[Debichem-devel] Bug#1126234: python-symfc: FTBFS: E ModuleNotFoundError: No module named 'spglib.spglib'
Santiago Vila
sanvila at debian.org
Fri Jan 23 11:38:19 GMT 2026
Package: src:python-symfc
Version: 1.6.0-1
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202601/
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 cannot 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 add an affects on src:python-symfc, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem pybuild
dh_auto_clean -O--buildsystem=pybuild
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --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:139: Building wheel for python3.14 with "build" module
I: pybuild base:384: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_python-symfc
* Building wheel...
No `packages` or `py_modules` configuration, performing automatic discovery.
[... snipped ...]
tests/test_api_linalg.py . [ 54%]
tests/test_sparse_solver.py . [ 55%]
tests/utils/test_block_tree.py . [ 56%]
tests/utils/test_cutoff_tools.py .. [ 59%]
tests/utils/test_eig_tools.py ... [ 63%]
tests/utils/test_graph.py . [ 64%]
tests/utils/test_permutation_tools_O2.py .. [ 67%]
tests/utils/test_permutation_tools_O3.py .. [ 70%]
tests/utils/test_permutation_tools_O4.py . [ 71%]
tests/utils/test_solver_funcs.py ... [ 75%]
tests/utils/test_translation_tools_O2.py . [ 77%]
tests/utils/test_translation_tools_O3.py . [ 78%]
tests/utils/test_utils.py .FFFFF [ 86%]
tests/utils/test_utils_O1.py . [ 87%]
tests/utils/test_utils_O2.py .... [ 93%]
tests/utils/test_utils_O2_2.py .. [ 95%]
tests/utils/test_utils_O3.py .. [ 98%]
tests/utils/test_utils_O4.py . [100%]
=================================== FAILURES ===================================
_________________________ test_compute_sg_permutations _________________________
ph_gan_222 = (<symfc.utils.utils.SymfcAtoms object at 0x7f1b19754ef0>, array([[[ 0.0005821 , 0.0087098 , -0.00487858],
[ 0... [-0.06985763, 0.19560211, -0.0771704 ],
[-0.11406107, 0.04719309, -0.17137264]]], shape=(40, 32, 3)))
cell_gan_111 = <symfc.utils.utils.SymfcAtoms object at 0x7f1b197217f0>
def test_compute_sg_permutations(
ph_gan_222: tuple[SymfcAtoms, NDArray, NDArray], cell_gan_111: SymfcAtoms
):
"""Test compute_sg_permutations."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:41: ModuleNotFoundError
_________________ test_compute_sg_permutations_compare_stable __________________
def test_compute_sg_permutations_compare_stable():
"""Test compute_sg_permutations and compare with compute_sg_permutations_stable."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:86: ModuleNotFoundError
_______________ test_compute_sg_permutations_compare_stable_nacl _______________
ph_nacl_222 = (<symfc.utils.utils.SymfcAtoms object at 0x7f1b19703850>, array([[[ 0.00605959, 0.02814605, 0.00843097],
[-0...565899e-02, 1.158060e-02, 6.284319e-02],
[-5.293000e-05, -2.349248e-02, 5.364267e-02]]], shape=(20, 64, 3)))
def test_compute_sg_permutations_compare_stable_nacl(
ph_nacl_222: tuple[SymfcAtoms, NDArray, NDArray],
):
"""Test of compute_sg_permutations for NaCl."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:226: ModuleNotFoundError
_______________ test_compute_sg_permutations_compare_stable_sio2 _______________
ph_sio2_221 = (<symfc.utils.utils.SymfcAtoms object at 0x7f1b198cc830>, array([[[ 1.30307014e-04, 7.52356158e-03, -6.58627673e-03],... [ 0.24715049, 0.2559772 , -0.49612488],
[-0.14193055, -0.51082636, 0.34255692]]], shape=(40, 36, 3)))
def test_compute_sg_permutations_compare_stable_sio2(
ph_sio2_221: tuple[SymfcAtoms, NDArray, NDArray],
):
"""Test of compute_sg_permutations for SiO2."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:252: ModuleNotFoundError
_____________ test_compute_sg_permutations_compare_stable_baal2o4 ______________
def test_compute_sg_permutations_compare_stable_baal2o4():
"""Test compute_sg_permutations for BaAl2O4."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:276: ModuleNotFoundError
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/spglib/spg.py:354: 8 warnings
tests/basis_sets/test_basis_sets_O2.py: 12 warnings
tests/basis_sets/test_basis_sets_O3.py: 11 warnings
tests/basis_sets/test_basis_sets_O4.py: 6 warnings
tests/spg_reps/test_spg_reps_O1.py: 2 warnings
tests/spg_reps/test_spg_reps_O2.py: 1 warning
tests/spg_reps/test_spg_reps_O3.py: 1 warning
tests/spg_reps/test_spg_reps_O4.py: 1 warning
tests/spg_reps/test_spg_reps_base.py: 2 warnings
tests/test_api.py: 24 warnings
tests/test_sparse_solver.py: 1 warning
tests/utils/test_utils.py: 1 warning
tests/utils/test_utils_O2.py: 3 warnings
tests/utils/test_utils_O3.py: 1 warning
/usr/lib/python3/dist-packages/spglib/spg.py:354: DeprecationWarning: Set OLD_ERROR_HANDLING to false and catch the errors directly.
