[Debian-pan-maintainers] Bug#1122490: tomoscan: FTBFS: Fatal Python error: Aborted
Santiago Vila
sanvila at debian.org
Wed Dec 10 20:41:30 GMT 2025
Package: src:tomoscan
Version: 2.3.1-2
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/202512/
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:tomoscan, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild
dh_auto_clean -O--buildsystem=pybuild
dh_autoreconf_clean -O--buildsystem=pybuild
dh_clean -O--buildsystem=pybuild
debian/rules binary
dh binary --buildsystem=pybuild
dh_update_autotools_config -O--buildsystem=pybuild
dh_autoreconf -O--buildsystem=pybuild
dh_auto_configure -O--buildsystem=pybuild
dh_auto_build -O--buildsystem=pybuild
I: pybuild plugin_pyproject:131: Building wheel for python3.14 with "build" module
I: pybuild base:317: python3.14 -m build --skip-dependency-check --no-isolation --wheel --outdir /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_tomoscan
* Building wheel...
/usr/lib/python3/dist-packages/setuptools/config/_apply_pyprojecttoml.py:82: SetuptoolsDeprecationWarning: `project.license` as a TOML table is deprecated
[... snipped ...]
adding 'build/lib/tomoscan/utils/__init__.py'
adding 'build/lib/tomoscan/utils/decorator.py'
adding 'build/lib/tomoscan/utils/geometry.py'
adding 'build/lib/tomoscan/utils/hdf5.py'
adding 'build/lib/tomoscan/utils/io.py'
adding 'build/lib/tomoscan/utils/volume.py'
adding 'build/lib/tomoscan/utils/drac/__init__.py'
adding 'build/lib/tomoscan/utils/drac/mapper.py'
adding 'build/lib/tomoscan/utils/drac/recons_vol_mapping.py'
adding 'doc/conf.py'
adding 'snippets/test_sinogram.py'
adding 'tomoscan/_CoordinateSystem.py'
adding 'tomoscan/__init__.py'
adding 'tomoscan/factory.py'
adding 'tomoscan/framereducerbase.py'
adding 'tomoscan/identifier.py'
adding 'tomoscan/io.py'
adding 'tomoscan/progress.py'
adding 'tomoscan/scanbase.py'
adding 'tomoscan/scanfactory.py'
adding 'tomoscan/serie.py'
adding 'tomoscan/series.py'
adding 'tomoscan/source.py'
adding 'tomoscan/test.py'
adding 'tomoscan/tomoobject.py'
adding 'tomoscan/validator.py'
adding 'tomoscan/version.py'
adding 'tomoscan/volumebase.py'
adding 'tomoscan/esrf/__init__.py'
adding 'tomoscan/esrf/edfscan.py'
adding 'tomoscan/esrf/hdf5scan.py'
adding 'tomoscan/esrf/mock.py'
adding 'tomoscan/esrf/utils.py'
adding 'tomoscan/esrf/identifier/__init__.py'
adding 'tomoscan/esrf/identifier/edfidentifier.py'
adding 'tomoscan/esrf/identifier/folderidentifier.py'
adding 'tomoscan/esrf/identifier/hdf5Identifier.py'
adding 'tomoscan/esrf/identifier/jp2kidentifier.py'
adding 'tomoscan/esrf/identifier/rawidentifier.py'
adding 'tomoscan/esrf/identifier/tiffidentifier.py'
adding 'tomoscan/esrf/identifier/url_utils.py'
adding 'tomoscan/esrf/identifier/tests/test_edfidentifier.py'
adding 'tomoscan/esrf/identifier/tests/test_hdf5identifier.py'
adding 'tomoscan/esrf/identifier/tests/test_rawidentifier.py'
adding 'tomoscan/esrf/scan/__init__.py'
adding 'tomoscan/esrf/scan/edfscan.py'
adding 'tomoscan/esrf/scan/fscan.py'
adding 'tomoscan/esrf/scan/fscan_scantypes.py'
adding 'tomoscan/esrf/scan/h5utils.py'
adding 'tomoscan/esrf/scan/hdf5scan.py'
adding 'tomoscan/esrf/scan/mock.py'
adding 'tomoscan/esrf/scan/nxtomoscan.py'
adding 'tomoscan/esrf/scan/utils.py'
adding 'tomoscan/esrf/scan/framereducer/__init__.py'
adding 'tomoscan/esrf/scan/framereducer/edfframereducer.py'
adding 'tomoscan/esrf/scan/framereducer/hdf5framereducer.py'
adding 'tomoscan/esrf/scan/framereducer/tests/test_edfframereducer.py'
adding 'tomoscan/esrf/scan/framereducer/tests/test_hdf5framereducer.py'
adding 'tomoscan/esrf/scan/tests/test_edfscan.py'
adding 'tomoscan/esrf/scan/tests/test_fscan.py'
adding 'tomoscan/esrf/scan/tests/test_mock.py'
adding 'tomoscan/esrf/scan/tests/test_nxtomoscan.py'
adding 'tomoscan/esrf/scan/tests/test_nxtomoscan_mcstas.py'
