[med-svn] [Git][med-team/salmon][master] 4 commits: Standards-Version: 4.7.3 (routine-update)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sun Feb 22 10:03:39 GMT 2026
Andreas Tille pushed to branch master at Debian Med / salmon
Commits:
ea221426 by Andreas Tille at 2026-02-22T09:30:50+01:00
Standards-Version: 4.7.3 (routine-update)
- - - - -
2b3a3f06 by Andreas Tille at 2026-02-22T09:43:52+01:00
debputy lint --auto-fix (routine-update)
- - - - -
61a8c65f by Andreas Tille at 2026-02-22T10:50:01+01:00
d/copyright: Review
- - - - -
0beb627c by Andreas Tille at 2026-02-22T10:54:23+01:00
Upload to unstable
- - - - -
3 changed files:
- debian/changelog
- debian/control
- debian/copyright
Changes:
=====================================
debian/changelog
=====================================
@@ -1,4 +1,4 @@
-salmon (1.10.3+ds1-2) UNRELEASED; urgency=medium
+salmon (1.10.3+ds1-2) unstable; urgency=medium
* Team upload.
* d/watch: Fix field names
@@ -6,8 +6,11 @@ salmon (1.10.3+ds1-2) UNRELEASED; urgency=medium
package)
* Remove libboost-system-dev from Build-Depends
Closes: #1127277
+ * Standards-Version: 4.7.3 (routine-update)
+ * debputy lint --auto-fix (routine-update)
+ * d/copyright: Review
- -- Andreas Tille <tille at debian.org> Sun, 22 Feb 2026 09:27:16 +0100
+ -- Andreas Tille <tille at debian.org> Sun, 22 Feb 2026 10:50:09 +0100
salmon (1.10.3+ds1-1) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,50 +1,53 @@
Source: salmon
+Standards-Version: 4.7.3
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <crusoe at debian.org>
+Uploaders:
+ Michael R. Crusoe <crusoe at debian.org>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- cmake,
- libboost-filesystem-dev,
- libboost-iostreams-dev,
- libboost-thread-dev,
- libboost-program-options-dev,
- libboost-timer-dev,
- libjellyfish-2.0-dev,
- libparallel-hashmap-dev,
- libpthread-stubs0-dev,
- libsparsehash-dev,
- libdivsufsort-dev,
- libbwa-dev,
- pkgconf,
- libjemalloc-dev,
- libcereal-dev,
- libtbb-dev,
- libgff-dev (>> 2.0),
- libstaden-read-dev,
- libtclap-dev,
- help2man,
- sphinx-doc,
- python3-sphinx,
- python3-sphinx-rtd-theme,
- python3-docs-theme,
- zlib1g-dev,
- libeigen3-dev,
- libbz2-dev,
- liblzma-dev,
- rapmap-dev,
- libsimde-dev
-Standards-Version: 4.7.2
+Build-Depends:
+ debhelper-compat (= 13),
+ cmake,
+ libboost-filesystem-dev,
+ libboost-iostreams-dev,
+ libboost-thread-dev,
+ libboost-program-options-dev,
+ libboost-timer-dev,
+ libjellyfish-2.0-dev,
+ libparallel-hashmap-dev,
+ libpthread-stubs0-dev,
+ libsparsehash-dev,
+ libdivsufsort-dev,
+ libbwa-dev,
+ pkgconf,
+ libjemalloc-dev,
+ libcereal-dev,
+ libtbb-dev,
+ libgff-dev,
+ libstaden-read-dev,
+ libtclap-dev,
+ help2man,
+ sphinx-doc,
+ python3-sphinx,
+ python3-sphinx-rtd-theme,
+ python3-docs-theme,
+ zlib1g-dev,
+ libeigen3-dev,
+ libbz2-dev,
+ liblzma-dev,
+ rapmap-dev,
+ libsimde-dev,
Vcs-Browser: https://salsa.debian.org/med-team/salmon
Vcs-Git: https://salsa.debian.org/med-team/salmon.git
Homepage: https://github.com/COMBINE-lab/salmon
Package: salmon
Architecture: any-amd64 arm64
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${sphinxdoc:Depends}
-Built-Using: ${sphinxdoc:Built-Using}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${sphinxdoc:Depends},
