Your message dated Sun, 20 Sep 2026 18:09:19 +0000
with message-id <[email protected]>
and subject line Bug#1143704: fixed in seqan3 3.4.0+ds-3
has caused the Debian Bug report #1143704,
regarding seqan3: FTBFS: /usr/include/c++/16/bits/shared_ptr_
[too-long-redacted] d [-Werror=maybe-uninitialized]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1143704: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1143704
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:seqan3
Version: 3.4.0+ds-2
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202608/
About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.
If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.
If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:seqan3, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
[316/1098] /usr/bin/x86_64-linux-gnu-g++ -DSEQAN3_DISABLE_DE
[too-long-redacted] ack-in-alignment-and-search.cpp
FAILED: [code=1]
CMakeFiles/3.0.2_user-callback-in-alignment-and-search_snippet.dir/release/3.0.2_user-callback-in-alignment-and-search.cpp.o
/usr/bin/x86_64-linux-gnu-g++ -DSEQAN3_DISABLE_DEPRECATED_WA
[too-long-redacted] ack-in-alignment-and-search.cpp
In file included from /usr/include/c++/16/bits/shared_ptr.h:53,
from /usr/include/c++/16/memory:82,
from
/<<PKGBUILDDIR>>/include/seqan3/utility/detail/type_name_as_string.hpp:18,
from
/<<PKGBUILDDIR>>/include/seqan3/core/debug_stream/debug_stream_type.hpp:18,
from
/<<PKGBUILDDIR>>/include/seqan3/core/detail/strong_type.hpp:16,
from
/<<PKGBUILDDIR>>/include/seqan3/alignment/configuration/align_config_gap_cost_affine.hpp:17,
from
/<<PKGBUILDDIR>>/include/seqan3/alignment/configuration/align_config_edit.hpp:12,
from
/<<PKGBUILDDIR>>/test/snippet/release/3.0.2_user-callback-in-alignment-and-search.cpp:8:
In member function âvoid std::_Sp_counted_ptr<_Ptr, _Lp>::_M
[too-long-redacted] y _Lp = __gnu_cxx::_S_atomic]â,
inlined from âvoid std::_Sp_counted_base<_Lp>::_M_release() [with
__gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]â at
/usr/include/c++/16/bits/shared_ptr_base.h:423:18,
inlined from âvoid std::_Sp_counted_base<_Lp>::_M_release() [with
__gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]â at
/usr/include/c++/16/bits/shared_ptr_base.h:392:5,
inlined from âstd::__shared_count<_Lp>::~__shared_count() [with
__gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]â at
/usr/include/c++/16/bits/shared_ptr_base.h:1136:21,
inlined from âstd::__shared_ptr<_Tp, _Lp>::~__shared_ptr
[too-long-redacted] /bits/shared_ptr_base.h:1610:7,
inlined from âstd::shared_ptr<seqan3::configuration<seqa
[too-long-redacted] ++/16/bits/shared_ptr.h:175:11,
inlined from âseqan3::detail::alignment_algorithm<config
[too-long-redacted] /alignment_algorithm.hpp:126:5,
inlined from âstatic constexpr function_wrapper_t seqan3
[too-long-redacted] gnment_configurator.hpp:495:58,
inlined from âstatic constexpr function_wrapper_t seqan3
[too-long-redacted] gnment_configurator.hpp:614:75,
inlined from âstatic constexpr auto
seqan3::detail::alignment_configurator::configure(const config_t&) [with
sequences_t =
std::ranges::ref_view<std::vector<std::pair<std::vector<seqan3::dna4>,
std::vector<seqan3::dna4> > > >; config_t =
seqan3::configuration<seqan3::align_cfg::method_global,
seqan3::align_cfg::scoring_scheme<seqan3::hamming_scoring_scheme>,
seqan3::align_cfg::gap_cost_affine,
seqan3::detail::parallel_mode<std::integral_constant<seqan3::detail::align_config_id,
seqan3::detail::align_config_id::parallel> >,
seqan3::align_cfg::on_result<main()::<lambda(auto:80&&)> > >]â at
/<<PKGBUILDDIR>>/include/seqan3/alignment/pairwise/alignment_configurator.hpp:350:70,
inlined from âconstexpr auto seqan3::align_pairwise(sequence_t&&, const
alignment_config_t&) [with sequence_t =
std::vector<std::pair<std::vector<dna4>, std::vector<dna4> > >&;
alignment_config_t = configuration<align_cfg::method_global,
align_cfg::scoring_scheme<hamming_scoring_scheme>, align_cfg::gap_cost_affine,
detail::parallel_mode<std::integral_constant<detail::align_config_id,
seqan3::detail::align_config_id::parallel> >,
align_cfg::on_result<main()::<lambda(auto:80&&)> > >]â at
/<<PKGBUILDDIR>>/include/seqan3/alignment/pairwise/align_pairwise.hpp:168:13,
inlined from âint main()â at
/<<PKGBUILDDIR>>/test/snippet/release/3.0.2_user-callback-in-alignment-and-search.cpp:35:27:
/usr/include/c++/16/bits/shared_ptr_base.h:487:9: error: â*(
[too-long-redacted] d [-Werror=maybe-uninitialized]
487 | { delete _M_ptr; }
| ^~~~~~~~~~~~~
cc1plus: all warnings being treated as errors
[317/1098] /usr/bin/x86_64-linux-gnu-g++ -DSEQAN3_DISABLE_DEPRECATED_WARNINGS
-I/<<PKGBUILDDIR>>/test/include -I/<<PKGBUILDDIR>>/include -g -O2
-ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-DNDEBUG -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++23 -pedantic -Wall -Wextra
-Werror -Wno-interference-size -Wnrvo -Wno-unused-variable
-Wno-unused-but-set-variable -MD -MT
CMakeFiles/3.0.3_io-record_snippet.dir/release/3.0.3_io-record.cpp.o -MF
CMakeFiles/3.0.3_io-record_snippet.dir/release/3.0.3_io-record.cpp.o.d -o
CMakeFiles/3.0.3_io-record_snippet.dir/release/3.0.3_io-record.cpp.o -c
/<<PKGBUILDDIR>>/test/snippet/release/3.0.3_io-record.cpp
ninja: build stopped: subcommand failed.
dh_auto_build: error: cd build_snippet && LC_ALL=C.UTF-8 ninja -j2 -v returned
exit code 1
make[1]: *** [debian/rules:42: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:24: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: seqan3
Source-Version: 3.4.0+ds-3
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
seqan3, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated seqan3 package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Sun, 20 Sep 2026 19:35:00 +0200
Source: seqan3
Architecture: source
Version: 3.4.0+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1143704
Changes:
seqan3 (3.4.0+ds-3) unstable; urgency=medium
.
* Team upload.
.
[ Adrian Bunk ]
* Don't build tests with -Werror. Closes: #1143704.
.
[ Santiago Vila ]
* Update standards-version.
* Disable Salsa CI job "debrebuild" instead of "reprotest".
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