[med-svn] r12560 - trunk/packages/ugene/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu Nov 22 09:14:36 UTC 2012
Author: tille
Date: 2012-11-22 09:14:36 +0000 (Thu, 22 Nov 2012)
New Revision: 12560
Modified:
trunk/packages/ugene/trunk/debian/copyright
Log:
DEP5 copyright; when checking the license I noticed two non-free components: src/plugins_3rdparty/psipred/src and src/plugins_3rdparty/phylyp/src - this needs to be sorted out before uploading the package
Modified: trunk/packages/ugene/trunk/debian/copyright
===================================================================
--- trunk/packages/ugene/trunk/debian/copyright 2012-11-22 06:54:34 UTC (rev 12559)
+++ trunk/packages/ugene/trunk/debian/copyright 2012-11-22 09:14:36 UTC (rev 12560)
@@ -1,168 +1,151 @@
-This package was debianized by Ivan Efremov <iefremov at unipro.ru> on
-Mon, 26 Jan 2009 19:18:51 +0600
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: UGENE
+Upstream-Contact: UniPro <ugene at unipro.ru>,
+ Ivan Efremov <iefremov at unipro.ru>
+Source: http://ugene.unipro.ru/downloads/ugene_get_latest_source.html
+Files-Excluded:
+ src/libs_3rdparty/zlib
-It was downloaded from: http://ugene.unipro.ru/download.html
+Files: *
+Copyright: © 2008-2012 UniPro <ugene at unipro.ru>
+License: GPL2+
-Modifications to the original source package:
- The following directories have been removed:
- ./installer/linux
- ./installer/macosx
- ./installer/windows
- ./src/libs_3rdparty/zlib
- since they contain useless for this package data.
-
-Upstream Author: UniPro <ugene at unipro.ru>
-
-Copyright:
- Copyright (C) 2008-2011 by UniPro <ugene at unipro.ru>
-
-License:
- This suite of programs 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.
-
- In other words, you are free to modify, copy, or redistribute this
- source code and its documentation in any way you like, but you must
- distribute all derivative versions as free software under the same
- terms that I've provided my code to you (i.e. the GNU General Public
- License). This precludes any use of the code in proprietary or
- commercial software unless your source code is made freely available.
-
- If you wish to use Unipro UGENE code under a different Open Source
- license that's not compatible with the GPL (like the Artistic License, BSD
- license, or the Netscape Public License), please contact us
- (ugene at unipro.ru) for permission.
-
- Incorporation into commercial software under non-GPL terms is possible
- by obtaining a specially licensed version from Unipro.
- Contact 'ugene at unipro.ru' to arrange licensing terms.
-
- This software 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 Unipro UGENE release, in the file LICENSE;
- if not, write to the Free Software Foundation, Inc.,
- 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
-
- On Debian systems, see /usr/share/common-licenses/GPL-2 for the complete
- text of the GPL.
-
-
Files: src/corelibs/U2Formats/src/ABIFormat.cpp
src/corelibs/U2Formats/src/SCFFormat.cpp
src/corelibs/U2Formats/src/IOLibUtils.cpp
-Copyright: 1994 Medical Research Council. All rights reserved.
-License:
- Permission to use, copy, modify and distribute this software and its
- documentation for any purpose is hereby granted without fee, provided that
- this copyright and notice appears in all copies.
+Copyright: © 1994 Medical Research Council. All rights reserved.
+License: MCR
+ Permission to use, copy, modify and distribute this software and its
+ documentation for any purpose is hereby granted without fee, provided that
+ this copyright and notice appears in all copies.
+ .
+ MRC disclaims all warranties with regard to this software.
- MRC disclaims all warranties with regard to this software.
+Files: src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp
+Copyright: © 1998 Todd C. Miller <Todd.Miller at courtesan.com>
+License: BSD
+ Permission to use, copy, modify, and distribute this software for any
+ purpose with or without fee is hereby granted, provided that the above
+ copyright notice and this permission notice appear in all copies.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+ WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+ MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
+ ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+ WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
+ ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
+ OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
+Files: src/plugins_3rdparty/hmm2/*
+Copyright: © 1992-2003 HHMI/Washington University School of Medicine
+License: GPL2+
-The File src/plugins_3rdparty/hmm2/src/hmmer2/sre_string.cpp
- Copyright (c) 1998 Todd C. Miller <Todd.Miller at courtesan.com>
+Files: src/plugins_3rdparty/umuscle/src/muscle
+Copyright: © 2004-2011 Robert C. Edgar <muscle at drive5.com>
+License: PD
+ The software is provided as PUBLIC DOMAIN
+ (see http://www.drive5.com/muscle/license.htm)
- Permission to use, copy, modify, and distribute this software for any
- purpose with or without fee is hereby granted, provided that the above
- copyright notice and this permission notice appear in all copies.
