Your message dated Tue, 16 Sep 2025 13:56:24 +0200
with message-id <[email protected]>
and subject line Re: augur: FTBFS: augur/io/shell_command_runner.py:11: error:
Cannot assign to final name "SIGKILL" [misc]
has caused the Debian Bug report #1115122,
regarding augur: FTBFS: augur/io/shell_command_runner.py:11: error: Cannot
assign to final name "SIGKILL" [misc]
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1115122: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1115122
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Version: 24.4.0-2
Fixed by upload earlier that day
OpenPGP_signature.asc
Description: OpenPGP digital signature
--- End Message ---
