[med-svn] [Git][med-team/ncbi-igblast][master] 8 commits: d/copyright: add missing license and do remaining work.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue May 17 21:39:29 BST 2022
Étienne Mollier pushed to branch master at Debian Med / ncbi-igblast
Commits:
bc448076 by Étienne Mollier at 2022-05-17T15:16:27+02:00
d/copyright: add missing license and do remaining work.
- - - - -
862f3b16 by Étienne Mollier at 2022-05-17T15:19:45+02:00
d/salsa-ci.yml: disable Salsa CI on i386
At the look of the build error, the programming of NCBI IgBlast seems
specific to 64-bit systems.
- - - - -
4a6ff911 by Étienne Mollier at 2022-05-17T18:27:15+02:00
d/copyright: add some more missing copyright texts.
- - - - -
d7c219c7 by Étienne Mollier at 2022-05-17T18:28:32+02:00
d/s/lintian-overrides: remove mismatched override.
- - - - -
61db7fea by Étienne Mollier at 2022-05-17T18:28:54+02:00
d/control: append missing shlib dependencies.
- - - - -
da450d24 by Étienne Mollier at 2022-05-17T19:25:27+02:00
d/copyright: clarify problematic json license statement.
- - - - -
0fdac9dc by Étienne Mollier at 2022-05-17T21:43:01+02:00
d/copyright: fixup for xmlwrapp
- - - - -
12c65c4d by Étienne Mollier at 2022-05-17T22:38:10+02:00
d/copyright: spare another json evil alarm bell.
- - - - -
4 changed files:
- debian/control
- debian/copyright
- debian/salsa-ci.yml
- debian/source/lintian-overrides
Changes:
=====================================
debian/control
=====================================
@@ -14,7 +14,7 @@ Rules-Requires-Root: no
Package: igblast
Architecture: any
-Depends: ${misc:Depends}
+Depends: ${misc:Depends}, ${shlibs:Depends}
Description: Immunoglobulin and T cell receptor variable domain sequence analysis
IgBLAST allows users to view the matches to the germline V, D, and J
genes, details at rearrangement junctions, the delineation of IG V
=====================================
debian/copyright
=====================================
@@ -81,6 +81,12 @@ License: LGPL-2+
Files: c++/include/misc/jsonwrapp/rapidjson11/*
Copyright: 2015, THL A29 Limited, a Tencent company, and Milo Yip.
License: Expat
+Comment:
+ The license.txt presents effectively the "Evil" statement which is problematic
+ regarding DFSG compatibility, however as documented in lintian-overrides:
+ .
+ > Aaron M. Ucko: As this file explains, the problematic JSON license applies
+ > only to a jsonchecker subtree NCBI already doesn't redistribute.
Files: c++/include/misc/jsonwrapp/rapidjson11/msinttypes/*
Copyright: 2006-2013, Alexander Chemeris
@@ -108,6 +114,25 @@ Files: c++/include/util/compress/zlib/*
c++/src/util/compress/zlib/*
Copyright: 1995-2013, Jean-loup Gailly and Mark Adler
License: Zlib
+ 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.
+
+Files: c++/src/util/compress/zlib/ncbi_z_compress.c
+Copyright: National Center for Biotechnology Information
+License: PD
Files: c++/include/util/impl/floating_point_comparison.hpp
Copyright: 2001-2008, Gennadiy Rozental
@@ -123,9 +148,10 @@ Files: c++/include/util/timsort.hpp
Copyright: 2011, Fuji, Goro (gfx) <gfuji at cpan.org>.
License: Expat
-Files: c++/scripts/xmlwrapp/*
+Files: c++/scripts/projects/xmlwrapp/*
Copyright: 2001-2003, Peter J Jones (pjones at pmade.org)
License: BSD-3-clause
+Comment: Modifications from NCBI released under Public Domain.
Files: c++/scripts/projects/quickblastp/*
Copyright: National Center for Biotechnology Information
@@ -173,8 +199,11 @@ License: GPL-2 or GPL-3
Files: c++/src/build-system/cmake/FindSqlite3.cmake
Copyright: 2007, Martin Dobias
-License: BSD
-# TODO: identify which BSD variant.
+License: BSD-3-clause
+Comment:
+ BSD variant determined by hunting down source code in cmake repository[1].
+ .
+ [1]: https://github.com/Kitware/CMake/blob/v3.23.1/Modules/FindSQLite3.cmake
Files: c++/src/build-system/cmake/HunterGate.cmake
Copyright: 2013-2017, Ruslan Baratov
@@ -203,9 +232,127 @@ License: BSD-2-clause
Files: c++/src/build-system/cmake/cmake-configure
Copyright: Evan Nemerson
License: CC-0
- To the extent possible under law, the author(s) hereby waive all
- copyright and related or neighboring rights to this work. For
- details, see <https://creativecommons.org/publicdomain/zero/1.0/>
+ Creative Commons Legal Code
+ .
