Your message dated Tue, 03 Jan 2023 10:53:54 +0000
with message-id <e1pceva-00eteh...@fasolo.debian.org>
and subject line Bug#1027460: fixed in scipy 1.8.1-19
has caused the Debian Bug report #1027460,
regarding scipy breaks scikit-learn autopkgtest: Segmentation fault
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1027460: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1027460
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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...@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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: scipy
Source-Version: 1.8.1-19
Done: Jochen Sprickerhof <jspri...@debian.org>
We believe that the bug you reported is fixed in the latest version of
scipy, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1027...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Jochen Sprickerhof <jspri...@debian.org> (supplier of updated scipy package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 03 Jan 2023 11:32:39 +0100
Source: scipy
Architecture: source
Version: 1.8.1-19
Distribution: unstable
Urgency: medium
Maintainer: Debian Python Team <team+pyt...@tracker.debian.org>
Changed-By: Jochen Sprickerhof <jspri...@debian.org>
Closes: 1027460
Changes:
scipy (1.8.1-19) unstable; urgency=medium
.
* Team upload.
* Add upstream patch to fix flapack (Closes: #1027460)
* Add upstream patch for numpy 1.24
* Use dh-sequence-*
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