ValueError: '_check_build.pyx' doesn't match any files

[jseps]

Description

Steps/Code to Reproduce

Expected Results

Actual Results

Versions

[jnothman]

Please provide code that can reproduce this error, and a full traceback

[jseps]

python setup.py install in mac terminal
resulting in
ValueError: '_check_build.pyx' doesn't match any files

import sklearn in python, resulting in

ImportError: No module named _check_build

---

Contents of /Users/jonathanepstein/venv/lib/python3.6/site-packages/sklearn/__check_build:
.DS_Store init.py init.pyc
pycache _check_build.cpython-36m-darwin.sosetup.py

---

It seems that scikit-learn has not been built correctly.

If you have installed scikit-learn from source, please do not forget
to build the package before using it: run python setup.py install or
make in the source directory.

If you have used an installer, please check that it is suited for your
Python version, your operating system and your platform.

[jnothman]

It's what's in the source dir, not what's in site-packages, that matters.

[jseps]

@jnothman /Users/jonathanepstein/venv/lib/python3.6/site-packages/sklearn is the source dir, correct?

I ran python setup.py install again in that directory, returning

non-existing path in '__check_build': '_check_build.pyx'
Appending sklearn.__check_build configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.__check_build')
Appending sklearn._build_utils configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn._build_utils')
Appending sklearn.compose configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.compose')
Appending sklearn.compose/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.compose/tests')
Appending sklearn.covariance configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.covariance')
Appending sklearn.covariance/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.covariance/tests')
Appending sklearn.cross_decomposition configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.cross_decomposition')
Appending sklearn.cross_decomposition/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.cross_decomposition/tests')
Appending sklearn.feature_selection configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.feature_selection')
Appending sklearn.feature_selection/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.feature_selection/tests')
Appending sklearn.gaussian_process configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.gaussian_process')
Appending sklearn.gaussian_process/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.gaussian_process/tests')
Appending sklearn.mixture configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.mixture')
Appending sklearn.mixture/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.mixture/tests')
Appending sklearn.model_selection configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.model_selection')
Appending sklearn.model_selection/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.model_selection/tests')
Appending sklearn.neural_network configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.neural_network')
Appending sklearn.neural_network/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.neural_network/tests')
Appending sklearn.preprocessing configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.preprocessing')
Appending sklearn.preprocessing/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.preprocessing/tests')
Appending sklearn.semi_supervised configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.semi_supervised')
Appending sklearn.semi_supervised/tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.semi_supervised/tests')
non-existing path in 'cluster': '_dbscan_inner.pyx'
non-existing path in 'cluster': '_hierarchical.pyx'
non-existing path in 'cluster': '_k_means_elkan.pyx'
non-existing path in 'cluster': '../src/cblas'
non-existing path in 'cluster': '_k_means.pyx'
Appending sklearn.cluster.tests configuration to sklearn.cluster
Ignoring attempt to set 'name' (from 'sklearn.cluster' to 'sklearn.cluster.tests')
Appending sklearn.cluster configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.cluster')
non-existing path in 'datasets': '_svmlight_format.pyx'
Appending sklearn.datasets.tests configuration to sklearn.datasets
