Source: q2-feature-classifier
Version: 2023.7.0-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20240115 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> PYTHONPATH=/<<PKGBUILDDIR>> \
> dh_auto_test -- -s custom --test-args="cd {build_dir}; py.test-3
> --cov=q2_feature_classifier"
> I: pybuild pybuild:310: python3.11 setup.py develop --install-dir
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build
> running develop
> /usr/lib/python3/dist-packages/setuptools/command/develop.py:40:
> EasyInstallDeprecationWarning: easy_install command is deprecated.
> !!
>
>
> ********************************************************************************
> Please avoid running ``setup.py`` and ``easy_install``.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://github.com/pypa/setuptools/issues/917 for details.
>
> ********************************************************************************
>
> !!
> easy_install.initialize_options(self)
> /usr/lib/python3/dist-packages/setuptools/_distutils/cmd.py:66:
> SetuptoolsDeprecationWarning: setup.py install is deprecated.
> !!
>
>
> ********************************************************************************
> Please avoid running ``setup.py`` directly.
> Instead, use pypa/build, pypa/installer or other
> standards-based tools.
>
> See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html
> for details.
>
> ********************************************************************************
>
> !!
> self.initialize_options()
> running egg_info
> creating q2_feature_classifier.egg-info
> writing q2_feature_classifier.egg-info/PKG-INFO
> writing dependency_links to
> q2_feature_classifier.egg-info/dependency_links.txt
> writing entry points to q2_feature_classifier.egg-info/entry_points.txt
> writing top-level names to q2_feature_classifier.egg-info/top_level.txt
> writing manifest file 'q2_feature_classifier.egg-info/SOURCES.txt'
> reading manifest file 'q2_feature_classifier.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> adding license file 'LICENSE'
> writing manifest file 'q2_feature_classifier.egg-info/SOURCES.txt'
> running build_ext
> Creating
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2-feature-classifier.egg-link
> (link to .)
> Adding q2-feature-classifier 2023.7.0 to easy-install.pth file
>
> Installed /<<PKGBUILDDIR>>
> Processing dependencies for q2-feature-classifier==2023.7.0
> Finished processing dependencies for q2-feature-classifier==2023.7.0
> I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build;
> py.test-3 --cov=q2_feature_classifier
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.7, pytest-7.4.4, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> plugins: cov-4.1.0
> collected 0 items / 5 errors
>
> ==================================== ERRORS
> ====================================
> _ ERROR collecting
> .pybuild/cpython3_3.11/build/q2_feature_classifier/tests/test_classifier.py _
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/__init__.py:15: in <module>
> importlib.import_module('q2_feature_classifier.classifier')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/classifier.py:17: in <module>
> from qiime2.plugin import Int, Str, Float, Bool, Choices, Range
> /usr/lib/python3/dist-packages/qiime2/__init__.py:23: in <module>
> __citations__ = tuple(Citations.load('citations.bib', package='qiime2'))
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load
> parser = bp.bparser.BibTexParser()
> E AttributeError: module 'bibtexparser' has no attribute 'bparser'
> _ ERROR collecting
> .pybuild/cpython3_3.11/build/q2_feature_classifier/tests/test_consensus_assignment.py
> _
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/__init__.py:15: in <module>
> importlib.import_module('q2_feature_classifier.classifier')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/classifier.py:18: in <module>
> from q2_types.feature_data import (
> /usr/lib/python3/dist-packages/q2_types/__init__.py:18: in <module>
> importlib.import_module('q2_types.multiplexed_sequences')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/__init__.py:11:
> in <module>
> from ._format import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/_format.py:9:
> in <module>
> import qiime2.plugin.model as model
> /usr/lib/python3/dist-packages/qiime2/__init__.py:23: in <module>
> __citations__ = tuple(Citations.load('citations.bib', package='qiime2'))
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load
> parser = bp.bparser.BibTexParser()
> E AttributeError: module 'bibtexparser' has no attribute 'bparser'
> _ ERROR collecting
> .pybuild/cpython3_3.11/build/q2_feature_classifier/tests/test_custom.py _
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/__init__.py:15: in <module>
> importlib.import_module('q2_feature_classifier.classifier')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/classifier.py:18: in <module>
> from q2_types.feature_data import (
> /usr/lib/python3/dist-packages/q2_types/__init__.py:18: in <module>
> importlib.import_module('q2_types.multiplexed_sequences')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/__init__.py:11:
> in <module>
> from ._format import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/_format.py:9:
> in <module>
> import qiime2.plugin.model as model
> /usr/lib/python3/dist-packages/qiime2/__init__.py:23: in <module>
> __citations__ = tuple(Citations.load('citations.bib', package='qiime2'))
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load
> parser = bp.bparser.BibTexParser()
> E AttributeError: module 'bibtexparser' has no attribute 'bparser'
> _ ERROR collecting
> .pybuild/cpython3_3.11/build/q2_feature_classifier/tests/test_cutter.py _
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/__init__.py:15: in <module>
> importlib.import_module('q2_feature_classifier.classifier')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/classifier.py:18: in <module>
> from q2_types.feature_data import (
> /usr/lib/python3/dist-packages/q2_types/__init__.py:18: in <module>
> importlib.import_module('q2_types.multiplexed_sequences')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/__init__.py:11:
> in <module>
> from ._format import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/_format.py:9:
> in <module>
> import qiime2.plugin.model as model
> /usr/lib/python3/dist-packages/qiime2/__init__.py:23: in <module>
> __citations__ = tuple(Citations.load('citations.bib', package='qiime2'))
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load
> parser = bp.bparser.BibTexParser()
> E AttributeError: module 'bibtexparser' has no attribute 'bparser'
> _ ERROR collecting
> .pybuild/cpython3_3.11/build/q2_feature_classifier/tests/test_taxonomic_classifier.py
> _
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1126: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/__init__.py:15: in <module>
> importlib.import_module('q2_feature_classifier.classifier')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> <frozen importlib._bootstrap>:1204: in _gcd_import
> ???
