyright
packages-metadata/b/bedtools.copyright
packages-metadata/e/emboss.upstream
packages-metadata/l/last-align.upstream
packages-metadata/m/mothur.copyright
packages-metadata/m/mothur.upstream
packages-metadata/m/multipath-tools.copyright
packages-metadata/p/poa.copyright
packages-metadata/p/poa.upstream
packages-metadata/r/r-bioc-limma.copyright
packages-metadata/r/r-bioc-limma.upstream
packages-metadata/r/raster3d.copyright
packages-metadata/r/raster3d.upstream
packages-metadata/t/tabix.copyright
packages-metadata/t/tm-align.copyright
packages-metadata/t/tm-align.upstream
Log:
Manual update of the previously collected files.
Modified: packages-metadata/a/ants.copyright
===================================================================
--- packages-metadata/a/ants.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/a/ants.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,6 +1,7 @@
-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-Upstream-Name: ANTs (AKA Advants)
-Upstream-Source-Location: https://advants.svn.sourceforge.net/svnroot/advants
+Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
+Name: ANTs (AKA Advants)
+Maintainer: Brian Avants <stnava at gmail.com>
+Source: https://advants.svn.sourceforge.net/svnroot/advants
Files: *
Copyright: Copyright (C) 2009, 2010 ConsortiumOfANTS
@@ -19,8 +20,17 @@
3. Neither the name of the consortium nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
-On Debian GNU/Linux systems, the complete text of the 3-clause BSD License
-can be found in `/usr/share/common-licenses/BSD'.
+ THIS SOFTWARE IS PROVIDED BY THE CONSORTIUM 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 REGENTS 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:
Examples/ConformalMapping.cxx
Modified: packages-metadata/b/bedtools.copyright
===================================================================
--- packages-metadata/b/bedtools.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/b/bedtools.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://bedtools.googlecode.com/files/BEDTools.v2.15.0.tar.gz
Files: *
@@ -6,33 +6,20 @@
© 2010 - Assaf Gordon, CSHL
License: GPL-2
+Files: src/expand/expand.cpp
+Copyright: © 2009, 2010, 2011 - Aaron Quinlan
+License: under-the-MIT-license
+ No further explanation about which MIT license to follow was provided.
+
Files: src/cuffToTrans/Fasta.cpp
src/cuffToTrans/Fasta.h
src/fastaFromBed/Fasta.cpp
src/fastaFromBed/Fasta.h
Copyright: © 2010 Erik Garrison <erik.garrison at bc.edu>
+License: GPL-2
Source: https://github.com/ekg/fastahack
-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 version 2 as
- published by the Free Software Foundation.
- .
- 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 Debian systems, you can find a copy of the GNU General Public License
- version 2 in ‘/usr/share/common-licenses/GPL-2’.
-
Files: src/utils/BamTools/*
-Source: https://github.com/pezmaster31/bamtools/wiki
Copyright: © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
License: MIT
Permission is hereby granted, free of charge, to any person obtaining a copy
@@ -53,6 +40,7 @@
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
Comment: see ‘https://github.com/pezmaster31/bamtools/blob/master/LICENSE’.
+Source: https://github.com/pezmaster31/bamtools/wiki
Files: debian/*
Copyright: © 2010–2011 Charles Plessy <plessy at debian.org>
@@ -80,7 +68,6 @@
6. Be tolerant. Everything that's good in nature comes from cooperation.
Files: src/utils/gzstream/gzstream.h
-Name: gzstream, C++ iostream classes wrapping the zlib compression library.
Copyright: © 2001 Deepak Bandyopadhyay, Lutz Kettner
License: LGPL-2.1
This library is free software; you can redistribute it and/or
@@ -96,6 +83,25 @@
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
-Comment:
+Comment:
On Debian systems, you can find a copy of the GNU Lesser General Public License
version 2.1 in ‘/usr/share/common-licenses/LGPL-2.1’.
+Name: gzstream, C++ iostream classes wrapping the zlib compression library.
+
+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 version 2 as
+ published by the Free Software Foundation.
+ .
+ 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 Debian systems, you can find a copy of the GNU General Public License
+ version 2 in ‘/usr/share/common-licenses/GPL-2’.