Ignoring attempt to set 'name' (from 'sklearn.datasets' to 'sklearn.datasets.tests')
Appending sklearn.datasets configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.datasets')
non-existing path in 'decomposition': '_online_lda.pyx'
non-existing path in 'decomposition': 'cdnmf_fast.pyx'
Appending sklearn.decomposition.tests configuration to sklearn.decomposition
Ignoring attempt to set 'name' (from 'sklearn.decomposition' to 'sklearn.decomposition.tests')
Appending sklearn.decomposition configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.decomposition')
non-existing path in 'ensemble': '_gradient_boosting.pyx'
Appending sklearn.ensemble.tests configuration to sklearn.ensemble
Ignoring attempt to set 'name' (from 'sklearn.ensemble' to 'sklearn.ensemble.tests')
Appending sklearn.ensemble configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.ensemble')
Appending sklearn.externals.joblib configuration to sklearn.externals
Ignoring attempt to set 'name' (from 'sklearn.externals' to 'sklearn.externals.joblib')
Appending sklearn.externals.joblib/externals configuration to sklearn.externals
Ignoring attempt to set 'name' (from 'sklearn.externals' to 'sklearn.externals.joblib/externals')
Appending sklearn.externals.joblib/externals/loky configuration to sklearn.externals
Ignoring attempt to set 'name' (from 'sklearn.externals' to 'sklearn.externals.joblib/externals/loky')
Appending sklearn.externals.joblib/externals/loky/backend configuration to sklearn.externals
Ignoring attempt to set 'name' (from 'sklearn.externals' to 'sklearn.externals.joblib/externals/loky/backend')
Appending sklearn.externals.joblib/externals/cloudpickle configuration to sklearn.externals
Ignoring attempt to set 'name' (from 'sklearn.externals' to 'sklearn.externals.joblib/externals/cloudpickle')
Appending sklearn.externals configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.externals')
non-existing path in 'feature_extraction': '_hashing.pyx'
Appending sklearn.feature_extraction.tests configuration to sklearn.feature_extraction
Ignoring attempt to set 'name' (from 'sklearn.feature_extraction' to 'sklearn.feature_extraction.tests')
Appending sklearn.feature_extraction configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.feature_extraction')
non-existing path in 'manifold': '_utils.pyx'
non-existing path in 'manifold': '../src/cblas'
non-existing path in 'manifold': '_barnes_hut_tsne.pyx'
Appending sklearn.manifold.tests configuration to sklearn.manifold
Ignoring attempt to set 'name' (from 'sklearn.manifold' to 'sklearn.manifold.tests')
Appending sklearn.manifold configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.manifold')
non-existing path in 'metrics/cluster': 'expected_mutual_info_fast.pyx'
Appending sklearn.metrics.cluster.tests configuration to sklearn.metrics.cluster
Ignoring attempt to set 'name' (from 'sklearn.metrics.cluster' to 'sklearn.metrics.cluster.tests')
Appending sklearn.metrics.cluster configuration to sklearn.metrics
Ignoring attempt to set 'name' (from 'sklearn.metrics' to 'sklearn.metrics.cluster')
non-existing path in 'metrics': '../src/cblas'
non-existing path in 'metrics': 'pairwise_fast.pyx'
Appending sklearn.metrics.tests configuration to sklearn.metrics
Ignoring attempt to set 'name' (from 'sklearn.metrics' to 'sklearn.metrics.tests')
Appending sklearn.metrics configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.metrics')
non-existing path in 'neighbors': 'ball_tree.pyx'
non-existing path in 'neighbors': 'kd_tree.pyx'
non-existing path in 'neighbors': 'dist_metrics.pyx'
non-existing path in 'neighbors': 'typedefs.pyx'
non-existing path in 'neighbors': 'quad_tree.pyx'
Appending sklearn.neighbors.tests configuration to sklearn.neighbors
Ignoring attempt to set 'name' (from 'sklearn.neighbors' to 'sklearn.neighbors.tests')
Appending sklearn.neighbors configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.neighbors')
non-existing path in 'tree': '_tree.pyx'
non-existing path in 'tree': '_splitter.pyx'
non-existing path in 'tree': '_criterion.pyx'
non-existing path in 'tree': '_utils.pyx'
Appending sklearn.tree.tests configuration to sklearn.tree
Ignoring attempt to set 'name' (from 'sklearn.tree' to 'sklearn.tree.tests')
Appending sklearn.tree configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.tree')