> <frozen importlib._bootstrap>:1176: in _find_and_load
> ???
> <frozen importlib._bootstrap>:1147: in _find_and_load_unlocked
> ???
> <frozen importlib._bootstrap>:690: in _load_unlocked
> ???
> <frozen importlib._bootstrap_external>:940: in exec_module
> ???
> <frozen importlib._bootstrap>:241: in _call_with_frames_removed
> ???
> q2_feature_classifier/classifier.py:18: in <module>
> from q2_types.feature_data import (
> /usr/lib/python3/dist-packages/q2_types/__init__.py:18: in <module>
> importlib.import_module('q2_types.multiplexed_sequences')
> /usr/lib/python3.11/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/__init__.py:11:
> in <module>
> from ._format import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
> /usr/lib/python3/dist-packages/q2_types/multiplexed_sequences/_format.py:9:
> in <module>
> import qiime2.plugin.model as model
> /usr/lib/python3/dist-packages/qiime2/__init__.py:23: in <module>
> __citations__ = tuple(Citations.load('citations.bib', package='qiime2'))
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:26: in load
> parser = bp.bparser.BibTexParser()
> E AttributeError: module 'bibtexparser' has no attribute 'bparser'
> =============================== warnings summary
> ===============================
> ../../../../../../usr/lib/python3/dist-packages/qiime2/core/cite.py:10
> /usr/lib/python3/dist-packages/qiime2/core/cite.py:10: DeprecationWarning:
> pkg_resources is deprecated as an API. See
> https://setuptools.pypa.io/en/latest/pkg_resources.html
> import pkg_resources
>
> ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
> /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871:
> DeprecationWarning: Deprecated call to
> `pkg_resources.declare_namespace('flufl')`.
> Implementing implicit namespace packages (as specified in PEP 420) is
> preferred to `pkg_resources.declare_namespace`. See
> https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
> declare_namespace(pkg)
>
> ../../../../../../usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871
> /usr/lib/python3/dist-packages/pkg_resources/__init__.py:2871:
> DeprecationWarning: Deprecated call to
> `pkg_resources.declare_namespace('mpl_toolkits')`.
> Implementing implicit namespace packages (as specified in PEP 420) is
> preferred to `pkg_resources.declare_namespace`. See
> https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
> declare_namespace(pkg)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
>
> ---------- coverage: platform linux, python 3.11.7-final-0 -----------
> Name Stmts Miss Cover
> ------------------------------------------------------------------------------
> q2_feature_classifier/__init__.py 8 3 62%
> q2_feature_classifier/_blast.py 54 54 0%
> q2_feature_classifier/_consensus_assignment.py 43 43 0%
> q2_feature_classifier/_cutter.py 100 100 0%
> q2_feature_classifier/_skl.py 58 58 0%
> q2_feature_classifier/_taxonomic_classifier.py 71 71 0%
> q2_feature_classifier/_version.py 4 0 100%
> q2_feature_classifier/_vsearch.py 91 91 0%
> q2_feature_classifier/classifier.py 199 190 5%
> q2_feature_classifier/custom.py 64 64 0%
> q2_feature_classifier/plugin_setup.py 4 4 0%
> q2_feature_classifier/tests/__init__.py 19 19 0%
> q2_feature_classifier/tests/test_classifier.py 147 147 0%
> q2_feature_classifier/tests/test_consensus_assignment.py 178 178 0%
> q2_feature_classifier/tests/test_custom.py 40 40 0%
> q2_feature_classifier/tests/test_cutter.py 67 67 0%
> q2_feature_classifier/tests/test_taxonomic_classifier.py 77 77 0%
> ------------------------------------------------------------------------------
> TOTAL 1224 1206 1%
>
> =========================== short test summary info
> ============================
> ERROR q2_feature_classifier/tests/test_classifier.py - AttributeError:
> module...
> ERROR q2_feature_classifier/tests/test_consensus_assignment.py -
> AttributeErr...
> ERROR q2_feature_classifier/tests/test_custom.py - AttributeError: module
> 'bi...
> ERROR q2_feature_classifier/tests/test_cutter.py - AttributeError: module
> 'bi...
> ERROR q2_feature_classifier/tests/test_taxonomic_classifier.py -
> AttributeErr...
> !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection
> !!!!!!!!!!!!!!!!!!!!
> ======================== 3 warnings, 5 errors in 1.38s
> =========================
> E: pybuild pybuild:391: test: plugin custom failed with: exit code=2: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; py.test-3
> --cov=q2_feature_classifier
> dh_auto_test: error: pybuild --test -i python{version} -p 3.11 -s custom
> "--test-args=cd {build_dir}; py.test-3 --cov=q2_feature_classifier" returned
> exit code 13
The full build log is available from:
http://qa-logs.debian.net/2024/01/15/q2-feature-classifier_2023.7.0-1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240115;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240115&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
