[Collab-qa-commits] r2627 - in packages-metadata: c e f g i o v
Charles Plessy
plessy at alioth.debian.org
Mon Feb 25 03:58:52 UTC 2013
Author: plessy
Date: 2013-02-25 03:58:51 +0000 (Mon, 25 Feb 2013)
New Revision: 2627
Added:
packages-metadata/c/cclib.control
packages-metadata/c/cclib.copyright
packages-metadata/c/cclib.upstream
packages-metadata/c/chemfp.control
packages-metadata/c/chemfp.copyright
packages-metadata/f/fmcs.control
packages-metadata/f/fmcs.copyright
packages-metadata/i/indigo.control
packages-metadata/i/indigo.copyright
packages-metadata/o/opsin.control
packages-metadata/o/opsin.copyright
Modified:
packages-metadata/e/emboss.copyright
packages-metadata/g/gamgi.control
packages-metadata/i/igv.control
packages-metadata/i/igv.copyright
packages-metadata/v/vcftools.control
Log:
Daily automatic umegaya push
Added: packages-metadata/c/cclib.control
===================================================================
--- packages-metadata/c/cclib.control (rev 0)
+++ packages-metadata/c/cclib.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,41 @@
+Source: cclib
+Section: science
+Priority: optional
+Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
+Uploaders: Karol M. Langner <karol.langner at gmail.com>,
+ Michael Banck <mbanck at debian.org>
+Build-Depends: debhelper (>= 7.0.50~),
+ python (>> 2.6.6-3~),
+ python-numpy (>> 1:1.4.1-4~)
+X-Python-Version: >= 2.4
+Standards-Version: 3.9.3
+Homepage: http://cclib.sourceforge.net
+Vcs-Svn: svn://svn.debian.org/debichem/unstable/cclib/
+Vcs-Browser: http://svn.debian.org/viewvc/debichem/unstable/cclib/
+
+Package: cclib
+Architecture: all
+Depends: python-cclib (= ${source:Version}), ${misc:Depends}, ${python:Depends}
+Suggests: cclib-data
+Description: Parsers and algorithms for computational chemistry
+ A Python library that provides parsers for computational
+ chemistry log files. It also provides a platform to implement
+ algorithms in a package-independent manner.
+ .
+ This package contains helper scripts for end users.
+ .
+ If you are looking for the unit tests and data files managed by cclib,
+ they are distributed separately as in non-free package cclib-data.
+
+Package: python-cclib
+Architecture: all
+Section: python
+Provides: ${python:Provides}
+Depends: python-numpy, ${misc:Depends}, ${python:Depends}
+Recommends: cclib
+Description: Parsers and algorithms for computational chemistry (Python module)
+ A Python library that provides parsers for computational
+ chemistry log files. It also provides a platform to implement
+ algorithms in a package-independent manner.
+ .
+ This package contains the Python module.
Added: packages-metadata/c/cclib.copyright
===================================================================
--- packages-metadata/c/cclib.copyright (rev 0)
+++ packages-metadata/c/cclib.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,37 @@
+This work was packaged for Debian by Karol M. Langner <karol.langner at gmail.com>
+on Wed, 27 Jul 2011 15:20:00 +0100 and is maintained with the help of
+the debichem team <debichem-devel at lists.alioth.debian.org>.
+
+It was originally downloaded from http://cclib.sf.net.
+
+Upstream Authors: cclib development team, which includes N. M. O'Boyle,
+A. L. Tenderholt, K. M. Langner and others.
+
+Copyright:
+
+ cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
+
+License: GNU Lesser General Public License, version 2.1
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+
+ On Debian GNU/Linux systems, the complete text of the license
+ can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+The Debian packaging is:
+
+ Copyright (C) 2011 Karol M. Langner <karol.langner at gmail.com>
+
+and is licensed under the GPL version 3, see "/usr/share/common-licenses/GPL-3".
Added: packages-metadata/c/cclib.upstream
===================================================================
--- packages-metadata/c/cclib.upstream (rev 0)
+++ packages-metadata/c/cclib.upstream 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,16 @@
+Name: cclib
+Homepage: http://cclib.sourceforge.net
+Contact: cclib-users at lists.sourceforge.net
+Reference:
+ - Author: Noel M. O'Boyle and Adam L. Tenderholt and Karol M. Langner
+ Title: "cclib: A library for package-independent computational chemistry algorithms"
+ Journal: J. Comp. Chem.
+ Year: 2008
+ Volume: 29
+ Number: 5
+ Pages: 839-845
+ URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20823/abstract
+ eprint: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20823/pdf
+ DOI: 10.1002/jcc.20823
+Repository: https://cclib.svn.sourceforge.net/svnroot/cclib/
+Repository-Browse: http://cclib.svn.sourceforge.net
Added: packages-metadata/c/chemfp.control
===================================================================
--- packages-metadata/c/chemfp.control (rev 0)
+++ packages-metadata/c/chemfp.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,37 @@
+Source: chemfp
+Section: science
+Priority: optional
+Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
+Uploaders: Michael Banck <mbanck at debian.org>
+Build-Depends: debhelper (>= 7.0.50~),
+ python-all-dev,
+ python-openbabel,
+ python-rdkit,
+ python-unit
+Standards-Version: 3.9.3
+Homepage: http://code.google.com/p/chem-fingerprints/
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/chemfp/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/chemfp
+
+Package: python-chemfp
+Section: python
+Architecture: any
+Provides: ${python:Provides}
+Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends}
+Recommends: python-openbabel, python-rdkit
+Description: cheminformatics fingerprints file formats and tools
+ Chem-fingerprints is a set of formats and related tools for the storage,
+ exchange, and search of cheminformatics fingerprint data sets.
+ .
+ It translates fingerprints from the OpenBabel and RDKIT and
+ cheminformatics packages (as well as the proprietary OEChem package)
+ into the binary FPS format.
+ .
+ Besides Python modules, it provides the following tools:
+ .
+ * sdf2fps - Extract fingerprint data from SD tags
+ * ob2fps - Use OpenBabel to generate fingerprints from structures
+ * rdkit2fps - Use RDKit to generate fingerprints from structures
+ * oe2fps - Use OEChem/OEGraphSim to generate fingerprints from structures
+ * simsearch - Do threshold or k-nearest neighbor Tanimoto similarity searches
+ between two FPS files
Added: packages-metadata/c/chemfp.copyright
===================================================================
--- packages-metadata/c/chemfp.copyright (rev 0)
+++ packages-metadata/c/chemfp.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,117 @@
+This work was packaged for Debian by:
+
+ Michael Banck <mbanck at debian.org> on Fri, 08 Jun 2012 16:04:49 +0200
+
+It was downloaded from:
+
+ http://code.google.com/p/chem-fingerprints/downloads/list
+
+Upstream Author:
+
+ Andrew Dalke
+
+General Copyright:
+
+ Copyright (c) 2010-2011 Andrew Dalke Scientific, AB
+
+General License:
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+License:
+
+chemfp/argparse.py Copyright:
+
+ Copyright (c) 2006-2009 Steven J. Bethard <steven.bethard at gmail.com>
+
+chemfp/argparse.py License:
+
+Licensed under the Apache License, Version 2.0 (the "License"); you may not
+use this file except in compliance with the License. You may obtain a copy
+of the License at
+
+ http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
+WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
+License for the specific language governing permissions and limitations
+under the License.
+
+chemfp/rdmaccs.patterns Copyright:
+
+ Copyright (c) 2006-2010 Rational Discovery LLC, Greg Landrum, and Julie
+ Penzotti
+ Copyright (c) 2001-2008 Greg Landrum and Rational Discovery LLC
+
+chemfp/rdmaccs.patterns License:
+
+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 Rational Discovery 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.
