Bug#908615: pyfai: FTBFS and autopkgtest fails with python3.7 in supported versions

Paul Gevers elbrus at debian.org
Tue Sep 11 20:31:26 BST 2018


Source: pyfai
Version: 0.15.0+dfsg1-1
Severity: serious
Tags: ftbfs
User: debian-ci at lists.debian.org
Usertags: needs-update
Control: affects -1 src:python3-defaults

[X-Debbugs-CC set to: debian-ci at lists.debian.org,
python3-defaults at packages.debian.org]

Dear maintainers,

Since the python3.7 transition started (which added python3.7 to the
supported Python versions) the autopkgtest of pyfai fails in testing
when that autopkgtest is run with the binary packages of
python3-defaults from unstable. It passes when run with only packages
from testing. I copied some of the output at the bottom of this report.
It seems that this failure also causes the package to FTBFS on
reproducible builds:
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/pyfai.html

If this is a real problem in your package (and not only in your
autopkgtest), the right binary package(s) from python3-defaults should
really add a versioned Breaks on the unfixed version of (one of your)
package(s). Note: the Breaks is nice even if the issue is only in the
autopkgtest as it helps the migration software to figure out the right
versions to combine in the tests.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/p/pyfai/972161/log.gz

autopkgtest [05:07:40]: test python3: [-----------------------
=== python3.7 ===
Unable to import pyFAI.ext.splitBBoxLUT for Look-up table based
azimuthal integration
Unable to import pyFAI.ext.splitPixel full pixel splitting: cannot
import name 'splitPixel' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitBBox Bounding Box pixel splitting:
cannot import name 'splitBBox' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.histogram Cython histogram implementation:
cannot import name 'histogram' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitBBoxCSR CSR based azimuthal integration:
cannot import name 'splitBBoxCSR' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitPixelFullCSR CSR based azimuthal
integration: cannot import name 'splitPixelFullCSR' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python3/dist-packages/pyFAI/__init__.py", line 73, in tests
    res = test.run_tests()
  File "/usr/lib/python3/dist-packages/pyFAI/test/__init__.py", line 59,
in run_tests
    if not runner.run(suite()).wasSuccessful():
  File "/usr/lib/python3/dist-packages/pyFAI/test/__init__.py", line 50,
in suite
    from . import test_all
  File "/usr/lib/python3/dist-packages/pyFAI/test/test_all.py", line 47,
in <module>
    from . import test_histogram
  File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py",
line 45, in <module>
    from ..ext.histogram import histogram, histogram2d
ModuleNotFoundError: No module named 'pyFAI.ext.histogram'
autopkgtest [05:07:41]: test python3: -----------------------]
autopkgtest [05:10:47]: test python3-dbg: [-----------------------
=== python3.7 ===
/usr/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't
resolve package from __spec__ or __package__, falling back on __name__
and __path__
  return f(*args, **kwds)
/usr/lib/python3/dist-packages/h5py/_hl/base.py:19: DeprecationWarning:
Using or importing the ABCs from 'collections' instead of from
'collections.abc' is deprecated, and in 3.8 it will stop working
  from collections import (Mapping, MutableMapping, KeysView,
/usr/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't
resolve package from __spec__ or __package__, falling back on __name__
and __path__
  return f(*args, **kwds)
Unable to import pyFAI.ext.splitBBoxLUT for Look-up table based
azimuthal integration
Unable to import pyFAI.ext.splitPixel full pixel splitting: cannot
import name 'splitPixel' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitBBox Bounding Box pixel splitting:
cannot import name 'splitBBox' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.histogram Cython histogram implementation:
cannot import name 'histogram' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitBBoxCSR CSR based azimuthal integration:
cannot import name 'splitBBoxCSR' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
Unable to import pyFAI.ext.splitPixelFullCSR CSR based azimuthal
integration: cannot import name 'splitPixelFullCSR' from 'pyFAI.ext'
(/usr/lib/python3/dist-packages/pyFAI/ext/__init__.py)
/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py:3245:
DeprecationWarning: Using or importing the ABCs from 'collections'
instead of from 'collections.abc' is deprecated, and in 3.8 it will stop
working
  elif isinstance( exprs, collections.Iterable ):
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python3/dist-packages/pyFAI/__init__.py", line 73, in tests
    res = test.run_tests()
  File "/usr/lib/python3/dist-packages/pyFAI/test/__init__.py", line 59,
in run_tests
    if not runner.run(suite()).wasSuccessful():
  File "/usr/lib/python3/dist-packages/pyFAI/test/__init__.py", line 50,
in suite
    from . import test_all
  File "/usr/lib/python3/dist-packages/pyFAI/test/test_all.py", line 47,
in <module>
    from . import test_histogram
  File "/usr/lib/python3/dist-packages/pyFAI/test/test_histogram.py",
line 45, in <module>
    from ..ext.histogram import histogram, histogram2d
ModuleNotFoundError: No module named 'pyFAI.ext.histogram'
* ob
object  : <refcnt 0 at 0x7f91283390c8>
type    : tuple
refcount: 0
address : 0x7f91283390c8
* op->_ob_prev->_ob_next
object  : <refcnt 0 at 0x7f91283390c7>Segmentation fault
autopkgtest [05:10:48]: test python3-dbg: -----------------------]


