[Debian-med-packaging] Bug#947717: pbcopper FTBFS on all architectures except x32

[Andreas Tille]

On Sun, Dec 29, 2019 at 07:00:54PM +0100, Michael Crusoe wrote:
> pbcopper's latest release has slipped in a code copy of libssw which uses
> x86 SIMD intrinsics. I've pushed up a fix along the lines I made to libssw
> to enable cross architecture compilation at
> https://salsa.debian.org/med-team/pbcopper/commit/f9678ed29590b57fe30638eed3d6819577b4ace1
> and it awaits sponsorship

Thanks a lot for the fix that is sponsored.  However, for s390[1]
there seems to be a timout problem:

...
   debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd build && meson test --no-rebuild --print-errorlogs
1/2 pbcopper formatting check               OK       0.01 s 
2/2 pbcopper gtest unittests                TIMEOUT 33.17 s 

Ok:                    1
Expected Fail:         0
Fail:                  0
Unexpected Pass:       0
Skipped:               0
Timeout:               1


The output from the failed tests:

2/2 pbcopper gtest unittests                TIMEOUT 33.17 s 

--- command ---
VERBOSE='1' ARGS='-V' /<<PKGBUILDDIR>>/build/tests/pbcopper_test --gtest_output=xml:/<<PKGBUILDDIR>>/build/pbcopper-gtest-unittests.xml
--- stdout ---
Running main() from /build/googletest-b6wiRD/googletest-1.9.0.20190831/googletest/src/gtest_main.cc
[==========] Running 355 tests from 53 test suites.
[----------] Global test environment set-up.
[----------] 6 tests from CLI_Runner
[ RUN      ] CLI_Runner.emits_tool_contract_when_requested_from_command_line
[       OK ] CLI_Runner.emits_tool_contract_when_requested_from_command_line (0 ms)
[ RUN      ] CLI_Runner.runs_application_from_vector_of_args
[       OK ] CLI_Runner.runs_application_from_vector_of_args (0 ms)
[ RUN      ] CLI_Runner.runs_application_from_C_style_args
[       OK ] CLI_Runner.runs_application_from_C_style_args (0 ms)
[ RUN      ] CLI_Runner.can_retrieve_input_commandline
[       OK ] CLI_Runner.can_retrieve_input_commandline (1 ms)
[ RUN      ] CLI_Runner.runs_application_from_resolved_tool_contract
[       OK ] CLI_Runner.runs_application_from_resolved_tool_contract (0 ms)
[ RUN      ] CLI_Runner.throws_on_invalid_choices
[       OK ] CLI_Runner.throws_on_invalid_choices (0 ms)
[----------] 6 tests from CLI_Runner (1 ms total)

[----------] 5 tests from Align_PairwiseAlignment
[ RUN      ] Align_PairwiseAlignment.calculates_metrics_from_input_aligned_sequences
[       OK ] Align_PairwiseAlignment.calculates_metrics_from_input_aligned_sequences (0 ms)
[ RUN      ] Align_PairwiseAlignment.can_generate_basic_global_alignments
[       OK ] Align_PairwiseAlignment.can_generate_basic_global_alignments (0 ms)
[ RUN      ] Align_PairwiseAlignment.maps_target_to_query_positions_from_transcript
[       OK ] Align_PairwiseAlignment.maps_target_to_query_positions_from_transcript (0 ms)
[ RUN      ] Align_PairwiseAlignment.check_justify_internals
[       OK ] Align_PairwiseAlignment.check_justify_internals (0 ms)
[ RUN      ] Align_PairwiseAlignment.can_left_and_right_justify_alignments
[       OK ] Align_PairwiseAlignment.can_left_and_right_justify_alignments (0 ms)
[----------] 5 tests from Align_PairwiseAlignment (0 ms total)

[----------] 3 tests from Align_AffineAlignment
[ RUN      ] Align_AffineAlignment.can_generate_basic_affine_alignments
[       OK ] Align_AffineAlignment.can_generate_basic_affine_alignments (0 ms)
[ RUN      ] Align_AffineAlignment.correctly_aligns_large_insertion
[       OK ] Align_AffineAlignment.correctly_aligns_large_insertion (10 ms)
[ RUN      ] Align_AffineAlignment.can_generate_IUPAC_aware_alignments
[       OK ] Align_AffineAlignment.can_generate_IUPAC_aware_alignments (0 ms)
[----------] 3 tests from Align_AffineAlignment (10 ms total)

[----------] 1 test from Align_LinearAlignment
[ RUN      ] Align_LinearAlignment.can_generate_basic_linear_alignments
[       OK ] Align_LinearAlignment.can_generate_basic_linear_alignments (2 ms)
[----------] 1 test from Align_LinearAlignment (2 ms total)

[----------] 1 test from Align_LocalAlignment
[ RUN      ] Align_LocalAlignment.can_generate_basic_local_alignments
-------

Full log written to /<<PKGBUILDDIR>>/build/meson-logs/testlog.txt
make[1]: *** [debian/rules:15: override_dh_auto_test] Error 1


Kind regards

      Andreas.


[1] https://buildd.debian.org/status/fetch.php?pkg=pbcopper&arch=s390x&ver=1.3.0%2Bdfsg-2&stamp=1577654596&raw=0

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