Package: src:python-dynasor Version: 2.1-2 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, this package failed to build. Below you will find the last part of the build log (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202606/ About the archive rebuild: The build was made on virtual machines from AWS, using sbuild and a reduced chroot with only build-essential packages. If you cannot reproduce the bug please contact me privately, as I am willing to provide ssh access to a virtual machine where the bug is fully reproducible. If this is really a bug in one of the build-depends, please use reassign and add an affects on src:python-dynasor, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] Notes ----- - If the file contains pickle data, then whatever object is stored in the pickle is returned. - If the file is a ``.npy`` file, then a single array is returned. - If the file is a ``.npz`` file, then a dictionary-like object is returned, containing ``{filename: array}`` key-value pairs, one for each file in the archive. - If the file is a ``.npz`` file, the returned value supports the context manager protocol in a similar fashion to the open function:: with load('foo.npz') as data: a = data['a'] The underlying file descriptor is closed when exiting the 'with' block. Examples -------- >>> import numpy as np Store data to disk, and load it again: >>> np.save('/tmp/123', np.array([[1, 2, 3], [4, 5, 6]])) >>> np.load('/tmp/123.npy') array([[1, 2, 3], [4, 5, 6]]) Store compressed data to disk, and load it again: >>> a=np.array([[1, 2, 3], [4, 5, 6]]) >>> b=np.array([1, 2]) >>> np.savez('/tmp/123.npz', a=a, b=b) >>> data = np.load('/tmp/123.npz') >>> data['a'] array([[1, 2, 3], [4, 5, 6]]) >>> data['b'] array([1, 2]) >>> data.close() Mem-map the stored array, and then access the second row directly from disk: >>> X = np.load('/tmp/123.npy', mmap_mode='r') >>> X[1, :] memmap([4, 5, 6]) """ if encoding not in ('ASCII', 'latin1', 'bytes'): # The 'encoding' value for pickle also affects what encoding # the serialized binary data of NumPy arrays is loaded # in. Pickle does not pass on the encoding information to # NumPy. The unpickling code in numpy._core.multiarray is # written to assume that unicode data appearing where binary # should be is in 'latin1'. 'bytes' is also safe, as is 'ASCII'. # # Other encoding values can corrupt binary data, and we # purposefully disallow them. For the same reason, the errors= # argument is not exposed, as values other than 'strict' # result can similarly silently corrupt numerical data. raise ValueError("encoding must be 'ASCII', 'latin1', or 'bytes'") pickle_kwargs = {'encoding': encoding, 'fix_imports': fix_imports} with contextlib.ExitStack() as stack: if hasattr(file, 'read'): fid = file own_fid = False else: fid = stack.enter_context(open(os.fspath(file), "rb")) own_fid = True # Code to distinguish from NumPy binary files and pickles. _ZIP_PREFIX = b'PK\x03\x04' _ZIP_SUFFIX = b'PK\x05\x06' # empty zip files start with this N = len(format.MAGIC_PREFIX) magic = fid.read(N) if not magic: > raise EOFError("No data left in file") E EOFError: No data left in file /usr/lib/python3/dist-packages/numpy/lib/_npyio_impl.py:463: EOFError ----------------------------- Captured stderr call ----------------------------- Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 94, in _get_next atoms = next(self._generator_xyz) StopIteration During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<string>", line 1, in <module> import sys; from multiprocessing.forkserver import main; main(12, 13, ['__main__'], sys_argv=sys.argv[1:], **{'sys_path': ['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/scripts', '/<<PKGBUILDDIR>>/debian/tmp/usr/lib/python3.14/dist-packages', '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build', '/usr/lib/python314.zip', '/usr/lib/python3.14', '/usr/lib/python3.14/lib-dynload', '/usr/local/lib/python3.14/dist-packages', '/usr/lib/python3/dist-packages', '/usr/lib/python3.14/dist-packages'], 'main_path': '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/scripts/dynasor', 'authkey_r': 15}) ~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 230, in main spawn.import_main_path(main_path) ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/spawn.py", line 307, in import_main_path _fixup_main_from_path(main_path) ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/spawn.py", line 297, in _fixup_main_from_path main_content = runpy.run_path(main_path, run_name="__mp_main__") File "<frozen runpy>", line 294, in run_path File "<frozen runpy>", line 98, in _run_module_code File "<frozen runpy>", line 88, in _run_code File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/scripts/dynasor", line 3, in <module> main() ~~~~^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/cli/main.py", line 176, in main traj = Trajectory(args.trajectory, trajectory_format=args.trajectory_format, ...