_set_no_error()
tests/basis_sets/test_basis_sets_O2.py: 2 warnings
tests/basis_sets/test_basis_sets_O3.py: 6 warnings
tests/basis_sets/test_basis_sets_O4.py: 4 warnings
tests/test_api.py: 1 warning
tests/utils/test_cutoff_tools.py: 8 warnings
tests/utils/test_permutation_tools_O2.py: 1 warning
tests/utils/test_permutation_tools_O3.py: 1 warning
tests/utils/test_translation_tools_O2.py: 1 warning
tests/utils/test_translation_tools_O3.py: 1 warning
tests/utils/test_utils_O3.py: 1 warning
/usr/lib/python3/dist-packages/spglib/reduce.py:131: DeprecationWarning: Set OLD_ERROR_HANDLING to false and catch the errors directly.
_set_no_error()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/utils/test_utils.py::test_compute_sg_permutations - ModuleNotFou...
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_nacl
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_sio2
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_baal2o4
================= 5 failed, 69 passed, 100 warnings in 16.37s ==================
E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_python-symfc/build; python3.14 -m pytest tests
I: pybuild base:384: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build; python3.13 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.13.11, pytest-9.0.2, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build
configfile: pyproject.toml
plugins: typeguard-4.4.4
collected 74 items
tests/basis_sets/test_basis_sets_O2.py .......... [ 13%]
tests/basis_sets/test_basis_sets_O3.py ..... [ 20%]
tests/basis_sets/test_basis_sets_O4.py ... [ 24%]
tests/basis_sets/test_basis_sets_base.py . [ 25%]
tests/solvers/test_solver_utils.py ... [ 29%]
tests/spg_reps/test_spg_reps_O1.py .. [ 32%]
tests/spg_reps/test_spg_reps_O2.py . [ 33%]
tests/spg_reps/test_spg_reps_O3.py . [ 35%]
tests/spg_reps/test_spg_reps_O4.py . [ 36%]
tests/spg_reps/test_spg_reps_base.py .. [ 39%]
tests/test_api.py .......... [ 52%]
tests/test_api_linalg.py . [ 54%]
tests/test_sparse_solver.py . [ 55%]
tests/utils/test_block_tree.py . [ 56%]
tests/utils/test_cutoff_tools.py .. [ 59%]
tests/utils/test_eig_tools.py ... [ 63%]
tests/utils/test_graph.py . [ 64%]
tests/utils/test_permutation_tools_O2.py .. [ 67%]
tests/utils/test_permutation_tools_O3.py .. [ 70%]
tests/utils/test_permutation_tools_O4.py . [ 71%]
tests/utils/test_solver_funcs.py ... [ 75%]
tests/utils/test_translation_tools_O2.py . [ 77%]
tests/utils/test_translation_tools_O3.py . [ 78%]
tests/utils/test_utils.py .FFFFF [ 86%]
tests/utils/test_utils_O1.py . [ 87%]
tests/utils/test_utils_O2.py .... [ 93%]
tests/utils/test_utils_O2_2.py .. [ 95%]
tests/utils/test_utils_O3.py .. [ 98%]
tests/utils/test_utils_O4.py . [100%]
=================================== FAILURES ===================================
_________________________ test_compute_sg_permutations _________________________
ph_gan_222 = (<symfc.utils.utils.SymfcAtoms object at 0x7fab97a70d50>, array([[[ 0.0005821 , 0.0087098 , -0.00487858],
[ 0... [-0.06985763, 0.19560211, -0.0771704 ],
[-0.11406107, 0.04719309, -0.17137264]]], shape=(40, 32, 3)))
cell_gan_111 = <symfc.utils.utils.SymfcAtoms object at 0x7fab9782a030>
def test_compute_sg_permutations(
ph_gan_222: tuple[SymfcAtoms, NDArray, NDArray], cell_gan_111: SymfcAtoms
):
"""Test compute_sg_permutations."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:41: ModuleNotFoundError
_________________ test_compute_sg_permutations_compare_stable __________________
def test_compute_sg_permutations_compare_stable():
"""Test compute_sg_permutations and compare with compute_sg_permutations_stable."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:86: ModuleNotFoundError