From the reproducible build log:

FAILED (failures=1, skipped=84)
WARNING:run_tests:Skipped
pyFAI.test.test_average.TestAverageMonitorName.test_edf_file_key ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_average.TestAverageMonitorName.test_edf_file_motor ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_geometry_refinement.TestGeometryRefinement.test_Spline
(tests geometric refinements with spline): network unreachable.
WARNING:run_tests:Skipped setUpClass
(pyFAI.test.test_azimuthal_integrator.TestAzimHalfFrelon) (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_azimuthal_integrator.TestSaxs.test_inpainting ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_azimuthal_integrator.TestSaxs.test_mask (test the
generation of mask): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_azimuthal_integrator.TestSaxs.test_normalization_factor
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_azimuthal_integrator.TestSaxs.test_variance (tests the
different variance model available): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_peak_picking.TestPeakPicking.test_peakPicking (first
test peak-picking then checks the geometry found is OK): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_geometry.TestSolidAngle.testSolidAngle (): skipping test
using >400M
WARNING:run_tests:Skipped pyFAI.test.test_mask.TestMask.test_mask_CSR
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMask.test_mask_CSR_OCL (): User request to skip
OpenCL tests
WARNING:run_tests:Skipped pyFAI.test.test_mask.TestMask.test_mask_LUT
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMask.test_mask_LUT_OCL (): User request to skip
OpenCL tests
WARNING:run_tests:Skipped pyFAI.test.test_mask.TestMask.test_mask_hist
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMask.test_mask_splitBBox (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMask.test_mask_splitfull (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_mask_LUT (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_mask_LUT_OCL (): User request
to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_mask_splitBBox (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_nomask (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_nomask_LUT (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_mask.TestMaskBeamstop.test_nomask_LUT_OCL (): User
request to skip OpenCL tests
WARNING:run_tests:Skipped pyFAI.test.test_openCL.TestMask.test_OpenCL
(): test using >200M
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestMask.test_OpenCL_CSR (): test using >200M
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestMask.test_OpenCL_LUT (): test using >500M
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestSort.test_reference_book (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestSort.test_reference_file (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped pyFAI.test.test_openCL.TestSort.test_sort_all
(): User request to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestSort.test_sort_horizontal (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_openCL.TestSort.test_sort_vertical (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped pyFAI.test.test_export.TestFIT2D.test_export
(): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_export.TestFIT2D.test_simple
(): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_export.TestSPD.test_simple ():
network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_saxs.TestSaxs.testCython ():
skipping test using >100M
WARNING:run_tests:Skipped pyFAI.test.test_saxs.TestSaxs.testMask ():
network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_saxs.TestSaxs.testNumpy ():
test using >100Mb
WARNING:run_tests:Skipped pyFAI.test.test_saxs.TestSaxs.testSplitBBox
(): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_saxs.TestSaxs.testSplitPixel
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate.TestIntegrate1D.test2th (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate.TestIntegrate1D.testQ (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate.TestIntegrate1D.testR (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate.TestIntegrate1D.test_defaultwriter (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate.TestIntegrate1D.test_filename (): network
unreachable.
WARNING:run_tests:Skipped setUpClass
(pyFAI.test.test_integrate.TestIntegrate2D) (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_counter_monitor
