[Debian-med-packaging] Bug#1060987: q2cli: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13
Lucas Nussbaum
lucas at debian.org
Tue Jan 16 19:42:08 GMT 2024
Source: q2cli
Version: 2022.11.1-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at 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):
> 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:305: python3.11 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> I: pybuild base:305: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> copying q2cli/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> copying q2cli/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> copying q2cli/__main__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> copying q2cli/commands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> copying q2cli/util.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_mystery_stew.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_cache_cli.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_dev.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_cli.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_core.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_usage.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> copying q2cli/tests/test_tools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/tests
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/completion.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/state.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/usage.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/config.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> copying q2cli/core/cache.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/core
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/builtin
> copying q2cli/builtin/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/builtin
> copying q2cli/builtin/tools.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/builtin
> copying q2cli/builtin/dev.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/builtin
> copying q2cli/builtin/info.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/builtin
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> copying q2cli/click/type.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> copying q2cli/click/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> copying q2cli/click/parser.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> copying q2cli/click/command.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> copying q2cli/click/option.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/click
> running egg_info
> creating q2cli.egg-info
> writing q2cli.egg-info/PKG-INFO
> writing dependency_links to q2cli.egg-info/dependency_links.txt
> writing entry points to q2cli.egg-info/entry_points.txt
> writing top-level names to q2cli.egg-info/top_level.txt
> writing manifest file 'q2cli.egg-info/SOURCES.txt'
> reading manifest file 'q2cli.egg-info/SOURCES.txt'
> reading manifest template 'MANIFEST.in'
> adding license file 'LICENSE'
> writing manifest file 'q2cli.egg-info/SOURCES.txt'
> UPDATING /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/_version.py
> set /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build/q2cli/_version.py to '2022.11.1'
> running build_scripts
> creating build
> creating build/scripts-3.11
> copying bin/tab-qiime -> build/scripts-3.11
> changing mode of build/scripts-3.11/tab-qiime from 644 to 755
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:305: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest --ignore=q2cli/tests/test_usage.py
> ============================= test session starts ==============================
> platform linux -- Python 3.11.7, pytest-7.4.4, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 0 items / 6 errors
>
> ==================================== ERRORS ====================================
> _ ERROR collecting .pybuild/cpython3_3.11/build/q2cli/tests/test_cache_cli.py __
> q2cli/tests/test_cache_cli.py:15: in <module>
> from qiime2 import Artifact
> /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/q2cli/tests/test_cli.py _____
> q2cli/tests/test_cli.py:18: in <module>
> from qiime2 import Artifact, Visualization
> /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/q2cli/tests/test_core.py ____
> q2cli/tests/test_core.py:16: in <module>
> from qiime2 import Artifact
> /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/q2cli/tests/test_dev.py _____
> q2cli/tests/test_dev.py:16: in <module>
> from qiime2 import Artifact
> /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/q2cli/tests/test_mystery_stew.py _
> q2cli/tests/test_mystery_stew.py:13: in <module>
> from q2cli.core.usage import CLIUsage
> q2cli/core/usage.py:14: in <module>
> import qiime2.sdk.usage as usage
> /usr/lib/python3/dist-packages/qiime2/sdk/usage.py:43: in <module>
> import qiime2
> /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/q2cli/tests/test_tools.py ____
> q2cli/tests/test_tools.py:16: in <module>
> from qiime2 import Artifact
> /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)
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> ERROR q2cli/tests/test_cache_cli.py - AttributeError: module 'bibtexparser' h...
> ERROR q2cli/tests/test_cli.py - AttributeError: module 'bibtexparser' has no ...
> ERROR q2cli/tests/test_core.py - AttributeError: module 'bibtexparser' has no...
> ERROR q2cli/tests/test_dev.py - AttributeError: module 'bibtexparser' has no ...
> ERROR q2cli/tests/test_mystery_stew.py - AttributeError: module 'bibtexparser...
> ERROR q2cli/tests/test_tools.py - AttributeError: module 'bibtexparser' has n...
> !!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!!
> ======================== 2 warnings, 6 errors in 1.06s =========================
> E: pybuild pybuild:391: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11/build; python3.11 -m pytest --ignore=q2cli/tests/test_usage.py
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.11 returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2024/01/15/q2cli_2022.11.1-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20240115;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20240115&fusertaguser=lucas@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.
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