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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