Appending sklearn.svm.tests configuration to sklearn.svm
Ignoring attempt to set 'name' (from 'sklearn.svm' to 'sklearn.svm.tests')
non-existing path in 'svm': 'src/libsvm/svm.cpp'
non-existing path in 'svm': 'src/libsvm/svm.h'
non-existing path in 'svm': 'src/libsvm/libsvm_template.cpp'
non-existing path in 'svm': 'src/libsvm'
non-existing path in 'svm': 'src/libsvm/libsvm_helper.c'
non-existing path in 'svm': 'src/libsvm/libsvm_template.cpp'
non-existing path in 'svm': 'src/libsvm/svm.cpp'
non-existing path in 'svm': 'src/libsvm/svm.h'
non-existing path in 'svm': 'libsvm.pyx'
non-existing path in 'svm': '../src/cblas'
could not resolve pattern in 'svm': 'src/liblinear/.h'
non-existing path in 'svm': 'src/liblinear/liblinear_helper.c'
non-existing path in 'svm': 'liblinear.pyx'
could not resolve pattern in 'svm': 'src/liblinear/.cpp'
non-existing path in 'svm': 'src/libsvm'
non-existing path in 'svm': 'src/libsvm/svm.h'
non-existing path in 'svm': 'src/libsvm/libsvm_sparse_helper.c'
non-existing path in 'svm': 'libsvm_sparse.pyx'
Appending sklearn.svm configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.svm')
non-existing path in '.': '_isotonic.pyx'
non-existing path in 'linear_model': '../src/cblas'
non-existing path in 'linear_model': 'cd_fast.pyx'
non-existing path in 'linear_model': '../src/cblas'
non-existing path in 'linear_model': 'sgd_fast.pyx'
non-existing path in 'linear_model': 'sag_fast.pyx'
Appending sklearn.linear_model.tests configuration to sklearn.linear_model
Ignoring attempt to set 'name' (from 'sklearn.linear_model' to 'sklearn.linear_model.tests')
Appending sklearn.linear_model configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.linear_model')
Appending sklearn.utils.sparsetools.tests configuration to sklearn.utils.sparsetools
Ignoring attempt to set 'name' (from 'sklearn.utils.sparsetools' to 'sklearn.utils.sparsetools.tests')
Appending sklearn.utils.sparsetools configuration to sklearn.utils
Ignoring attempt to set 'name' (from 'sklearn.utils' to 'sklearn.utils.sparsetools')
non-existing path in 'utils': 'sparsefuncs_fast.pyx'
non-existing path in 'utils': 'src/cholesky_delete.h'
non-existing path in 'utils': '../src/cblas'
non-existing path in 'utils': 'arrayfuncs.pyx'
non-existing path in 'utils': 'src'
non-existing path in 'utils': 'murmurhash.pyx'
non-existing path in 'utils': 'src/MurmurHash3.cpp'
non-existing path in 'utils': 'src'
non-existing path in 'utils': 'lgamma.pyx'
non-existing path in 'utils': 'src/gamma.c'
non-existing path in 'utils': 'graph_shortest_path.pyx'
non-existing path in 'utils': 'fast_dict.pyx'
non-existing path in 'utils': 'seq_dataset.pyx'
non-existing path in 'utils': '../src/cblas'
non-existing path in 'utils': 'weight_vector.pyx'
non-existing path in 'utils': '_random.pyx'
non-existing path in 'utils': '_logistic_sigmoid.pyx'
Appending sklearn.utils.tests configuration to sklearn.utils
Ignoring attempt to set 'name' (from 'sklearn.utils' to 'sklearn.utils.tests')
Appending sklearn.utils configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.utils')
Appending sklearn.tests configuration to sklearn
Ignoring attempt to set 'name' (from 'sklearn' to 'sklearn.tests')
Warning: Assuming default configuration (./_build_utils/{setup__build_utils,setup}.py was not found)Warning: Assuming default configuration (./compose/{setup_compose,setup}.py was not found)Warning: Assuming default configuration (./compose/tests/setup_compose/{setup_compose/tests,setup}.py was not found)Warning: Assuming default configuration (./covariance/{setup_covariance,setup}.py was not found)Warning: Assuming default configuration (./covariance/tests/setup_covariance/{setup_covariance/tests,setup}.py was not found)Warning: Assuming default configuration (./cross_decomposition/{setup_cross_decomposition,setup}.py was not found)Warning: Assuming default configuration (./cross_decomposition/tests/setup_cross_decomposition/{setup_cross_decomposition/tests,setup}.py was not found)Warning: Assuming default configuration (./feature_selection/{setup_feature_selection,setup}.py was not found)Warning: Assuming default configuration (./feature_selection/tests/setup_feature_selection/{setup_feature_selection/tests,setup}.py was not found)Warning: Assuming default configuration (./gaussian_process/{setup_gaussian_process,setup}.py was not found)Warning: Assuming default configuration (./gaussian_process/tests/setup_gaussian_process/{setup_gaussian_process/tests,setup}.py was not found)Warning: Assuming default configuration (./mixture/{setup_mixture,setup}.py was not found)Warning: Assuming default configuration (./mixture/tests/setup_mixture/{setup_mixture/tests,setup}.py was not found)Warning: Assuming default configuration (./model_selection/{setup_model_selection,setup}.py was not found)Warning: Assuming default configuration (./model_selection/tests/setup_model_selection/{setup_model_selection/tests,setup}.py was not found)Warning: Assuming default configuration (./neural_network/{setup_neural_network,setup}.py was not found)Warning: Assuming default configuration (./neural_network/tests/setup_neural_network/{setup_neural_network/tests,setup}.py was not found)Warning: Assuming default configuration (./preprocessing/{setup_preprocessing,setup}.py was not found)Warning: Assuming default configuration (./preprocessing/tests/setup_preprocessing/{setup_preprocessing/tests,setup}.py was not found)Warning: Assuming default configuration (./semi_supervised/{setup_semi_supervised,setup}.py was not found)Warning: Assuming default configuration (./semi_supervised/tests/setup_semi_supervised/{setup_semi_supervised/tests,setup}.py was not found)Warning: Assuming default configuration (cluster/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (datasets/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (decomposition/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (ensemble/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (externals/joblib/{setup_joblib,setup}.py was not found)Warning: Assuming default configuration (externals/joblib/externals/setup_joblib/{setup_joblib/externals,setup}.py was not found)Warning: Assuming default configuration (externals/joblib/externals/loky/setup_joblib/externals/{setup_joblib/externals/loky,setup}.py was not found)Warning: Assuming default configuration (externals/joblib/externals/loky/backend/setup_joblib/externals/loky/{setup_joblib/externals/loky/backend,setup}.py was not found)Warning: Assuming default configuration (externals/joblib/externals/cloudpickle/setup_joblib/externals/{setup_joblib/externals/cloudpickle,setup}.py was not found)Warning: Assuming default configuration (feature_extraction/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (manifold/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (metrics/cluster/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (metrics/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (neighbors/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (tree/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (svm/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (linear_model/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (utils/sparsetools/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (utils/tests/{setup_tests,setup}.py was not found)Warning: Assuming default configuration (./tests/{setup_tests,setup}.py was not found)Traceback (most recent call last):
File "setup.py", line 89, in
setup(**configuration(top_path='').todict())
File "setup.py", line 83, in configuration
maybe_cythonize_extensions(top_path, config)
File "/Users/jonathanepstein/venv/lib/python3.6/site-packages/sklearn/_build_utils/init.py", line 84, in maybe_cythonize_extensions
config.ext_modules = cythonize(config.ext_modules)
File "/Users/jonathanepstein/venv/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 967, in cythonize
aliases=aliases)
File "/Users/jonathanepstein/venv/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 812, in create_extension_list
for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern):
File "/Users/jonathanepstein/venv/lib/python3.6/site-packages/Cython/Build/Dependencies.py", line 111, in nonempty
raise ValueError(error_msg)
ValueError: '_check_build.pyx' doesn't match any files

[jnothman]

No that is not the source dir.

[jnothman]

You're asking a usage question. The issue tracker is mainly for bugs and new features. For usage questions, it is recommended to try Stack Overflow or the Mailing List.

[maqingyue]

Have you solved this problem? I have encountered similar problems. I look forward to your reply