Bug#1101031: marked as done (cctbx: autopkgtest regression in testing)

Thu, 29 May 2025 10:07:30 -0700 

Your message dated Thu, 29 May 2025 17:05:15 +0000
with message-id <[email protected]>
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.
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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-- 
1101031: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1101031
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message --- 
Source: cctbx
Version: 2024.10+ds2+~3.22.1+ds1-4
Severity: serious
User: [email protected]
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

--- End Message ---
--- Begin Message --- 
Source: cctbx
Source-Version: 2024.10+ds2+~3.22.1+ds1-5
Done: Roland Mas <[email protected]>

We believe that the bug you reported is fixed in the latest version of
cctbx, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Roland Mas <[email protected]> (supplier of updated cctbx 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 [email protected])


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 1.8
Date: Thu, 29 May 2025 18:19:06 +0200
Source: cctbx
Architecture: source
Version: 2024.10+ds2+~3.22.1+ds1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers 
<[email protected]>
Changed-By: Roland Mas <[email protected]>
Closes: 1101031
Changes:
 cctbx (2024.10+ds2+~3.22.1+ds1-5) unstable; urgency=medium
 .
   [ Michael R. Crusoe ]
   * Team upload.
   * d/rules: use DEB_BUILD_OPTION_PARALLEL instead of nproc to respect
     Debian Policy 4.9.1.
 .
   [ Roland Mas ]
   * Backport upstream patch to fix: "autopkgtest regression in testing",
     thanks to Graham Inggs (Closes: #1101031).
   * Fix pip invocation to help with autopkgtests.
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cctbx_2024.10+ds2+~3.22.1+ds1-5.debian.tar.xz
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cctbx_2024.10+ds2+~3.22.1+ds1-5_amd64.buildinfo
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Files:
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cctbx_2024.10+ds2+~3.22.1+ds1-5.dsc
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cctbx_2024.10+ds2+~3.22.1+ds1-5.debian.tar.xz
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--- End Message ---
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