[Debian-med-packaging] Bug#1090269: python-cogent: FTBFS: E ImportError: Numba could not be imported.
Santiago Vila
sanvila at debian.org
Mon Dec 16 17:51:47 GMT 2024
Package: src:python-cogent
Version: 2024.5.7a1+dfsg-3
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
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[...]
debian/rules binary
dh binary --with sphinxdoc --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module
I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_cogent3
* Building wheel...
Successfully built cogent3-2024.5.7a1-py3-none-any.whl
I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module
I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module
I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3
* Building wheel...
[... snipped ...]
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writing output... [ 31%] api/tree/classes/cogent3.core.tree.PhyloNode
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writing output... [ 86%] examples/align_codons_to_protein
writing output... [ 86%] examples/calculate_UPGMA_cluster
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writing output... [ 90%] examples/hmm_par_heterogeneity
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writing output... [ 98%] index
writing output... [ 98%] install
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writing output... [ 99%] pycogent
writing output... [100%] templates/class
generating indices... genindex done
copying linked files...
copying notebooks ...
writing additional pages... search done
dumping search index in English (code: en)... done
dumping object inventory... done
Highlighting style a11y-high-contrast-light not found by pygments, falling back to tango.
Highlighting style a11y-high-contrast-dark not found by pygments, falling back to monokai.
build succeeded, 1169 warnings.
The HTML pages are in _build/html.
Build finished. The HTML pages are in _build/html.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc'
# remove superfluous files and dirs
find doc/_build -name "*.doctree*" -delete
rm -f doc/_build/html/_sources/COGENT_LICENSE.txt
rm -f doc/_build/html/_static/jquery.js
rm -f doc/_build/html/_static/underscore.js
rm -rf doc/_build/html/_images/math/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -O--buildsystem=pybuild
I: pybuild pybuild:308: cp -r /<<PKGBUILDDIR>>/tests/data /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_cogent3/build
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
ImportError while loading conftest '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_cogent3/build/tests/conftest.py'.
__init__.py:11: in <module>
exec(f"from {__name__} import {sub_module}")
test_phylo.py:10: in <module>
from cogent3 import get_model, load_aligned_seqs, load_tree, make_tree
../cogent3/__init__.py:14: in <module>
from cogent3.app import app_help, available_apps, get_app, open_data_store
../cogent3/app/__init__.py:14: in <module>
from .io import open_data_store
../cogent3/app/io.py:23: in <module>
from cogent3.evolve.fast_distance import DistanceMatrix
../cogent3/evolve/fast_distance.py:16: in <module>
from .pairwise_distance_numba import fill_diversity_matrix
../cogent3/evolve/pairwise_distance_numba.py:1: in <module>
from numba import njit
/usr/lib/python3/dist-packages/numba/__init__.py:74: 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
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=4: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_cogent3/build; python3.13 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
I: pybuild pybuild:308: cp -r /<<PKGBUILDDIR>>/tests/data /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build; python3.12 -m pytest -k 'not test_pickleable_member_roundtrip and not test_pickleable_roundtrip'
============================= test session starts ==============================
platform linux -- Python 3.12.8, pytest-8.3.4, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build
configfile: pyproject.toml
plugins: xdist-3.6.1, typeguard-4.4.1, cov-5.0.0, anyio-4.6.2
collected 11030 items / 4 deselected / 11026 selected
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=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500
/usr/lib/python3/dist-packages/_pytest/config/__init__.py:1500: PytestConfigWarning: No files were found in testpaths; consider removing or adjusting your testpaths configuration. Searching recursively from the current directory instead.
self.args, self.args_source = self._decide_args(
tests/test_maths/test_stats/test_test.py::StatTests::test_t_two_sample_switch
/usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning:
Degrees of freedom <= 0 for slice
tests/test_util/test_deserialise.py::test_convert_annotation_to_annotation_db
tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated
tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated
tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated
tests/test_util/test_deserialise.py::test_deserialise_old_style_annotated
tests/test_util/test_deserialise.py::test_deser_annotated_aln
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_cogent3/build/cogent3/util/warning.py:226: DeprecationWarning:
class Map is discontinued and will be removed in version 2024.6
reason='Replaced by IndelMap and FeatureMap'
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
= 11014 passed, 9 skipped, 4 deselected, 1 xfailed, 2 xpassed, 8 warnings in 136.30s (0:02:16) =
dh_auto_test: error: pybuild --test -i python{version} -p "3.13 3.12" returned exit code 13
make: *** [debian/rules:20: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202412/
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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
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