Bug#1027460: scipy breaks scikit-learn autopkgtest: Segmentation fault

Paul Gevers elbrus at debian.org
Sat Dec 31 21:55:13 GMT 2022 

Source: scipy, scikit-learn
Control: found -1 scipy/1.8.1-18
Control: found -1 scikit-learn/1.1.2+dfsg-91
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

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

                        pass            fail
scipy                  from testing    1.8.1-18
scikit-learn           from testing    1.1.2+dfsg-91
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 of scipy to testing 
[1]. Due to the nature of this issue, I filed this bug report against 
both packages. Can you please investigate the situation and reassign the 
bug to the right package?

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=scipy

https://ci.debian.net/data/autopkgtest/testing/amd64/s/scikit-learn/29794749/log.gz

../../../../usr/lib/python3/dist-packages/sklearn/decomposition/tests/test_kernel_pca.py::test_kernel_pca_raise_not_fitted_error 
PASSED
../../../../usr/lib/python3/dist-packages/sklearn/decomposition/tests/test_kernel_pca.py::test_32_64_decomposition_shape 
PASSEDFatal Python error: Segmentation fault

Current thread 0x00007ff05b47d040 (most recent call first):
   File "<frozen os>", line 685 in __setitem__
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 195 in 
_update_current_test_var
   File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 178 in 
pytest_runtest_teardown
   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 131 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 "<frozen runpy>", line 88 in _run_code
   File "<frozen runpy>", line 198 in _run_module_as_main

Extension modules: sklearn.__check_build._check_build, 
numpy.core._multiarray_umath, numpy.core._multiarray_tests, 
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, 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, 
sklearn.utils.murmurhash, lz4._version, lz4.frame._frame, 
scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, 
scipy.spatial._voronoi, 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.spatial._distance_wrap, 
scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, 
scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 
scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, 
scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, 
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, 
numpy.linalg.lapack_lite, 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, 
scipy.interpolate._fitpack, scipy.interpolate.dfitpack, 
scipy.interpolate._bspl, scipy.interpolate._ppoly, 
scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, 
scipy.special.cython_special, scipy.stats._stats, beta_ufunc, 
scipy.stats._boost.beta_ufunc, binom_ufunc, 
scipy.stats._boost.binom_ufunc, nbinom_ufunc, 
scipy.stats._boost.nbinom_ufunc, hypergeom_ufunc, 
scipy.stats._boost.hypergeom_ufunc, scipy.stats._biasedurn, 
scipy.stats._hypotests_pythran, scipy.stats._statlib, scipy.stats._mvn, 
scipy.stats._sobol, scipy.stats._qmc_cy, 
scipy.stats._unuran.unuran_wrapper, sklearn.utils._openmp_helpers, 
sklearn.utils._logistic_sigmoid, sklearn.utils.sparsefuncs_fast, 
sklearn.preprocessing._csr_polynomial_expansion, 
sklearn.utils._vector_sentinel, 
sklearn.feature_extraction._hashing_fast, sklearn.utils._random, 
sklearn.datasets._svmlight_format_fast, scipy.io.matlab._mio_utils, 
scipy.io.matlab._streams, scipy.io.matlab._mio5_utils, 
matplotlib._c_internal_utils, PIL._imaging, matplotlib._path, 
kiwisolver, sklearn._loss._loss, sklearn.utils._readonly_array_wrapper, 
sklearn.utils._typedefs, sklearn.metrics._dist_metrics, 
sklearn.metrics.cluster._expected_mutual_info_fast, 
sklearn.utils._cython_blas, sklearn.utils._heap, sklearn.utils._sorting, 
sklearn.metrics._pairwise_distances_reduction, 
sklearn.metrics._pairwise_fast, sklearn.neighbors._partition_nodes, 
sklearn.neighbors._ball_tree, sklearn.neighbors._kd_tree, 
sklearn.decomposition._cdnmf_fast, sklearn.utils._seq_dataset, 
sklearn.utils.arrayfuncs, sklearn.linear_model._cd_fast, 
sklearn.utils._weight_vector, sklearn.linear_model._sgd_fast, 
sklearn.linear_model._sag_fast, sklearn.svm._libsvm, 
sklearn.svm._liblinear, sklearn.svm._libsvm_sparse, 
sklearn.decomposition._online_lda_fast, sklearn._isotonic, 
sklearn.manifold._utils, sklearn.tree._utils, sklearn.tree._tree, 
sklearn.tree._splitter, sklearn.tree._criterion, 
sklearn.neighbors._quad_tree, sklearn.manifold._barnes_hut_tsne, 
sklearn.cluster._k_means_common, sklearn.cluster._k_means_minibatch, 
sklearn.cluster._k_means_lloyd, sklearn.cluster._k_means_elkan, 
sklearn.utils._fast_dict, sklearn.cluster._hierarchical_fast, 
sklearn.cluster._dbscan_inner, scipy.cluster._vq, 
scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, 
sklearn.ensemble._gradient_boosting, 
sklearn.ensemble._hist_gradient_boosting.common, 
sklearn.ensemble._hist_gradient_boosting._gradient_boosting, 
sklearn.ensemble._hist_gradient_boosting._binning, 
sklearn.ensemble._hist_gradient_boosting._bitset, 
sklearn.ensemble._hist_gradient_boosting.splitting, 
sklearn.ensemble._hist_gradient_boosting.histogram, 
sklearn.ensemble._hist_gradient_boosting._predictor, 
sklearn.ensemble._hist_gradient_boosting.utils, 
scipy._lib._uarray._uarray, sklearn.svm._newrand (total: 170)
Segmentation fault
autopkgtest [22:15:36]: test python3

-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-science-maintainers/attachments/20221231/6eba3a99/attachment-0001.sig>

More information about the debian-science-maintainers mailing list