[Debian-med-packaging] Bug#996280: seqan3: autopkgtest needs update for new version of gcc-defaults

Paul Gevers elbrus at debian.org
Tue Oct 12 21:17:02 BST 2021 

Source: seqan3
Version: 3.0.2+ds-9
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: needs-update
Control: affects -1 src:gcc-defaults

[X-Debbugs-CC: debian-ci at lists.debian.org, gcc-defaults at packages.debian.org]

Dear maintainer(s),

With a recent upload of gcc-defaults the autopkgtest of seqan3 fails in
testing when that autopkgtest is run with the binary packages of
gcc-defaults from unstable. It passes when run with only packages from
testing. In tabular form:

                       pass            fail
gcc-defaults           from testing    1.194
seqan3                 from testing    3.0.2+ds-9
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of gcc-defaults to
testing [1].

If this is a real problem in your package (and not only in your
autopkgtest), the right binary package(s) from gcc-defaults should
really add a versioned Breaks on the unfixed version of (one of your)
package(s). Note: the Breaks is nice even if the issue is only in the
autopkgtest as it helps the migration software to figure out the right
versions to combine in the tests.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=gcc-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/s/seqan3/15914132/log.gz

/tmp/autopkgtest-lxc.yel9kndg/downtmp/autopkgtest_tmp/unit/alignment/pairwise/pairwise_alignment_single_test_template.hpp:101:48:
  required from ‘void
gtest_suite_pairwise_alignment_test_::alignment<gtest_TypeParam_>::TestBody()
[with gtest_TypeParam_ = pairwise_alignment_fixture<(&
seqan3::test::alignment::fixture::global::affine::banded::dna4_single_diagonal)>]’
/tmp/autopkgtest-lxc.yel9kndg/downtmp/autopkgtest_tmp/unit/alignment/pairwise/pairwise_alignment_single_test_template.hpp:89:1:
  required from here
/usr/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp:946:19: error:
‘struct
seqan3::detail::edit_distance_unbanded<std::vector<seqan3::dna4>&,
std::vector<seqan3::dna4>&,
seqan3::configuration<seqan3::align_cfg::method_global,
seqan3::align_cfg::gap_cost_affine, seqan3::align_cfg::band_fixed_size,
seqan3::align_cfg::scoring_scheme<seqan3::nucleotide_scoring_scheme<signed
char> >, seqan3::align_cfg::output_score,
seqan3::align_cfg::output_end_position,
seqan3::align_cfg::output_begin_position,
seqan3::align_cfg::output_alignment,
seqan3::detail::debug_mode<std::integral_constant<seqan3::detail::align_config_id,
seqan3::detail::align_config_id::debug> >,
seqan3::align_cfg::detail::result_type<seqan3::alignment_result<seqan3::detail::alignment_result_value_type<std::nullopt_t*,
std::nullopt_t*, int, seqan3::alignment_coordinate,
seqan3::alignment_coordinate,
std::tuple<seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> >, seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> > >,
seqan3::detail::two_dimensional_matrix<std::optional<int>,
std::allocator<std::optional<int> >,
seqan3::detail::matrix_major_order::column>,
seqan3::detail::two_dimensional_matrix<std::optional<seqan3::detail::trace_directions>,
std::allocator<std::optional<seqan3::detail::trace_directions> >,
seqan3::detail::matrix_major_order::column> > > > >,
seqan3::detail::default_edit_distance_trait_type<std::vector<seqan3::dna4>&,
std::vector<seqan3::dna4>&,
seqan3::configuration<seqan3::align_cfg::method_global,
seqan3::align_cfg::gap_cost_affine, seqan3::align_cfg::band_fixed_size,
seqan3::align_cfg::scoring_scheme<seqan3::nucleotide_scoring_scheme<signed
char> >, seqan3::align_cfg::output_score,
seqan3::align_cfg::output_end_position,
seqan3::align_cfg::output_begin_position,
seqan3::align_cfg::output_alignment,
seqan3::detail::debug_mode<std::integral_constant<seqan3::detail::align_config_id,
seqan3::detail::align_config_id::debug> >,
seqan3::align_cfg::detail::result_type<seqan3::alignment_result<seqan3::detail::alignment_result_value_type<std::nullopt_t*,
std::nullopt_t*, int, seqan3::alignment_coordinate,
seqan3::alignment_coordinate,
std::tuple<seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> >, seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> > >,