<4 lines>... frame_step=args.step, ) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/trajectory.py", line 105, in __init__ frame0 = next(self._reader_obj) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 121, in __next__ self._get_next() ~~~~~~~~~~~~~~^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 98, in _get_next raise StopIteration StopIteration Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 94, in _get_next atoms = next(self._generator_xyz) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 26, in iread buff.append(ex.submit(chunk_to_atoms, chunk)) ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.14/concurrent/futures/process.py", line 816, in submit self._adjust_process_count() ~~~~~~~~~~~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3.14/concurrent/futures/process.py", line 775, in _adjust_process_count self._spawn_process() ~~~~~~~~~~~~~~~~~~~^^ File "/usr/lib/python3.14/concurrent/futures/process.py", line 793, in _spawn_process p.start() ~~~~~~~^^ File "/usr/lib/python3.14/multiprocessing/process.py", line 121, in start self._popen = self._Popen(self) ~~~~~~~~~~~^^^^^^ File "/usr/lib/python3.14/multiprocessing/context.py", line 306, in _Popen return Popen(process_obj) File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 35, in __init__ super().__init__(process_obj) ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/popen_fork.py", line 20, in __init__ self._launch(process_obj) ~~~~~~~~~~~~^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/popen_forkserver.py", line 51, in _launch self.sentinel, w = forkserver.connect_to_new_process(self._fds) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/forkserver.py", line 106, in connect_to_new_process connection.answer_challenge( ~~~~~~~~~~~~~~~~~~~~~~~~~~~^ wrapped_client, self._forkserver_authkey) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.14/multiprocessing/connection.py", line 995, in answer_challenge message = connection.recv_bytes(256) # reject large message File "/usr/lib/python3.14/multiprocessing/connection.py", line 226, in recv_bytes buf = self._recv_bytes(maxlength) File "/usr/lib/python3.14/multiprocessing/connection.py", line 451, in _recv_bytes buf = self._recv(4) File "/usr/lib/python3.14/multiprocessing/connection.py", line 416, in _recv chunk = read(handle, to_read) ConnectionResetError: [Errno 104] Connection reset by peer During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/scripts/dynasor", line 3, in <module> main() ~~~~^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/cli/main.py", line 176, in main traj = Trajectory(args.trajectory, trajectory_format=args.trajectory_format, ...<4 lines>... frame_step=args.step, ) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/trajectory.py", line 105, in __init__ frame0 = next(self._reader_obj) File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 121, in __next__ self._get_next() ~~~~~~~~~~~~~~^^ File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build/dynasor/trajectory/extxyz_trajectory_reader.py", line 98, in _get_next raise StopIteration StopIteration =============================== warnings summary =============================== .pybuild/cpython3_3.14/build/tests/test_trajectory_and_window_iterator.py::test_trajectory_with_mdanalysis_reader_xtc .pybuild/cpython3_3.14/build/tests/test_trajectory_frame.py::test_read_indices_from_trajectory .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_only_from_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_matching_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_not_matching_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_stopiteration_of_closed_file /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:1916: UserWarning: there is no reference attributes in this universe to guess types from warnings.warn(str(e)) .pybuild/cpython3_3.14/build/tests/test_trajectory_and_window_iterator.py::test_trajectory_with_mdanalysis_reader_xtc .pybuild/cpython3_3.14/build/tests/test_trajectory_frame.py::test_read_indices_from_trajectory .