[Debian-astro-maintainers] Bug#1145593: yt: FTBFS: E UserWarning: h5py is running against HDF5 2.2.0 when it was built against 2.1.0, this may cause problems
Santiago Vila
sanvila at debian.org
Tue Aug 25 21:34:33 BST 2026
Package: src:yt
Version: 4.4.2-1
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/202608/
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:yt, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
# H5PY_ALWAYS_USE_MPI takes precedence if H5PY_NEVER_USE_MPI is also set
if _MPI_ACTIVE or _MPI_USE_ALWAYS:
try:
from . import _debian_h5py_mpi as _h5py
except:
from . import _debian_h5py_serial as _h5py
else:
try:
from . import _debian_h5py_serial as _h5py
except:
> from . import _debian_h5py_mpi as _h5py
E ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py)
E Something went wrong while trying to lazy-import h5py. Please make sure that h5py is properly installed.
E If the problem persists, please file an issue at https://github.com/yt-project/yt/issues/new
/usr/lib/python3/dist-packages/h5py/__init__.py:26: ImportError
__________________ test_all_invalid_with_missing_requirements __________________
# avoid running mpi with serial (1 process) jobs
# by checking whether mpi is actually being used over multiple processes
# Probe number of processes with OMPI_COMM_WORLD_SIZE (openmpi) and MPI_LOCALNRANKS (mpich)
from os import getenv as os_getenv
from sys import modules as sys_modules
from importlib import import_module
_OPENMPI_MULTIPROC = os_getenv('OMPI_COMM_WORLD_SIZE') is not None
_MPICH_MULTIPROC = os_getenv('MPI_LOCALNRANKS') is not None
_MPI_USE_ALWAYS = os_getenv('H5PY_ALWAYS_USE_MPI') is not None
_MPI_USE_NEVER = os_getenv('H5PY_NEVER_USE_MPI') is not None
_MPI_ACTIVE = (_OPENMPI_MULTIPROC or _MPICH_MULTIPROC) and not _MPI_USE_NEVER
# H5PY_ALWAYS_USE_MPI takes precedence if H5PY_NEVER_USE_MPI is also set
if _MPI_ACTIVE or _MPI_USE_ALWAYS:
try:
from . import _debian_h5py_mpi as _h5py
except:
from . import _debian_h5py_serial as _h5py
else:
try:
> from . import _debian_h5py_serial as _h5py
/usr/lib/python3/dist-packages/h5py/__init__.py:24:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
This is the h5py package, a Python interface to the HDF5
scientific data format.
"""
from warnings import warn as _warn
import atexit
# --- Library setup -----------------------------------------------------------
# When importing from the root of the unpacked tarball or git checkout,
# Python sees the "h5py" source directory and tries to load it, which fails.
# We tried working around this by using "package_dir" but that breaks Cython.
try:
from . import _errors
except ImportError:
import os.path as _op
if _op.exists(_op.join(_op.dirname(__file__), '..', 'setup.py')):
raise ImportError("You cannot import h5py from inside the install directory.\nChange to another directory first.")
else:
raise
from . import version
if version.hdf5_version_tuple[0:2] != version.hdf5_built_version_tuple[0:2]:
> _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
"this may cause problems").format(
'{0}.{1}.{2}'.format(*version.hdf5_version_tuple),
'{0}.{1}.{2}'.format(*version.hdf5_built_version_tuple)
))
E UserWarning: h5py is running against HDF5 2.2.0 when it was built against 2.1.0, this may cause problems
/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py:36: UserWarning
During handling of the above exception, another exception occurred:
tmp_path = PosixPath('/tmp/pytest-of-sbuild/pytest-1/test_all_invalid_with_missing_0')
@pytest.mark.usefixtures("invalid_dataset_class_with_missing_requirements")
def test_all_invalid_with_missing_requirements(tmp_path):
with pytest.raises(
YTUnidentifiedDataType,
match=re.compile(
re.escape(f"Could not determine input format from {tmp_path!r}\n")
+ "The following types could not be thorougly checked against your data because "
"their requirements are missing. "
"You may want to inspect this list and check your installation:\n"
r".*"
r"- MockDataset \(requires: mock_package_name\)"
r".*"
"\n\n"
"Please make sure you are running a sufficiently recent version of yt.",
re.DOTALL,
),
):
> load(tmp_path)
yt/tests/test_load_errors.py:258:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
yt/_maintenance/deprecation.py:68: in inner
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
