tslearnのインストール時のエラーを解決したい

Question

tslearnを使用できるようにしたい

最近，pythonでkShapeによるクラスタリングをしたいと思い，ターミナル上でtslearnをインストールしようとしたのですが，以下のようなエラー文が表示されました．
何が原因かわかりません．
どなたかご教授いただけますと幸いです．

Building wheels for collected packages: tslearn
  Building wheel for tslearn (PEP 517) ... error
  ERROR: Command errored out with exit status 1:
   command: /usr/local/opt/python@3.9/bin/python3.9 /usr/local/lib/python3.9/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /var/folders/s8/kl7xtlk11dl94wg8wj3gjbbr0000gn/T/tmprfdn9co7
       cwd: /private/var/folders/s8/kl7xtlk11dl94wg8wj3gjbbr0000gn/T/pip-install-384240s3/tslearn_64344a8a487b4eba9671f849e381d7ab
  Complete output (98 lines):
  /usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/setuptools/dist.py:697: UserWarning: Usage of dash-separated 'description-file' will not be supported in future versions. Please use the underscore name 'description_file' instead
    warnings.warn(
  running bdist_wheel
  running build
  running build_py
  creating build
  creating build/lib.macosx-11-x86_64-3.9
  creating build/lib.macosx-11-x86_64-3.9/tslearn
  copying tslearn/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn
  creating build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/softdtw_variants.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/dtw_variants.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/sax.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/utils.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  copying tslearn/metrics/ctw.py -> build/lib.macosx-11-x86_64-3.9/tslearn/metrics
  creating build/lib.macosx-11-x86_64-3.9/tslearn/piecewise
  copying tslearn/piecewise/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/piecewise
  copying tslearn/piecewise/piecewise.py -> build/lib.macosx-11-x86_64-3.9/tslearn/piecewise
  creating build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  copying tslearn/barycenters/softdtw.py -> build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  copying tslearn/barycenters/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  copying tslearn/barycenters/dba.py -> build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  copying tslearn/barycenters/utils.py -> build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  copying tslearn/barycenters/euclidean.py -> build/lib.macosx-11-x86_64-3.9/tslearn/barycenters
  creating build/lib.macosx-11-x86_64-3.9/tslearn/datasets
  copying tslearn/datasets/datasets.py -> build/lib.macosx-11-x86_64-3.9/tslearn/datasets
  copying tslearn/datasets/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/datasets
  copying tslearn/datasets/cached.py -> build/lib.macosx-11-x86_64-3.9/tslearn/datasets
  copying tslearn/datasets/ucr_uea.py -> build/lib.macosx-11-x86_64-3.9/tslearn/datasets
  creating build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_utils.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_estimators.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_matrixprofile.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_metrics.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_barycenters.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_piecewise.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_variablelength.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_preprocessing.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_svm.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_serialize_models.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/sklearn_patches.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_shapelets.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_neighbors.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  copying tslearn/tests/test_clustering.py -> build/lib.macosx-11-x86_64-3.9/tslearn/tests
  creating build/lib.macosx-11-x86_64-3.9/tslearn/clustering
  copying tslearn/clustering/kshape.py -> build/lib.macosx-11-x86_64-3.9/tslearn/clustering
  copying tslearn/clustering/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/clustering
  copying tslearn/clustering/kmeans.py -> build/lib.macosx-11-x86_64-3.9/tslearn/clustering
  copying tslearn/clustering/utils.py -> build/lib.macosx-11-x86_64-3.9/tslearn/clustering
  creating build/lib.macosx-11-x86_64-3.9/tslearn/hdftools
  copying tslearn/hdftools/hdftools.py -> build/lib.macosx-11-x86_64-3.9/tslearn/hdftools