+Files: src/plugins_3rdparty/psipred/src/seq2mtx.cpp
+ src/plugins_3rdparty/psipred/src/sspred_avpred.cpp
+ src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp
+Copyright: © 2000 D.T. Jones <dtj at cs.ucl.ac.uk>
+License: non-free_in_clause_8
+ BY USING THE PROGRAM YOU ARE ACKNOWLEDGING THE FACT THAT YOU AGREE TO
+ THE TERMS OUTLINED IN THIS AGREEMENT. USERS WISHING TO USE THE SOFTWARE
+ FOR COMMERCIAL ACTIVITIES NOT COVERED BY THIS AGREEMENT SHOULD SEND
+ E-MAIL TO: dtj at cs.ucl.ac.uk
+ .
+ * NOTE RECENT CHANGES TO PARAGRAPH 8 *
+ .
+ In regard to the protein structure prediction program (PSIPRED2)
+ herewith (the Software) the copyright and other intellectual property
+ rights to which belong to the Author(s).
+ .
+ Any user (the User) of the program undertakes to the Copyright holder that he
+ or she shall be bound by the following terms and conditions:
+ .
+ 1. The User will receive the Software and any related documentation in
+ confidence and will not use the same except for the purpose of their own
+ research. The Software will be used only by such of the User's officers or
+ employees to whom it must reasonably be communicated to enable them to
+ undertake their research and who agree to be bound by the same confidence.
+ The User shall procure and enforce such agreement from his or her staff for
+ the benefit of the Copyright holder.
+ .
+ 2. The publication of research using the Software must include an
+ appropriate citation to the method:
+ .
+ Jones, D.T. (1999) Protein secondary structure prediction based on
+ position-specific scoring matrices. J. Mol. Biol. 292:195-202.
+ .
+ 3. All forms of the Software will be kept in a reasonably secure place to
+ prevent unauthorised access.
+ .
+ 4. Each copy of the Software or, if not practicable then, any package
+ associated therewith shall be suitably marked (and such marking maintained)
+ with the following copyright notice: "Copyright 2000 D.T.Jones. All Rights
+ Reserved.".
+ .
+ 5. The Software may be modified, but any changes made shall be communicated
+ to the Author(s) and made freely available.
+ .
+ 6. The Software may not be sold as a standalone package, or incorporated into
+ a commercial software package without the written permission of the Copyright
+ holder. The Software may be used freely for individual academic or commercial
+ research. The Software may also be made freely available for training or
+ teaching purposes.
+ .
+ 7. The results produced by the Software may not be incorporated into any
+ data banks or databases which are subject to the payment of access or
+ license fees without the written permission of the Copyright holder.
+ .
+ 8. The Software may be made available to users over a local network or
+ wide area network (including the Internet), but only if access is granted
+ free of charge to all authorised users. Incorporation of the Software into
+ a commercial Web site or other fee paying service is not allowed without
+ the written permission of the Copyright holder. If PSIPRED results are
+ returned to the user via such a network service, then a suitable
+ acknowledgement of the PSIPRED method must be returned somewhere in the
+ output text.
+ .
+ 9. The confidentiality obligation in paragraph one shall not apply:
+ .
+ (i) to information and data known to the User at the time of
+ receipt hereunder (as evidenced by its written records);
+ .
+ (ii) to information and data which was at the time of receipt in the
+ public domain or thereafter becomes so through no wrongful act of
+ the User;
+ .
+ (iii) to information and data which the User receives from a third
+ party not in breach of any obligation of confidentiality owed to
+ the Author(s).
+ .
+ 10. The User understands that the Software is supplied "as is". No warranty
+ as to its fitness or suitability for any purpose whatsoever is made or
+ implied. In no event shall the Author(s) or Copyright holder be held
+ responsible for any direct or indirect damages arising through the use
+ of the Software.
- THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
- WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
- MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
- ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
- WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
- ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
- OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-
-
-The Files in src/plugins_3rdparty/hmm2
- HMMER - Biological sequence analysis with profile hidden Markov models
- Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
-
- This suite of programs 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.
-
- In other words, you are free to modify, copy, or redistribute this
- source code and its documentation in any way you like, but you must
- distribute all derivative versions as free software under the same
- terms that I've provided my code to you (i.e. the GNU General Public
- License). This precludes any use of the code in proprietary or
- commercial software unless your source code is made freely available.
-
- If you wish to use HMMER code under a different Open Source license
- that's not compatible with the GPL (like the Artistic License, BSD
- license, or the Netscape Public License), please contact me
- (eddy at genetics.wustl.edu) for permission.
-
- Incorporation into commercial software under non-GPL terms is possible
- by obtaining a specially licensed version from Washington University
- School of Medicine. Contact Jack Pincus (jhpincus at cris.com) to arrange
- licensing terms.
-
- This software 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 HMMER release, in the file LICENSE; if not, write to
- the Free Software Foundation, Inc.,
- 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
-
- On Debian systems, see /usr/share/common-licenses/GPL-2 for the
- complete text of the GPL.
-
-Note:
-The Files in src/plugins_3rdparty/uhmmer/src/u_spu and
- src/plugins_3rdparty/uhmmer/src/uhmmsearch_cell.cpp
- are modified sources from the HMMER-Cell project
- (ftp://selab.janelia.org/pub/software/hmmer/contrib-2.3.2/HMMerCell_src_02272008.tar.gz)
-
- Original Copyright: 2008, International Business Machines Corporation
- Authors: Kursad Albayraktaroglu, Jizhu Lu
-
- This files are released under the terms of GPL (v2 or any later version).
-
-
-The Files in src/plugins_3rdparty/umuscle/src/muscle
- are PUBLIC DOMAIN (see http://www.drive5.com/muscle/license.htm)
-
-
-The Files src/plugins_3rdparty/psipred/src/seq2mtx.cpp
- src/plugins_3rdparty/psipred/src/sspred_avpred.cpp
- src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp
- Copyright (C) 2000 D.T. Jones
- These files are distributed under the terms of custom GPL-compatible
- license. See src/plugins_3rdparty/psipred/src/license for details.
-
-
-The Files in src/plugins_3rdparty/primer3/src/primer3_core
- Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006,2007
- Whitehead Institute for Biomedical Research, Steve Rozen
+Files: src/plugins_3rdparty/primer3/src/primer3_core
+Copyright: © 1996-2007 Whitehead Institute for Biomedical Research, Steve Rozen
(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
- All rights reserved.
-
- 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
+License: BSDlike
+ 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
+ * 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 names of the copyright holders nor contributors may
+ * Neither the names of the copyright holders nor 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
@@ -175,227 +158,195 @@
(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: src/plugins_3rdparty/hmm3/src/hmmer3/*
+Copyright: © 2000-2009 Howard Hughes Medical Institute (and others)
+License: GPL3+
-The Files in src/plugins_3rdparty/hmm3/src/hmmer3
-(except files in src/plugins_3rdparty/hmm3/src/hmmer3/easel)
- Copyright (C) 2009 Howard Hughes Medical Institute.
- Other copyrights also apply. See the
- src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT file for a full list.
-
- HMMER is distributed under the terms of the GNU General Public License
- (GPLv3). On Debian systems, see /usr/share/common-licenses/GPL-3 for
- the full text of the license.
-
+Files: src/plugins_3rdparty/hmm3/src/hmmer3/easel/*
+Copyright: © 2006-2009 Howard Hughes Medical Institute (and others)
+License: JaneliaFarm
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ 1. Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ 2. Redistributions in binary form must reproduce the above copyright
+ notice, this list of conditions and the following disclaimer in
+ the documentation and/or other materials provided with the
+ distribution.
+ .
+ 3. Neither the name of the Howard Hughes Medical Institute nor the
+ names of its contributors may be used to endorse or promote
+ products derived from this software without specific prior written
+ permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, ANY IMPLIED WARRANTIES OF MERCHANTABILITY,
+ NON-INFRINGEMENT, OR FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+ REASONABLE ROYALTIES; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
+ TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
+ USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+ DAMAGE.
-
-The Files in src/plugins_3rdparty/hmm3/src/hmmer3/easel
- Copyright (C) 2009 Howard Hughes Medical Institute.