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_only_from_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_matching_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_not_matching_traj .pybuild/cpython3_3.14/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_stopiteration_of_closed_file /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:1916: UserWarning: there is no reference attributes (elements, types, or names) in this universe to guess mass from warnings.warn(str(e)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html =========================== short test summary info ============================ FAILED tests/test_cli.py::test_dynasor_CLI - EOFError: No data left in file ===== 1 failed, 132 passed, 1 deselected, 12 warnings in 91.65s (0:01:31) ====== E: pybuild pybuild:485: test: plugin pyproject failed with: exit code=1: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14/build; python3.14 -m pytest -k 'not test_integration_static_structure_factor' I: pybuild base:385: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13/build; python3.13 -m pytest -k 'not test_integration_static_structure_factor' ============================= test session starts ============================== platform linux -- Python 3.13.12, pytest-9.0.3, pluggy-1.6.0 rootdir: /<<PKGBUILDDIR>> plugins: typeguard-4.4.4 collected 134 items / 1 deselected / 133 selected tests/filon/test_filon.py ... [ 2%] tests/test_SED.py ... [ 4%] tests/test_average_independent_samples.py .. [ 6%] tests/test_cli.py . [ 6%] tests/test_dho.py .... [ 9%] tests/test_dynasor_API.py ...... [ 14%] tests/test_integration.py . [ 15%] tests/test_lattice.py .. [ 16%] tests/test_logging.py . [ 17%] tests/test_normalization.py .. [ 18%] tests/test_numba.py . [ 19%] tests/test_parse_gromacs_index_file.py ... [ 21%] tests/test_qpoints.py ...... [ 26%] tests/test_regression_vs_old_cmdline_results.py . [ 27%] tests/test_sample_class.py ........... [ 35%] tests/test_spherical_average.py ..... [ 39%] tests/test_time_averager.py . [ 39%] tests/test_tools.py ..... [ 43%] tests/test_trajectory_and_window_iterator.py ............ [ 52%] tests/test_trajectory_frame.py ... [ 54%] tests/test_units.py . [ 55%] tests/test_utils.py . [ 56%] tests/test_weighting.py .............................. [ 78%] tests/test_weights.py .. [ 80%] tests/trajectory_reader/test_ase_trajectory_reader.py ....... [ 85%] tests/trajectory_reader/test_extxyz_trajectory_reader.py ....... [ 90%] tests/trajectory_reader/test_lammps_trajectory_reader.py ...... [ 95%] tests/trajectory_reader/test_mdanalysis_trajectory_reader.py ...... [100%] =============================== warnings summary =============================== .pybuild/cpython3_3.13/build/tests/test_dynasor_API.py: 10 warnings .pybuild/cpython3_3.13/build/tests/test_trajectory_and_window_iterator.py: 12 warnings .pybuild/cpython3_3.13/build/tests/test_trajectory_frame.py: 2 warnings /usr/lib/python3.13/multiprocessing/popen_fork.py:67: DeprecationWarning: This process (pid=463) is multi-threaded, use of fork() may lead to deadlocks in the child. self.pid = os.fork() .pybuild/cpython3_3.13/build/tests/test_trajectory_and_window_iterator.py::test_trajectory_with_mdanalysis_reader_xtc .pybuild/cpython3_3.13/build/tests/test_trajectory_frame.py::test_read_indices_from_trajectory .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_only_from_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_matching_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_not_matching_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_stopiteration_of_closed_file /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:1916: UserWarning: there is no reference attributes in this universe to guess types from warnings.warn(str(e)) .pybuild/cpython3_3.13/build/tests/test_trajectory_and_window_iterator.py::test_trajectory_with_mdanalysis_reader_xtc .pybuild/cpython3_3.13/build/tests/test_trajectory_frame.py::test_read_indices_from_trajectory .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_only_from_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_matching_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_units_from_user_not_matching_traj .pybuild/cpython3_3.13/build/tests/trajectory_reader/test_mdanalysis_trajectory_reader.py::test_stopiteration_of_closed_file /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:1916: UserWarning: there is no reference attributes (elements, types, or names) in this universe to guess mass from warnings.warn(str(e)) -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ========== 133 passed, 1 deselected, 36 warnings in 101.80s (0:01:41) ========== dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" --parallel=2 returned exit code 13 make: *** [debian/rules:6: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2 --------------------------------------------------------------------------------