seqan3::detail::two_dimensional_matrix<std::optional<int>,
std::allocator<std::optional<int> >,
seqan3::detail::matrix_major_order::column>,
seqan3::detail::two_dimensional_matrix<std::optional<seqan3::detail::trace_directions>,
std::allocator<std::optional<seqan3::detail::trace_directions> >,
seqan3::detail::matrix_major_order::column> > > > >,
std::integral_constant<bool, false>, long unsigned int>
>::compute_state’ has no member named ‘db’; did you mean ‘b’?
  946 |             state.db =
proxy_reference<word_type>{this->db[current_block]};
      |             ~~~~~~^~
      |             b
/usr/include/seqan3/alignment/pairwise/edit_distance_unbanded.hpp:952:19: error:
‘struct
seqan3::detail::edit_distance_unbanded<std::vector<seqan3::dna4>&,
std::vector<seqan3::dna4>&,
seqan3::configuration<seqan3::align_cfg::method_global,
seqan3::align_cfg::gap_cost_affine, seqan3::align_cfg::band_fixed_size,
seqan3::align_cfg::scoring_scheme<seqan3::nucleotide_scoring_scheme<signed
char> >, seqan3::align_cfg::output_score,
seqan3::align_cfg::output_end_position,
seqan3::align_cfg::output_begin_position,
seqan3::align_cfg::output_alignment,
seqan3::detail::debug_mode<std::integral_constant<seqan3::detail::align_config_id,
seqan3::detail::align_config_id::debug> >,
seqan3::align_cfg::detail::result_type<seqan3::alignment_result<seqan3::detail::alignment_result_value_type<std::nullopt_t*,
std::nullopt_t*, int, seqan3::alignment_coordinate,
seqan3::alignment_coordinate,
std::tuple<seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> >, seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> > >,
seqan3::detail::two_dimensional_matrix<std::optional<int>,
std::allocator<std::optional<int> >,
seqan3::detail::matrix_major_order::column>,
seqan3::detail::two_dimensional_matrix<std::optional<seqan3::detail::trace_directions>,
std::allocator<std::optional<seqan3::detail::trace_directions> >,
seqan3::detail::matrix_major_order::column> > > > >,
seqan3::detail::default_edit_distance_trait_type<std::vector<seqan3::dna4>&,
std::vector<seqan3::dna4>&,
seqan3::configuration<seqan3::align_cfg::method_global,
seqan3::align_cfg::gap_cost_affine, seqan3::align_cfg::band_fixed_size,
seqan3::align_cfg::scoring_scheme<seqan3::nucleotide_scoring_scheme<signed
char> >, seqan3::align_cfg::output_score,
seqan3::align_cfg::output_end_position,
seqan3::align_cfg::output_begin_position,
seqan3::align_cfg::output_alignment,
seqan3::detail::debug_mode<std::integral_constant<seqan3::detail::align_config_id,
seqan3::detail::align_config_id::debug> >,
seqan3::align_cfg::detail::result_type<seqan3::alignment_result<seqan3::detail::alignment_result_value_type<std::nullopt_t*,
std::nullopt_t*, int, seqan3::alignment_coordinate,
seqan3::alignment_coordinate,
std::tuple<seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> >, seqan3::gap_decorator<std::span<seqan3::dna4,
18446744073709551615> > >,
seqan3::detail::two_dimensional_matrix<std::optional<int>,
std::allocator<std::optional<int> >,
seqan3::detail::matrix_major_order::column>,
seqan3::detail::two_dimensional_matrix<std::optional<seqan3::detail::trace_directions>,
std::allocator<std::optional<seqan3::detail::trace_directions> >,
seqan3::detail::matrix_major_order::column> > > > >,
std::integral_constant<bool, false>, long unsigned int>
>::compute_state’ has no member named ‘db’; did you mean ‘b’?
  952 |             state.db = ~(state.b ^ state.d0);
      |             ~~~~~~^~
      |             b
make[2]: ***
[alignment/pairwise/CMakeFiles/global_affine_banded_test.dir/build.make:79:
alignment/pairwise/CMakeFiles/global_affine_banded_test.dir/global_affine_banded_test.cpp.o]
Error 1
make[2]: Leaving directory
'/tmp/autopkgtest-lxc.yel9kndg/downtmp/autopkgtest_tmp/build_unit'
make[1]: *** [CMakeFiles/Makefile2:2825:
alignment/pairwise/CMakeFiles/global_affine_banded_test.dir/all] Error 2
make[1]: Leaving directory
'/tmp/autopkgtest-lxc.yel9kndg/downtmp/autopkgtest_tmp/build_unit'
make: *** [Makefile:104: all] Error 2

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