+
+tests/unittest2/* Copyright:
+
+ Copyright (c) 1999-2003 Steve Purcell
+ Copyright (c) 2003-2010 Python Software Foundation
+
+tests/unittest2/* License:
+
+This module is free software, and you may redistribute it and/or modify
+it under the same terms as Python itself, so long as this copyright message
+and disclaimer are retained in their original form.
+
+IN NO EVENT SHALL THE AUTHOR BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT,
+SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OF
+THIS CODE, EVEN IF THE AUTHOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.
+
+THE AUTHOR SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE. THE CODE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS,
+AND THERE IS NO OBLIGATION WHATSOEVER TO PROVIDE MAINTENANCE,
+SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+
+The Debian packaging is:
+
+ Copyright (C) 2012 Michael Banck <mbanck at debian.org>
+
+and is licensed under the same (MIT license) terms as the upstream project.
Modified: packages-metadata/e/emboss.copyright
===================================================================
--- packages-metadata/e/emboss.copyright 2013-02-24 03:58:50 UTC (rev 2626)
+++ packages-metadata/e/emboss.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -317,16 +317,22 @@
See http://www.sequenceontology.org/resources/faq.html#lic
Files: debian/*
-Copyright: the developers
-License: unclear
+Copyright: 2002-2004 Matt Hope <dopey at debian.org>
+ 2007-2013 Charles Plessy <plessy at debian.org>
+ 2012-2013 Andreas Tille <tille at debian.org>
+License: LGPL-2.1+
+Comment:
The EMBOSS package for Debian was initially prepared by Matt Hope
(dopey at debian.org) in 2002-2004 and released on
(http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian
was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope
- as a starting point. The packaging work of the pkg-emboss project is in the
- public domain unless stated otherwise.
+ as a starting point. Feel free to use the work of the pkg-emboss project as if
+ it were in the public domain. The license of the packaging (LGPL-2.1+) was
+ chosen in 2013 to be as close as possible to upstream's licenses (LGPL-2.1+
+ for the libraries, GPL-2+ for the applications, and GFDL-NIV-1.1 for some of
+ the documentation). After applyint patches, please be kind to submit them to
+ Upstream under terms that are convenient for them.
-
License: CC-BY-3.0
Attribution 3.0 Unported
.
Added: packages-metadata/f/fmcs.control
===================================================================
--- packages-metadata/f/fmcs.control (rev 0)
+++ packages-metadata/f/fmcs.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,27 @@
+Source: fmcs
+Section: science
+Priority: optional
+Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
+Uploaders: Michael Banck <mbanck at debian.org>
+Build-Depends: debhelper (>> 8), python-all, python-argparse, python-rdkit
+Standards-Version: 3.9.3
+Homepage: https://bitbucket.org/dalke/fmcs/overview
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/fmcs/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/fmcs/
+DM-Upload-Allowed: yes
+
+Package: python-fmcs
+Section: python
+Architecture: all
+Provides: ${python:Provides}
+Depends: python-argparse,
+ python-rdkit,
+ ${misc:Depends},
+ ${python:Depends},
+ ${shlibs:Depends}
+Description: Find Maximum Common Substructure
+ Fcms finds the maximum common substructure (MCS) of a group (or cluster) of
+ chemical structures and report the result as a SMARTS string.
+ .
+ More specifically, the MCS found is a common edge subgraph, and not a
+ common induced subgraph. Only connected MCSes are found.
Added: packages-metadata/f/fmcs.copyright
===================================================================
--- packages-metadata/f/fmcs.copyright (rev 0)
+++ packages-metadata/f/fmcs.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,47 @@
+This work was packaged for Debian by:
+
+ Michael Banck <mbanck at debian.org> on Fri, 08 Jun 2012 18:34:35 +0200
+
+It was downloaded from:
+
+ https://bitbucket.org/dalke/fmcs/downloads
+
+Upstream Author:
+
+ Andrew Dalke <dalke at dalkescientific.com>
+
+Copyright:
+
+ Copyright (c) 2012 Andrew Dalke Scientific AB
+
+License:
+
+ 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.
+
+ 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
+ HOLDER 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.
+
+The Debian packaging is:
+
+ Copyright (C) 2012 Michael Banck <mbanck at debian.org>
+
+and is licensed under the same BSD license as the upstream project.
Modified: packages-metadata/g/gamgi.control
===================================================================
--- packages-metadata/g/gamgi.control 2013-02-24 03:58:50 UTC (rev 2626)
+++ packages-metadata/g/gamgi.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -2,7 +2,8 @@
Section: science
Priority: optional
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
-Uploaders: Daniel Leidert (dale) <daniel.leidert at wgdd.de>
+Uploaders: Daniel Leidert (dale) <daniel.leidert at wgdd.de>,
+ Michael Banck <mbanck at debian.org>
Build-Depends: debhelper (>> 7.0.50~),
libatk1.0-dev,
libcairo2-dev,
Modified: packages-metadata/i/igv.control
===================================================================
--- packages-metadata/i/igv.control 2013-02-24 03:58:50 UTC (rev 2626)
+++ packages-metadata/i/igv.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -4,7 +4,8 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Shaun Jackman <sjackman at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Olivier Sallou <osallou at debian.org>
Build-Depends: ant, junit4, default-jdk|java-compiler, debhelper (>= 7.0.50~),
libbatik-java (>>1.7),
libcommons-logging-java, libcommons-math-java, libcommons-net-java,
@@ -12,7 +13,8 @@
libhttpclient-java (>>4.1), libhttpcore-java (>>4.1),
libjcommon-java, libjfreechart-java, libjhdf5-java, libjlibeps-java,
libjama-java, libjargs-java, libjaxp1.3-java, liblog4j1.2-java,
- libsam-java, libswing-layout-java, libxml-commons-external-java
+ libsam-java, libswing-layout-java, libxml-commons-external-java,
+ libguava-java
Standards-Version: 3.9.3
Homepage: http://www.broadinstitute.org/igv/
Vcs-Git: git://git.debian.org/debian-med/igv.git
@@ -27,7 +29,8 @@
libhttpclient-java (>>4.1), libhttpcore-java (>>4.1),
libjcommon-java, libjfreechart-java, libjhdf5-java, libjlibeps-java,
libjama-java, libjargs-java, libjaxp1.3-java, liblog4j1.2-java,
- libsam-java, libswing-layout-java, libxml-commons-external-java
+ libsam-java, libswing-layout-java, libxml-commons-external-java,
+ libguava-java
Description: Integrative Genomics Viewer
The Integrative Genomics Viewer (IGV) is a high-performance viewer that
efficiently handles large heterogeneous data sets, while providing a
Modified: packages-metadata/i/igv.copyright
===================================================================
--- packages-metadata/i/igv.copyright 2013-02-24 03:58:50 UTC (rev 2626)
+++ packages-metadata/i/igv.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -3,12 +3,14 @@
Files-Excluded:
igv.jar
batik-codec.jar
+ goby-io-igv.jar
igv.bat
igv.command
lib/Jama-*
lib/batik*
lib/commons*
lib/concurrent*
+ lib/guava*
lib/jargs*
lib/jcommon*
lib/jfreechart*
Added: packages-metadata/i/indigo.control
===================================================================
--- packages-metadata/i/indigo.control (rev 0)
+++ packages-metadata/i/indigo.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,146 @@
+Source: indigo
+Section: science
+Priority: extra
+Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
+Uploaders: Michael Banck <mbanck at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), javahelper, default-jdk, libjna-java, libcairo2-dev, libtinyxml-dev
+Standards-Version: 3.9.2
+Homepage: http://ggasoftware.com/opensource/indigo
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/indigo/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/indigo/
+
+Package: indigo-utils
+Architecture: any
+Section: science
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Organic Chemistry Toolkit Utilities
+ Indigo is a C++ based organic chemistry and cheminformatics software
+ environment. Features Include:
+ .
