Bug#1023222: python-xarray: autopkgtest regression on s390x: segmentation fault

Paul Gevers elbrus at debian.org
Mon Oct 31 19:52:14 GMT 2022 

Source: python-xarray
Version: 2022.10.0-1
Severity: serious
User: debian-ci at lists.debian.org
Usertags: regression

Dear maintainer(s),

With a recent upload of python-xarray the autopkgtest of python-xarray 
fails in testing on s390x when that autopkgtest is run with the binary 
packages of python-xarray from unstable. It passes when run with only 
packages from testing. In tabular form:

                        pass            fail
python-xarray          from testing    2022.10.0-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration to testing [1]. Can 
you please investigate the situation and fix it?

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=python-xarray

https://ci.debian.net/data/autopkgtest/testing/s390x/p/python-xarray/27672266/log.gz

[ 90%]
tests/test_sparse.py::test_variable_property[nbytes] PASSED 
[ 90%]
tests/test_sparse.py::test_variable_property[ndim] PASSED 
[ 90%]
tests/test_sparse.py::test_variable_property[values] XFAIL (Coercion...) 
[ 90%]
tests/test_sparse.py::test_variable_method[obj.all(*(), **{})-False] 
Fatal Python error: Segmentation fault

Current thread 0x000003ff91575040 (most recent call first):
   File "/usr/lib/python3/dist-packages/sparse/_coo/core.py", line 1562 
in _grouped_reduce
   File "/usr/lib/python3/dist-packages/sparse/_coo/core.py", line 687 
in _reduce_calc
   File "/usr/lib/python3/dist-packages/sparse/_sparse_array.py", line 
360 in reduce
   File "/usr/lib/python3/dist-packages/sparse/_sparse_array.py", line 
278 in _reduce
   File "/usr/lib/python3/dist-packages/sparse/_sparse_array.py", line 
307 in __array_ufunc__
   File "/usr/lib/python3/dist-packages/sparse/_sparse_array.py", line 
490 in all
   File "/usr/lib/python3/dist-packages/sparse/_sparse_array.py", line 
268 in __array_function__
   File "<__array_function__ internals>", line 5 in all
   File "/usr/lib/python3/dist-packages/xarray/core/variable.py", line 
1901 in reduce
   File "/usr/lib/python3/dist-packages/xarray/core/common.py", line 73 
in wrapped_func
   File "/usr/lib/python3/dist-packages/xarray/tests/test_sparse.py", 
line 69 in __call__
   File "/usr/lib/python3/dist-packages/xarray/tests/test_sparse.py", 
line 231 in test_variable_method
   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 192 in 
pytest_pyfunc_call
   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in 
_multicall
   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in 
_hookexec
   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in 
__call__
   File "/usr/lib/python3/dist-packages/_pytest/python.py", line 1761 in 
runtest
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 166 in 
pytest_runtest_call
   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in 
_multicall
   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in 
_hookexec
   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in 
__call__
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 259 in 
<lambda>
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 338 in 
from_call
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 258 in 
call_runtest_hook
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 219 in 
call_and_report
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 130 in 
runtestprotocol
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 111 in 
pytest_runtest_protocol
   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in 
_multicall
   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in 
_hookexec
   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in 
__call__
   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347 in 
pytest_runtestloop
   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in 
_multicall
   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in 
_hookexec
   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in 
__call__
   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 322 in _main
   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 268 in 
wrap_session
   File "/usr/lib/python3/dist-packages/_pytest/main.py", line 315 in 
pytest_cmdline_main
   File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 39 in 
_multicall
   File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 80 in 
_hookexec
   File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 265 in 
__call__
   File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", 
line 164 in main
   File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", 
line 187 in console_main
   File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 5 in 
<module>
   File "/usr/lib/python3.10/runpy.py", line 86 in _run_code
   File "/usr/lib/python3.10/runpy.py", line 196 in _run_module_as_main