adding 'tomoscan/esrf/scan/tests/test_utils.py'
adding 'tomoscan/esrf/volume/__init__.py'
adding 'tomoscan/esrf/volume/edfvolume.py'
adding 'tomoscan/esrf/volume/hdf5volume.py'
adding 'tomoscan/esrf/volume/jp2kvolume.py'
adding 'tomoscan/esrf/volume/mock.py'
adding 'tomoscan/esrf/volume/rawvolume.py'
adding 'tomoscan/esrf/volume/singleframebase.py'
adding 'tomoscan/esrf/volume/tiffvolume.py'
adding 'tomoscan/esrf/volume/utils.py'
adding 'tomoscan/esrf/volume/helpers/__init__.py'
adding 'tomoscan/esrf/volume/helpers/single_frame_saver.py'
adding 'tomoscan/esrf/volume/helpers/test/test_single_frame_saver.py'
adding 'tomoscan/esrf/volume/tests/test_edfvolume.py'
adding 'tomoscan/esrf/volume/tests/test_hdf5volume.py'
adding 'tomoscan/esrf/volume/tests/test_jp2kvolume.py'
adding 'tomoscan/esrf/volume/tests/test_raw_volume.py'
adding 'tomoscan/esrf/volume/tests/test_single_frame_volume.py'
adding 'tomoscan/esrf/volume/tests/test_tiffvolume.py'
adding 'tomoscan/esrf/volume/tests/test_volume_esrf_utils.py'
adding 'tomoscan/framereducer/ReduceFrameSaver.py'
adding 'tomoscan/framereducer/__init__.py'
adding 'tomoscan/framereducer/framereducerbase.py'
adding 'tomoscan/framereducer/method.py'
adding 'tomoscan/framereducer/reducedframesinfos.py'
adding 'tomoscan/framereducer/target.py'
adding 'tomoscan/framereducer/tests/test_ReduceFrameSaver.py'
adding 'tomoscan/framereducer/tests/test_framereducerbase.py'
adding 'tomoscan/nexus/__init__.py'
adding 'tomoscan/nexus/paths/__init__.py'
adding 'tomoscan/nexus/paths/nxdetector.py'
adding 'tomoscan/nexus/paths/nxinstrument.py'
adding 'tomoscan/nexus/paths/nxmonitor.py'
adding 'tomoscan/nexus/paths/nxsample.py'
adding 'tomoscan/nexus/paths/nxsource.py'
adding 'tomoscan/nexus/paths/nxtomo.py'
adding 'tomoscan/nexus/paths/nxtransformations.py'
adding 'tomoscan/nexus/utils/__init__.py'
adding 'tomoscan/normalization/__init__.py'
adding 'tomoscan/normalization/calculationmode.py'
adding 'tomoscan/normalization/datasetscope.py'
adding 'tomoscan/normalization/method.py'
adding 'tomoscan/normalization/methodmode.py'
adding 'tomoscan/normalization/normalization.py'
adding 'tomoscan/normalization/tests/test_normalization.py'
adding 'tomoscan/tests/__init__.py'
adding 'tomoscan/tests/conftest.py'
adding 'tomoscan/tests/datasets.py'
adding 'tomoscan/tests/test_drac_utils.py'
adding 'tomoscan/tests/test_factory.py'
adding 'tomoscan/tests/test_hdf5_utils.py'
adding 'tomoscan/tests/test_io.py'
adding 'tomoscan/tests/test_progress.py'
adding 'tomoscan/tests/test_scanbase.py'
adding 'tomoscan/tests/test_serie.py'
adding 'tomoscan/tests/test_tomoobject.py'
adding 'tomoscan/tests/test_utils.py'
adding 'tomoscan/tests/test_validator.py'
adding 'tomoscan/tests/test_version.py'
adding 'tomoscan/tests/test_volume_base.py'
adding 'tomoscan/tests/test_volume_utils.py'
adding 'tomoscan/tests/utils.py'
adding 'tomoscan/utils/__init__.py'
adding 'tomoscan/utils/decorator.py'
adding 'tomoscan/utils/geometry.py'
adding 'tomoscan/utils/hdf5.py'
adding 'tomoscan/utils/io.py'
adding 'tomoscan/utils/volume.py'
adding 'tomoscan/utils/drac/__init__.py'
adding 'tomoscan/utils/drac/mapper.py'
adding 'tomoscan/utils/drac/recons_vol_mapping.py'
adding 'tomoscan-2.3.1.dist-info/licenses/LICENSE'
adding 'tomoscan-2.3.1.dist-info/METADATA'
adding 'tomoscan-2.3.1.dist-info/WHEEL'
adding 'tomoscan-2.3.1.dist-info/entry_points.txt'
adding 'tomoscan-2.3.1.dist-info/top_level.txt'
adding 'tomoscan-2.3.1.dist-info/RECORD'
removing build/bdist.linux-x86_64/wheel
Successfully built tomoscan-2.3.1-py3-none-any.whl
I: pybuild plugin_pyproject:155: Unpacking wheel built for python3.13 with "installer" module
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_tomoscan/build; python3.14 -m pytest
Fatal Python error: Aborted