+
Modified: packages-metadata/e/emboss.upstream
===================================================================
--- packages-metadata/e/emboss.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/e/emboss.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,16 +1,17 @@
Contact: EMBOSS core development team <emboss-bug at emboss.open-bio.org>
Homepage: http://emboss.sourceforge.net
Name: EMBOSS
-Reference-title: >
- EMBOSS: The European Molecular Biology Open Software Suite
-Reference-journal: Trends in Genetics
-Reference-volume: 16
-Reference-number: 6
-Reference-pages: 276 - 277
-Reference-year: 2000
-Reference-issn: 0168-9525
-Reference-url: http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317
-Reference-author: Peter Rice and Ian Longden and Alan Bleasby
-Reference-PMID: 10827456
-Reference-DOI: 10.1016/S0168-9525(00)02024-2
+Reference:
+ title: >
+ EMBOSS: The European Molecular Biology Open Software Suite
+ journal: Trends in Genetics
+ volume: 16
+ number: 6
+ pages: 276 - 277
+ year: 2000
+ issn: 0168-9525
+ url: http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317
+ author: Peter Rice and Ian Longden and Alan Bleasby
+ PMID: 10827456
+ DOI: 10.1016/S0168-9525(00)02024-2
Watch: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz
Modified: packages-metadata/l/last-align.upstream
===================================================================
--- packages-metadata/l/last-align.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/l/last-align.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,8 +1,6 @@
Contact: last (ATmark) cbrc (dot) jp
-Reference-DOI: 10.1093/nar/gkq010
Name: LAST
Homepage: http://last.cbrc.jp/
-Reference-PMID: 20110255
Reference:
author: Frith, Martin C. and Wan, Raymond and Horton, Paul
title: Incorporating sequence quality data into alignment improves DNA read mapping
Modified: packages-metadata/m/mothur.copyright
===================================================================
--- packages-metadata/m/mothur.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/m/mothur.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,9 +1,10 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: Mothur
+Upstream-Contact: Patrick D. Schloss <pschloss at umich.edu>
Source: http://www.mothur.org/wiki/Download_mothur
Files: *
-Copyright: © 2009-2011 Schloss Lab UMASS Amhers., Patrick Schloss <pschloss at umich.edu>
+Copyright: © 2009-2012 Schloss Lab UMASS Amhers., Patrick Schloss <pschloss at umich.edu>
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
@@ -28,7 +29,7 @@
Files: clearcut.* cmdargs.* common.h dayhoff.h distclearcut.* dmat.* fasta.* prng.*
Copyright: © 2004, Luke Sheneman
- © 1997 - 2002, Makoto Matsumoto and Takuji Nishimura
+ © 1997 - 2002, Makoto Matsumoto and Takuji Nishimura
License: Clearcut
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
@@ -57,8 +58,6 @@
POSSIBILITY OF SUCH DAMAGE.
Files: getopt_long.*
-Comment: This getopt_long() is compatible with GNU's, however, added original
- extension (short 1 byte option).
Copyright: © 2004 Koji Arai
License: MIT
Permission is hereby granted, free of charge, to any person
@@ -80,10 +79,13 @@
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.
+Comment: This getopt_long() is compatible with GNU's, however, added original
+ extension (short 1 byte option).
Files: debian/*
Copyright: © 2010 Sri Girish Srinivasa Murthy <srigirish at evolbio.mpg.de>
- © 2011 Andreas Tille <tille at debian.org>
-License: Same as Mothur itself (GPL-3)
+ © 2011-2012 Andreas Tille <tille at debian.org>
+License: GPL-3
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'.
+
Modified: packages-metadata/m/mothur.upstream
===================================================================
--- packages-metadata/m/mothur.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/m/mothur.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,11 +1,9 @@
Contact: Patrick D. Schloss <pschloss at umich.edu>
-Reference-DOI: 10.1128/AEM.01541-09
Homepage: http://www.mothur.org
-Reference-PMID: 19801464
Name: Mothur
Reference:
AUTHOR: Schloss, P.D., et al.
- TITILE: >
+ TITLE: >
Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities
JOURNAL: Appl Environ Microbiol
YEAR: 2009
@@ -14,3 +12,5 @@
NUMBER: 23
URL: http://aem.asm.org/cgi/content/full/75/23/7537
ISSN: 1098-5336
+ DOI: 10.1128/AEM.01541-09
+ PMID: 19801464
Modified: packages-metadata/m/multipath-tools.copyright
===================================================================
--- packages-metadata/m/multipath-tools.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/m/multipath-tools.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -7,6 +7,6 @@
libdevmapper is licensed under the GNU LGPL version 2.
On Debian systems, the complete text of the GNU General Public License
-and of the GNU Lesser Public License can be found in
+and of the GNU Lesser General Public License can be found in
/usr/share/common-licenses/GPL-2 and /usr/share/common-licenses/LGPL-2 .