_______________ test_compute_sg_permutations_compare_stable_nacl _______________
ph_nacl_222 = (<symfc.utils.utils.SymfcAtoms object at 0x7fab9794b250>, array([[[ 0.00605959, 0.02814605, 0.00843097],
[-0...565899e-02, 1.158060e-02, 6.284319e-02],
[-5.293000e-05, -2.349248e-02, 5.364267e-02]]], shape=(20, 64, 3)))
def test_compute_sg_permutations_compare_stable_nacl(
ph_nacl_222: tuple[SymfcAtoms, NDArray, NDArray],
):
"""Test of compute_sg_permutations for NaCl."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:226: ModuleNotFoundError
_______________ test_compute_sg_permutations_compare_stable_sio2 _______________
ph_sio2_221 = (<symfc.utils.utils.SymfcAtoms object at 0x7fab978f19b0>, array([[[ 1.30307014e-04, 7.52356158e-03, -6.58627673e-03],... [ 0.24715049, 0.2559772 , -0.49612488],
[-0.14193055, -0.51082636, 0.34255692]]], shape=(40, 36, 3)))
def test_compute_sg_permutations_compare_stable_sio2(
ph_sio2_221: tuple[SymfcAtoms, NDArray, NDArray],
):
"""Test of compute_sg_permutations for SiO2."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:252: ModuleNotFoundError
_____________ test_compute_sg_permutations_compare_stable_baal2o4 ______________
def test_compute_sg_permutations_compare_stable_baal2o4():
"""Test compute_sg_permutations for BaAl2O4."""
pytest.importorskip("spglib")
import spglib
> from spglib.spglib import Cell as SpgCell
E ModuleNotFoundError: No module named 'spglib.spglib'
tests/utils/test_utils.py:276: ModuleNotFoundError
=============================== warnings summary ===============================
../../../../../../usr/lib/python3/dist-packages/spglib/spg.py:354: 8 warnings
tests/basis_sets/test_basis_sets_O2.py: 12 warnings
tests/basis_sets/test_basis_sets_O3.py: 11 warnings
tests/basis_sets/test_basis_sets_O4.py: 6 warnings
tests/spg_reps/test_spg_reps_O1.py: 2 warnings
tests/spg_reps/test_spg_reps_O2.py: 1 warning
tests/spg_reps/test_spg_reps_O3.py: 1 warning
tests/spg_reps/test_spg_reps_O4.py: 1 warning
tests/spg_reps/test_spg_reps_base.py: 2 warnings
tests/test_api.py: 24 warnings
tests/test_sparse_solver.py: 1 warning
tests/utils/test_utils.py: 1 warning
tests/utils/test_utils_O2.py: 3 warnings
tests/utils/test_utils_O3.py: 1 warning
/usr/lib/python3/dist-packages/spglib/spg.py:354: DeprecationWarning: Set OLD_ERROR_HANDLING to false and catch the errors directly.
_set_no_error()
tests/basis_sets/test_basis_sets_O2.py: 2 warnings
tests/basis_sets/test_basis_sets_O3.py: 6 warnings
tests/basis_sets/test_basis_sets_O4.py: 4 warnings
tests/test_api.py: 1 warning
tests/utils/test_cutoff_tools.py: 8 warnings
tests/utils/test_permutation_tools_O2.py: 1 warning
tests/utils/test_permutation_tools_O3.py: 1 warning
tests/utils/test_translation_tools_O2.py: 1 warning
tests/utils/test_translation_tools_O3.py: 1 warning
tests/utils/test_utils_O3.py: 1 warning
/usr/lib/python3/dist-packages/spglib/reduce.py:131: DeprecationWarning: Set OLD_ERROR_HANDLING to false and catch the errors directly.
_set_no_error()
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/utils/test_utils.py::test_compute_sg_permutations - ModuleNotFou...
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_nacl
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_sio2
FAILED tests/utils/test_utils.py::test_compute_sg_permutations_compare_stable_baal2o4
================= 5 failed, 69 passed, 100 warnings in 16.64s ==================
E: pybuild pybuild:483: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_python-symfc/build; python3.13 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
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