Copyright and licence information for the r2sbml package ======================================================== The r2sbml package as a whole is distributed under GPL (>= 2). Parts of it are derived from, or are linked against, third-party code held by other copyright holders and released under other (compatible) terms. Those parts are itemised below. 1. The R package itself ----------------------------------------------------------------------- Files: everything not listed under the sections below. Copyright: Satyaprakash Nayak Licence: GPL (>= 2) 2. Code adapted from the libSBML example programs ----------------------------------------------------------------------- Files: src/convertReactions.cpp src/getMath.cpp Authors: Sarah Keating, Frank T. Bergmann Copyright: (c) 2013-2016 by the California Institute of Technology (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK) and the University of Heidelberg (Germany), with support from the National Institutes of Health (USA) under grant R01GM070923. Licence: MIT These two files are adapted from example programs shipped with libSBML. Those examples are distributed under a different licence from the rest of libSBML: the MIT licence. The full licence text and the accompanying non-endorsement clause are retained verbatim in the header comment of each of the two files. 3. libSBML ----------------------------------------------------------------------- Copyright: (C) 2020 jointly by the California Institute of Technology (Pasadena, CA, USA), the University of Heidelberg (Heidelberg, Germany) and University College London (London, UK) (C) 2019 jointly by the California Institute of Technology and the University of Heidelberg (C) 2013-2018 jointly by the California Institute of Technology (Pasadena, CA, USA), the EMBL European Bioinformatics Institute (EMBL-EBI, Hinxton, UK) and the University of Heidelberg (Heidelberg, Germany) (C) 2009-2013 jointly by the California Institute of Technology and the EMBL European Bioinformatics Institute (C) 2006-2008 by the California Institute of Technology (C) 2002-2005 jointly by the California Institute of Technology and the Japan Science and Technology Agency (Japan) Licence: GNU Lesser General Public License (LGPL), version 2.1 or, at your option, any later version. libSBML source code IS shipped inside this package, as the archive src/libsbml-mod-5.21.0.tar.gz. tools/cmake_call.sh unpacks it at build time, builds it as a static library and links it into the r2sbml shared object, so both the package sources and the installed binary contain libSBML code. That archive is the official libSBML 5.21.0 release from https://github.com/sbmlteam/libsbml with whole directories removed -- the language bindings, documentation, examples, development tooling, autotools build system, test suites, and the SBML Level 3 package sources this build does not enable. The files it does retain are byte-for-byte upstream. tools/strip_libsbml_tarball.sh regenerates the archive from an official release and documents exactly what it drops. libSBML sources ARE modified during the build, after unpacking and before compiling: tools/cmake_call.sh applies a set of patches required by CRAN policy (removing calls to the system random number generator, output to stdout/stderr, and [v]sprintf). Those patches are applied to the unpacked copy only; the archive itself is left as distributed upstream. libSBML's own licence files are included in the archive and are installed alongside the built library, at src/libsbml-install/share/libsbml/LICENSE.txt (terms and copyright summary) and src/libsbml-install/share/libsbml/COPYING.txt (the full LGPL 2.1 text). Both are also available from https://sbml.org/software/libsbml/ and from the libSBML source repository. libSBML's main authors are Sarah M. Keating, Frank T. Bergmann, Lucian P. Smith, Brett G. Olivier, Akiya Jouraku, Michael Hucka and Ben Bornstein, with contributions from many others. Note: libSBML also carries a copyright statement for the "SBML Layout" code, (C) 2004-2008 by European Media Laboratories Research gGmbH (Heidelberg, Germany). That code is not compiled into r2sbml, because the build enables no SBML Level 3 packages. It would need to be listed here if tools/cmake_call.sh were ever changed to enable them. 4. MiniZip, incorporated into libSBML ----------------------------------------------------------------------- Files: compiled into libSBML from src/sbml/compress/ in the libSBML source tree: zip.c/.h, unzip.c/.h, ioapi.c/.h, iowin32.c/.h (MiniZip 1.1), ioapi_mem.c/.h, and crypt.h (MiniZip 1.01e) Copyright: (C) 1998-2010 Gilles Vollant (http://www.winimage.com/zLibDll/minizip.html) (C) 2009-2010 Mathias Svensson (Zip64 support) (C) 2007-2008 Even Rouault (Zip64 support in unzip) (C) 2010-2014 Nathan Moinvaziri (AES and PKWARE disk spanning, in zip.c and unzip.c) (C) 2003 Terry Thorsen (crypt.h) (C) 1990-2000 Info-ZIP (crypt.h, which is a modified version of the encryption code in the Info-ZIP distribution) Licence: zlib licence, reproduced below; crypt.h is additionally subject to the Info-ZIP licence (version 2000-Apr-09 or later, https://infozip.sourceforge.net/license.html), a permissive BSD-style licence. libSBML's own src/sbml/compress/00README.txt describes all of these files as MiniZip 1.01e, but the headers of every file except crypt.h say version 1.1. The headers are what is recorded here. 