Public bug reported: Imported from Debian bug http://bugs.debian.org/1101031:
Source: cctbx Version: 2024.10+ds2+~3.22.1+ds1-4 Severity: serious User: debian...@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 ** Affects: cctbx (Ubuntu) Importance: Undecided Status: New ** Affects: dials (Ubuntu) Importance: Undecided Status: New ** Affects: libobjcryst (Ubuntu) Importance: Undecided Status: New ** Affects: pyobjcryst (Ubuntu) Importance: Undecided Status: New ** Affects: cctbx (Debian) Importance: Undecided Status: New ** Tags: update-excuse ** Bug watch added: Debian Bug tracker #1101031 https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1101031 ** Changed in: cctbx (Debian) Remote watch: None => Debian Bug tracker #1101031 ** Tags added: update-excuse ** Also affects: libobjcryst (Ubuntu) Importance: Undecided Status: New ** Also affects: dials (Ubuntu) Importance: Undecided Status: New ** Also affects: pyobjcryst (Ubuntu) Importance: Undecided Status: New -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/2103848 Title: cctbx: autopkgtest regression in testing To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/cctbx/+bug/2103848/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