+ * Molecule and reaction rendering including SVG support
+ * Automatic layout for SMILES-represented molecules and reactions
+ * Canonical (isomeric) SMILES computation
+ * Exact matching, substructure matching, SMARTS matching
+ * Matching of tautomers and resonance structures
+ * Molecule fingerprinting, molecule similarity computation
+ * Fast enumeration of SSSR rings, subtrees, and edge sugraphs
+ * Molecular weight, molecular formula computation
+ * R-Group deconvolution and scaffold detection
+ * Computation of the exact maximum common substructure for an
+ arbitrary amount of input structures
+ * Combinatorial chemistry * Plugin support in the API
+ .
+ File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
+ SMARTS.
+ .
+ This package contains the following utilities:
+ .
+ * indigo-depict: Molecule and reaction rendering utility
+ * indigo-cano: Canonical SMILES generator
+ * indigo-deco: R-Group deconvolution utility
+ * chemdiff: Visual comparison of two SDF or SMILES files
+
+Package: libindigo0d
+Architecture: any
+Section: libs
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: Organic Chemistry Toolkit
+ Indigo is a C++ based organic chemistry and cheminformatics software
+ environment. Features Include:
+ .
+ * Molecule and reaction rendering including SVG support
+ * Automatic layout for SMILES-represented molecules and reactions
+ * Canonical (isomeric) SMILES computation
+ * Exact matching, substructure matching, SMARTS matching
+ * Matching of tautomers and resonance structures
+ * Molecule fingerprinting, molecule similarity computation
+ * Fast enumeration of SSSR rings, subtrees, and edge sugraphs
+ * Molecular weight, molecular formula computation
+ * R-Group deconvolution and scaffold detection
+ * Computation of the exact maximum common substructure for an
+ arbitrary amount of input structures
+ * Combinatorial chemistry * Plugin support in the API
+ .
+ File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
+ SMARTS.
+
+Package: libindigo-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends}, ${misc:Depends}, libindigo0d
+Description: Organic Chemistry Toolkit (development files)
+ Indigo is a C++ based organic chemistry and cheminformatics software
+ environment. Features Include:
+ .
+ * Molecule and reaction rendering including SVG support
+ * Automatic layout for SMILES-represented molecules and reactions
+ * Canonical (isomeric) SMILES computation
+ * Exact matching, substructure matching, SMARTS matching
+ * Matching of tautomers and resonance structures
+ * Molecule fingerprinting, molecule similarity computation
+ * Fast enumeration of SSSR rings, subtrees, and edge sugraphs
+ * Molecular weight, molecular formula computation
+ * R-Group deconvolution and scaffold detection
+ * Computation of the exact maximum common substructure for an
+ arbitrary amount of input structures
+ * Combinatorial chemistry
+ * Plugin support in the API
+ .
+ File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
+ SMARTS.
+ .
+ This package contains the static libary and header files.
+
+Package: python-indigo
+Architecture: all
+Section: python
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libindigo0d
+Description: Organic Chemistry Toolkit (python module)
+ Indigo is a C++ based organic chemistry and cheminformatics software
+ environment. Features Include:
+ .
+ * Molecule and reaction rendering including SVG support
+ * Automatic layout for SMILES-represented molecules and reactions
+ * Canonical (isomeric) SMILES computation
+ * Exact matching, substructure matching, SMARTS matching
+ * Matching of tautomers and resonance structures
+ * Molecule fingerprinting, molecule similarity computation
+ * Fast enumeration of SSSR rings, subtrees, and edge sugraphs
+ * Molecular weight, molecular formula computation
+ * R-Group deconvolution and scaffold detection
+ * Computation of the exact maximum common substructure for an
+ arbitrary amount of input structures
+ * Combinatorial chemistry
+ * Plugin support in the API
+ .
+ File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
+ SMARTS.
+ .
+ This package contains the python modules.
+
+Package: libindigo-java
+Architecture: all
+Section: java
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}, libindigo0d
+Description: Organic Chemistry Toolkit (Java package)
+ Indigo is a C++ based organic chemistry and cheminformatics software
+ environment. Features Include:
+ .
+ * Molecule and reaction rendering including SVG support
+ * Automatic layout for SMILES-represented molecules and reactions
+ * Canonical (isomeric) SMILES computation
+ * Exact matching, substructure matching, SMARTS matching
+ * Matching of tautomers and resonance structures
+ * Molecule fingerprinting, molecule similarity computation
+ * Fast enumeration of SSSR rings, subtrees, and edge sugraphs
+ * Molecular weight, molecular formula computation
+ * R-Group deconvolution and scaffold detection
+ * Computation of the exact maximum common substructure for an
+ arbitrary amount of input structures
+ * Combinatorial chemistry
+ * Plugin support in the API
+ .
+ File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and
+ SMARTS.
+ .
+ This package contains the Java packages.
Added: packages-metadata/i/indigo.copyright
===================================================================
--- packages-metadata/i/indigo.copyright (rev 0)
+++ packages-metadata/i/indigo.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,808 @@
+This work was packaged for Debian by:
+
+ Michael Banck <mbanck at debian.org> on Sun, 04 Mar 2012 21:14:05 +0100
+
+It was downloaded from:
+
+ http://ggasoftware.com/download/indigo
+
+api,bingo,common,graph,layout,legio,molecule,oci,reaction,render2d,utils:
+
+Upstream Author:
+
+ GGA Software Services LLC
+
+Copyright:
+
+ Copyright (C) 2009-2011 GGA Software Services LLC
+
+License:
+
+ This program 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 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 "/usr/share/common-licenses/GPL-3".
