Package: src:augur Version: 24.4.0-1 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, your package failed to build. Below you will find how the build ends (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202509/ 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 could not 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:augur, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean I: pybuild base:311: python3.13 setup.py clean /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Affero General Public License v3 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running clean removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.13' does not exist -- can't clean it rm -rf .pytest_cache nextstrain_augur.egg-info make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:311: python3.13 setup.py config /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Affero General Public License v3 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:311: /usr/bin/python3 setup.py build /usr/lib/python3/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. !! ******************************************************************************** Please consider removing the following classifiers in favor of a SPDX license expression: License :: OSI Approved :: GNU Affero General Public License v3 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. ******************************************************************************** !! self._finalize_license_expression() running build running build_py creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/types.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/refine.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/traits.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/lbi.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/mask.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/filenames.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/reconstruct_sequences.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/export_v2.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/distance.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/translate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/index.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/parse.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/titers.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/frequency_estimators.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/align.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/tree.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/frequencies.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/export_v1.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/errors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/sequence_traits.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/titer_model.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/validate.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/validate_export.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/__version__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/export.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/clades.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/ancestral.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur copying augur/argparse_.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/measurements copying augur/measurements/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/measurements copying augur/measurements/concat.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/measurements copying augur/measurements/export.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/measurements creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/titlecase.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/normalize_strings.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/format_dates_directives.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/format_dates.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate copying augur/curate/passthru.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/curate creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/metadata.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/print.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/shell_command_runner.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/file.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/sequences.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/vcf.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/strains.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io copying augur/io/json.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/io creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/dates copying augur/dates/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/dates copying augur/dates/ambiguous_date.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/dates copying augur/dates/errors.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/dates creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/import_ copying augur/import_/beast.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/import_ copying augur/import_/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/import_ creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/color_parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/color_parser_line.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/node_data_reader.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/node_data_file.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support copying augur/util_support/node_data.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/util_support creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/constants.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/_run.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/subsample.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/io.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/include_exclude_rules.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/filter/validate_arguments.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/filter copying augur/data/colors.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-export-v2.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-export-root-sequence.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-export-v1-tree.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-auspice-config-v2.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-annotations.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-export-v1-meta.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-measurements.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-tip-frequencies.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-measurements-collection-config.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/schema-frequencies.json -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data copying augur/data/lat_longs.tsv -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/data debian/rules execute_before_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' cp -v mypy.ini /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build && : 'mypy.ini' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/mypy.ini' cp -v .flake8 /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build && : '.flake8' -> '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/.flake8' make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_test -O--buildsystem=pybuild I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest tests ============================= test session starts ============================== platform linux -- Python 3.13.7, pytest-8.4.2, pluggy-1.6.0 rootdir: /<<PKGBUILDDIR>> plugins: typeguard-4.4.4, mock-3.15.0 collected 351 items tests/dates/test_ambiguous_date.py ............................. [ 8%] tests/dates/test_dates.py ....... [ 10%] tests/filter/test_relative_dates.py ................ [ 14%] tests/filter/test_subsample.py ................ [ 19%] tests/io/test_file.py ............. [ 23%] tests/io/test_metadata.py .......................................... [ 35%] tests/io/test_sequences.py .................... [ 40%] tests/io/test_shell_command_runner.py .......... [ 43%] tests/io/test_strains.py . [ 43%] tests/io/test_vcf.py ....... [ 45%] tests/test_align.py ............................................... [ 59%] tests/test_ancestral.py ... [ 60%] tests/test_clades.py ......... [ 62%] tests/test_flake8.py . [ 62%] tests/test_frequencies.py ........................ [ 69%] tests/test_mask.py ....................................... [ 80%] tests/test_mypy.py F [ 81%] tests/test_parse.py ... [ 82%] tests/test_schemas.py .......... [ 84%] tests/test_titer_models.py . [ 85%] tests/test_translate.py .. [ 85%] tests/test_utils.py .......... [ 88%] tests/test_validate.py ................... [ 94%] tests/test_validate_export.py .. [ 94%] tests/util_support/test_color_parser.py .... [ 95%] tests/util_support/test_node_data.py ... [ 96%] tests/util_support/test_node_data_file.py ...... [ 98%] tests/util_support/test_node_data_reader.py ...... [100%] =================================== FAILURES =================================== __________________________________ test_mypy ___________________________________ def test_mypy(): # Check the exit status ourselves for nicer test output on failure result = run(["mypy"], cwd = topdir) > assert result.returncode == 0, "mypy exited with errors" E AssertionError: mypy exited with errors E assert 1 == 0 E + where 1 = CompletedProcess(args=['mypy'], returncode=1).returncode tests/test_mypy.py:9: AssertionError ----------------------------- Captured stdout call ----------------------------- augur/io/shell_command_runner.py:11: error: Cannot assign to final name "SIGKILL" [misc] augur/io/shell_command_runner.py:11: note: Error code "misc" not covered by "type: ignore" comment Found 1 error in 1 file (checked 69 source files) =============================== warnings summary =============================== .pybuild/cpython3_3.13/build/tests/test_validate.py: 10 warnings .pybuild/cpython3_3.13/build/tests/util_support/test_node_data_file.py: 2 warnings /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build/augur/validate.py:65: DeprecationWarning: Accessing Draft6Validator.resolver is deprecated as of v4.18.0, in favor of the https://github.com/python-jsonschema/referencing library, which provides more compliant referencing behavior as well as more flexible APIs for customization. schema_validator.resolver.resolve_remote = resolve_remote -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_mypy.py::test_mypy - AssertionError: mypy exited with errors ================= 1 failed, 350 passed, 12 warnings in 11.06s ================== E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest tests dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.13 returned exit code 13 make: *** [debian/rules:7: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