Current thread 0x00007f2463f96200 [python3.14] (most recent call first):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_tomoscan/build/snippets/test_sinogram.py", line 119 in <module>
File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 186 in exec_module
File "<frozen importlib._bootstrap>", line 938 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1342 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1371 in _find_and_load
File "<frozen importlib._bootstrap>", line 1398 in _gcd_import
File "/usr/lib/python3.14/importlib/__init__.py", line 88 in import_module
File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 498 in importtestmodule
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 551 in _getobj
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 280 in obj
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 567 in _register_setup_module_fixture
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 554 in collect
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 344 in from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 839 in _collect_one_node
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 974 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 979 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 979 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 813 in perform_collect
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 353 in pytest_collection
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 342 in _main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 289 in wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Current thread's C stack trace (most recent call first):
Binary file "python3.14", at _Py_DumpStack+0x4a [0x472522]
Binary file "python3.14" [0x4fc6c7]
Binary file "/usr/lib/x86_64-linux-gnu/libc.so.6", at +0x40590 [0x7f2463c40590]
Binary file "/usr/lib/x86_64-linux-gnu/libc.so.6", at +0x9569c [0x7f2463c9569c]
Binary file "/usr/lib/x86_64-linux-gnu/libc.so.6", at gsignal+0x12 [0x7f2463c40462]
Binary file "/usr/lib/x86_64-linux-gnu/libc.so.6", at abort+0x22 [0x7f2463c284ac]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Core.so.5", at +0x92514 [0x7f245c692514]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Gui.so.5", at _ZN22QGuiApplicationPrivate25createPlatformIntegrationEv+0x17bf [0x7f245933d31f]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Gui.so.5", at _ZN22QGuiApplicationPrivate21createEventDispatcherEv+0x38 [0x7f245933d858]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Core.so.5", at _ZN23QCoreApplicationPrivate4initEv+0x8f5 [0x7f245c8f05c5]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Gui.so.5", at _ZN22QGuiApplicationPrivate4initEv+0x2e [0x7f245934090e]
Binary file "/usr/lib/x86_64-linux-gnu/libQt5Widgets.so.5", at _ZN19QApplicationPrivate4initEv+0xd [0x7f2458168a5d]
Binary file "/usr/lib/python3/dist-packages/PyQt5/QtWidgets.abi3.so", at +0x3b6b8d [0x7f2458bb6b8d]
Binary file "/usr/lib/python3/dist-packages/PyQt5/QtWidgets.abi3.so", at +0x3b6c69 [0x7f2458bb6c69]
Binary file "/usr/lib/python3/dist-packages/PyQt5/sip.cpython-314-x86_64-linux-gnu.so", at +0x1c6f1 [0x7f245cbf36f1]
Binary file "python3.14", at _PyObject_MakeTpCall+0x282 [0x526f92]
Binary file "python3.14", at _PyEval_EvalFrameDefault+0x3607 [0x548757]
Binary file "python3.14", at PyEval_EvalCode+0xf1 [0x53ffa1]
Binary file "python3.14" [0x696957]
Binary file "python3.14", at _PyEval_EvalFrameDefault+0x3421 [0x548571]
Binary file "python3.14" [0x583944]
Binary file "python3.14" [0x58e15e]
Binary file "python3.14", at _PyObject_GenericGetAttrWithDict+0xfc [0x56c80c]
Binary file "python3.14", at PyObject_GetAttr+0x42 [0x52dbc2]
Binary file "python3.14", at _PyEval_EvalFrameDefault+0x9e9 [0x545b39]
Binary file "python3.14" [0x583944]
Binary file "python3.14" [0x52e8be]