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_default_output_azim
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_default_output_dat
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_file_output_dat
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_monitor
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_app.TestIntegrateApp.test_integrate_no_monitor
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestImplementations.test_calc_pos (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestImplementations.test_size (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestImplementations.test_lut (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestHalfCCD.test_pos_lut (): skipping test
using >100M
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestHalfCCD.test_ref_vs_fit2d (Compare
reference spline correction vs fit2d's code): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestHalfCCD.test_lut_vs_fit2d (Compare
reference spline correction vs fit2d's code): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_distortion.TestHalfCCD.test_csr_vs_fit2d (Compare
reference spline correction vs fit2d's code): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_sparse.TestSparseBBox.test_CSR
(): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_sparse.TestSparseBBox.test_LUT
(): network unreachable.
WARNING:run_tests:Skipped setUpClass (pyFAI.test.test_csr.TestCSR) ():
network unreachable.
WARNING:run_tests:Skipped setUpClass (pyFAI.test.test_csr.TestOpenClCSR)
(): network unreachable.
WARNING:run_tests:Skipped pyFAI.test.test_bispev.TestBispev.test_bispev
(): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_bug_regression.TestBug170.test_bug170 (): test using >100Mb
WARNING:run_tests:Skipped
pyFAI.test.test_bug_regression.TestBugRegression.test_bug_174 ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_watershed.TestWatershed.test_init (): network unreachable.
WARNING:run_tests:Skipped setUpClass
(pyFAI.test.test_multi_geometry.TestMultiGeometry) (): network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_filter_hor (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_filter_vert (): User request
to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_mean_hor (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_mean_vert (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_sigma_clip_hor (): User
request to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_sigma_clip_vert (): User
request to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_sort_hor (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_ocl_sort.TestOclSort.test_sort_vert (): User request to
skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_widget.TestAIWidget.test_process_array_1d ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_widget.TestAIWidget.test_process_array_2d ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_widget.TestAIWidget.test_process_no_data ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_widget.TestAIWidget.test_process_numpy_1d ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_integrate_widget.TestAIWidget.test_process_numpy_2d ():
network unreachable.
WARNING:run_tests:Skipped
pyFAI.test.test_preproc.TestPreproc.test_opencl (): User request to skip
OpenCL tests
WARNING:run_tests:Skipped
pyFAI.test.test_spline.TestSpline.test_tilt_coverage (): network
unreachable.
WARNING:run_tests:Skipped
pyFAI.opencl.test.test_addition.TestAddition.test_add (): User request
to skip OpenCL tests
WARNING:run_tests:Skipped
pyFAI.opencl.test.test_addition.TestAddition.test_measurement (): User
request to skip OpenCL tests
WARNING:run_tests:Test suite failed
numpy 1.14.5 from ['/usr/lib/python3/dist-packages/numpy']
Scipy 1.1.0 from ['/usr/lib/python3/dist-packages/scipy']
FabIO 0.7.0
h5py 2.8.0
Cython 0.28.4
* ob
object  : <refcnt 0 at 0x7fc29a89fbb8>
type    : tuple
refcount: 0
address : 0x7fc29a89fbb8
* op->_ob_prev->_ob_next
object  : <refcnt 0 at 0x7fc29a89fbb7>Segmentation fault
E: pybuild pybuild:338: test: plugin custom failed with: exit code=139:
PYTHONPATH=/build/1st/pyfai-0.15.0+dfsg1/.pybuild/cpython3_3.7_dbg_pyfai/build
http_proxy='127.0.0.1:9' PYFAI_TESTIMAGES=testimages
PYFAI_DATA=/build/1st/pyfai-0.15.0+dfsg1 xvfb-run -a
--server-args="-screen 0 1024x768x24" python3.7-dbg ./run_tests.py
--low-mem --no-opencl --installed


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