+
+cairo-src:
+
+Upstream Authors:
+
+ Josh Aas <joshmoz at gmail.com>
+ Daniel Amelang <dan at amelang.net>
+ Shawn T. Amundson <amundson at gtk.org>
+ Olivier Andrieu <oliv__a at users.sourceforge.net>
+ Peter Dennis Bartok <peter at novonyx.com>
+ Dave Beckett <dajobe at debian.org>
+ Kai-Uwe Behrmann <ku.b at gmx.de>
+ Christian Biesinger <cbiesinger at web.de>
+ Billy Biggs <vektor at dumbterm.net>
+ Hans Breuer <hans at breuer.org>
+ Brian Cameron <brian.cameron at sun.com>
+ Carlos Garcia Campos <carlosgc at gnome.org>
+ Damien Carbery <damien.carbery at sun.com>
+ Andrew Chant <andrew.chant at utoronto.ca>
+ Steve Chaplin <stevech1097 at yahoo.com.au>
+ Tomasz Cholewo <cholewo at ieee-cis.org>
+ Manu Cornet <manu at manucornet.net>
+ Frederic Crozat <fcrozat at mandriva.com>
+ Julien Danjou <julien at danjou.info>
+ Radek Doulík <rodo at novell.com>
+ John Ehresman <jpe at wingide.com>
+ John Ellson <ellson at research.att.com>
+ Michael Emmel <mike.emmel at gmail.com>
+ Miklós Erdélyi <erdelyim at gmail.com>
+ Behdad Esfahbod <behdad at behdad.org>
+ Brian Ewins <Brian.Ewins at gmail.com>
+ Bertram Felgenhauer <int-e at gmx.de>
+ Damian Frank <damian.frank at gmail.com>
+ Bdale Garbee <bdale at gag.com>
+ Jens Granseuer <jensgr at gmx.net>
+ Laxmi Harikumar <laxmi.harikumar at digital.com>
+ J. Ali Harlow <ali at avrc.city.ac.uk>
+ Mathias Hasselmann <mathias.hasselmann at gmx.de>
+ Richard Henderson <rth at twiddle.net>
+ James Henstridge <james at daa.com.au>
+ Graydon Hoare <graydon at redhat.com>
+ Thomas Hunger <info at teh-web.de>
+ Björn Lindqvist <bjourne at gmail.com>
+ Kristian Høgsberg <krh at redhat.com>
+ Amaury Jacquot <sxpert at esitcom.org>
+ Adrian Johnson <ajohnson at redneon.com>
+ Michael Johnson <ahze at ahze.net>
+ Jonathon Jongsma <jonathon.jongsma at gmail.com>
+ Øyvind Kolås <pippin at freedesktop.org>
+ Martin Kretzschmar <martink at gnome.org>
+ Mathieu Lacage <Mathieu.Lacage at sophia.inria.fr>
+ Dominic Lachowicz <domlachowicz at gmail.com>
+ Alexander Larsson <alexl at redhat.com>
+ Tor Lillqvist <tml at novell.com>
+ Jinghua Luo <sunmoon1997 at gmail.com>
+ Luke-Jr <luke-jr at utopios.org>
+ Kjartan Maraas <kmaraas at gnome.org>
+ Nis Martensen <nis.martensen at web.de>
+ Jordi Mas <jordi at ximian.com>
+ Nicholas Miell <nmiell at gmail.com>
+ Eugeniy Meshcheryakov <eugen at debian.org>
+ Zakharov Mikhail <zmey20000 at yahoo.com>
+ Christopher (Monty) Montgomery <xiphmont at gmail.com>
+ Tim Mooney <enchanter at users.sourceforge.net>
+ Jeff Muizelaar <jeff at infidigm.net>
+ Yevgen Muntyan <muntyan at tamu.edu>
+ Declan Naughton <piratepenguin at gmail.com>
+ Peter Nilsson <c99pnn at cs.umu.se>
+ Henning Noren <henning.noren.402 at student.lu.se>
+ Geoff Norton <gnorton at customerdna.com>
+ Robert O'Callahan <rocallahan at novell.com>
+ Ian Osgood <iano at quirkster.com>
+ Benjamin Otte <in7y118 at public.uni-hamburg.de>
+ Mike Owens <etc at filespanker.com>
+ Emmanuel Pacaud <emmanuel.pacaud at lapp.in2p3.fr>
+ Keith Packard <keithp at keithp.com>
+ Stuart Parmenter <pavlov at pavlov.net>
+ Alfred Peng <alfred.peng at sun.com>
+ Christof Petig <christof at petig-baender.de>
+ Joonas Pihlaja <jpihlaja at cc.helsinki.fi>
+ Mart Raudsepp <leio at dustbite.net>
+ David Reveman <davidr at novell.com>
+ Calum Robinson <calumr at mac.com>
+ Pavel Roskin <proski at gnu.org>
+ Tim Rowley <tim.rowley at gmail.com>
+ Soeren Sandmann <sandmann at daimi.au.dk>
+ Torsten Schönfeld <kaffeetisch at gmx.de>
+ Jamey Sharp <jamey at minilop.net>
+ Jason Dorje Short <jdorje at users.sf.net>
+ Jeff Smith <whydoubt at yahoo.com>
+ Travis Spencer <tspencer at cs.pdx.edu>
+ Bill Spitzak <spitzak at d2.com>
+ Zhe Su <james.su at gmail.com>
+ Owen Taylor <otaylor at redhat.com>
+ Karl Tomlinson <karlt+ at karlt.net>
+ Alp Toker <alp at atoker.com>
+ Malcolm Tredinnick <malcolm at commsecure.com.au>
+ David Turner <david at freetype.org>
+ Kalle Vahlman <kalle.vahlman at gmail.com>
+ Sasha Vasko <sasha at aftercode.net>
+ Vladimir Vukicevic <vladimir at pobox.com>
+ Jonathan Watt <jwatt at jwatt.org>
+ Peter Weilbacher <pmw at avila.aip.de>
+ Dan Williams <dcbw at redhat.com>
+ Chris Wilson <chris at chris-wilson.co.uk>
+ Carl Worth <cworth at isi.edu>
+ Richard D. Worth <richard at theworths.org>
+ Kent Worsnop <kworsnop at accesswave.ca>
+ Dave Yeo <daveryeo at telus.net>
+
+Copyright:
+
+ Copyright 1999 Tom Tromey
+ Copyright 2002, 2003 University of Southern California, Information
+ Sciences Institute (ISI)
+ Copyright 2000, 2002, 2004, 2005 Keith Packard
+ Copyright 2004 Calum Robinson
+ Copyright 2004 Richard D. Worth
+ Copyright 2004, 2005 Red Hat, Inc.
+ Copyright 2004 David Reveman
+
+License:
+
+ Cairo is free software.
+
+ Every source file in the implementation of cairo is available to be
+ redistributed and/or modified under the terms of either the GNU Lesser
+ General Public License (LGPL) version 2.1 or the Mozilla Public
+ License (MPL) version 1.1. Some files are available under more
+ liberal terms, but we believe that in all cases, each file may be used
+ under either the LGPL or the MPL.
+
+ On Debian systems, the complete text of the GNU General Lesser Public
+ License 2.1 can be found in /usr/share/common-licenses/LGPL-2.1
+
+ MOZILLA PUBLIC LICENSE
+ Version 1.1
+
+ ---------------
+
+ 1. Definitions.
+
+ 1.0.1. "Commercial Use" means distribution or otherwise making the
+ Covered Code available to a third party.
+
+ 1.1. "Contributor" means each entity that creates or contributes to
+ the creation of Modifications.
+
+ 1.2. "Contributor Version" means the combination of the Original
+ Code, prior Modifications used by a Contributor, and the Modifications
+ made by that particular Contributor.
+
+ 1.3. "Covered Code" means the Original Code or Modifications or the
+ combination of the Original Code and Modifications, in each case
+ including portions thereof.
+
+ 1.4. "Electronic Distribution Mechanism" means a mechanism generally
+ accepted in the software development community for the electronic
+ transfer of data.
+
+ 1.5. "Executable" means Covered Code in any form other than Source
+ Code.
+
+ 1.6. "Initial Developer" means the individual or entity identified
+ as the Initial Developer in the Source Code notice required by Exhibit
+ A.
+
+ 1.7. "Larger Work" means a work which combines Covered Code or
+ portions thereof with code not governed by the terms of this License.
+
+ 1.8. "License" means this document.
+
+ 1.8.1. "Licensable" means having the right to grant, to the maximum
+ extent possible, whether at the time of the initial grant or
+ subsequently acquired, any and all of the rights conveyed herein.
+
+ 1.9. "Modifications" means any addition to or deletion from the
+ substance or structure of either the Original Code or any previous
+ Modifications. When Covered Code is released as a series of files, a
+ Modification is:
+ A. Any addition to or deletion from the contents of a file
+ containing Original Code or previous Modifications.
+
+ B. Any new file that contains any part of the Original Code or
+ previous Modifications.
+
+ 1.10. "Original Code" means Source Code of computer software code
+ which is described in the Source Code notice required by Exhibit A as
+ Original Code, and which, at the time of its release under this
+ License is not already Covered Code governed by this License.
+
+ 1.10.1. "Patent Claims" means any patent claim(s), now owned or
+ hereafter acquired, including without limitation, method, process,
+ and apparatus claims, in any patent Licensable by grantor.
+
+ 1.11. "Source Code" means the preferred form of the Covered Code for
+ making modifications to it, including all modules it contains, plus
+ any associated interface definition files, scripts used to control
+ compilation and installation of an Executable, or source code
+ differential comparisons against either the Original Code or another
+ well known, available Covered Code of the Contributor's choice. The
+ Source Code can be in a compressed or archival form, provided the
+ appropriate decompression or de-archiving software is widely available
+ for no charge.
+
+ 1.12. "You" (or "Your") means an individual or a legal entity
+ exercising rights under, and complying with all of the terms of, this
+ License or a future version of this License issued under Section 6.1.