yt/loaders.py:121: in load
if cls._is_valid(fn, *args, **kwargs):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
yt/frontends/swift/data_structures.py:205: in _is_valid
handle = h5py.File(filename, mode="r")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
yt/utilities/on_demand_imports.py:39: in __call__
raise self.error
yt/utilities/on_demand_imports.py:77: in inner
return func(self)
^^^^^^^^^^
yt/utilities/on_demand_imports.py:305: in File
from h5py import File
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
# avoid running mpi with serial (1 process) jobs
# by checking whether mpi is actually being used over multiple processes
# Probe number of processes with OMPI_COMM_WORLD_SIZE (openmpi) and MPI_LOCALNRANKS (mpich)
from os import getenv as os_getenv
from sys import modules as sys_modules
from importlib import import_module
_OPENMPI_MULTIPROC = os_getenv('OMPI_COMM_WORLD_SIZE') is not None
_MPICH_MULTIPROC = os_getenv('MPI_LOCALNRANKS') is not None
_MPI_USE_ALWAYS = os_getenv('H5PY_ALWAYS_USE_MPI') is not None
_MPI_USE_NEVER = os_getenv('H5PY_NEVER_USE_MPI') is not None
_MPI_ACTIVE = (_OPENMPI_MULTIPROC or _MPICH_MULTIPROC) and not _MPI_USE_NEVER
# H5PY_ALWAYS_USE_MPI takes precedence if H5PY_NEVER_USE_MPI is also set
if _MPI_ACTIVE or _MPI_USE_ALWAYS:
try:
from . import _debian_h5py_mpi as _h5py
except:
from . import _debian_h5py_serial as _h5py
else:
try:
from . import _debian_h5py_serial as _h5py
except:
> from . import _debian_h5py_mpi as _h5py
E ImportError: cannot import name '_debian_h5py_mpi' from partially initialized module 'h5py' (most likely due to a circular import) (/usr/lib/python3/dist-packages/h5py/__init__.py)
E Something went wrong while trying to lazy-import h5py. Please make sure that h5py is properly installed.
E If the problem persists, please file an issue at https://github.com/yt-project/yt/issues/new
/usr/lib/python3/dist-packages/h5py/__init__.py:26: ImportError
_________________ test_single_valid_with_missing_requirements __________________
tmp_path = PosixPath('/tmp/pytest-of-sbuild/pytest-1/test_single_valid_with_missing0')
@pytest.mark.usefixtures("valid_dataset_class_with_missing_requirements")
def test_single_valid_with_missing_requirements(tmp_path):
> with pytest.warns(
UserWarning,
match=(
"This dataset appears to be of type MockDataset, "
"but the following requirements are currently missing: mock_package_name\n"
"Please verify your installation."
),
):
E UserWarning: h5py is running against HDF5 2.2.0 when it was built against 2.1.0, this may cause problems
yt/tests/test_load_errors.py:294: UserWarning
=========================== short test summary info ============================
SKIPPED [2] yt/testing.py:1253: Missing required file WDMerger_hdf5_chk_1000/WDMerger_hdf5_chk_1000.hdf5
SKIPPED [1] yt/testing.py:1253: Missing required module xarray
SKIPPED [1] yt/testing.py:1253: Missing required file IsothermalCollapse/snap_505
SKIPPED [5] yt/testing.py:1253: Missing required file IsolatedGalaxy/galaxy0030/galaxy0030
SKIPPED [13] yt/testing.py:1253: Missing required module firefly
SKIPPED [1] yt/data_objects/tests/test_glue.py:15: missing requirement(s): glue, astropy
SKIPPED [3] yt/testing.py:1253: Missing required module astropy
SKIPPED [1] yt/testing.py:1253: Missing required module pandas
SKIPPED [1] yt/testing.py:1253: Missing required file GadgetDiskGalaxy/snapshot_200.hdf5
SKIPPED [2] yt/testing.py:1253: Missing required file TNGHalo/halo_59.hdf5
SKIPPED [2] yt/testing.py:1253: Missing required module miniball
SKIPPED [1] yt/testing.py:1253: Missing required file enzo_tiny_cosmology/DD0046/DD0046
SKIPPED [1] yt/testing.py:1253: See https://github.com/yt-project/yt/issues/3909
SKIPPED [3] yt/testing.py:1253: Missing required module f90nml
SKIPPED [1] yt/frontends/cf_radial/tests/test_cf_radial_pytest.py:36: missing requirement(s): xarray, netCDF4, pyart
SKIPPED [1] yt/testing.py:1253: Missing required file snapshot_033/snap_033.0.hdf5
SKIPPED [7] yt/testing.py:1253: Missing required file output_00080/info_00080.txt
SKIPPED [2] yt/testing.py:1253: Missing required file ramses_new_format/output_00002/info_00002.txt
SKIPPED [1] yt/testing.py:1253: Missing required file UnigridData/turb_vels.h5