+Built-Using:
+ ${sphinxdoc:Built-Using},
Description: wicked-fast transcript quantification from RNA-seq data
Salmon is a wicked-fast program to produce a highly-accurate, transcript-level
quantification estimates from RNA-seq data. Salmon achieves is accuracy and
=====================================
debian/copyright
=====================================
@@ -17,10 +17,6 @@ Copyright: © 2015 The Salmon Authors
(C) 1997 Makoto Matsumoto and Takuji Nishimura
License: GPL-3+
-Files: debian/*
-Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
-License: GPL-3+
-
Files: cmake/Modules/FindJemalloc.cmake
include/VersionChecker.hpp
src/VersionChecker.cpp
@@ -39,16 +35,97 @@ Copyright: 2011, 2012 Remik Ziemlinski
(c) 2008 Yuta Mori All Rights Reserved
License: Expat
+Files: include/spline.h
+Copyright: 2011, 2014 Tino Kluge (ttk448 at gmail.com)
+License: GPL-2+
+ On Debian systems, the full text of the GNU General Public License
+ version 2 can be found in the file `/usr/share/common-licenses/GPL-2'.
+
+Files: include/stx/*
+Copyright: 2016 Denilson das Mercês Amorim
+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.
+
Files: include/format.h
Copyright: (c) 2012 - 2015, Victor Zverovich
License: BSD-2-clause
+Files: include/kseq.h
+Copyright: 2008, 2009, 2011 Attractive Chaos <attractor at live.co.uk>
+License: Expat
+
+Files: include/xxhash.h
+Copyright: 2012-2016, Yann Collet.
+License: BSD-2-Clause
+
Files: include/atomicops.h
include/concurrentqueue.h
include/readerwriterqueue.h
Copyright: ©2013 Cameron Desrochers
License: BSD-cameron-descrochers
+Files: debian/*
+Copyright: © 2015 Michael R. Crusoe <crusoe at ucdavis.edu>
+License: GPL-3+
+
+Files: include/spdlog/*
+ debian/external/pufferfish/include/spdlog/*
+Copyright: 2014-2016 Gabi Melman <gmelman1 at gmail.com>
+License: Expat
+
+Files: debian/external/pufferfish/src/metro/*
+ debian/external/pufferfish/include/metro/*
+Copyright: 2015 J. Andrew Rogers
+License: Expat
+
+Files: debian/external/pufferfish/include/tsl/*
+Copyright: 2017 Tessil
+License: Expat
+
+Files: debian/external/pufferfish/include/simde/*
+Copyright: 2020 Evan Nemerson <evan at nemerson.com>
+ 2020 Himanshi Mathur <himanshi18037 at iiitd.ac.in>
+ 2020 Hidayat Khan <huk2209 at gmail.com>
+License: expat
+
+Files: debian/external/pufferfish/src/xxhash.c
+Copyright: 2012-2016, Yann Collet
+License: BSD-2-clause
+
+Files: debian/external/pufferfish/external/asyncplusplus/*
+Copyright: 2015 Amanieu d'Antras
+License: Expat
+
+Files: debian/external/pufferfish/include/itlib/*
+Copyright: 2021 Borislav Stanimirov
+License: Expat
+
+Files: debian/external/pufferfish/src/rank9b.cpp
+Copyright: 2007-2013 Sebastiano Vigna
+License: LGPL-3+
+ On Debian systems, the full text of the GNU Lesser General Public
+ License version 3 can be found in the file `/usr/share/common-licenses/LGPL-3'.
+
License: BSD-cameron-descrochers
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/e77b686cfcffaa575027fd9d174c6dfa521cb989...0beb627ca1163ebb61792a7dbb71d4086ac37568
--
View it on GitLab: https://salsa.debian.org/med-team/salmon/-/compare/e77b686cfcffaa575027fd9d174c6dfa521cb989...0beb627ca1163ebb61792a7dbb71d4086ac37568
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