+ For legal entities, "You" includes any entity which controls, is
+ controlled by, or is under common control with You. For purposes of
+ this definition, "control" means (a) the power, direct or indirect,
+ to cause the direction or management of such entity, whether by
+ contract or otherwise, or (b) ownership of more than fifty percent
+ (50%) of the outstanding shares or beneficial ownership of such
+ entity.
+
+ 2. Source Code License.
+
+ 2.1. The Initial Developer Grant.
+ The Initial Developer hereby grants You a world-wide, royalty-free,
+ non-exclusive license, subject to third party intellectual property
+ claims:
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Initial Developer to use, reproduce,
+ modify, display, perform, sublicense and distribute the Original
+ Code (or portions thereof) with or without Modifications, and/or
+ as part of a Larger Work; and
+
+ (b) under Patents Claims infringed by the making, using or
+ selling of Original Code, to make, have made, use, practice,
+ sell, and offer for sale, and/or otherwise dispose of the
+ Original Code (or portions thereof).
+
+ (c) the licenses granted in this Section 2.1(a) and (b) are
+ effective on the date Initial Developer first distributes
+ Original Code under the terms of this License.
+
+ (d) Notwithstanding Section 2.1(b) above, no patent license is
+ granted: 1) for code that You delete from the Original Code; 2)
+ separate from the Original Code; or 3) for infringements caused
+ by: i) the modification of the Original Code or ii) the
+ combination of the Original Code with other software or devices.
+
+ 2.2. Contributor Grant.
+ Subject to third party intellectual property claims, each Contributor
+ hereby grants You a world-wide, royalty-free, non-exclusive license
+
+ (a) under intellectual property rights (other than patent or
+ trademark) Licensable by Contributor, to use, reproduce, modify,
+ display, perform, sublicense and distribute the Modifications
+ created by such Contributor (or portions thereof) either on an
+ unmodified basis, with other Modifications, as Covered Code
+ and/or as part of a Larger Work; and
+
+ (b) under Patent Claims infringed by the making, using, or
+ selling of Modifications made by that Contributor either alone
+ and/or in combination with its Contributor Version (or portions
+ of such combination), to make, use, sell, offer for sale, have
+ made, and/or otherwise dispose of: 1) Modifications made by that
+ Contributor (or portions thereof); and 2) the combination of
+ Modifications made by that Contributor with its Contributor
+ Version (or portions of such combination).
+
+ (c) the licenses granted in Sections 2.2(a) and 2.2(b) are
+ effective on the date Contributor first makes Commercial Use of
+ the Covered Code.
+
+ (d) Notwithstanding Section 2.2(b) above, no patent license is
+ granted: 1) for any code that Contributor has deleted from the
+ Contributor Version; 2) separate from the Contributor Version;
+ 3) for infringements caused by: i) third party modifications of
+ Contributor Version or ii) the combination of Modifications made
+ by that Contributor with other software (except as part of the
+ Contributor Version) or other devices; or 4) under Patent Claims
+ infringed by Covered Code in the absence of Modifications made by
+ that Contributor.
+
+ 3. Distribution Obligations.
+
+ 3.1. Application of License.
+ The Modifications which You create or to which You contribute are
+ governed by the terms of this License, including without limitation
+ Section 2.2. The Source Code version of Covered Code may be
+ distributed only under the terms of this License or a future version
+ of this License released under Section 6.1, and You must include a
+ copy of this License with every copy of the Source Code You
+ distribute. You may not offer or impose any terms on any Source Code
+ version that alters or restricts the applicable version of this
+ License or the recipients' rights hereunder. However, You may include
+ an additional document offering the additional rights described in
+ Section 3.5.
+
+ 3.2. Availability of Source Code.
+ Any Modification which You create or to which You contribute must be
+ made available in Source Code form under the terms of this License
+ either on the same media as an Executable version or via an accepted
+ Electronic Distribution Mechanism to anyone to whom you made an
+ Executable version available; and if made available via Electronic
+ Distribution Mechanism, must remain available for at least twelve (12)
+ months after the date it initially became available, or at least six
+ (6) months after a subsequent version of that particular Modification
+ has been made available to such recipients. You are responsible for
+ ensuring that the Source Code version remains available even if the
+ Electronic Distribution Mechanism is maintained by a third party.
+
+ 3.3. Description of Modifications.
+ You must cause all Covered Code to which You contribute to contain a
+ file documenting the changes You made to create that Covered Code and
+ the date of any change. You must include a prominent statement that
+ the Modification is derived, directly or indirectly, from Original
+ Code provided by the Initial Developer and including the name of the
+ Initial Developer in (a) the Source Code, and (b) in any notice in an
+ Executable version or related documentation in which You describe the
+ origin or ownership of the Covered Code.
+
+ 3.4. Intellectual Property Matters
+ (a) Third Party Claims.
+ If Contributor has knowledge that a license under a third party's
+ intellectual property rights is required to exercise the rights
+ granted by such Contributor under Sections 2.1 or 2.2,
+ Contributor must include a text file with the Source Code
+ distribution titled "LEGAL" which describes the claim and the
+ party making the claim in sufficient detail that a recipient will
+ know whom to contact. If Contributor obtains such knowledge after
+ the Modification is made available as described in Section 3.2,
+ Contributor shall promptly modify the LEGAL file in all copies
+ Contributor makes available thereafter and shall take other steps
+ (such as notifying appropriate mailing lists or newsgroups)
+ reasonably calculated to inform those who received the Covered
+ Code that new knowledge has been obtained.
+
+ (b) Contributor APIs.
+ If Contributor's Modifications include an application programming
+ interface and Contributor has knowledge of patent licenses which
+ are reasonably necessary to implement that API, Contributor must
+ also include this information in the LEGAL file.
+
+ (c) Representations.
+ Contributor represents that, except as disclosed pursuant to
+ Section 3.4(a) above, Contributor believes that Contributor's
+ Modifications are Contributor's original creation(s) and/or
+ Contributor has sufficient rights to grant the rights conveyed by
+ this License.
+
+ 3.5. Required Notices.
+ You must duplicate the notice in Exhibit A in each file of the Source
+ Code. If it is not possible to put such notice in a particular Source
+ Code file due to its structure, then You must include such notice in a
+ location (such as a relevant directory) where a user would be likely
+ to look for such a notice. If You created one or more Modification(s)
+ You may add your name as a Contributor to the notice described in
+ Exhibit A. You must also duplicate this License in any documentation
+ for the Source Code where You describe recipients' rights or ownership
+ rights relating to Covered Code. You may choose to offer, and to
+ charge a fee for, warranty, support, indemnity or liability
+ obligations to one or more recipients of Covered Code. However, You
+ may do so only on Your own behalf, and not on behalf of the Initial
+ Developer or any Contributor. You must make it absolutely clear than
+ any such warranty, support, indemnity or liability obligation is
+ offered by You alone, and You hereby agree to indemnify the Initial
+ Developer and every Contributor for any liability incurred by the
+ Initial Developer or such Contributor as a result of warranty,
+ support, indemnity or liability terms You offer.
+
+ 3.6. Distribution of Executable Versions.
+ You may distribute Covered Code in Executable form only if the
+ requirements of Section 3.1-3.5 have been met for that Covered Code,
+ and if You include a notice stating that the Source Code version of
+ the Covered Code is available under the terms of this License,
+ including a description of how and where You have fulfilled the
+ obligations of Section 3.2. The notice must be conspicuously included
+ in any notice in an Executable version, related documentation or
+ collateral in which You describe recipients' rights relating to the
+ Covered Code. You may distribute the Executable version of Covered
+ Code or ownership rights under a license of Your choice, which may
+ contain terms different from this License, provided that You are in
+ compliance with the terms of this License and that the license for the
+ Executable version does not attempt to limit or alter the recipient's
+ rights in the Source Code version from the rights set forth in this
+ License. If You distribute the Executable version under a different
+ license You must make it absolutely clear that any terms which differ
+ from this License are offered by You alone, not by the Initial
+ Developer or any Contributor. You hereby agree to indemnify the
+ Initial Developer and every Contributor for any liability incurred by
+ the Initial Developer or such Contributor as a result of any such
+ terms You offer.
