Error on Cythonizing sklearn/utils/sparsefuncs_fast.pyx

[toncho11]

I get this error no matter what hacks I try:

[53/53] Cythonizing sklearn/utils/sparsefuncs_fast.pyx
main()
File "/home/toncho/.local/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/toncho/.local/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 487, in run_setup
super().run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/setuptools/build_meta.py", line 311, in run_setup
exec(code, locals())
File "", line 301, in
File "", line 297, in setup_package
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/numpy/distutils/core.py", line 136, in setup
config = configuration()
File "", line 188, in configuration
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/numpy/distutils/misc_util.py", line 1050, in add_subpackage
config_list = self.get_subpackage(subpackage_name, subpackage_path,
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/numpy/distutils/misc_util.py", line 1016, in get_subpackage
config = self._get_configuration_from_setup_py(
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/numpy/distutils/misc_util.py", line 958, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "/tmp/pip-install-isn9jct7/scikit-learn_5c93d3f4287e428bae9240467ba18b26/sklearn/setup.py", line 83, in configuration
cythonize_extensions(top_path, config)
File "/tmp/pip-install-isn9jct7/scikit-learn_5c93d3f4287e428bae9240467ba18b26/sklearn/_build_utils/init.py", line 70, in cythonize_extensions
config.ext_modules = cythonize(
File "/tmp/pip-build-env-pe1m9p4j/overlay/local/lib/python3.10/dist-packages/Cython/Build/Dependencies.py", line 1145, in cythonize
result.get(99999) # seconds
File "/usr/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
Cython.Compiler.Errors.CompileError: sklearn/ensemble/_hist_gradient_boosting/splitting.pyx
[end of output]

[JacksonBurns]

Looks like you are using Python 3.10. The latest version of Python in which I have been able to install auto-sklearn is 3.9, try downgrading.

[tbarbette]

Had the same problem with Python 3.10 and indeed going back to 3.9 worked. Steps on Ubuntu:

sudo add-apt-repository ppa:deadsnakes/ppa                                                                                                                                                                               
sudo apt-get update
sudo apt-get install python3.9 python3.9-venv
python3.9 -m venv venv
source venv/bin/activate
pip install auto-sklearn