[med-svn] [Git][med-team/rapmap][master] 7 commits: Fix FTBFS with GCC 15. (Closes: #1097770)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Oct 9 21:22:10 BST 2025
Andreas Tille pushed to branch master at Debian Med / rapmap
Commits:
1e69191c by Andreas Tille at 2025-10-09T21:54:21+02:00
Fix FTBFS with GCC 15. (Closes: #1097770)
- - - - -
e68ef2c6 by Andreas Tille at 2025-10-09T21:58:53+02:00
d/watch: version = 5
- - - - -
faefe797 by Andreas Tille at 2025-10-09T21:59:14+02:00
Standards-Version: 4.7.2 (routine-update)
- - - - -
44f41aed by Andreas Tille at 2025-10-09T22:00:22+02:00
Replace transitional package pkg-config by pkgconf in Build-Depends (routine-update)
- - - - -
60285c49 by Andreas Tille at 2025-10-09T22:00:26+02:00
debputy lint --auto-fix (routine-update)
- - - - -
c7c7b59b by Andreas Tille at 2025-10-09T22:16:32+02:00
d/copyright: review
- - - - -
7a0405cf by Andreas Tille at 2025-10-09T22:18:30+02:00
Upload to unstable
- - - - -
7 changed files:
- debian/TODO
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/gcc-15.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/TODO
=====================================
@@ -1,3 +1,6 @@
+Replace code copy of
+ libbitarray-dev
+
Replace code copy of spdlog by Debian packaged version once either
upstream might have switched (see
https://github.com/COMBINE-lab/RapMap/issues/44
=====================================
debian/changelog
=====================================
@@ -1,3 +1,18 @@
+rapmap (0.15.0+dfsg-5) unstable; urgency=medium
+
+ [ Adrian Bunk ]
+ * Fix FTBFS with GCC 15. (Closes: #1097770)
+
+ [ Andreas Tille ]
+ * d/watch: version = 5
+ * Standards-Version: 4.7.2 (routine-update)
+ * Replace transitional package pkg-config by pkgconf in Build-Depends
+ (routine-update)
+ * debputy lint --auto-fix (routine-update)
+ * d/copyright: review
+
+ -- Andreas Tille <tille at debian.org> Thu, 09 Oct 2025 22:16:49 +0200
+
rapmap (0.15.0+dfsg-4) unstable; urgency=medium
* d/rules: enable "-fopenmp-simd" and other SIMDe recommended build
=====================================
debian/control
=====================================
@@ -1,24 +1,26 @@
Source: rapmap
+Standards-Version: 4.7.2
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Michael R. Crusoe <crusoe at debian.org>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Michael R. Crusoe <crusoe at debian.org>,
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 13),
- cmake,
- zlib1g-dev,
- libdivsufsort-dev,
- libcereal-dev,
- libjellyfish-2.0-dev,
- libjemalloc-dev,
- libsimde-dev,
- libsparsehash-dev,
- libspdlog-dev,
- libtclap-dev,
- pkg-config,
- python3-markdown,
- python3
-Standards-Version: 4.6.2
+Build-Depends:
+ debhelper-compat (= 13),
+ cmake,
+ zlib1g-dev,
+ libdivsufsort-dev,
+ libcereal-dev,
+ libjellyfish-2.0-dev,
+ libjemalloc-dev,
+ libsimde-dev,
+ libsparsehash-dev,
+ libspdlog-dev,
+ libtclap-dev,
+ pkgconf,
+ python3-markdown,
+ python3,
Vcs-Browser: https://salsa.debian.org/med-team/rapmap
Vcs-Git: https://salsa.debian.org/med-team/rapmap.git
Homepage: https://github.com/COMBINE-lab/RapMap
@@ -26,9 +28,11 @@ Rules-Requires-Root: no
Package: rapmap
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Built-Using: ${simde:Built-Using}
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+Built-Using:
+ ${simde:Built-Using},
Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
@@ -57,8 +61,10 @@ Description: rapid sensitive and accurate DNA read mapping via quasi-mapping
Package: rapmap-example-data
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends}
-Recommends: rapmap
+Depends:
+ ${misc:Depends},
+Recommends:
+ rapmap,
Description: example data for rapmap - rapid sensitive and accurate DNA read mapping
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
@@ -76,7 +82,8 @@ Description: example data for rapmap - rapid sensitive and accurate DNA read map
Package: rapmap-dev
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends}
+Depends:
+ ${misc:Depends},
Description: rapmap - rapid sensitive and accurate DNA read mapping (some headers)
RapMap is a testing ground for ideas in quasi-mapping / (lightweight /
pseudo) transcriptome alignment. That means that, at this point, it is
=====================================
debian/copyright
=====================================
@@ -27,6 +27,59 @@ Comment: Since RapMap uses Jellyfish, it must be released under the GPL.