+
+ 3.7. Larger Works.
+ You may create a Larger Work by combining Covered Code with other code
+ not governed by the terms of this License and distribute the Larger
+ Work as a single product. In such a case, You must make sure the
+ requirements of this License are fulfilled for the Covered Code.
+
+ 4. Inability to Comply Due to Statute or Regulation.
+
+ If it is impossible for You to comply with any of the terms of this
+ License with respect to some or all of the Covered Code due to
+ statute, judicial order, or regulation then You must: (a) comply with
+ the terms of this License to the maximum extent possible; and (b)
+ describe the limitations and the code they affect. Such description
+ must be included in the LEGAL file described in Section 3.4 and must
+ be included with all distributions of the Source Code. Except to the
+ extent prohibited by statute or regulation, such description must be
+ sufficiently detailed for a recipient of ordinary skill to be able to
+ understand it.
+
+ 5. Application of this License.
+
+ This License applies to code to which the Initial Developer has
+ attached the notice in Exhibit A and to related Covered Code.
+
+ 6. Versions of the License.
+
+ 6.1. New Versions.
+ Netscape Communications Corporation ("Netscape") may publish revised
+ and/or new versions of the License from time to time. Each version
+ will be given a distinguishing version number.
+
+ 6.2. Effect of New Versions.
+ Once Covered Code has been published under a particular version of the
+ License, You may always continue to use it under the terms of that
+ version. You may also choose to use such Covered Code under the terms
+ of any subsequent version of the License published by Netscape. No one
+ other than Netscape has the right to modify the terms applicable to
+ Covered Code created under this License.
+
+ 6.3. Derivative Works.
+ If You create or use a modified version of this License (which you may
+ only do in order to apply it to code which is not already Covered Code
+ governed by this License), You must (a) rename Your license so that
+ the phrases "Mozilla", "MOZILLAPL", "MOZPL", "Netscape",
+ "MPL", "NPL" or any confusingly similar phrase do not appear in your
+ license (except to note that your license differs from this License)
+ and (b) otherwise make it clear that Your version of the license
+ contains terms which differ from the Mozilla Public License and
+ Netscape Public License. (Filling in the name of the Initial
+ Developer, Original Code or Contributor in the notice described in
+ Exhibit A shall not of themselves be deemed to be modifications of
+ this License.)
+
+ 7. DISCLAIMER OF WARRANTY.
+
+ COVERED CODE IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS,
+ WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING,
+ WITHOUT LIMITATION, WARRANTIES THAT THE COVERED CODE IS FREE OF
+ DEFECTS, MERCHANTABLE, FIT FOR A PARTICULAR PURPOSE OR NON-INFRINGING.
+ THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE COVERED CODE
+ IS WITH YOU. SHOULD ANY COVERED CODE PROVE DEFECTIVE IN ANY RESPECT,
+ YOU (NOT THE INITIAL DEVELOPER OR ANY OTHER CONTRIBUTOR) ASSUME THE
+ COST OF ANY NECESSARY SERVICING, REPAIR OR CORRECTION. THIS DISCLAIMER
+ OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF THIS LICENSE. NO USE OF
+ ANY COVERED CODE IS AUTHORIZED HEREUNDER EXCEPT UNDER THIS DISCLAIMER.
+
+ 8. TERMINATION.
+
+ 8.1. This License and the rights granted hereunder will terminate
+ automatically if You fail to comply with terms herein and fail to cure
+ such breach within 30 days of becoming aware of the breach. All
+ sublicenses to the Covered Code which are properly granted shall
+ survive any termination of this License. Provisions which, by their
+ nature, must remain in effect beyond the termination of this License
+ shall survive.
+
+ 8.2. If You initiate litigation by asserting a patent infringement
+ claim (excluding declatory judgment actions) against Initial Developer
+ or a Contributor (the Initial Developer or Contributor against whom
+ You file such action is referred to as "Participant") alleging that:
+
+ (a) such Participant's Contributor Version directly or indirectly
+ infringes any patent, then any and all rights granted by such
+ Participant to You under Sections 2.1 and/or 2.2 of this License
+ shall, upon 60 days notice from Participant terminate prospectively,
+ unless if within 60 days after receipt of notice You either: (i)
+ agree in writing to pay Participant a mutually agreeable reasonable
+ royalty for Your past and future use of Modifications made by such
+ Participant, or (ii) withdraw Your litigation claim with respect to
+ the Contributor Version against such Participant. If within 60 days
+ of notice, a reasonable royalty and payment arrangement are not
+ mutually agreed upon in writing by the parties or the litigation claim
+ is not withdrawn, the rights granted by Participant to You under
+ Sections 2.1 and/or 2.2 automatically terminate at the expiration of
+ the 60 day notice period specified above.
+
+ (b) any software, hardware, or device, other than such Participant's
+ Contributor Version, directly or indirectly infringes any patent, then
+ any rights granted to You by such Participant under Sections 2.1(b)
+ and 2.2(b) are revoked effective as of the date You first made, used,
+ sold, distributed, or had made, Modifications made by that
+ Participant.
+
+ 8.3. If You assert a patent infringement claim against Participant
+ alleging that such Participant's Contributor Version directly or
+ indirectly infringes any patent where such claim is resolved (such as
+ by license or settlement) prior to the initiation of patent
+ infringement litigation, then the reasonable value of the licenses
+ granted by such Participant under Sections 2.1 or 2.2 shall be taken
+ into account in determining the amount or value of any payment or
+ license.
+
+ 8.4. In the event of termination under Sections 8.1 or 8.2 above,
+ all end user license agreements (excluding distributors and resellers)
+ which have been validly granted by You or any distributor hereunder
+ prior to termination shall survive termination.
+
+ 9. LIMITATION OF LIABILITY.
+
+ UNDER NO CIRCUMSTANCES AND UNDER NO LEGAL THEORY, WHETHER TORT
+ (INCLUDING NEGLIGENCE), CONTRACT, OR OTHERWISE, SHALL YOU, THE INITIAL
+ DEVELOPER, ANY OTHER CONTRIBUTOR, OR ANY DISTRIBUTOR OF COVERED CODE,
+ OR ANY SUPPLIER OF ANY OF SUCH PARTIES, BE LIABLE TO ANY PERSON FOR
+ ANY INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES OF ANY
+ CHARACTER INCLUDING, WITHOUT LIMITATION, DAMAGES FOR LOSS OF GOODWILL,
+ WORK STOPPAGE, COMPUTER FAILURE OR MALFUNCTION, OR ANY AND ALL OTHER
+ COMMERCIAL DAMAGES OR LOSSES, EVEN IF SUCH PARTY SHALL HAVE BEEN
+ INFORMED OF THE POSSIBILITY OF SUCH DAMAGES. THIS LIMITATION OF
+ LIABILITY SHALL NOT APPLY TO LIABILITY FOR DEATH OR PERSONAL INJURY
+ RESULTING FROM SUCH PARTY'S NEGLIGENCE TO THE EXTENT APPLICABLE LAW
+ PROHIBITS SUCH LIMITATION. SOME JURISDICTIONS DO NOT ALLOW THE
+ EXCLUSION OR LIMITATION OF INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO
+ THIS EXCLUSION AND LIMITATION MAY NOT APPLY TO YOU.
+
+ 10. U.S. GOVERNMENT END USERS.
