[Debian-med-packaging] Bug#1143704: seqan3: FTBFS: /usr/include/c++/16/bits/shared_ptr_ [too-long-redacted] d [-Werror=maybe-uninitialized]

[Santiago Vila]

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.

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[...]
[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 ‘void std::_Sp_counted_ptr<_Ptr, _Lp>::_M [too-long-redacted] y _Lp = __gnu_cxx::_S_atomic]’,
    inlined from ‘void std::_Sp_counted_base<_Lp>::_M_release() [with __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]’ at /usr/include/c++/16/bits/shared_ptr_base.h:423:18,
    inlined from ‘void std::_Sp_counted_base<_Lp>::_M_release() [with __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]’ at /usr/include/c++/16/bits/shared_ptr_base.h:392:5,
    inlined from ‘std::__shared_count<_Lp>::~__shared_count() [with __gnu_cxx::_Lock_policy _Lp = __gnu_cxx::_S_atomic]’ at /usr/include/c++/16/bits/shared_ptr_base.h:1136:21,
    inlined from ‘std::__shared_ptr<_Tp, _Lp>::~__shared_ptr [too-long-redacted] /bits/shared_ptr_base.h:1610:7,
    inlined from ‘std::shared_ptr<seqan3::configuration<seqa [too-long-redacted] ++/16/bits/shared_ptr.h:175:11,
    inlined from ‘seqan3::detail::alignment_algorithm<config [too-long-redacted] /alignment_algorithm.hpp:126:5,
    inlined from ‘static constexpr function_wrapper_t seqan3 [too-long-redacted] gnment_configurator.hpp:495:58,
    inlined from ‘static constexpr function_wrapper_t seqan3 [too-long-redacted] gnment_configurator.hpp:614:75,
    inlined from ‘static 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&&)> > >]’ at /<<PKGBUILDDIR>>/include/seqan3/alignment/pairwise/alignment_configurator.hpp:350:70,
    inlined from ‘constexpr 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&&)> > >]’ at /<<PKGBUILDDIR>>/include/seqan3/alignment/pairwise/align_pairwise.hpp:168:13,
    inlined from ‘int main()’ 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: ‘*( [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
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