[Python-modules-team] Bug#966463: openblas breaks scipy autopkgtest: tests/test_vq.py::TestKMean::test_krandinit Segmentation fault

Paul Gevers elbrus at debian.org
Tue Jul 28 20:14:57 BST 2020 

Source: openblas, scipy
Control: found -1 openblas/0.3.10+ds-1
Control: found -1 scipy/1.4.1-2
Severity: serious
Tags: sid bullseye
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update

Dear maintainer(s),

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

                       pass            fail
openblas               from testing    0.3.10+ds-1
scipy                  from testing    1.4.1-2
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 openblas 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=openblas

https://ci.debian.net/data/autopkgtest/testing/amd64/s/scipy/6418132/log.gz

=== Testing: python3.8 scipy.cluster ===
============================= test session starts
==============================
platform linux -- Python 3.8.5, pytest-4.6.11, py-1.8.1, pluggy-0.13.0
-- /usr/bin/python3.8
cachedir: .pytest_cache
rootdir: /tmp/autopkgtest-lxc.5e7uwcse/downtmp/autopkgtest_tmp
collecting ... collected 111 items

tests/test_hierarchy.py::TestLinkage::test_linkage_non_finite_elements_in_distance_matrix
PASSED [  0%]
tests/test_hierarchy.py::TestLinkage::test_linkage_empty_distance_matrix
PASSED [  1%]
tests/test_hierarchy.py::TestLinkage::test_linkage_tdist PASSED
[  2%]
tests/test_hierarchy.py::TestLinkage::test_linkage_X PASSED
[  3%]
tests/test_hierarchy.py::TestLinkage::test_compare_with_trivial PASSED
[  4%]
tests/test_hierarchy.py::TestLinkage::test_optimal_leaf_ordering PASSED
[  5%]
tests/test_hierarchy.py::TestLinkageTies::test_linkage_ties PASSED
[  6%]
tests/test_hierarchy.py::TestInconsistent::test_inconsistent_tdist
PASSED [  7%]
tests/test_hierarchy.py::TestCopheneticDistance::test_linkage_cophenet_tdist_Z
PASSED [  8%]
tests/test_hierarchy.py::TestCopheneticDistance::test_linkage_cophenet_tdist_Z_Y
PASSED [  9%]
tests/test_hierarchy.py::TestMLabLinkageConversion::test_mlab_linkage_conversion_empty
PASSED [  9%]
tests/test_hierarchy.py::TestMLabLinkageConversion::test_mlab_linkage_conversion_single_row
PASSED [ 10%]
tests/test_hierarchy.py::TestMLabLinkageConversion::test_mlab_linkage_conversion_multiple_rows
PASSED [ 11%]
tests/test_hierarchy.py::TestFcluster::test_fclusterdata PASSED
[ 12%]
tests/test_hierarchy.py::TestFcluster::test_fcluster PASSED
[ 13%]
tests/test_hierarchy.py::TestFcluster::test_fcluster_monocrit PASSED
[ 14%]
tests/test_hierarchy.py::TestLeaders::test_leaders_single PASSED
[ 15%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_1 PASSED
[ 16%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_2 PASSED
[ 17%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_3 PASSED
[ 18%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_4A PASSED
[ 18%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_4B PASSED
[ 19%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_4C PASSED
[ 20%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_5 PASSED
[ 21%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_6 PASSED
[ 22%]
tests/test_hierarchy.py::TestIsIsomorphic::test_is_isomorphic_7 PASSED
[ 23%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_various_size
PASSED [ 24%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_int_type
PASSED [ 25%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_empty
PASSED [ 26%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_4_and_up
PASSED [ 27%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_4_and_up_neg_index_left
PASSED [ 27%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_4_and_up_neg_index_right
PASSED [ 28%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_4_and_up_neg_dist
PASSED [ 29%]
tests/test_hierarchy.py::TestIsValidLinkage::test_is_valid_linkage_4_and_up_neg_counts
PASSED [ 30%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_int_type
PASSED [ 31%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_various_size
PASSED [ 32%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_empty
PASSED [ 33%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_4_and_up
PASSED [ 34%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_4_and_up_neg_index_left
PASSED [ 35%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_4_and_up_neg_index_right
PASSED [ 36%]
tests/test_hierarchy.py::TestIsValidInconsistent::test_is_valid_im_4_and_up_neg_dist
PASSED [ 36%]
tests/test_hierarchy.py::TestNumObsLinkage::test_num_obs_linkage_empty
PASSED [ 37%]
tests/test_hierarchy.py::TestNumObsLinkage::test_num_obs_linkage_1x4
PASSED [ 38%]
tests/test_hierarchy.py::TestNumObsLinkage::test_num_obs_linkage_2x4
PASSED [ 39%]