- Other copyrights also apply. See the
- src/plugins_3rdparty/hmm3/src/hmmer3/easel/COPYRIGHT file for a full list.
-
- Easel is distributed under the Janelia Farm Software License, a BSD
- license. See the src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE file
- for more details.
-
- On Debian systems, see /usr/share/common-licenses/BSD for the full
- text of the license.
-
-
-The Files in src/plugins/biostruct3d_view/src/gl2ps
- GL2PS, an OpenGL to PostScript Printing Library
- Copyright (C) 1999-2006 Christophe Geuzaine <geuz at geuz.org>
-
- This program is free software; you can redistribute it and/or
- modify it under the terms of either:
-
- a) the GNU Library General Public License as published by the Free
- Software Foundation, either version 2 of the License, or (at your
- option) any later version; or
-
- b) the GL2PS License as published by Christophe Geuzaine, either
- version 2 of the License, or (at your option) any later version.
-
+Files: src/plugins/biostruct3d_view/src/gl2ps
+Copyright: © 1999-2006 Christophe Geuzaine <geuz at geuz.org>
+License: GPL2+
+Note: Alternatively you can choose
+ the GL2PS License as published by Christophe Geuzaine, either
+ version 2 of the License, or (at your option) any later version.
+ .
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See either
the GNU Library General Public License or the GL2PS License for
more details.
+Comment: Debian just contains this code in libgl2ps-dev
- On Debian systems, see /usr/share/common-licenses/GPL-2 for the
- full text of the GPL version 2.
-
+Files: src/plugins_3rdparty/ball/include/*
+ src/plugins_3rdparty/ball/source/*
+Copyright: © 1996-2012 Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt
+License: LGPL-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.
+ .
+ On Debian systems, see /usr/share/common-licenses/LGPL-2.1 for the
+ full text of the license.
-The Files in src/plugins_3rdparty/ball/include and
- src/plugins_3rdparty/ball/source
- Copyright (C) Oliver Kohlbacher, Hans-Peter Lenhof, Andreas Hildebrandt
- and others 1996-2009
+Files: src/plugins_3rdparty/phylyp/src
+Copyright: © 1993-2004 by the University of Washington.
+ Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
+License: non-free_phylip
+ Permission is granted to copy and use this program provided no fee is
+ charged for it and provided that this copyright notice is not removed.
- 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.
+Files: src/plugins_3rdparty/kalign/src
+Copyright: © 2006 Timo Lassmann <timolassmann at gmail.com>
+License: GPL2+
- 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.
-
- On Debian systems, see /usr/share/common-licenses/LGPL-2 for the
- full text of the license.
-
-
-The Files in src/plugins_3rdparty/phylyp/src
- version 3.6. (c) Copyright 1993-2004 by the University of Washington.
- Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, and Andrew Keeffe.
- Permission is granted to copy and use this program provided no fee is
- charged for it and provided that this copyright notice is not removed.
-
-
-The Files in src/plugins_3rdparty/kalign/src
-
- Released under GPL - see the 'COPYING' file
-
- Copyright (C) 2006 Timo Lassmann <timolassmann at gmail.com>
-
- This program is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- any later version.
-
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 51 Franklin Street, Fifth Floor,
- Boston, MA 02110-1301 USA
-
- Please send bug reports, comments etc. to:
- timolassmann at gmail.com
-
- On Debian systems, see /usr/share/common-licenses/GPL-2 for the
- full text of the license.
-
-
-The Files in src/plugins_3rdparty/bowtie/src/bowtie/SeqAn-1.1
- Copyright (C) 2007
-
- 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 3 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.
-
- On Debian systems, see /usr/share/common-licenses/GPL-3 for the
- full text of the license.
-
-
-The Files in src/plugins_3rdparty/bowtie/src/bowtie/visualstudio
- ISO C9x compliant inttypes.h for Microsoft Visual Studio
- Based on ISO/IEC 9899:TC2 Committee draft (May 6, 2005) WG14/N1124
-
- Copyright (c) 2006 Alexander Chemeris
-
- Redistribution and use in source and binary forms, with or without
- modification, are permitted provided that the following conditions are met:
-
- 1. Redistributions of source code must retain the above copyright notice,
- this list of conditions and the following disclaimer.
-
- 2. Redistributions in binary form must reproduce the above copyright
- notice, this list of conditions and the following disclaimer in the
- documentation and/or other materials provided with the distribution.
