[Debichem-devel] Bug#1151795: python-pymzml: FTBFS: ModuleNotFoundError: No module named 'numpy._core._multiarray_umath'
Santiago Vila
sanvila at debian.org
Fri Oct 23 17:27:56 BST 2026
Package: src:python-pymzml
Version: 2.5.10+repack1-5
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/202610/
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-pymzml, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
from . import multiarray
File "/usr/lib/python3/dist-packages/numpy/_core/multiarray.py", line 11, in <module>
from . import _multiarray_umath, overrides
File "/usr/lib/python3/dist-packages/numpy/_core/overrides.py", line 6, in <module>
from numpy._core._multiarray_umath import (
ModuleNotFoundError: No module named 'numpy._core._multiarray_umath'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "<frozen runpy>", line 201, in _run_module_as_main
File "<frozen runpy>", line 87, in _run_code
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9, in <module>
raise SystemExit(_console_main())
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 253, in _console_main
code = _main(prog=_get_prog_name(sys.argv))
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 229, in _main
ret: ExitCode | int = config.hook.pytest_cmdline_main(config=config)
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512, in __call__
return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120, in _hookexec
return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 167, in _multicall
raise exception
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121, in _multicall
res = hook_impl.function(*args)
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 377, in pytest_cmdline_main
return wrap_session(config, _main)
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 350, in wrap_session
config.notify_exception(excinfo, config.option)
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 1264, in notify_exception
excrepr = excinfo.getrepr(
File "/usr/lib/python3/dist-packages/_pytest/_code/code.py", line 755, in getrepr
format_exception(
File "/usr/lib/python3.15/traceback.py", line 199, in format_exception
te = TracebackException(type(value), value, tb, limit=limit, compact=True)
File "/usr/lib/python3.15/traceback.py", line 1259, in __init__
cause = TracebackException(
File "/usr/lib/python3.15/traceback.py", line 1206, in __init__
elif abi_tag := _find_incompatible_extension_module(module_name):
File "/usr/lib/python3.15/traceback.py", line 2075, in _find_incompatible_extension_module
traversable = importlib.resources.files(parent)
File "/usr/lib/python3.15/importlib/resources/_common.py", line 22, in files
return from_package(resolve(anchor))
File "/usr/lib/python3.15/functools.py", line 1003, in wrapper
return dispatch(args[0].__class__)(*args, **kw)
File "/usr/lib/python3.15/importlib/resources/_common.py", line 48, in _
return importlib.import_module(cand)
File "/usr/lib/python3.15/importlib/__init__.py", line 88, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1390, in _gcd_import
File "<frozen importlib._bootstrap>", line 1350, in _find_and_load
File "<frozen importlib._bootstrap>", line 1277, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 549, in _call_with_frames_removed
File "<frozen importlib._bootstrap>", line 1390, in _gcd_import
File "<frozen importlib._bootstrap>", line 1350, in _find_and_load
File "<frozen importlib._bootstrap>", line 1309, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 915, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 747, in exec_module
File "<frozen importlib._bootstrap>", line 549, in _call_with_frames_removed
File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 112, in <module>
from numpy.__config__ import show_config
File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in <module>
from numpy._core._multiarray_umath import (
File "/usr/lib/python3/dist-packages/numpy/_core/__init__.py", line 85, in <module>
raise ImportError(msg) from exc
ImportError:
IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!
Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.
The following compiled module files exist, but seem incompatible
with with either python 'cpython-315' or the platform 'linux':
* _multiarray_umath.cpython-314-x86_64-linux-gnu.so
We have compiled some common reasons and troubleshooting tips at:
https://numpy.org/devdocs/user/troubleshooting-importerror.html
Please note and check the following:
* The Python version is: Python 3.15 from "/usr/bin/python3.15"
* The NumPy version is: "2.4.6"
and make sure that they are the versions you expect.
Please carefully study the information and documentation linked above.
This is unlikely to be a NumPy issue but will be caused by a bad install
or environment on your machine.