+
+ The Covered Code is a "commercial item," as that term is defined in
+ 48 C.F.R. 2.101 (Oct. 1995), consisting of "commercial computer
+ software" and "commercial computer software documentation," as such
+ terms are used in 48 C.F.R. 12.212 (Sept. 1995). Consistent with 48
+ C.F.R. 12.212 and 48 C.F.R. 227.7202-1 through 227.7202-4 (June 1995),
+ all U.S. Government End Users acquire Covered Code with only those
+ rights set forth herein.
+
+ 11. MISCELLANEOUS.
+
+ This License represents the complete agreement concerning subject
+ matter hereof. If any provision of this License is held to be
+ unenforceable, such provision shall be reformed only to the extent
+ necessary to make it enforceable. This License shall be governed by
+ California law provisions (except to the extent applicable law, if
+ any, provides otherwise), excluding its conflict-of-law provisions.
+ With respect to disputes in which at least one party is a citizen of,
+ or an entity chartered or registered to do business in the United
+ States of America, any litigation relating to this License shall be
+ subject to the jurisdiction of the Federal Courts of the Northern
+ District of California, with venue lying in Santa Clara County,
+ California, with the losing party responsible for costs, including
+ without limitation, court costs and reasonable attorneys' fees and
+ expenses. The application of the United Nations Convention on
+ Contracts for the International Sale of Goods is expressly excluded.
+ Any law or regulation which provides that the language of a contract
+ shall be construed against the drafter shall not apply to this
+ License.
+
+ 12. RESPONSIBILITY FOR CLAIMS.
+
+ As between Initial Developer and the Contributors, each party is
+ responsible for claims and damages arising, directly or indirectly,
+ out of its utilization of rights under this License and You agree to
+ work with Initial Developer and Contributors to distribute such
+ responsibility on an equitable basis. Nothing herein is intended or
+ shall be deemed to constitute any admission of liability.
+
+ 13. MULTIPLE-LICENSED CODE.
+
+ Initial Developer may designate portions of the Covered Code as
+ "Multiple-Licensed". "Multiple-Licensed" means that the Initial
+ Developer permits you to utilize portions of the Covered Code under
+ Your choice of the NPL or the alternative licenses, if any, specified
+ by the Initial Developer in the file described in Exhibit A.
+
+ EXHIBIT A -Mozilla Public License.
+
+ ``The contents of this file are subject to the Mozilla Public License
+ Version 1.1 (the "License"); you may not use this file except in
+ compliance with the License. You may obtain a copy of the License at
+ http://www.mozilla.org/MPL/
+
+ Software distributed under the License is distributed on an "AS IS"
+ basis, WITHOUT WARRANTY OF ANY KIND, either express or implied. See the
+ License for the specific language governing rights and limitations
+ under the License.
+
+ The Original Code is ______________________________________.
+
+ The Initial Developer of the Original Code is ________________________.
+ Portions created by ______________________ are Copyright (C) ______
+ _______________________. All Rights Reserved.
+
+ Contributor(s): ______________________________________.
+
+ Alternatively, the contents of this file may be used under the terms
+ of the _____ license (the "[___] License"), in which case the
+ provisions of [______] License are applicable instead of those
+ above. If you wish to allow use of your version of this file only
+ under the terms of the [____] License and not to allow others to use
+ your version of this file under the MPL, indicate your decision by
+ deleting the provisions above and replace them with the notice and
+ other provisions required by the [___] License. If you do not delete
+ the provisions above, a recipient may use your version of this file
+ under either the MPL or the [___] License."
+
+ [NOTE: The text of this Exhibit A may differ slightly from the text of
+ the notices in the Source Code files of the Original Code. You should
+ use the text of this Exhibit A rather than the text found in the
+ Original Code Source Code for Your Modifications.]
+
+libpng-src:
+
+ libpng version 1.2.26 - April 2, 2008
+ Copyright (c) 1998-2008 Glenn Randers-Pehrson
+ (Version 0.96 Copyright (c) 1996, 1997 Andreas Dilger)
+ (Version 0.88 Copyright (c) 1995, 1996 Guy Eric Schalnat, Group 42, Inc.)
+
+ Authors and maintainers:
+ libpng versions 0.71, May 1995, through 0.88, January 1996: Guy Schalnat
+ libpng versions 0.89c, June 1996, through 0.96, May 1997: Andreas Dilger
+ libpng versions 0.97, January 1998, through 1.2.26 - April 2, 2008: Glenn
+ See also "Contributing Authors", below.
+
+
+ COPYRIGHT NOTICE, DISCLAIMER, and LICENSE:
+
+ If you modify libpng you may insert additional notices immediately following
+ this sentence.
+
+ libpng versions 1.2.6, August 15, 2004, through 1.2.26, April 2, 2008, are
+ Copyright (c) 2004, 2006-2008 Glenn Randers-Pehrson, and are
+ distributed according to the same disclaimer and license as libpng-1.2.5
+ with the following individual added to the list of Contributing Authors:
+
+ Cosmin Truta
+
+ libpng versions 1.0.7, July 1, 2000, through 1.2.5, October 3, 2002, are
+ Copyright (c) 2000-2002 Glenn Randers-Pehrson, and are
+ distributed according to the same disclaimer and license as libpng-1.0.6
+ with the following individuals added to the list of Contributing Authors:
+
+ Simon-Pierre Cadieux
+ Eric S. Raymond
+ Gilles Vollant
+
+ and with the following additions to the disclaimer:
+
+ There is no warranty against interference with your enjoyment of the
+ library or against infringement. There is no warranty that our
+ efforts or the library will fulfill any of your particular purposes
+ or needs. This library is provided with all faults, and the entire
+ risk of satisfactory quality, performance, accuracy, and effort is with
+ the user.
+
+ libpng versions 0.97, January 1998, through 1.0.6, March 20, 2000, are
+ Copyright (c) 1998, 1999, 2000 Glenn Randers-Pehrson, and are
+ distributed according to the same disclaimer and license as libpng-0.96,
+ with the following individuals added to the list of Contributing Authors:
+
+ Tom Lane
+ Glenn Randers-Pehrson
+ Willem van Schaik
+
+ libpng versions 0.89, June 1996, through 0.96, May 1997, are
+ Copyright (c) 1996, 1997 Andreas Dilger
+ Distributed according to the same disclaimer and license as libpng-0.88,
+ with the following individuals added to the list of Contributing Authors:
+
+ John Bowler
+ Kevin Bracey
+ Sam Bushell
+ Magnus Holmgren
+ Greg Roelofs
+ Tom Tanner
+
+ libpng versions 0.5, May 1995, through 0.88, January 1996, are
+ Copyright (c) 1995, 1996 Guy Eric Schalnat, Group 42, Inc.
+
+ For the purposes of this copyright and license, "Contributing Authors"
+ is defined as the following set of individuals:
+
+ Andreas Dilger
+ Dave Martindale
+ Guy Eric Schalnat
+ Paul Schmidt
+ Tim Wegner
+
+ The PNG Reference Library is supplied "AS IS". The Contributing Authors
+ and Group 42, Inc. disclaim all warranties, expressed or implied,
+ including, without limitation, the warranties of merchantability and of
+ fitness for any purpose. The Contributing Authors and Group 42, Inc.
+ assume no liability for direct, indirect, incidental, special, exemplary,
+ or consequential damages, which may result from the use of the PNG
+ Reference Library, even if advised of the possibility of such damage.
+
+ Permission is hereby granted to use, copy, modify, and distribute this
+ source code, or portions hereof, for any purpose, without fee, subject
+ to the following restrictions:
+
+ 1. The origin of this source code must not be misrepresented.
+
+ 2. Altered versions must be plainly marked as such and
+ must not be misrepresented as being the original source.
+
+ 3. This Copyright notice may not be removed or altered from
+ any source or altered source distribution.
