tests fail on Mac with Python 3.7.4, built with Spack. #6263
Description
Describe the bug
I'm updating the Spack package for statsmodels (in this Pull Request) to include v0.10.1. I'm on a Mac running OS X 10.13.6 and am using a mixed toolchain that combines clang v10.0.0 with gfortran from gcc 9.2.0.
It previously only supported v0.8.0. The previous version of the package did not run statsmodels' tests.
When I enable statsmodels' tests, it crashes with the following error, ultimately from scipy:
Traceback (most recent call last):
File "setup.py", line 346, in <module>
data_files=[('', ['LICENSE.txt', 'setup.cfg'])]
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/__init__.py", line 145, in setup
return distutils.core.setup(**attrs)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/distutils/core.py", line 148, in setup
dist.run_commands()
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/command/test.py", line 229, in run
self.run_tests()
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/command/test.py", line 251, in run_tests
exit=False,
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/main.py", line 100, in __init__
self.parseArgs(argv)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/main.py", line 124, in parseArgs
self._do_discovery(argv[2:])
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/main.py", line 244, in _do_discovery
self.createTests(from_discovery=True, Loader=Loader)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/main.py", line 154, in createTests
self.test = loader.discover(self.start, self.pattern, self.top)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 349, in discover
tests = list(self._find_tests(start_dir, pattern))
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 406, in _find_tests
full_path, pattern, namespace)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 483, in _find_test_path
tests = self.loadTestsFromModule(package, pattern=pattern)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/command/test.py", line 55, in loadTestsFromModule
tests.append(self.loadTestsFromName(submodule))
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 191, in loadTestsFromName
return self.loadTestsFromModule(obj)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/command/test.py", line 55, in loadTestsFromModule
tests.append(self.loadTestsFromName(submodule))
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 191, in loadTestsFromName
return self.loadTestsFromModule(obj)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-setuptools-41.4.0-auj3fiauezrmusmyjbzphcpjuqhqsbta/lib/python3.7/site-packages/setuptools/command/test.py", line 55, in loadTestsFromModule
tests.append(self.loadTestsFromName(submodule))
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/lib/python3.7/unittest/loader.py", line 154, in loadTestsFromName
module = __import__(module_name)
File "/private/var/folders/f7/fcb363190nz0jbypndp3nj_m0000gn/T/hartzell/spack-stage/spack-stage-py-statsmodels-0.10.1-ud4qbhmf7ffyidkdehobbg2idavdfbt4/spack-src/statsmodels/sandbox/tsa/try_var_convolve.py", line 147, in <module>
yff = fftconvolve(x.astype(float)[:,:,None],a3f)
File "/private/var/folders/f7/fcb363190nz0jbypndp3nj_m0000gn/T/hartzell/spack-stage/spack-stage-py-statsmodels-0.10.1-ud4qbhmf7ffyidkdehobbg2idavdfbt4/spack-src/statsmodels/tsa/filters/filtertools.py", line 77, in fftconvolveinv
IN1 = fft.fftn(in1,fsize)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy/fftpack/basic.py", line 624, in fftn
return _raw_fftn_dispatch(x, shape, axes, overwrite_x, 1)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy/fftpack/basic.py", line 639, in _raw_fftn_dispatch
return _raw_fftnd(tmp, shape, axes, direction, overwrite_x, work_function)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy/fftpack/basic.py", line 530, in _raw_fftnd
s, axes = _init_nd_shape_and_axes_sorted(x, s, axes)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy/fftpack/helper.py", line 271, in _init_nd_shape_and_axes_sorted
shape, axes = _init_nd_shape_and_axes(x, shape, axes)
File "/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy/fftpack/helper.py", line 226, in _init_nd_shape_and_axes
raise ValueError("when given, shape values must be integers")
ValueError: when given, shape values must be integers
==> Error: ProcessError: Command exited with status 1:
'/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/python-3.7.4-ew4djiffqu2foj6hqix6xtacn33iwul2/bin/python3.7' '-s' 'setup.py' '--no-user-cfg' 'test'
Code Sample, a copy-pastable example if possible
I realize/apologize that this is a heavyweight recreation example. Given the PR branch, you can recreate the error with:
spack install -v --test=root py-statsmodelsI do not see any similar issues in the statsmodels or scipy repositories. I have not tried the current master version.
Expected Output
I expect the test to pass.
Output of import statsmodels.api as sm; sm.show_versions()
The following output uses the library after installing it without running its tests.
Details
(alice)[09:57:06]spack>>module load py-statsmodels
(alice)[09:57:24]spack>>python
Python 3.7.4 (default, Nov 19 2019, 10:42:46)
[Clang 10.0.0 (clang-1000.10.44.4)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
import statsmodels.api as sm; sm.show_versions()
INSTALLED VERSIONS
Python: 3.7.4.final.0
OS: Darwin 17.7.0 Darwin Kernel Version 17.7.0: Fri Oct 4 23:08:59 PDT 2019; root:xnu-4570.71.57~1/RELEASE_X86_64 x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
Statsmodels
Installed: 0.10.1 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-statsmodels-0.10.1-ud4qbhmf7ffyidkdehobbg2idavdfbt4/lib/python3.7/site-packages/statsmodels)
Required Dependencies
cython: Not installed
numpy: 1.17.4 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-numpy-1.17.4-3in4mcicpsphvuu2yff6t5q3ebe53jyq/lib/python3.7/site-packages/numpy)
scipy: 1.3.2 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-scipy-1.3.2-t4ns676iwabls65jakratet2d5leqcoy/lib/python3.7/site-packages/scipy)
pandas: 0.25.1 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-pandas-0.25.1-jlqq2j72mehrre43e6v6b72jgdwtkal7/lib/python3.7/site-packages/pandas)
dateutil: 2.8.0 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-python-dateutil-2.8.0-ievtkb7dvscoip3h2gd3evvoasxfqqul/lib/python3.7/site-packages/dateutil)
patsy: 0.4.1 (/Users/hartzell/tmp/spack/opt/spack/darwin-highsierra-x86_64/clang-10.0.0-apple/py-patsy-0.4.1-7wxkn2mcajxqvfclxxsrsuqnbupn2njd/lib/python3.7/site-packages/patsy)
Optional Dependencies
matplotlib: Not installed
cvxopt: Not installed
joblib: Not installed
Developer Tools
IPython: Not installed
jinja2: Not installed
sphinx: Not installed
pygments: Not installed
pytest: Not installed
virtualenv: Not installed