+ CC0 1.0 Universal
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+ CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE
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Files: c++/src/build-system/m4/*
Copyright: 2015, Enrico M. Crisostomo <enrico.m.crisostomo at gmail.com>
@@ -213,6 +360,10 @@ Copyright: 2015, Enrico M. Crisostomo <enrico.m.crisostomo at gmail.com>
2008, Don Anderson <dda at sleepycat.com>
2008, Paolo Bonzini <bonzini at gnu.org>
License: FSFAP
+ Copying and distribution of this file, with or without modification, are
+ permitted in any medium without royalty provided the copyright notice
+ and this notice are preserved. This file is offered as-is, without any
+ warranty.
Files: c++/src/connect/parson.c
c++/src/connect/parson.h
@@ -221,7 +372,7 @@ License: Expat
Files: c++/src/connect/mbedtls/*
Copyright: The Mbed TLS Contributors
-License: Apache-2.0 or GPL-2+ and/or GPL-2+
+License: Apache-2.0 or GPL-2+ or GPL-2+
Files: c++/src/html/*.js
Copyright: 1997-1999, Netscape Communications Corp.
@@ -240,8 +391,6 @@ Copyright: 2013, 2014, RAD Game Tools and Valve Software
2010-2014, Rich Geldreich and Tenacious Software LLC
License: Expat
-## TODO below that point ######################################################
-
Files: c++/src/util/lmdb/*
Copyright: 1999-2003, The OpenLDAP Foundation, Redwood City
2011-2019 Howard Chu, Symas Corp.
@@ -387,7 +536,7 @@ License: LGPL-2+
On Debian systems, a full copy of the LGPL 2 should be available
in /usr/share/common-licenses/LGPL-2.
-License: LGPL-2.1+
+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
@@ -401,6 +550,60 @@ License: LGPL-2.1+
On Debian systems, a full copy of the LGPL 2.1 should be available
in /usr/share/common-licenses/LGPL-2.1.
+License: GPL-2
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; version 2 of the License.
+ .
+ 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, a full copy of the GPL 2 should be available
+ in /usr/share/common-licenses/GPL-2.
+
+License: GPL-2+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; 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 the
+ GNU General Public License for more details.
+ .
+ On Debian systems, a full copy of the GPL 2 should be available
+ in /usr/share/common-licenses/GPL-2.
+
+License: GPL-3
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, version 3 of the License.
+ .
+ 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, a full copy of the GPL 3 should be available
+ in /usr/share/common-licenses/GPL-3.
+
+License: GPL-3+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ 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, a full copy of the GPL 3 should be available
+ in /usr/share/common-licenses/GPL-3.
+
License: Expat
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
@@ -419,3 +622,51 @@ License: Expat
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: BSD-3-clause
+ 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 University 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 REGENTS AND CONTRIBUTORS ``AS IS'' AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE
+ FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS
+ OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+ HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+ LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+ OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
+ SUCH DAMAGE.
+
+License: BSL-1.0
+ Permission is hereby granted, free of charge, to any person or organization
+ obtaining a copy of the software and accompanying documentation covered by
+ this license (the "Software") to use, reproduce, display, distribute,
+ execute, and transmit the Software, and to prepare derivative works of the
+ Software, and to permit third-parties to whom the Software is furnished to
+ do so, all subject to the following:
+ .
+ The copyright notices in the Software and this entire statement, including
+ the above license grant, this restriction and the following disclaimer,
+ must be included in all copies of the Software, in whole or in part, and
+ all derivative works of the Software, unless such copies or derivative
+ works are solely in the form of machine-executable object code generated by
+ a source language processor.
+ .
+ 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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+ SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+ FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ DEALINGS IN THE SOFTWARE.
=====================================
debian/salsa-ci.yml
=====================================
@@ -2,3 +2,7 @@
include:
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
- https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
+
+# i386 CI disabled: the package programming seems 64-bit specific.
+variables:
+ SALSA_CI_DISABLE_BUILD_PACKAGE_I386: "true"
=====================================
debian/source/lintian-overrides
=====================================
@@ -6,5 +6,4 @@ ncbi-igblast source: source-is-missing c++/src/html/ncbi_menu_dnd.js
ncbi-igblast source: source-is-missing c++/src/html/ncbi_menu_dyn.js
# JSON not evil license, related code is not present
# Aaron M. Ucko: As this file explains, the problematic JSON license applies only to a jsonchecker subtree NCBI already doesn't redistribute
-ncbi-igblast source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson10/license.txt
ncbi-igblast source: license-problem-json-evil c++/include/misc/jsonwrapp/rapidjson11/license.txt
View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/1a830a5337e2d795231852f8ca8a555b190e8a95...12c65c4d3bc8413d27b6caf172a3c8e294f6eeac
--
View it on GitLab: https://salsa.debian.org/med-team/ncbi-igblast/-/compare/1a830a5337e2d795231852f8ca8a555b190e8a95...12c65c4d3bc8413d27b6caf172a3c8e294f6eeac
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