[med-svn] [Git][med-team/bedtools][master] 2 commits: d/copyright: review
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Dec 24 14:13:58 GMT 2025
Andreas Tille pushed to branch master at Debian Med / bedtools
Commits:
5cb4a24f by Andreas Tille at 2025-12-24T15:10:07+01:00
d/copyright: review
- - - - -
6a7ea893 by Andreas Tille at 2025-12-24T15:12:45+01:00
Upload to unstable
- - - - -
2 changed files:
- debian/changelog
- debian/copyright
Changes:
=====================================
debian/changelog
=====================================
@@ -1,16 +1,17 @@
-bedtools (2.31.1+dfsg-3) UNRELEASED; urgency=medium
+bedtools (2.31.1+dfsg-3) unstable; urgency=medium
[ Andreas Tille ]
* d/watch: version=5
* Standards-Version: 4.7.3 (routine-update)
* Remove Priority field to comply with Debian Policy 4.7.3 (routine-
update)
+ * d/copyright: review
[ Lucas Nussbaum ]
* Fix FTBFS with GNUMAKEFLAGS=--shuffle=random
Closes: #1104751, #1105730
- -- Andreas Tille <tille at debian.org> Wed, 24 Dec 2025 14:47:50 +0100
+ -- Andreas Tille <tille at debian.org> Wed, 24 Dec 2025 15:10:11 +0100
bedtools (2.31.1+dfsg-2) unstable; urgency=medium
=====================================
debian/copyright
=====================================
@@ -13,6 +13,55 @@ Copyright: © 2009,2010,2011 Aaron Quinlan
© 2010 - Assaf Gordon, CSHL
License: GPL-2
+Files: src/utils/htslib/*
+Copyright: 2009, 2010, 2012-2015, 2017 Genome Research Ltd.
+ 2010-2012 Broad Institute.
+License: Expat
+
+Files: src/utils/htslib/cram/*
+Copyright: 2012-2013 Genome Research Ltd.
+ James Bonfield <jkb at sanger.ac.uk>
+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 names Genome Research Ltd and Wellcome Trust Sanger
+ 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 GENOME RESEARCH LTD 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 GENOME RESEARCH LTD 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: src/utils/htslib/md5.c
+Copyright: 2001 Alexander Peslyak, better known as Solar Designer <solar at openwall.com>
+License: public_domain
+ This software was written by Alexander Peslyak in 2001. No copyright is
+ claimed, and the software is hereby placed in the public domain.
+ In case this attempt to disclaim copyright and place the software in the
+ public domain is deemed null and void, then the software is
+ Copyright (c) 2001 Alexander Peslyak and it is hereby released to the
+ general public under the following terms:
+ .
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted.
+ .
+ There's ABSOLUTELY NO WARRANTY, express or implied.
+
Files: src/expand/expand.cpp
Copyright: © 2009, 2010, 2011 - Aaron Quinlan
License: under-the-MIT-license
@@ -26,24 +75,7 @@ Source: https://github.com/ekg/fastahack
Files: src/utils/BamTools/*
Copyright: © 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
-License: MIT
- Permission is hereby granted, free of charge, to any person obtaining a copy
- 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: Expat
Comment: see ‘https://github.com/pezmaster31/bamtools/blob/master/LICENSE’.
Source: https://github.com/pezmaster31/bamtools/wiki
@@ -60,10 +92,6 @@ License: LGPL-2.1+
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
-Comment:
On Debian systems, you can find a copy of the GNU Lesser General Public License
version 2.1 in ‘/usr/share/common-licenses/LGPL-2.1’.
Name: gzstream, C++ iostream classes wrapping the zlib compression library.
@@ -106,9 +134,24 @@ License: GPL-2
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
.
- You should have received a copy of the GNU General Public License along
- with this program; if not, write to the Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-Comment:
On Debian systems, you can find a copy of the GNU General Public License
version 2 in ‘/usr/share/common-licenses/GPL-2’.
+
+License: Expat
+ 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.
View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/102cd0b57161f9d773eee33f9d3ef20c9a0cb235...6a7ea893d4a9053930e4e29672c43c21991f3a88
--
View it on GitLab: https://salsa.debian.org/med-team/bedtools/-/compare/102cd0b57161f9d773eee33f9d3ef20c9a0cb235...6a7ea893d4a9053930e4e29672c43c21991f3a88
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