Closed
Description
Describe the bug
on running pytest on a fresh clone of the scikit-learn repository in a virtual env(properly setup), I get
Fatal Python error: Segmentation fault
Steps/Code to Reproduce
- clone the scikit-learn repository
- python3.7 -m venv venv
- source venv/bin/activate
- run
pip install -ein the scikit-learn repo. - run pytest
Platform:
Debian 10
4gb RAM
python 3.7
Expected Results
pytest runs without error (or one or two known errors)
Actual Results
pytest throws a segmentation fault.
The traceback is as follows:
Traceback
Fatal Python error: Segmentation fault
Thread 0x00007f931f3a5700 (most recent call first):
File "/usr/lib/python3.7/threading.py", line 296 in wait
File "/home/neil/testing/venv/lib/python3.7/site-packages/joblib/externals/loky/backend/queues.py", line 138 in _feed
File "/usr/lib/python3.7/threading.py", line 865 in run
File "/usr/lib/python3.7/threading.py", line 917 in _bootstrap_inner
File "/usr/lib/python3.7/threading.py", line 885 in _bootstrap
Thread 0x00007f931eba4700 (most recent call first):
File "/usr/lib/python3.7/selectors.py", line 415 in select
File "/usr/lib/python3.7/multiprocessing/connection.py", line 920 in wait
File "/home/neil/testing/venv/lib/python3.7/site-packages/joblib/externals/loky/process_executor.py", line 609 in wait_result_broken_or_wakeup
File "/home/neil/testing/venv/lib/python3.7/site-packages/joblib/externals/loky/process_executor.py", line 555 in run
File "/usr/lib/python3.7/threading.py", line 917 in _bootstrap_inner
File "/usr/lib/python3.7/threading.py", line 885 in _bootstrap
Current thread 0x00007f9342504740 (most recent call first):
File "/home/neil/testing/scikit-learn/sklearn/svm/_base.py", line 276 in _dense_fit
File "/home/neil/testing/scikit-learn/sklearn/svm/_base.py", line 217 in fit
File "/home/neil/testing/scikit-learn/sklearn/utils/estimator_checks.py", line 1834 in check_classifiers_train
File "/home/neil/testing/scikit-learn/sklearn/utils/_testing.py", line 299 in wrapper
File "/home/neil/testing/scikit-learn/sklearn/tests/test_common.py", line 85 in test_estimators
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/python.py", line 182 in pytest_pyfunc_call
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/python.py", line 1477 in runtest
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 135 in pytest_runtest_call
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 217 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 244 in from_call
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 217 in call_runtest_hook
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 186 in call_and_report
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 100 in runtestprotocol
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/runner.py", line 85 in pytest_runtest_protocol
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/main.py", line 272 in pytest_runtestloop
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/main.py", line 247 in _main
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/main.py", line 191 in wrap_session
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/main.py", line 240 in pytest_cmdline_main
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/callers.py", line 187 in _multicall
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 87 in <lambda>
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/manager.py", line 93 in _hookexec
File "/home/neil/testing/venv/lib/python3.7/site-packages/pluggy/hooks.py", line 286 in __call__
File "/home/neil/testing/venv/lib/python3.7/site-packages/_pytest/config/__init__.py", line 125 in main
File "/home/neil/testing/venv/bin/pytest", line 10 in <module>
I've also uploaded the entire output of running the pytest command(as it is too long to paste in the issue) here:
pytest_output.txt