happy to accept pull-requests that replace the Jellyfish components
with a library released under a more liberal license (BSD-compatible
+Files: include/bar.h
+ include/bit_array.h
+ include/bit_macros.h
+ src/bit_array.c
+Copyright: Isaac Turner <turner.isaac at gmail.com>
+License: public-domain
+ Public Domain, no warranty
+ .
+ https://github.com/noporpoise/BitArray/
+
+Files: include/concurrentqueue.h
+Copyright: 2013-2016, Cameron Desrochers
+License: BSD-2-clause
+
+Files: include/metro/*
+ src/metro/*
+Copyright: 2015 J. Andrew Rogers
+License: Expat
+
+Files: include/tsl/*
+Copyright: 2017 Tessil
+License: Expat
+
+Files: include/nonstd/*
+Copyright: 2014-2018 Martin Moene
+License: BSL-1.0
+ Boost Software License - Version 1.0 - August 17th, 2003
+ .
+ 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: src/EnumCoderTest.cpp
src/EnumCoder.cpp
src/UtilTest.cpp
@@ -62,26 +115,8 @@ License: LGPL-3+
Files: include/kseq.h
Copyright: 2008-2011 Attractive Chaos <attractor at live.co.uk>
-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
+
Files: include/btree/*
Copyright: 2013 Google Inc. All Rights Reserved.
@@ -104,24 +139,6 @@ License: Apache-2.0
Files: include/spdlog/*
Copyright: (c) 2014-2016 Gabi Melman <gmelman1 at gmail.com>
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.
Files: include/spdlog/fmt/bundled/*
Copyright: (c) 2012 - 2016, Victor Zverovich
@@ -166,3 +183,24 @@ License: BSD-2-clause
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: 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.
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,14 @@
+Description: Fix FTBFS with GCC 15
+Author: Adrian Bunk <bunk at debian.org>
+Bug-Debian: https://bugs.debian.org/1097770
+
+--- rapmap-0.15.0+dfsg.orig/include/BooPHF.hpp
++++ rapmap-0.15.0+dfsg/include/BooPHF.hpp
+@@ -17,6 +17,7 @@
+ #include <string.h>
+ #include <memory> // for make_shared
+ #include <unistd.h>
++#include <cstdint>
+
+
+
=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ spelling
portable_pause
no_gomp_needed
simde
+gcc-15.patch
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://github.com/COMBINE-lab/RapMap/tags .*/[salmon-]*v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+Source: https://github.com/COMBINE-lab/RapMap/tags
+Matching-Pattern: .*/[salmon-]*v?(\d[\d.-]+)@ARCHIVE_EXT@
+Filename-Mangle: s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%
+Repack-Suffix: +dfsg
+Dversion-Mangle: auto
View it on GitLab: https://salsa.debian.org/med-team/rapmap/-/compare/1cb1948660d2e8f811f7dd4e5338df251b647fc7...7a0405cf161191e2431d52d0128b92a66070906a
--
View it on GitLab: https://salsa.debian.org/med-team/rapmap/-/compare/1cb1948660d2e8f811f7dd4e5338df251b647fc7...7a0405cf161191e2431d52d0128b92a66070906a
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