SKIPPED [2] yt/testing.py:1253: Missing required file KeplerianRing/keplerian_ring_0020.hdf5
SKIPPED [2] yt/testing.py:1253: Missing required file EAGLE_6/eagle_0005.hdf5
SKIPPED [1] yt/testing.py:1253: Missing required file MagneticumCluster/snap_132
SKIPPED [2] yt/geometry/tests/test_geometries.py:27: cannot test this case with vanilla yt (requires cartopy) see https://github.com/yt-project/yt/issues/4182
SKIPPED [4] yt/tests/test_load_archive.py:31: missing requirement(s): ratarmount
SKIPPED [1] yt/tests/test_load_archive.py:96: missing requirement(s): ratarmount
SKIPPED [1] yt/tests/test_load_errors.py:201: Deprecation warnings are disabled
SKIPPED [4] yt/tests/test_load_sample.py:46: missing requirement(s): pandas, f90nml
SKIPPED [1] yt/tests/test_load_sample.py:113: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:130: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:145: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:152: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:157: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:164: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py:189: missing requirement(s): pandas
SKIPPED [1] yt/tests/test_load_sample.py: unconditional skip
SKIPPED [1] yt/tests/test_testing.py:12: https://github.com/yt-project/yt/issues/2533
SKIPPED [1] yt/tests/test_testing.py:27: https://github.com/yt-project/yt/issues/2533
SKIPPED [1] yt/testing.py:1253: Missing required file MOOSE_sample_data/out.e-s010
SKIPPED [3] yt/testing.py:1253: Missing required module cartopy
SKIPPED [1] yt/testing.py:1253: missing external executable(s): tex
SKIPPED [10] yt/testing.py:1253: Missing required module scipy
SKIPPED [23] yt/visualization/tests/test_image_comp_geo.py:20: missing requirement(s): cartopy, scipy
SKIPPED [1] yt/visualization/volume_rendering/tests/test_zbuff.py:54: Leads to memory alloc error on mipsel
FAILED yt/data_objects/tests/test_image_array.py::TestImageArray::test_image_array_hdf5
FAILED yt/data_objects/tests/test_io_geometry.py::test_preserve_geometric_properties
FAILED yt/data_objects/tests/test_io_geometry.py::test_default_to_cartesian
FAILED yt/data_objects/tests/test_profiles.py::TestBadProfiles::test_unequal_bin_field_profile
FAILED yt/data_objects/tests/test_profiles.py::TestBadProfiles::test_unequal_data_shape_profile
FAILED yt/data_objects/tests/test_time_series.py::test_init_fake_dataseries
FAILED yt/data_objects/tests/test_time_series.py::test_init_fake_dataseries2
FAILED yt/data_objects/tests/test_time_series.py::test_get_by_key - ImportErr...
FAILED yt/frontends/ytdata/tests/test_data_reload.py::test_save_as_data_unit_system
FAILED yt/geometry/tests/test_particle_octree.py::test_bitmap_save_load - Imp...
FAILED yt/tests/test_external_frontends.py::test_external_frontend - ImportEr...
FAILED yt/tests/test_load_errors.py::test_load_unidentified_data_dir - Import...
FAILED yt/tests/test_load_errors.py::test_load_unidentified_data_file - Impor...
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data - ImportError: ...
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[alpha-AlphaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[al-AlphaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[ph-AlphaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[beta-BetaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[BeTA-BetaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[b-BetaDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[mock-MockDataset]
FAILED yt/tests/test_load_errors.py::test_load_ambiguous_data_with_hint[MockDataset-MockDataset]
FAILED yt/tests/test_load_errors.py::test_all_invalid_with_missing_requirements
FAILED yt/tests/test_load_errors.py::test_single_valid_with_missing_requirements
====== 24 failed, 738 passed, 115 skipped, 2 xpassed in 259.21s (0:04:19) ======
E: pybuild pybuild:485: test: plugin distutils failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_yt/build; python3.14 -m pytest --confcutdir=.
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.13 3.14" --parallel=2 returned exit code 13
make: *** [debian/rules:25: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
--------------------------------------------------------------------------------
More information about the Debian-astro-maintainers
mailing list