Original error was: No module named 'numpy._core._multiarray_umath'
============================= test session starts ==============================
platform linux -- Python 3.15.0, pytest-9.1.1, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>
collected 0 items
============================ no tests ran in 0.12s =============================
E: pybuild pybuild:485: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.15_pymzml/build; python3.15 -m pytest tests
I: pybuild base:383: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build; python3.14 -m pytest tests
============================= test session starts ==============================
platform linux -- Python 3.14.8, pytest-9.1.1, pluggy-1.6.0
rootdir: /<<PKGBUILDDIR>>
collected 98 items
tests/file_io_file_interface_test.py .. [ 2%]
tests/file_io_indexed_gzip_reader_test.py ..... [ 7%]
tests/file_io_indexed_gzip_test.py ... [ 10%]
tests/file_io_indexed_gzip_writer_test.py ....... [ 17%]
tests/file_io_standard_gzip_test.py .. [ 19%]
tests/file_io_standard_mzml_test.py .. [ 21%]
tests/main_chromatogram_test.py ... [ 24%]
tests/main_reader_test.py .......... [ 34%]
tests/main_spec_test.py ................................................ [ 83%]
.... [ 87%]
tests/ms2_spec_test.py s..... [ 93%]
tests/plot_spec_test.py ... [ 96%]
tests/regex_test.py ... [100%]/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning:
Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
=============================== warnings summary ===============================
pymzml/file_classes/standardMzml.py:384
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:384: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
chromexp = re.compile(b'<\s*chromatogram[^>]*id="([^"]*)"')
pymzml/file_classes/standardMzml.py:385
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:385: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
chromcntexp = re.compile(b'<\s*chromatogramList\s*count="([^"]*)"')
pymzml/file_classes/standardMzml.py:386
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:386: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
specexp = re.compile(b'<\s*spectrum[^>]*id="([^"]*)"')
pymzml/file_classes/standardMzml.py:387
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:387: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
speccntexp = re.compile(b'<\s*spectrumList\s*count="([^"]*)"')
pymzml/file_classes/standardMzml.py:735
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:735: SyntaxWarning: "\s" is an invalid escape sequence. Such sequences will not work in the future. Did you mean "\\s"? A raw string is also an option.
'<\s*spectrum[^>]*index="[0-9]+"\sid="({0})"\sdefaultArrayLength="[0-9]+">'.format(
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_file_interface_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_mzml_test.py: 2 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_reader_test.py: 74 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 7 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/file_classes/standardMzml.py:68: DeprecationWarning: codecs.open() is deprecated. Use open() instead.
return codecs.open(self.path, mode="r", encoding=encoding)
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_indexed_gzip_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_gzip_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_mzml_test.py: 2 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_reader_test.py: 6 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 82 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/ms2_spec_test.py: 5 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py: 2 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:472: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if self.element:
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_indexed_gzip_test.py::IndexedGzipTest::test_getitem_5
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_gzip_test.py::StandardGzipTest::test_getitem_5
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_mzml_test.py::StandardMzmlTest::test_getitem
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitem_2_times_standard_mzml
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitem_2_times_standard_mzml
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitem_index_gzip
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitem_index_mzml
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitem_index_mzml_last
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py::SpectrumTest::test_getitems_end_standard_mzml
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:819: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if self.element:
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_indexed_gzip_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_gzip_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_mzml_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/main_chromatogram_test.py: 3 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:1772: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if self.element:
.pybuild/cpython3_3.14_pymzml/build/tests/file_io_standard_gzip_test.py: 2 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_chromatogram_test.py: 1 warning
.pybuild/cpython3_3.14_pymzml/build/tests/main_reader_test.py: 6 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 76 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/ms2_spec_test.py: 7 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py: 1 warning
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if self.element:
.pybuild/cpython3_3.14_pymzml/build/tests/main_chromatogram_test.py: 4 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 76 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/ms2_spec_test.py: 2 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:169: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if not b_data_array:
.pybuild/cpython3_3.14_pymzml/build/tests/main_chromatogram_test.py: 4 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/main_spec_test.py: 76 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/ms2_spec_test.py: 2 warnings
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py: 4 warnings
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:177: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
if b_data_array:
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:472: DeprecationWarning:
Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:169: DeprecationWarning:
Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:177: DeprecationWarning:
Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning:
Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
.pybuild/cpython3_3.14_pymzml/build/tests/plot_spec_test.py::PlotTest::test_save_plot
/usr/lib/python3/dist-packages/plotly/basedatatypes.py:2314: DeprecationWarning:
The append_trace method is deprecated and will be removed in a future version.
Please use the add_trace method with the row and col parameters.
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================= 97 passed, 1 skipped, 484 warnings in 1.09s ==================
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_pymzml/build/pymzml/spec.py:487: DeprecationWarning: Testing an element's truth value will always return True in future versions. Use specific 'len(elem)' or 'elem is not None' test instead.
rm -fr -- /tmp/dh-xdg-rundir-KDo6kOsm
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.15 3.14" --parallel=2 returned exit code 13
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
More information about the Debichem-devel
mailing list