Source: cctbx
Version: 2024.10+ds2+~3.22.1+ds1-4
Severity: serious
User: debian-ci@lists.debian.org
Usertags: regression

Hi Maintainer

Sometime between 2025-01-25 and 2025-02-01, cctbx's autopkgtest
regressed in testing [1]. I've copied what I hope is the relevant
part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/c/cctbx/testing/amd64/


266s autopkgtest [06:45:11]: test dxtbx: [-----------------------
267s Testing dxtbx with python3.13:
271s Fatal Python error: Segmentation fault
271s
271s Current thread 0x00007fc2049cf100 (most recent call first):
271s File "/usr/lib/python3/dist-packages/cctbx/sgtbx/__init__.py",
line 102 in __init__
271s File "/usr/lib/python3/dist-packages/cctbx/crystal/__init__.py",
line 75 in __init__
271s File "/tmp/autopkgtest-lxc.b4ym3mfk/downtmp/autopkgtest_tmp/tests/test_crystal_model_equivalence.py",
line 28 in <module>
271s File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py",
line 184 in exec_module
271s File "<frozen importlib._bootstrap>", line 935 in _load_unlocked
271s File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked 271s File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
271s File "<frozen importlib._bootstrap>", line 1387 in _gcd_import
271s File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module 271s File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line
587 in import_path
271s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 493
in importtestmodule
271s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 546
in _getobj
271s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 284 in obj 271s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 562
in _register_setup_module_fixture
271s File "/usr/lib/python3/dist-packages/_pytest/python.py", line 549
in collect
271s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389
in collect
271s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 341
in from_call
271s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391
in pytest_make_collect_report
271s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line
103 in _multicall
271s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line
120 in _hookexec
271s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513
in __call__
271s File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567
in collect_one_node
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 835
in _collect_one_node
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 970 in genitems
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 975 in genitems
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 809
in perform_collect
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 347
in pytest_collection
271s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line
103 in _multicall
271s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line
120 in _hookexec
271s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513
in __call__
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in _main 271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 283
in wrap_session
271s File "/usr/lib/python3/dist-packages/_pytest/main.py", line 330
in pytest_cmdline_main
271s File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line
103 in _multicall
271s File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line
120 in _hookexec
271s File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 513
in __call__
271s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 175 in main
271s File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py",
line 201 in console_main
271s File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9
in <module>
271s File "<frozen runpy>", line 88 in _run_code
271s File "<frozen runpy>", line 198 in _run_module_as_main
271s
271s Extension modules: _brotli, charset_normalizer.md, yaml._yaml, h5py._debian_h5py_serial._errors, h5py._debian_h5py_serial.defs, h5py._debian_h5py_serial._objects, h5py._debian_h5py_serial.h5, numpy._core._multiarray_umath, numpy.linalg._umath_linalg, h5py._debian_h5py_serial.utils, h5py._debian_h5py_serial.h5t, h5py._debian_h5py_serial.h5s, h5py._debian_h5py_serial.h5ac, h5py._debian_h5py_serial.h5p, h5py._debian_h5py_serial.h5r, h5py._debian_h5py_serial._proxy, h5py._debian_h5py_serial._conv, h5py._debian_h5py_serial.h5z, h5py._debian_h5py_serial.h5a, h5py._debian_h5py_serial.h5d, h5py._debian_h5py_serial.h5ds, h5py._debian_h5py_serial.h5g, h5py._debian_h5py_serial.h5i, h5py._debian_h5py_serial.h5o, h5py._debian_h5py_serial.h5f, h5py._debian_h5py_serial.h5fd, h5py._debian_h5py_serial.h5pl, h5py._debian_h5py_serial.h5l, h5py._debian_h5py_serial._selector,
h5py.atexit, h5py._errors, h5py.defs, h5py._objects, h5py.h5,
h5py.utils, h5py.h5t, h5py.h5s, h5py.h5ac, h5py.h5p, h5py.h5r,
h5py._proxy, h5py._conv, h5py.h5z, h5py.h5a, h5py.h5d, h5py.h5ds,
h5py.h5g, h5py.h5i, h5py.h5o, h5py.h5f, h5py.h5fd, h5py.h5pl,
h5py.h5l, h5py._selector, scipy._lib._ccallback_c,
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.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack,
scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack,
scipy.sparse.linalg._propack._dpropack,
scipy.sparse.linalg._propack._cpropack,
scipy.sparse.linalg._propack._zpropack, 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.spatial._ckdtree, scipy._lib.messagestream,
scipy.spatial._qhull, scipy.spatial._voronoi,
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, boost_python_meta_ext, boost_optional_ext, std_pair_ext, scitbx_array_family_flex_ext, scitbx_stl_set_ext,
scitbx_stl_vector_ext, scitbx_stl_map_ext, scitbx_random_ext, cctbx_array_family_flex_ext, cctbx_crystal_ext,
scitbx_array_family_shared_ext, cctbx_uctbx_ext, cctbx_sgtbx_ext, boost_rational_ext, cctbx_covariance_ext, cctbx_geometry_ext, scitbx_cubicle_neighbors_ext, dxtbx_format_image_ext,
dxtbx_imageset_ext, dxtbx_ext, _pycbf, dxtbx_model_ext, cctbx_eltbx_attenuation_coefficient_ext, iotbx_detectors_ext, iotbx_detectors_bruker_ext, omptbx_ext, dxtbx_masking_ext, dxtbx_format_nexus_ext, scitbx_math_ext, scitbx_linalg_ext, cctbx_orientation_ext, scipy.interpolate._fitpack,
scipy.interpolate._dfitpack, 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._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,
scipy.optimize._direct, scipy.interpolate._bspl,
scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, iotbx_cif_ext, cctbx_miller_ext, cctbx_asymmetric_map_ext,
cctbx_maptbx_ext, cctbx_adptbx_ext, scitbx_fftpack_ext,
cctbx_xray_ext, cctbx_eltbx_xray_scattering_ext, cctbx_math_ext, cctbx_eltbx_neutron_ext, scitbx_lbfgs_ext (total: 169)
271s Segmentation fault

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

I think I see the problem.

The test run on 2025-01-29 03:55:04 UTC [1] against numpy/1:2.2.2+ds-2
should have failed, and prevented numpy from migrating to testing, but debian/tests/control has all tests marked 'skip-not-installable'
(please don't do that), so the test result was considered 'neutral'
and numpy was eventually allowed to migrate.


[1] https://ci.debian.net/packages/c/cctbx/testing/amd64/
[2] https://salsa.debian.org/science-team/cctbx/-/blob/master/debian/tests/control?ref_type=heads

--- SoupGate-Win32 v1.05
* Origin: fsxNet Usenet Gateway (21:1/5)

This is a multi-part message in MIME format...

Your message dated Thu, 29 May 2025 17:05:15 +0000
with message-id <E1uKggt-0064sk-0v@fasolo.debian.org>
and subject line Bug#1101031: fixed in cctbx 2024.10+ds2+~3.22.1+ds1-5
has caused the Debian Bug report #1101031,
regarding cctbx: autopkgtest regression in testing
to be marked as done.

This means that you claim that the problem has been dealt with.
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Bug report if necessary, and/or fix the problem forthwith.

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--
1101031: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1101031
Debian Bug Tracking System
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