libgssw 0.0~git20211210.14b4d43+ds-1

Package Information

Description	graph SIMD Smith-Waterman C library GSSW is a generalization of the striped Smith-Waterman algorithm to graphs. It is used by the vg toolkit for partial order alignment and supports affine gap penalties, traceback across graph nodes, pinned alignments and a bonus for full-length alignments. This package contains the shared library.
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed By	Andreas Tille <tille@debian.org>
Sponsor	tille@debian.org
Distribution	unstable
Architecture	any
VCS	git: https://salsa.debian.org/med-team/libgssw.git (browse)
Closes	#1151713
Tracker	https://tracker.debian.org/pkg/libgssw
Uploaded	4 hours ago

New Package Report

.changes◂

Changed-By	Andreas Tille <tille@debian.org>
Architecture	source amd64
Distribution	unstable
Date	Fri, 23 Oct 2026 13:20:40 +0200
Source	libgssw
Version	0.0~git20211210.14b4d43+ds-1

Changelog◂

libgssw (0.0~git20211210.14b4d43+ds-1) unstable; urgency=medium
 .
   * Initial release (Closes: #1151713).

.dsc◂

Section	libdevel
Priority	optional
Component	main
Package-List	libgssw-dev deb libdevel optional arch=any libgssw1 deb libs optional arch=any

debian/copyright◂

Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: gssw
Source: https://github.com/vgteam/gssw
# The only consumer of this 22 MB demo data set is src/main.c, a legacy
# ssw_test port that no longer compiles against gssw. The demo binaries
# (gssw_example, gssw_example_adj) and the gssw-test unit suite all run
# without it, so it is not shipped.
Files-Excluded: demo

Files: *
Copyright: 2012-2015 Boston College
 2014-2018 Wellcome Trust Sanger Institute
 2012-2016 Mengyao Zhao
 2014-2026 Erik Garrison
 2015-2026 Adam Novak
 2016-2026 Jordan Eizenga
 2014-2026 the gssw contributors
License: MIT

Files: src/kseq.h
Copyright: 2008 Genome Research Ltd (GRL)
License: MIT

Files: debian/*
Copyright: 2026 Andreas Tille <tille@debian.org>
License: MIT

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.

DFSG Assistant LLM REVIEW 0 blocker, 1 important, 0 minor

This is an LLM based review using a Debian Inference based workflow. It was not written by a member of the DFSG team and has not been checked by one. It is not a decision on the package: it may be wrong, and it may have missed things.

Reviewed 3 hours ago.

Report◂

DFSG NEW review for libgssw version 0.0~git20211210.14b4d43+ds-1

Summary

Licensing is DFSG-compliant and debian/copyright is accurate: Yes
Packaging is of good quality: No
Issues: 0 blocker, 1 important, 0 minor
debian/watch: version 5
debian/copyright: machine-readable
Scan before the review: nothing found

Licensing

debian/copyright is DEP-5 machine-readable with an accurate Format URL. Every upstream file is MIT; the repo carries no built artifacts, fonts or vendored code, and the only embedded pre-release (simde, empty dir) is replaced by the system libsimde-dev. All copyright holders seen in the sources (Boston College, Wellcome Sanger/Trust Institute, Mengyao Zhao, Erik Garrison, GRL for kseq.h) are named in the relevant stanzas; full MIT text is inlined. No non-free terms, no unlicensed files, no missing preferred form. DFSG-compliant.

Packaging

The packaging is generally clean (compat 13, dh cmake, hardening, MA:same split dev/lib, sane build deps and standards-version), but the autopkgtest smoke test will fail in its libgssw1 instance because it is written to compile against gssw.h and link -lgssw, which live only in libgssw-dev, while the test's own Depends only installs the runtime package for that run.

Issues

1. [important] [packaging] Autopkgtest smoke test fails in the libgssw1 instance

Files: debian/tests/control (Depends: @, build-essential); debian/tests/smoke (compile of smoke.c)
Basis: checked, in the package or with a reference tool
Evidence: Depends: @, build-essential; the smoke test runs cc ... smoke.c -lgssw -lm with #include <gssw.h>. Per the autopkgtest spec, @ replicates per binary package, so one run installs only libgssw1 + build-essential. debian/rules' d-shlibmove --movedev debian/tmp/usr/include/* moves gssw.h and the libgssw.so symlink to libgssw-dev, leaving libgssw1 with only libgssw.so.1.
Problem: In the libgssw1 autopkgtest copy, neither gssw.h nor libgssw.so is installed, so cc fails (gssw.h: No such file or directory / cannot find -lgssw) and the test fails for that package. libgssw1 has no dependency on libgssw-dev, so the header and linker symlink are not pulled in.
Fix: Change the test's Depends: to libgssw-dev, build-essential (libgssw-dev already Depends on libgssw1), so both binary-package runs get the header and the unversioned .so.

Verified

All upstream sources under src/ and the root (gssw.c, gssw.h, ssw_cpp.{h,cpp}, main.c, example*.{c,cpp}, gssw_test.c, kseq.h, Makefile, CMakeLists.txt, README.md) are MIT; gssw.c and README carry the MIT header. kseq.h has its own MIT header (GRL 2008).
gssw.c:3 holder 'Boston College' is present in debian/copyright (Copyright: 2012-2015 Boston College); the prescan's flagged holder is covered, not missing.
No binary/prebuilt artifacts, minified code, fonts, images, or unlicensed files in the tree; demo/ is excluded via Files-Excluded and absent.
src/simde/ is an empty directory and simde headers come from the system libsimde-dev (Build-Depends and libgssw-dev Depends), so there is no embedded third-party copy.
src/main.c and ssw_cpp.cpp reference a non-shipped ssw.h, but neither is compiled by the CMake build (only gssw.c and gssw_test.c are built); main.c is documented as a legacy non-compiling port, so this is not a build failure.
Build-Depends (debhelper-compat (=13), cmake, libsimde-dev, d-shlibs) all exist in the archive; Standards-Version 4.7.4 is current.
debian/copyright is machine-readable and its Format URL, Files stanzas, standalone MIT License paragraph and full MIT text are correct (already DEP-5).
libgssw1.symbols MINVER 0.0~git20211209.14b4d43 is below the package version, so dependencies on the listed symbols are satisfiable.
uscan found the packaged version as the newest upstream release (upstream 0.0~git20211210.14b4d43, packaged 0.0~git20211210.14b4d43+ds).

Not confirmed

Symbol names in debian/libgssw1.symbols were not cross-checked against the compiled library (cannot build); a wrong/missing symbol would surface at build or via lintian.
Whether d-shlibmove moves libgssw.h into libgssw-dev as assumed was taken from the rules invocation, not from running it.

Proposed changes

None.

Uploader's response to the LLM review

There will be about 10 further rdepends for the new version of the vg package of Debian Med - so some more libs to come ...

— Andreas Tille (tille), 2 hours ago

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