Modified: packages-metadata/p/poa.copyright
===================================================================
--- packages-metadata/p/poa.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/p/poa.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,32 +1,31 @@
-This package was debianized by Charles Plessy
-<charles-debian-nospam at plessy.org> on Sun, 20 Aug 2006 11:21:24 +0900. The
-packaging work is in the public domain unless stated otherwise. The manpage for
-poa and its source are licenced under the GPL.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: POA
+Upstream-Contact: Christopher Lee <leec at mbi.ucla.edu>
+Source: http://sourceforge.net/projects/poamsa/files/poamsa/2.0/
-It was downloaded from http://sourceforge.net/project/showfiles.php?group_id=168080&package_id=191162&release_id=418237
-
-Copyright 2001, 2006 Christopher Lee <leec at mbi.ucla.edu>
-
-The project page on the SourceForge website indicates that this program is
-licenced under the GNU General Public Licence.
-(see: http://sourceforge.net/projects/poamsa/)
-
-License:
-
+Files: *
+Copyright: 2004-2006 Christopher Lee <leec at mbi.ucla.edu>
+License: GPL2+
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 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'.
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
+Files: debian/*
+Copyright: 2006 Charles Plessy <plessy at debian.org>,
+ 2012 Andreas Tille <tille at debian.org>
+License: GPL-2+
+ Same as software itself.
Modified: packages-metadata/p/poa.upstream
===================================================================
--- packages-metadata/p/poa.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/p/poa.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,8 +1,5 @@
Contact: Christopher Lee <leec at mbi.ucla.edu>
-Reference-DOI: 10.1093/bioinformatics/bth126
-Homepage: http://www.bioinformatics.ucla.edu/poa
Name: POA
-Reference-PMID: 14962922
Reference:
author: Grasso, Catherine and Lee, Christopher
title: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
@@ -11,8 +8,6 @@
number: 10
pages: 1546-1556
year: 2004
- URL: http:°bioinformatics.oxfordjournals.org¢gi¢ontentåbstract½0/10/1546
- eprint: http:°bioinformatics.oxfordjournals.org¢gi/reprint½0/10/1546.pdf
-Watch: |
- opts="uversionmangle=s/$/.0/,dversionmangle=s/\+.*$//" \
- http://sf.net/poamsa/ poaV(.*)\.tar\.gz
+ DOI: 10.1093/bioinformatics/bth126
+ PMID: 14962922
+ URL: http://bioinformatics.oxfordjournals.org/content/20/10/1546
Modified: packages-metadata/r/r-bioc-limma.copyright
===================================================================
--- packages-metadata/r/r-bioc-limma.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/r/r-bioc-limma.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,6 +1,8 @@
-Format: http://dep.debian.net/deps/dep5/
-Source: http://www.bioconductor.org/packages/2.9/bioc/src/contrib/limma_3.10.0.tar.gz
-Comment: discussed on https://stat.ethz.ch/pipermail/bioc-devel/2011-May/002620.html
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://www.bioconductor.org/packages/2.9/bioc/src/contrib/limma_3.10.3.tar.gz
+ inst/doc/usersguide.pdf is not accompanied by its source, and therefore removed in the “dfsg” version.
+Removed: inst/doc/usersguide.pdf
+Comment: licensing discussed on https://stat.ethz.ch/pipermail/bioc-devel/2011-May/002620.html
Files: *
Copyright: Gordon Smyth <smyth at wehi.edu.au>
Modified: packages-metadata/r/r-bioc-limma.upstream
===================================================================
--- packages-metadata/r/r-bioc-limma.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/r/r-bioc-limma.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,3 +1,4 @@
Archive: Bioconductor
Homepage: http://bioinf.wehi.edu.au/limma/
Name: limma
+References: http://bioinf.wehi.edu.au/limma/
Modified: packages-metadata/r/raster3d.copyright
===================================================================
--- packages-metadata/r/raster3d.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/r/raster3d.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,103 +1,102 @@
-Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135
-Maintainer: Ethan Merritt <merritt at u.washington.edu>
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Raster3D
+Upstream-Contact: Ethan Merritt <merritt at u.washington.edu>
Source: http://skuld.bmsc.washington.edu/raster3d/raster3d.html
-Name: Raster3D
Files: *
-Copyright 1996-2011 © Ethan Merritt, David J. Bacon and Wayne F. Anderson
-License: Artistic License 2.0
-
- Copyright (c) 2000-2006, The Perl Foundation.
-
+Copyright: 1996-2011 Ethan Merritt, David J. Bacon and Wayne F. Anderson
+License: Artistic
+ Artistic License 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.