tests/test_hierarchy.py::TestNumObsLinkage::test_num_obs_linkage_4_and_up
PASSED [ 40%]
tests/test_hierarchy.py::TestLeavesList::test_leaves_list_1x4 PASSED
[ 41%]
tests/test_hierarchy.py::TestLeavesList::test_leaves_list_2x4 PASSED
[ 42%]
tests/test_hierarchy.py::TestLeavesList::test_leaves_list_Q PASSED
[ 43%]
tests/test_hierarchy.py::TestLeavesList::test_Q_subtree_pre_order PASSED
[ 44%]
tests/test_hierarchy.py::TestCorrespond::test_correspond_empty PASSED
[ 45%]
tests/test_hierarchy.py::TestCorrespond::test_correspond_2_and_up PASSED
[ 45%]
tests/test_hierarchy.py::TestCorrespond::test_correspond_4_and_up PASSED
[ 46%]
tests/test_hierarchy.py::TestCorrespond::test_correspond_4_and_up_2
PASSED [ 47%]
tests/test_hierarchy.py::TestCorrespond::test_num_obs_linkage_multi_matrix
PASSED [ 48%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_empty PASSED
[ 49%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_1x4 PASSED
[ 50%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_2x4_T PASSED
[ 51%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_2x4_F PASSED
[ 52%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_3x4_T PASSED
[ 53%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_3x4_F1
PASSED [ 54%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_3x4_F2
PASSED [ 54%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_3x4_F3
PASSED [ 55%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_tdist_linkage1
PASSED [ 56%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_tdist_linkage2
PASSED [ 57%]
tests/test_hierarchy.py::TestIsMonotonic::test_is_monotonic_Q_linkage
PASSED [ 58%]
tests/test_hierarchy.py::TestMaxDists::test_maxdists_empty_linkage
PASSED [ 59%]
tests/test_hierarchy.py::TestMaxDists::test_maxdists_one_cluster_linkage
PASSED [ 60%]
tests/test_hierarchy.py::TestMaxDists::test_maxdists_Q_linkage PASSED
[ 61%]
tests/test_hierarchy.py::TestMaxInconsts::test_maxinconsts_empty_linkage
PASSED [ 62%]
tests/test_hierarchy.py::TestMaxInconsts::test_maxinconsts_difrow_linkage
PASSED [ 63%]
tests/test_hierarchy.py::TestMaxInconsts::test_maxinconsts_one_cluster_linkage
PASSED [ 63%]
tests/test_hierarchy.py::TestMaxInconsts::test_maxinconsts_Q_linkage
PASSED [ 64%]
tests/test_hierarchy.py::TestMaxRStat::test_maxRstat_invalid_index
PASSED [ 65%]
tests/test_hierarchy.py::TestMaxRStat::test_maxRstat_empty_linkage
PASSED [ 66%]
tests/test_hierarchy.py::TestMaxRStat::test_maxRstat_difrow_linkage
PASSED [ 67%]
tests/test_hierarchy.py::TestMaxRStat::test_maxRstat_one_cluster_linkage
PASSED [ 68%]
tests/test_hierarchy.py::TestMaxRStat::test_maxRstat_Q_linkage PASSED
[ 69%]
tests/test_hierarchy.py::TestDendrogram::test_dendrogram_single_linkage_tdist
PASSED [ 70%]
tests/test_hierarchy.py::TestDendrogram::test_valid_orientation PASSED
[ 71%]
tests/test_hierarchy.py::TestDendrogram::test_dendrogram_plot SKIPPED
[ 72%]
tests/test_hierarchy.py::TestDendrogram::test_dendrogram_truncate_mode
SKIPPED [ 72%]
tests/test_hierarchy.py::TestDendrogram::test_dendrogram_colors PASSED
[ 73%]
tests/test_hierarchy.py::test_unsupported_uncondensed_distance_matrix_linkage_warning
PASSED [ 74%]
tests/test_hierarchy.py::test_euclidean_linkage_value_error PASSED
[ 75%]
tests/test_hierarchy.py::test_2x2_linkage PASSED
[ 76%]
tests/test_hierarchy.py::test_node_compare PASSED
[ 77%]
tests/test_hierarchy.py::test_cut_tree PASSED
[ 78%]
tests/test_hierarchy.py::test_optimal_leaf_ordering PASSED
[ 79%]
tests/test_hierarchy.py::test_Heap PASSED
[ 80%]
tests/test_vq.py::TestWhiten::test_whiten PASSED
[ 81%]
tests/test_vq.py::TestWhiten::test_whiten_zero_std PASSED
[ 81%]
tests/test_vq.py::TestWhiten::test_whiten_not_finite PASSED
[ 82%]
tests/test_vq.py::TestVq::test_py_vq PASSED
[ 83%]
tests/test_vq.py::TestVq::test_vq PASSED
[ 84%]
tests/test_vq.py::TestVq::test_vq_1d PASSED
[ 85%]
tests/test_vq.py::TestVq::test__vq_sametype PASSED
[ 86%]
tests/test_vq.py::TestVq::test__vq_invalid_type PASSED
[ 87%]
tests/test_vq.py::TestVq::test_vq_large_nfeat PASSED
[ 88%]
tests/test_vq.py::TestVq::test_vq_large_features PASSED
[ 89%]
tests/test_vq.py::TestKMean::test_large_features PASSED
[ 90%]
tests/test_vq.py::TestKMean::test_kmeans_simple PASSED
[ 90%]
tests/test_vq.py::TestKMean::test_kmeans_lost_cluster PASSED
[ 91%]
tests/test_vq.py::TestKMean::test_kmeans2_simple PASSED
[ 92%]
tests/test_vq.py::TestKMean::test_kmeans2_rank1 PASSED
[ 93%]
tests/test_vq.py::TestKMean::test_kmeans2_rank1_2 PASSED
[ 94%]
tests/test_vq.py::TestKMean::test_kmeans2_high_dim PASSED
[ 95%]
tests/test_vq.py::TestKMean::test_kmeans2_init PASSED
[ 96%]
tests/test_vq.py::TestKMean::test_krandinit Segmentation fault
autopkgtest [00:02:42]: test openblas: -----------------------]

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