[Debian-med-packaging] Bug#1058321: python-loompy: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Tue Dec 12 08:24:17 GMT 2023
Source: python-loompy
Version: 3.0.7+dfsg-2
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20231212 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
> pybuild --configure -i python{version} -p "3.12 3.11"
> I: pybuild base:310: python3.12 setup.py config
> running config
> I: pybuild base:310: python3.11 setup.py config
> running config
> dh_auto_build -O--buildsystem=pybuild
> pybuild --build -i python{version} -p "3.12 3.11"
> I: pybuild base:310: /usr/bin/python3.12 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_view.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/cell_calling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/normalize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/to_html.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/layer_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loompy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/graph_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/bus_file.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_validator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/attribute_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/metadata_loaders.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/loom_layer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/commands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/global_attribute_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> copying loompy/view_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy
> I: pybuild base:310: /usr/bin/python3 setup.py build
> running build
> running build_py
> creating /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/utils.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/__init__.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_view.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/cell_calling.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/normalize.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/_version.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/to_html.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/layer_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loompy.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/graph_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/bus_file.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_validator.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/attribute_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/metadata_loaders.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/loom_layer.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/commands.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/global_attribute_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> copying loompy/view_manager.py -> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy
> dh_auto_test -O--buildsystem=pybuild
> pybuild --test --test-pytest -i python{version} -p "3.12 3.11"
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build; python3.12 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.12.1, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 0 items / 5 errors
>
> ==================================== ERRORS ====================================
> _ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_attribute_manager.py _
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_attribute_manager.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_attribute_manager.py:3: in <module>
> from loompy import AttributeManager
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_connection.py _
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_connection.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_connection.py:6: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_file_attribute_manager.py _
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_file_attribute_manager.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_file_attribute_manager.py:8: in <module>
> from loompy import GlobalAttributeManager
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> ___ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_main.py ____
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_main.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_main.py:1: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> _ ERROR collecting .pybuild/cpython3_3.12_loompy/build/tests/test_validator.py _
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/tests/test_validator.py'.
> Hint: make sure your test modules/packages have valid Python names.
> Traceback:
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:4: in <module>
> from numba.core.typeconv import _typeconv
> E ImportError: cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)
>
> During handling of the above exception, another exception occurred:
> /usr/lib/python3.12/importlib/__init__.py:90: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_validator.py:6: in <module>
> import loompy
> loompy/__init__.py:14: in <module>
> from .bus_file import create_from_fastq
> loompy/bus_file.py:14: in <module>
> from numba import jit
> /usr/lib/python3/dist-packages/numba/__init__.py:73: in <module>
> from numba.misc.special import (
> /usr/lib/python3/dist-packages/numba/misc/special.py:3: in <module>
> from numba.core.typing.typeof import typeof
> /usr/lib/python3/dist-packages/numba/core/typing/__init__.py:1: in <module>
> from .context import BaseContext, Context
> /usr/lib/python3/dist-packages/numba/core/typing/context.py:11: in <module>
> from numba.core.typeconv import Conversion, rules
> /usr/lib/python3/dist-packages/numba/core/typeconv/rules.py:2: in <module>
> from .typeconv import TypeManager, TypeCastingRules
> /usr/lib/python3/dist-packages/numba/core/typeconv/typeconv.py:16: in <module>
> raise ImportError(msg)
> E ImportError: Numba could not be imported.
> E --------------------------------------------------------------------------------
> E If you are seeing this message and are undertaking Numba development work, you may need to rebuild Numba.
> E Please see the development set up guide:
> E
> E https://numba.readthedocs.io/en/stable/developer/contributing.html.
> E
> E --------------------------------------------------------------------------------
> E If you are not working on Numba development, the original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'.
> E For help, please visit:
> E
> E https://numba.readthedocs.io/en/stable/user/faq.html#numba-could-not-be-imported
> =============================== warnings summary ===============================
> loompy/view_manager.py:23
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build/loompy/view_manager.py:23: SyntaxWarning: "is not" with 'int' literal. Did you mean "!="?
> if type(slice_) is not tuple or len(slice_) is not 2:
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info ============================
> ERROR tests/test_attribute_manager.py
> ERROR tests/test_connection.py
> ERROR tests/test_file_attribute_manager.py
> ERROR tests/test_main.py
> ERROR tests/test_validator.py
> !!!!!!!!!!!!!!!!!!! Interrupted: 5 errors during collection !!!!!!!!!!!!!!!!!!!!
> ========================= 1 warning, 5 errors in 1.30s =========================
> E: pybuild pybuild:395: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_loompy/build; python3.12 -m pytest tests
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build; python3.11 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 7 items
>
> tests/test_attribute_manager.py .. [ 28%]
> tests/test_connection.py . [ 42%]
> tests/test_file_attribute_manager.py . [ 57%]
> tests/test_main.py .. [ 85%]
> tests/test_validator.py . [100%]
>
> =============================== warnings summary ===============================
> loompy/view_manager.py:23
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/view_manager.py:23: SyntaxWarning: "is not" with a literal. Did you mean "!="?
> if type(slice_) is not tuple or len(slice_) is not 2:
>
> loompy/bus_file.py:67
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:67: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m
> @jit
>
> loompy/bus_file.py:84
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:84: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m
> @jit
>
> loompy/bus_file.py:101
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_loompy/build/loompy/bus_file.py:101: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m
> @jit
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> ======================== 7 passed, 4 warnings in 2.40s =========================
> rm -fr -- /tmp/dh-xdg-rundir-QcowctYQ
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12 3.11" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/12/12/python-loompy_3.0.7+dfsg-2_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231212;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231212&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.
More information about the Debian-med-packaging
mailing list