@@ -116,7 +115,7 @@
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
@@ -126,13 +125,13 @@
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
@@ -140,37 +139,37 @@
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
@@ -180,7 +179,7 @@
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
@@ -196,14 +195,9 @@
The next upstream version will feature the license change also in the
source code.
-REFERENCES
-Bacon, D.J., & Anderson, W.F. (1988) ``A Fast Algorithm for
-Rendering Space-Filling Molecule Pictures''. (abstract of paper
-presented at the Seventh Annual Meeting of the Molecular Graphics
-Society). J. Molec. Graphics 6, 219-220.
-Kraulis, P.J. (1991) ``MOLSCRIPT: a program to produce both detailed
-and schematic plots of protein structures''. J. Appl. Cryst. 24, 946-950.
-Merritt, E.A. & Murphy, M.E.P. (1994) ``Raster3D Version 2.0 - A Program
-for Photorealistic Molecular Graphics''. Acta Cryst. D50, 869-873.
-Merritt, E.A. & Bacon, D.J. (1997) ``Raster3D Photorealistic Molecular
-Graphics''. Methods in Enzymology 277, 505-524.
+Files: debian/*
+Copyright: 2005-2008 Nelson A. de Oliveira <naoliv at gmail.com>
+ 2008-2012 Andreas Tille <tille at debian.org>
+License: Artistic
+ Same as program itself
+
Modified: packages-metadata/r/raster3d.upstream
===================================================================
--- packages-metadata/r/raster3d.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/r/raster3d.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,11 +1,13 @@
Homepage: http://skuld.bmsc.washington.edu/raster3d/
Name: Raster3D
-Reference-PMID: 18488322
Reference:
Article: MerrittBacon1997
Author: Merritt, E.A. and Bacon, D.J.
Title: Raster3D Photorealistic Molecular Graphics
Journal: Methods in Enzymology
+ PMID: 18488322
+ DOI: 10.1016/S0076-6879(97)77028-9
Volume: 277
Pages: 505-524
Year: 1997
+ URL: http://www.sciencedirect.com/science/article/pii/S0076687997770289
Modified: packages-metadata/t/tabix.copyright
===================================================================
--- packages-metadata/t/tabix.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/t/tabix.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://sourceforge.net/projects/samtools/files/tabix/tabix-0.2.5.tar.bz2
Files: *
@@ -32,3 +32,4 @@
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.
+
Modified: packages-metadata/t/tm-align.copyright
===================================================================
--- packages-metadata/t/tm-align.copyright 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/t/tm-align.copyright 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,11 +1,11 @@
-Format: http://dep.debian.net/deps/dep5/
-Upstream-Name: TM-align
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: TM-align
Upstream-Contact: Yang Zhang <zhng at umich.edu>
Source: http://zhanglab.ccmb.med.umich.edu/TM-align/
Files: *
-Copyright: © 2005-2011 Yang Zhang, Jeffrey Skolnick
-License:
+Copyright: © 2005-2012 Yang Zhang, Jeffrey Skolnick
+License: other
Permission to use, copy, modify, and distribute this program for
any purpose, with or without fee, is hereby granted, provided that
the notices on the head, the reference information, and this
@@ -14,8 +14,9 @@
warranty.
Files: debian/*
-Copyright: © 2007 Steffen Moeller <moeller at debian.org>
Copyright: © 2011 Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>
-License: The Debian packaging is licensed under the GPL, see
- `/usr/share/common-licenses/GPL'.
+ © 2011-2012 Andreas Tille <tille at debian.org>
+License: GPL
+ The Debian packaging is licensed under the GPL, see
+ `/usr/share/common-licenses/GPL'.
+
Modified: packages-metadata/t/tm-align.upstream
===================================================================
--- packages-metadata/t/tm-align.upstream 2012-03-08 00:00:19 UTC (rev 2172)
+++ packages-metadata/t/tm-align.upstream 2012-03-17 04:30:35 UTC (rev 2173)
@@ -1,11 +1,9 @@
Contact: Yang Zhang <zhng at umich.edu>
-Reference-DOI: 10.1093/nar/gki524
Homepage: http://zhanglab.ccmb.med.umich.edu/TM-align/
-Reference-PMID: 15849316
Name: TM-align & TM-score
Reference:
AUTHOR: Y. Zhang, J. Skolnick
- TITILE: >
+ TITLE: >
TM-align: A protein structure alignment algorithm based on TM-score
JOURNAL: Nucleic Acids Research
YEAR: 2005
@@ -14,3 +12,5 @@
NUMBER: 7
URL: http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.pdf
ISSN: 1362-4962
+ DOI: 10.1093/nar/gki524
+ PMID: 15849316
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