[Debian-med-packaging] Bug#1002335: python-epimodels: FTBFS: dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13
Lucas Nussbaum
lucas at debian.org
Wed Dec 22 07:55:42 GMT 2021
Source: python-epimodels
Version: 0.3.20-1
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20211220 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_auto_test
> I: pybuild base:237: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_epimodels/build; python3.10 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.10.1, pytest-6.2.5, py-1.10.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
> plugins: cov-3.0.0
> collected 11 items / 1 error / 10 selected
>
> ==================================== ERRORS ====================================
> _ ERROR collecting .pybuild/cpython3_3.10_epimodels/build/tests/test_continuous_models.py _
> ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_epimodels/build/tests/test_continuous_models.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/python3.10/importlib/__init__.py:126: in import_module
> return _bootstrap._gcd_import(name[level:], package, level)
> tests/test_continuous_models.py:8: in <module>
> from epimodels.continuous.models import *
> epimodels/continuous/models.py:12: in <module>
> import numba
> /usr/lib/python3/dist-packages/numba/__init__.py:24: 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:17: in <module>
> raise ImportError(msg % (url, reportme, str(e), sys.executable))
> E ImportError: Numba could not be imported.
> E If you are seeing this message and are undertaking Numba development work, you may need to re-run:
> E
> E python setup.py build_ext --inplace
> E
> E (Also, please check the development set up guide https://numba.pydata.org/numba-doc/latest/developer/contributing.html.)
> E
> E If you are not working on Numba development:
> E
> E Please report the error message and traceback, along with a minimal reproducer
> E at: https://github.com/numba/numba/issues/new
> E
> E If more help is needed please feel free to speak to the Numba core developers
> E directly at: https://gitter.im/numba/numba
> E
> E Thanks in advance for your help in improving Numba!
> E
> E The original error was: 'cannot import name '_typeconv' from 'numba.core.typeconv' (/usr/lib/python3/dist-packages/numba/core/typeconv/__init__.py)'
> E --------------------------------------------------------------------------------
> E If possible please include the following in your error report:
> E
> E sys.executable: /usr/bin/python3.10
> =============================== warnings summary ===============================
> ../../../../../../usr/lib/python3/dist-packages/numba/core/types/__init__.py:108
> /usr/lib/python3/dist-packages/numba/core/types/__init__.py:108: DeprecationWarning: `np.long` is a deprecated alias for `np.compat.long`. To silence this warning, use `np.compat.long` by itself. In the likely event your code does not need to work on Python 2 you can use the builtin `int` for which `np.compat.long` is itself an alias. Doing this will not modify any behaviour and is safe. When replacing `np.long`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> long_ = _make_signed(np.long)
>
> ../../../../../../usr/lib/python3/dist-packages/numba/core/types/__init__.py:109
> /usr/lib/python3/dist-packages/numba/core/types/__init__.py:109: DeprecationWarning: `np.long` is a deprecated alias for `np.compat.long`. To silence this warning, use `np.compat.long` by itself. In the likely event your code does not need to work on Python 2 you can use the builtin `int` for which `np.compat.long` is itself an alias. Doing this will not modify any behaviour and is safe. When replacing `np.long`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> ulong = _make_unsigned(np.long)
>
> -- Docs: https://docs.pytest.org/en/stable/warnings.html
> =========================== short test summary info ============================
> ERROR tests/test_continuous_models.py
> !!!!!!!!!!!!!!!!!!!! Interrupted: 1 error during collection !!!!!!!!!!!!!!!!!!!!
> ========================= 2 warnings, 1 error in 0.82s =========================
> E: pybuild pybuild:355: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10_epimodels/build; python3.10 -m pytest tests
> I: pybuild base:237: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build; python3.9 -m pytest tests
> ============================= test session starts ==============================
> platform linux -- Python 3.9.9, pytest-6.2.5, py-1.10.0, pluggy-0.13.0
> rootdir: /<<PKGBUILDDIR>>, configfile: setup.cfg
> plugins: cov-3.0.0
> collected 17 items
>
> tests/test_continuous_models.py ...... [ 35%]
> tests/test_discrete_models.py ........... [100%]
>
> =============================== warnings summary ===============================
> ../../../../../../usr/lib/python3/dist-packages/numba/core/types/__init__.py:108
> /usr/lib/python3/dist-packages/numba/core/types/__init__.py:108: DeprecationWarning: `np.long` is a deprecated alias for `np.compat.long`. To silence this warning, use `np.compat.long` by itself. In the likely event your code does not need to work on Python 2 you can use the builtin `int` for which `np.compat.long` is itself an alias. Doing this will not modify any behaviour and is safe. When replacing `np.long`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> long_ = _make_signed(np.long)
>
> ../../../../../../usr/lib/python3/dist-packages/numba/core/types/__init__.py:109
> /usr/lib/python3/dist-packages/numba/core/types/__init__.py:109: DeprecationWarning: `np.long` is a deprecated alias for `np.compat.long`. To silence this warning, use `np.compat.long` by itself. In the likely event your code does not need to work on Python 2 you can use the builtin `int` for which `np.compat.long` is itself an alias. Doing this will not modify any behaviour and is safe. When replacing `np.long`, you may wish to use e.g. `np.int64` or `np.int32` to specify the precision. If you wish to review your current use, check the release note link for additional information.
> Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
> ulong = _make_unsigned(np.long)
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIR
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py:63: NumbaWarning:
> Compilation is falling back to object mode WITH looplifting enabled because Function "_model" failed type inference due to: non-precise type pyobject
> During: typing of argument at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py (72)
>
> File "epimodels/continuous/models.py", line 72:
> def _model(self, t: float, y: list, params: dict) -> list:
> <source elided>
> """
> S, I, R = y
> ^
>
> @numba.jit
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:151: NumbaWarning: Function "_model" was compiled in object mode without forceobj=True.
>
> File "epimodels/continuous/models.py", line 64:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaWarning(warn_msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:161: NumbaDeprecationWarning:
> Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.
>
> For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
>
> File "epimodels/continuous/models.py", line 64:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaDeprecationWarning(msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIS
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py:89: NumbaWarning:
> Compilation is falling back to object mode WITH looplifting enabled because Function "_model" failed type inference due to: non-precise type pyobject
> During: typing of argument at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py (98)
>
> File "epimodels/continuous/models.py", line 98:
> def _model(self, t: float, y: list, params: dict) -> list:
> <source elided>
> """
> S, I = y
> ^
>
> @numba.jit
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIS
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:151: NumbaWarning: Function "_model" was compiled in object mode without forceobj=True.
>
> File "epimodels/continuous/models.py", line 90:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaWarning(warn_msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIS
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:161: NumbaDeprecationWarning:
> Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.
>
> For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
>
> File "epimodels/continuous/models.py", line 90:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaDeprecationWarning(msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIRS
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py:113: NumbaWarning:
> Compilation is falling back to object mode WITH looplifting enabled because Function "_model" failed type inference due to: non-precise type pyobject
> During: typing of argument at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py (122)
>
> File "epimodels/continuous/models.py", line 122:
> def _model(self, t: float, y: list, params: dict) -> list:
> <source elided>
> """
> S, I, R = y
> ^
>
> @numba.jit
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIRS
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:151: NumbaWarning: Function "_model" was compiled in object mode without forceobj=True.
>
> File "epimodels/continuous/models.py", line 114:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaWarning(warn_msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SIRS
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:161: NumbaDeprecationWarning:
> Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.
>
> For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
>
> File "epimodels/continuous/models.py", line 114:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaDeprecationWarning(msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEIR
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py:138: NumbaWarning:
> Compilation is falling back to object mode WITH looplifting enabled because Function "_model" failed type inference due to: non-precise type pyobject
> During: typing of argument at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py (140)
>
> File "epimodels/continuous/models.py", line 140:
> def _model(self, t: float, y: list, params: dict) -> list:
> S, E, I, R = y
> ^
>
> @numba.jit
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEIR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:151: NumbaWarning: Function "_model" was compiled in object mode without forceobj=True.
>
> File "epimodels/continuous/models.py", line 139:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaWarning(warn_msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEIR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:161: NumbaDeprecationWarning:
> Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.
>
> For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
>
> File "epimodels/continuous/models.py", line 139:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaDeprecationWarning(msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEQIAHR
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py:163: NumbaWarning:
> Compilation is falling back to object mode WITH looplifting enabled because Function "_model" failed type inference due to: non-precise type pyobject
> During: typing of argument at /<<PKGBUILDDIR>>/.pybuild/cpython3_3.9_epimodels/build/epimodels/continuous/models.py (165)
>
> File "epimodels/continuous/models.py", line 165:
> def _model(self, t: float, y: list, params: dict) -> list:
> S, E, I, A, H, R, C, D = y
> ^
>
> @numba.jit
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEQIAHR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:151: NumbaWarning: Function "_model" was compiled in object mode without forceobj=True.
>
> File "epimodels/continuous/models.py", line 164:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaWarning(warn_msg,
>
> .pybuild/cpython3_3.9_epimodels/build/tests/test_continuous_models.py::test_SEQIAHR
> /usr/lib/python3/dist-packages/numba/core/object_mode_passes.py:161: NumbaDeprecationWarning:
> Fall-back from the nopython compilation path to the object mode compilation path has been detected, this is deprecated behaviour.
>
> For more information visit https://numba.pydata.org/numba-doc/latest/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit
>
> File "epimodels/continuous/models.py", line 164:
> @numba.jit
> def _model(self, t: float, y: list, params: dict) -> list:
> ^
>
> warnings.warn(errors.NumbaDeprecationWarning(msg,
>
> -- Docs: https://docs.pytest.org/en/stable/warnings.html
> ======================= 17 passed, 17 warnings in 1.95s ========================
> dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.10 3.9" returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2021/12/20/python-epimodels_0.3.20-1_unstable.log
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 marking 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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