[MacPorts] #58332: py27-astropy segfaults at 14% in tests

MacPorts noreply at macports.org
Sun Nov 3 22:41:48 UTC 2019 

#58332: py27-astropy segfaults at 14% in tests
-----------------------------------+----------------------------
  Reporter:  Russell-Jones-OxPhys  |      Owner:  duncanmmacleod
      Type:  defect                |     Status:  assigned
  Priority:  Normal                |  Milestone:
 Component:  ports                 |    Version:  2.5.4
Resolution:                        |   Keywords:
      Port:  py-astropy            |
-----------------------------------+----------------------------

Comment (by Schamschula):

 I've update py-astropy to 3.2.3. I ran the tests (using python 3.7) and
 got a bit farther:

 {{{
 In [3]: import astropy;astropy.test()
 /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/conftest.py:38: MatplotlibDeprecationWarning:
 The examples.directory rcparam was deprecated in Matplotlib 3.0 and will
 be removed in 3.2. In the future, examples will be found relative to the
 'datapath' directory.
   matplotlibrc_cache.update(matplotlib.rcParams)
 ====================================================================================================================================================
 test session starts
 =====================================================================================================================================================
 platform darwin -- Python 3.7.5, pytest-5.2.1, py-1.8.0, pluggy-0.13.0

 Running tests with Astropy version 3.2.3.
 Running tests in
 /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy.

 Date: 2019-11-03T10:55:28

 Platform: Darwin-18.7.0-x86_64-i386-64bit

 Executable:
 /opt/local/Library/Frameworks/Python.framework/Versions/3.7/bin/python3.7

 Full Python Version:
 3.7.5 (default, Oct 19 2019, 01:20:12)
 [Clang 10.0.1 (clang-1001.0.46.4)]

 encodings: sys: utf-8, locale: UTF-8, filesystem: utf-8
 byteorder: little
 float info: dig: 15, mant_dig: 15

 Numpy: 1.17.3
 Scipy: 1.3.1
 Matplotlib: 3.1.1
 h5py: not available
 Pandas: 0.25.2
 Cython: 0.29.14
 Scikit-image: not available
 asdf: not available
 astropy_helpers: 3.2.2
 Using Astropy options: remote_data: none.

 rootdir:
 /opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy
 plugins: openfiles-0.4.0, remotedata-0.3.2, arraydiff-0.3, astropy-
 header-0.1, doctestplus-0.4.0
 collected 12757 items / 14 skipped / 12743 selected

 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/_erfa/tests/test_erfa.py ........
 [  0%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/config/tests/test_configs.py ...............
 [  0%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/constants/tests/test_constant.py ........
 [  0%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/constants/tests/test_pickle.py xxxxxxxxx
 [  0%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/constants/tests/test_prior_version.py .........
 [  0%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_convolve.py
 ..............................................................................................................................................................................
 [  1%]
 ..................................................................................................................................................................................x.x.x.x.x.x.x.x.....................................................................................................................
 [  4%]
 [  4%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_convolve_fft.py
 ..........................................................................................................................................................................
 [  5%]
 ......................................................................................................................................................................................................................................................................................................................
 [  7%]
 ..........
 [  8%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_convolve_kernels.py
 ..............................................................................................................
 [  8%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_convolve_models.py
 ............
 [  8%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_convolve_nddata.py ...
 [  8%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_discretize.py
 ...s...........s...................
 [  9%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_kernel_class.py
 ..........................................................................................................................................................................
 [ 10%]
 ...........
 [ 10%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/convolution/tests/test_pickle.py .xx.xx.xx
 [ 10%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_angles.py
 ..........................................
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_angular_separation.py ....
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_api_ape5.py ....s
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_arrays.py .............
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_atc_replacements.py ....
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_celestial_transformations.py
 ............ss..
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_distance.py ..........
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_earth.py ..............s..
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-
 packages/astropy/coordinates/tests/test_finite_difference_velocities.py
 ......s..xx
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_formatting.py ..........
 [ 11%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_frames.py
 ..........................s.............
 [ 12%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_frames_with_velocity.py
 ................................................
 [ 12%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_funcs.py .....
 [ 12%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_iau_fullstack.py
 sssssssssssssssssssssssssssssssssssssssssssssssssss.
 [ 12%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-
 packages/astropy/coordinates/tests/test_intermediate_transformations.py
 .....sssssssssssssssssssssssssssssss..........ssssssssss.s
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_matching.py .............
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_matrix_utilities.py ..
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_name_resolve.py s.ss
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_pickle.py
 ....xx.x...xx.x...xx.x.
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_regression.py
 .ss.s.....s.sss.s....s....s....
 [ 13%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_representation.py
 ................................................................................s.................
 [ 14%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_representation_arithmetic.py
 .........................................................................................
 [ 15%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_representation_methods.py
 ............
 [ 15%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_shape_manipulation.py
 sssssssss
 [ 15%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_sites.py .ss.s...
 [ 15%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_sky_coord.py
 .............................................................................................................................................................................
 [ 17%]
 ................................................................................................s.............................................................................................................x...............s...........
 [ 18%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_sky_coord_velocities.py
 .........x...........x.x...........
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_skyoffset_transformations.py
 ...........s.................
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_solar_system.py
 s....ssssssssssssss....sss
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_transformations.py
 ..........................s...
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_unit_representation.py s
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/test_velocity_corrs.py ssssss
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_altaz_icrs.py ssss
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_ecliptic.py
 .........
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_fk4_no_e_fk4.py .
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_fk4_no_e_fk5.py .
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_galactic_fk4.py .
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/coordinates/tests/accuracy/test_icrs_fk5.py .
 [ 19%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/cosmology/tests/test_cosmology.py
 ..........................................
 [ 20%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/cosmology/tests/test_pickle.py ...
 [ 20%]
 ../../opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7
 /site-packages/astropy/io/ascii/tests/test_c_reader.py .....
 ^C
 }}}

 There it hung for over an hour, so I stopped it using the keyboard. I
 suspect there are issues with the pytest packages.

 Note: I made local Portfiles for the missing py-pytest-* packages. See:
 https://github.com/Schamschula/macports/tree/master/python

-- 
Ticket URL: <https://trac.macports.org/ticket/58332#comment:16>
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