-
- 3. The name of the author may be used to endorse or promote products
- derived from this software without specific prior written permission.
-
- THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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 Files in src/plugins_3rdparty/bowtie/src/bowtie
- This files are distributed under Artistic License. See the 'COPYING' file
- for details.
-
-
-The Files in src/libs_3rdparty/sqlite3/src
-
- The author disclaims copyright to this source code. In place of
- a legal notice, here is a blessing:
-
+Files: src/libs_3rdparty/sqlite3/src
+Copyright: The author D. Richard Hipp <drh at hwaci.com> disclaims copyright
+ to this source code.
+License: PD+blessing
+ In place of a legal notice, here is a blessing:
+ .
May you do good and not evil.
May you find forgiveness for yourself and forgive others.
May you share freely, never taking more than you give.
+Files: src/include/opencl/legacy/*
+Copyright: © 2008-2010 The Khronos Group Inc.
+License: BSD+Khronos
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and/or associated documentation files (the
+ "Materials"), to deal in the Materials without restriction, including
+ without limitation the rights to use, copy, modify, merge, publish,
+ distribute, sublicense, and/or sell copies of the Materials, and to
+ permit persons to whom the Materials are 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 Materials.
+ .
+ THE MATERIALS ARE 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
+ MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
-The Files src/include/opencl/legacy/cl.h
- src/include/opencl/legacy/cl_platform.h
- Copyright (c) 2008-2010 The Khronos Group Inc.
- Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and/or associated documentation files (the
- "Materials"), to deal in the Materials without restriction, including
- without limitation the rights to use, copy, modify, merge, publish,
- distribute, sublicense, and/or sell copies of the Materials, and to
- permit persons to whom the Materials are furnished to do so, subject to
- the following conditions:
+Files: src/corelibs/U2Private/src/StackWalker.*
+Copyright: © 2005-2011 Jochen Kalmbach
+License: BSD-like
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+ .
+ Redistributions of source code must retain the above copyright notice,
+ this list of conditions and the following disclaimer.
+ Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ Neither the name of Jochen Kalmbach 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.
- The above copyright notice and this permission notice shall be included
- in all copies or substantial portions of the Materials.
+Files: debian/*
+Copyright: © 2008-2011 Ivan Efremov <iefremov at unipro.ru>
+ © 2012 Andreas Tille <tille at debian.org>
+License: GPL3+
- THE MATERIALS ARE 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
- MATERIALS OR THE USE OR OTHER DEALINGS IN THE MATERIALS.
+License: GPL2+
+ This suite of programs 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.
+ .
+ In other words, you are free to modify, copy, or redistribute this
+ source code and its documentation in any way you like, but you must
+ distribute all derivative versions as free software under the same
+ terms that I've provided my code to you (i.e. the GNU General Public
+ License). This precludes any use of the code in proprietary or
+ commercial software unless your source code is made freely available.
+ .
+ If you wish to use Unipro UGENE code under a different Open Source
+ license that's not compatible with the GPL (like the Artistic License, BSD
+ license, or the Netscape Public License), please contact us
+ (ugene at unipro.ru) for permission.
+ .
+ Incorporation into commercial software under non-GPL terms is possible
+ by obtaining a specially licensed version from Unipro.
+ Contact 'ugene at unipro.ru' to arrange licensing terms.
+ .
+ This software 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 Unipro UGENE release, in the file LICENSE;
+ if not, write to the Free Software Foundation, Inc.,
+ 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA.
+ .
+ On Debian systems, see /usr/share/common-licenses/GPL-2 for the complete
+ text of the GPL.
-
-The Files src/corelibs/U2Private/src/StackWalker.cpp
- src/corelibs/U2Private/src/StackWalker.cpp
- Copyright (c) 2005-2011, Jochen Kalmbach
- All rights reserved.
-
- 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 Jochen Kalmbach nor the names of its contributors may be
- used to endorse or promote products derived from this software without
- specific prior written permission.
- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
- THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
- (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
- LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
- ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
- (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
- SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
-
-Files: debian/*
-License:
- Copyright (C) 2008-2011 by Ivan Efremov <iefremov at unipro.ru>
- released under the GPL. On Debian systems, see
- /usr/share/common-licenses/GPL-3 for the full text of the license.
+License: GPL3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or (at
+ your option) any later version.
+ .
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ On Debian systems, see /usr/share/common-licenses/GPL-3 for the complete
+ text of the GPL.
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