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 <[email protected]> +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 <[email protected]> +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 <[email protected]> @@ -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 <[email protected]> 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 <[email protected]> Source: http://www.mothur.org/wiki/Download_mothur Files: * -Copyright: © 2009-2011 Schloss Lab UMASS Amhers., Patrick Schloss <[email protected]> +Copyright: © 2009-2012 Schloss Lab UMASS Amhers., Patrick Schloss <[email protected]> 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 <[email protected]> - © 2011 Andreas Tille <[email protected]> -License: Same as Mothur itself (GPL-3) + © 2011-2012 Andreas Tille <[email protected]> +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 <[email protected]> -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 -<[email protected]> 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 <[email protected]> +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 <[email protected]> - -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 <[email protected]> +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 <[email protected]>, + 2012 Andreas Tille <[email protected]> +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 <[email protected]> -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 <[email protected]> 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 <[email protected]> +Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Upstream-Name: Raster3D +Upstream-Contact: Ethan Merritt <[email protected]> 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 <[email protected]> + 2008-2012 Andreas Tille <[email protected]> +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 <[email protected]> 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 <[email protected]> Copyright: © 2011 Tim Booth <[email protected]>, - Andreas Tille <[email protected]> -License: The Debian packaging is licensed under the GPL, see - `/usr/share/common-licenses/GPL'. + © 2011-2012 Andreas Tille <[email protected]> +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 <[email protected]> -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 _______________________________________________ Collab-qa-commits mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/collab-qa-commits