Binary file "python3.14" [0x626aff]
Binary file "python3.14", at _PyObject_MakeTpCall+0x36c [0x52707c]
Binary file "python3.14", at _PyEval_EvalFrameDefault+0x63eb [0x54b53b]
Binary file "python3.14" [0x5c1080]
Binary file "python3.14" [0x5bdf30]
<truncated rest of calls>
Extension modules: h5py._debian_h5py_serial._errors, h5py._d [too-long-redacted] q, tornado.speedups (total: 77)
Aborted
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=134: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.14_tomoscan/build; python3.14 -m pytest
I: pybuild base:317: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_tomoscan/build; python3.13 -m pytest
Fatal Python error: Aborted
Current thread 0x00007f1215f76200 (most recent call first):
File "/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_tomoscan/build/snippets/test_sinogram.py", line 119 in <module>
File "/usr/lib/python3/dist-packages/_pytest/assertion/rewrite.py", line 186 in exec_module
File "<frozen importlib._bootstrap>", line 935 in _load_unlocked
File "<frozen importlib._bootstrap>", line 1331 in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 1360 in _find_and_load
File "<frozen importlib._bootstrap>", line 1387 in _gcd_import
File "/usr/lib/python3.13/importlib/__init__.py", line 88 in import_module
File "/usr/lib/python3/dist-packages/_pytest/pathlib.py", line 587 in import_path
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 498 in importtestmodule
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 551 in _getobj
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 280 in obj
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 567 in _register_setup_module_fixture
File "/usr/lib/python3/dist-packages/_pytest/python.py", line 554 in collect
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 389 in collect
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 344 in from_call
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 391 in pytest_make_collect_report
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/runner.py", line 567 in collect_one_node
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 839 in _collect_one_node
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 974 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 979 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 979 in genitems
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 813 in perform_collect
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 353 in pytest_collection
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 342 in _main
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 289 in wrap_session
File "/usr/lib/python3/dist-packages/_pytest/main.py", line 336 in pytest_cmdline_main
File "/usr/lib/python3/dist-packages/pluggy/_callers.py", line 121 in _multicall
File "/usr/lib/python3/dist-packages/pluggy/_manager.py", line 120 in _hookexec
File "/usr/lib/python3/dist-packages/pluggy/_hooks.py", line 512 in __call__
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 175 in main
File "/usr/lib/python3/dist-packages/_pytest/config/__init__.py", line 201 in console_main
File "/usr/lib/python3/dist-packages/pytest/__main__.py", line 9 in <module>
File "<frozen runpy>", line 88 in _run_code
File "<frozen runpy>", line 198 in _run_module_as_main
Extension modules: h5py._debian_h5py_serial._errors, h5py._d [too-long-redacted] q, tornado.speedups (total: 77)
Aborted
E: pybuild pybuild:389: test: plugin pyproject failed with: exit code=134: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_tomoscan/build; python3.13 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.14 3.13" returned exit code 13
make: *** [debian/rules:5: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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