Extension modules: numpy.core._multiarray_umath, 
numpy.core._multiarray_tests, numpy.linalg.lapack_lite, 
numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, 
numpy.random._common, numpy.random.bit_generator, 
numpy.random._bounded_integers, numpy.random._mt19937, 
numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, 
numpy.random._sfc64, numpy.random._generator, 
pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, 
pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.nattype, 
pandas._libs.tslibs.timezones, pandas._libs.tslibs.ccalendar, 
pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.strptime, 
pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, 
pandas._libs.tslibs.timestamps, pandas._libs.properties, 
pandas._libs.tslibs.offsets, pandas._libs.tslibs.parsing, 
pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, 
pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, 
pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, 
pandas._libs.interval, pandas._libs.tslib, pandas._libs.lib, 
pandas._libs.hashing, pandas._libs.ops, bottleneck.reduce, 
bottleneck.nonreduce, bottleneck.nonreduce_axis, bottleneck.move, 
pandas._libs.arrays, pandas._libs.index, pandas._libs.join, 
pandas._libs.sparse, pandas._libs.reduction, pandas._libs.indexing, 
pandas._libs.internals, pandas._libs.writers, 
pandas._libs.window.aggregations, pandas._libs.window.indexers, 
pandas._libs.reshape, pandas._libs.groupby, pandas._libs.parsers, 
pandas._libs.json, pandas._libs.testing, yaml._yaml, 
markupsafe._speedups, lz4._version, lz4.frame._frame, 
numba.core.typeconv._typeconv, numba._helperlib, numba._dynfunc, 
numba._dispatcher, numba.core.runtime._nrt_python, 
numba.np.ufunc._internal, numba.experimental.jitclass._box, 
scipy._lib._ccallback_c, scipy.sparse._sparsetools, 
scipy.sparse._csparsetools, scipy.sparse.csgraph._tools, 
scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, 
scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, 
scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, 
scipy._lib._uarray._uarray, scipy.special._ufuncs_cxx, 
scipy.special._ufuncs, scipy.special._specfun, scipy.linalg._fblas, 
scipy.linalg._flapack, scipy.linalg._cythonized_array_utils, 
scipy.linalg._flinalg, scipy.linalg._solve_toeplitz, 
scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, 
scipy.linalg.cython_lapack, scipy.linalg._decomp_update, 
scipy.special._comb, scipy.special._ellip_harm_2, 
scipy.fftpack.convolve, cftime._cftime, netCDF4._netCDF4, 
scipy.io.matlab._mio_utils, scipy.io.matlab._streams, 
scipy.io.matlab._mio5_utils, matplotlib._c_internal_utils, PIL._imaging, 
matplotlib._path, kiwisolver, rasterio._version, rasterio._err, 
rasterio._filepath, rasterio._env, rasterio._transform, rasterio._base, 
rasterio.crs, rasterio._features, rasterio._warp, rasterio._io, 
matplotlib._image, scipy.interpolate._fitpack, 
scipy.interpolate.dfitpack, scipy.interpolate._bspl, 
scipy.interpolate._ppoly, scipy.spatial._ckdtree, 
scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, 
scipy.spatial._distance_wrap, scipy.spatial._hausdorff, 
scipy.spatial.transform._rotation, scipy.interpolate.interpnd, 
scipy.interpolate._rbfinterp_pythran, 
scipy.sparse.linalg._isolve._iterative, 
scipy.sparse.linalg._dsolve._superlu, 
scipy.sparse.linalg._eigen.arpack._arpack, scipy.optimize._minpack2, 
scipy.optimize._group_columns, scipy.optimize._trlib._trlib, 
scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, 
scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, 
scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, 
scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, 
scipy.optimize._highs._highs_wrapper, 
scipy.optimize._highs.cython.src._highs_constants, 
scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, 
scipy.optimize._bglu_dense, scipy.optimize._lsap_module, 
scipy.integrate._odepack, scipy.integrate._quadpack, 
scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda 
(total: 156)
bash: line 1:  6460 Segmentation fault      $py -m pytest -v --pyargs xarray
autopkgtest [16:26:52]: test command1

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