+
+ The Contributing Authors and Group 42, Inc. specifically permit, without
+ fee, and encourage the use of this source code as a component to
+ supporting the PNG file format in commercial products. If you use this
+ source code in a product, acknowledgment is not required but would be
+ appreciated.
+
+tinyxml:
+
+Upstream authors:
+
+ Lee Thomason, Yves Berquin, Andrew Ellerton and Tyge Lovset
+
+Copyright:
+
+ Copyright (C) 2000-2007 Lee Thomason
+ Copyright (C) 2002-2004 Yves Berquin
+ Copyright (C) 2005 Tyge Lovset
+
+License:
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any
+ damages arising from the use of this software.
+ .
+ Permission is granted to anyone to use this software for any
+ purpose, including commercial applications, and to alter it and
+ redistribute it freely, subject to the following restrictions:
+ .
+ 1. The origin of this software must not be misrepresented; you must
+ not claim that you wrote the original software. If you use this
+ software in a product, an acknowledgment in the product documentation
+ would be appreciated but is not required.
+ .
+ 2. Altered source versions must be plainly marked as such, and
+ must not be misrepresented as being the original software.
+ .
+ 3. This notice may not be removed or altered from any source
+ distribution.
+
+zlib-src:
+
+Upstream Authors:
+
+ Jean-loup Gailly and Mark Adler
+
+Copyright:
+
+ Copyright (C) 1995-2010 Jean-loup Gailly and Mark Adler
+
+License:
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+The Debian packaging is:
+
+ Copyright (C) 2012 Michael Banck <mbanck at debian.org>
+
+and is licensed under the GPL version 3, see above.
Added: packages-metadata/o/opsin.control
===================================================================
--- packages-metadata/o/opsin.control (rev 0)
+++ packages-metadata/o/opsin.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,19 @@
+Source: opsin
+Section: science
+Priority: extra
+Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
+Uploaders: Michael Banck <mbanck at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), javahelper, default-jdk, ant, libautomaton-java, libxom-java, liblog4j1.2-java, libcommons-cli-java, libcommons-io-java, libmockito-java, junit4
+Standards-Version: 3.9.2
+Homepage: http://www-ucc.ch.cam.ac.uk/products/software/opsin
+Vcs-Browser: http://svn.debian.org/wsvn/debichem/unstable/opsin/
+Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/opsin/
+
+Package: libopsin-java
+Architecture: all
+Section: java
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${java:Depends}
+Description: Chemical name to structure converter
+ OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound
+ names to semantic chemical information and outputs a structure either as as
+ CML (Chemical Markup Language), SMILES, or InChI.
Added: packages-metadata/o/opsin.copyright
===================================================================
--- packages-metadata/o/opsin.copyright (rev 0)
+++ packages-metadata/o/opsin.copyright 2013-02-25 03:58:51 UTC (rev 2627)
@@ -0,0 +1,193 @@
+This work was packaged for Debian by:
+
+ Michael Banck <mbanck at debian.org> on Mon, 05 Mar 2012 22:01:45 +0100
+
+It was downloaded from:
+
+ https://bitbucket.org/dan2097/opsin/downloads
+
+Upstream Authors:
+
+ Albina Absdulina, Rich Apodaca, Peter Corbett, Daniel Lowe and Peter
+ Murray-Rust
+
+Copyright:
+
+ Copyright (C) Daniel Lowe, Peter Corbett and Peter Murray-Rust
+
+License:
+
+ 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. (b)
+ ensure that installation of your Modified Version does not prevent the
+ user installing or running the Standard Version. In addition, the
+ Modified Version must bear a name that is different from the name of the
+ Standard Version. (c) allow anyone who receives a copy of the Modified
+ Version to make the Source form of the Modified Version available to
+ others under (i) the Original License or (ii) a license that permits the
+ licensee to freely copy, modify and redistribute the Modified Version
+ using the same licensing terms that apply to the copy that the licensee
+ received, and requires that the Source form of the Modified Version, and
+ of any works derived from it, be made freely available in that license
+ fees are prohibited but Distributor Fees are allowed. Distribution of
+ Compiled Forms of the Standard Version or Modified Versions without the
+ Source
+
+ (5) You may Distribute Compiled forms of the Standard Version without
+ the Source, provided that you include complete instructions on how to
+ get the Source of the Standard Version. Such instructions must be valid
+ at the time of your distribution. If these instructions, at any time
+ while you are carrying out such distribution, become invalid, you must
+ provide new instructions on demand or cease further distribution. If you
+ provide valid instructions or cease distribution within thirty days
+ after you become aware that the instructions are invalid, then you do
+ not forfeit any of your rights under this license.
+
+ (6) You may Distribute a Modified Version in Compiled form without the
+ Source, provided that you comply with Section 4 with respect to the
+ Source of the Modified Version. Aggregating or Linking the Package
+
+ (7) You may aggregate the Package (either the Standard Version or
+ Modified Version) with other packages and Distribute the resulting
+ aggregation provided that you do not charge a licensing fee for the
+ Package. Distributor Fees are permitted, and licensing fees for other
+ components in the aggregation are permitted. The terms of this license
+ apply to the use and Distribution of the Standard or Modified Versions
+ as included in the aggregation.
+
+ (8) You are permitted to link Modified and Standard Versions with other
+ works, to embed the Package in a larger work of your own, or to build
+ stand-alone binary or bytecode versions of applications that include the
+ Package, and Distribute the result without restriction, provided the
+ result does not expose a direct interface to the Package. Items That
+ are Not Considered Part of a Modified Version
+
+ (9) Works (including, but not limited to, modules and scripts) that
+ merely extend or make use of the Package, do not, by themselves, cause
+ the Package to be a Modified Version. In addition, such works are not
+ considered parts of the Package itself, and are not subject to the terms
+ of this license. General Provisions
+
+ (10) Any use, modification, and distribution of the Standard or Modified
+ Versions is governed by this Artistic License. By using, modifying or
+ distributing the Package, you accept this license. Do not use, modify,
+ or distribute the Package, if you do not accept this license.
+
+ (11) If your Modified Version has been derived from a Modified Version
+ made by someone other than you, you are nevertheless required to ensure
+ that your Modified Version complies with the requirements of this
+ license.
+
+ (12) This license does not grant you the right to use any trademark,
+ service mark, tradename, or logo of the Copyright Holder.
+
+ (13) This license includes the non-exclusive, worldwide, free-of-charge
+ patent license to make, have made, use, offer to sell, sell, import and
+ otherwise transfer the Package with respect to any patent claims
+ licensable by the Copyright Holder that are necessarily infringed by the
+ Package. If you institute patent litigation (including a cross-claim or
+ counterclaim) against any party alleging that the Package constitutes
+ direct or contributory patent infringement, then this Artistic License
+ to you shall terminate on the date that such litigation is filed.
+
+ (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
+ HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES. THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+ PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
+ PERMITTED BY YOUR LOCAL LAW. UNLESS REQUIRED BY LAW, NO COPYRIGHT HOLDER
+ OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, OR
+ CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE OF THE PACKAGE,
+ EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+The Debian packaging is:
+
+ Copyright (C) 2012 Michael Banck <mbanck at debian.org>
+
+and is licensed under the same license as above.
Modified: packages-metadata/v/vcftools.control
===================================================================
--- packages-metadata/v/vcftools.control 2013-02-24 03:58:50 UTC (rev 2626)
+++ packages-metadata/v/vcftools.control 2013-02-25 03:58:51 UTC (rev 2627)
@@ -2,10 +2,9 @@
Section: science
Priority: extra
Build-Depends: debhelper (>= 9), zlib1g-dev
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
Homepage: http://vcftools.sourceforge.net
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
Uploaders: Thorsten Alteholz <debian at alteholz.de>,
Andreas Tille <tille at debian.org>
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/vcftools/trunk/
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