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. Some of these files were modified by the libSBML developers to address compiler warnings. r2sbml additionally patches crypt.h at build time (see tools/cmake_call.sh) to remove calls to the system random number generator, which CRAN policy does not permit in compiled code. 5. iostream wrappers derived from zlib contributed code, incorporated into libSBML ----------------------------------------------------------------------- Files: compiled into libSBML from src/sbml/compress/ in the libSBML source tree: zfstream.cpp/.h, and bzfstream and zipfstream which are based on them Authors: Ludwig Schwardt , from an original implementation by Kevin Ruland Origin: contributed sample files of zlib 1.2.3 (http://www.zlib.net/) Licence: zlib licence, as reproduced in section 4 above. 6. maddy, incorporated into libSBML ----------------------------------------------------------------------- Files: compiled into libSBML from src/sbml/maddy/ in the libSBML source tree (header-only) Version: 1.4.0 (https://github.com/progsource/maddy) Copyright: (C) 2017, 2018, 2019, 2020, 2023 M. Petra Baranski Licence: MIT licence, reproduced below. 7. html2md, incorporated into libSBML ----------------------------------------------------------------------- Files: compiled into libSBML from src/sbml/html2md/ in the libSBML source tree: html2md.cpp/.h, table.cpp/.h Version: 1.6.6 (https://github.com/tim-gromeyer/html2md) Copyright: (C) 2022 Tim Gromeyer Licence: MIT licence, reproduced below. Both libraries carry the same MIT licence text, differing only in the copyright line given above. The original licence files are retained in the bundled archive as src/sbml/maddy/LICENSE and src/sbml/html2md/COPYING. 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. 8. Example SBML models ----------------------------------------------------------------------- Files: inst/examples/*.xml Source: the worked examples in Section 7 of "The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core, Release 2" (29 March 2019), M. Hucka, F. T. Bergmann, C. Chaouiya, A. Draeger, S. Hoops, S. M. Keating, M. Koenig, N. Le Novere, C. J. Myers, B. G. Olivier, S. Sahle, J. C. Schaff, R. Sheriff, L. P. Smith, D. Waltemath, D. J. Wilkinson and F. Zhang. https://sbml.org/specifications/sbml-level-3/version-2/core/release-2/ The specification carries no copyright or licence statement of its own. inst/examples/sbmlsimple.xml Section 7.1 inst/examples/sbmlconversionfactor.xml Section 7.2 inst/examples/sbmlconversionfactor-alternative.xml Section 7.3 inst/examples/sbmlassignmentrules.xml Section 7.5 inst/examples/sbmlalgebraicrules.xml Section 7.6 inst/examples/sbmlboundaryconditions.xml Section 7.7 inst/examples/sbmlmutlicompartment.xml Section 7.8 inst/examples/sbmlfunctiondefinition.xml Section 7.9 inst/examples/sbmldelay.xml Section 7.10 inst/examples/sbmlevent.xml Section 7.11 Every line of each file appears in the corresponding listing, except the opening tag of sbmlevent.xml: the listing in Section 7.11 closes that tag before its namespace declarations, which is not well-formed XML, and the copy here was corrected. 9. SBML Test Suite cases ----------------------------------------------------------------------- Files: tests/testthat/sbml-test-suite/*/ (each -sbml-l3v2.xml, -results.csv, -settings.txt) Source: the semantic test cases of the SBML Test Suite 3.3.0, https://github.com/sbmlteam/sbml-test-suite, cases/semantic/, commit d6dcd2cc6408d5eb881638ac6ce7a05fd7d2e4d1 Copyright: (C) 2016-2017 jointly by the California Institute of Technology (Pasadena, CA, USA), the EMBL European Bioinformatics Institute (EMBL-EBI, Hinxton, UK), the University of Heidelberg (Heidelberg, Germany), the University of Tuebingen (Tuebingen, Germany) and the Babraham Institute (Cambridge, UK) (C) 2010-2016 jointly by the California Institute of Technology, the EMBL European Bioinformatics Institute and the University of Heidelberg (C) 2008-2009 by the California Institute of Technology (C) 2004-2007 jointly by the California Institute of Technology and the University of Hertfordshire (UK) Licence: GNU Lesser General Public License (LGPL), version 2.1 or, at your option, any later version. These are test data only: they are read by the package's tests and are not installed with the package. The files are copied unchanged; each directory is named after its case number in the suite. Only the three files the tests read are kept from each case, out of the several the suite provides. None of them comes from the suite's separately licensed contributions (the DSMTS stochastic cases and sbmltest2archive), which live outside cases/semantic/.