Your message dated Wed, 27 May 2026 07:04:47 +0000
with message-id <[email protected]>
and subject line Bug#1090269: fixed in python-cogent 2026.5.25a0+dfsg-1
has caused the Debian Bug report #1090269,
regarding python-cogent: FTBFS: E ImportError: Numba could not be imported.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1090269: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1090269
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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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api/sequence/classes/cogent3.core.sequence.ProteinSequence
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generating indices... genindex done
copying linked files...
copying notebooks ...
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dumping object inventory... done
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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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tests/test_util/test_parallel.py ... [ 98%]
tests/test_util/test_recode_alignment.py ............... [ 98%]
tests/test_util/test_table.py .......................................... [ 99%]
............................................................... [ 99%]
tests/test_util/test_transform.py ..... [ 99%]
tests/test_util/test_union_dict.py ........... [ 99%]
tests/test_util/test_warning.py ......................... [100%]
=============================== 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.
--- End Message ---
--- Begin Message ---
Source: python-cogent
Source-Version: 2026.5.25a0+dfsg-1
Done: Karsten Schöke <[email protected]>
We believe that the bug you reported is fixed in the latest version of
python-cogent, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Karsten Schöke <[email protected]> (supplier of updated
python-cogent package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 26 May 2026 09:56:09 +0200
Source: python-cogent
Architecture: source
Version: 2026.5.25a0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Karsten Schöke <[email protected]>
Closes: 1058479 1090269 1123705
Changes:
python-cogent (2026.5.25a0+dfsg-1) unstable; urgency=medium
.
* Team upload.
* New upstream version
Closes: #1090269, #1058479, #1123705
* Standards-Version: 4.7.4 (routine-update)
* Patches cleaned up following upstream update.
* d/control: Update B-D
* d/rules: Update PYTHONPATH for docu build environment.
* d/watch: convert to v5 Github template.
* NumPy Python headers integrated into the build environment.
* Tackle privacy breaches caused by MathML.
* Clean fonts that made their way to the documentation package
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