  copying tslearn/hdftools/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/hdftools
  creating build/lib.macosx-11-x86_64-3.9/tslearn/bases
  copying tslearn/bases/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/bases
  copying tslearn/bases/bases.py -> build/lib.macosx-11-x86_64-3.9/tslearn/bases
  creating build/lib.macosx-11-x86_64-3.9/tslearn/early_classification
  copying tslearn/early_classification/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/early_classification
  copying tslearn/early_classification/early_classification.py -> build/lib.macosx-11-x86_64-3.9/tslearn/early_classification
  creating build/lib.macosx-11-x86_64-3.9/tslearn/utils
  copying tslearn/utils/cast.py -> build/lib.macosx-11-x86_64-3.9/tslearn/utils
  copying tslearn/utils/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/utils
  copying tslearn/utils/utils.py -> build/lib.macosx-11-x86_64-3.9/tslearn/utils
  creating build/lib.macosx-11-x86_64-3.9/tslearn/neural_network
  copying tslearn/neural_network/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/neural_network
  copying tslearn/neural_network/neural_network.py -> build/lib.macosx-11-x86_64-3.9/tslearn/neural_network
  creating build/lib.macosx-11-x86_64-3.9/tslearn/shapelets
  copying tslearn/shapelets/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/shapelets
  copying tslearn/shapelets/shapelets.py -> build/lib.macosx-11-x86_64-3.9/tslearn/shapelets
  creating build/lib.macosx-11-x86_64-3.9/tslearn/svm
  copying tslearn/svm/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/svm
  copying tslearn/svm/svm.py -> build/lib.macosx-11-x86_64-3.9/tslearn/svm
  creating build/lib.macosx-11-x86_64-3.9/tslearn/matrix_profile
  copying tslearn/matrix_profile/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/matrix_profile
  copying tslearn/matrix_profile/matrix_profile.py -> build/lib.macosx-11-x86_64-3.9/tslearn/matrix_profile
  creating build/lib.macosx-11-x86_64-3.9/tslearn/preprocessing
  copying tslearn/preprocessing/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/preprocessing
  copying tslearn/preprocessing/preprocessing.py -> build/lib.macosx-11-x86_64-3.9/tslearn/preprocessing
  creating build/lib.macosx-11-x86_64-3.9/tslearn/generators
  copying tslearn/generators/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/generators
  copying tslearn/generators/generators.py -> build/lib.macosx-11-x86_64-3.9/tslearn/generators
  creating build/lib.macosx-11-x86_64-3.9/tslearn/neighbors
  copying tslearn/neighbors/neighbors.py -> build/lib.macosx-11-x86_64-3.9/tslearn/neighbors
  copying tslearn/neighbors/__init__.py -> build/lib.macosx-11-x86_64-3.9/tslearn/neighbors
  creating build/lib.macosx-11-x86_64-3.9/tslearn/.cached_datasets
  copying tslearn/.cached_datasets/Trace.npz -> build/lib.macosx-11-x86_64-3.9/tslearn/.cached_datasets
  running build_ext
  building 'tslearn.metrics.cycc' extension
  creating build/temp.macosx-11-x86_64-3.9
  creating build/temp.macosx-11-x86_64-3.9/tslearn
  creating build/temp.macosx-11-x86_64-3.9/tslearn/metrics
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX11.sdk -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python@3.9/3.9.7/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c tslearn/metrics/cycc.c -o build/temp.macosx-11-x86_64-3.9/tslearn/metrics/cycc.o
  tslearn/metrics/cycc.c:633:10: fatal error: 'numpy/arrayobject.h' file not found
  #include "numpy/arrayobject.h"
           ^~~~~~~~~~~~~~~~~~~~~
  1 error generated.
  error: command '/usr/bin/clang' failed with exit code 1
  ----------------------------------------
  ERROR: Failed building wheel for tslearn
Failed to build tslearn
ERROR: Could not build wheels for tslearn which use PEP 517 and cannot be installed directly

Comments

[jbpb0]

これが参考になるかも
https://github.com/tslearn-team/tslearn/issues/196

Answer 1

私の環境では問題なかったですね。
Python関連の環境やXcodeCLT等を最新にしてみてはいかがでしょう。

Python 3.9.7
macOS Big Sur 11.6

$ pip install tslearn

Collecting tslearn
  Downloading tslearn-0.5.2.tar.gz (484 kB)
     |████████████████████████████████| 484 kB 3.5 MB/s 
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
    Preparing wheel metadata ... done
Collecting scikit-learn
  Using cached scikit_learn-0.24.2-cp39-cp39-macosx_10_13_x86_64.whl (7.3 MB)
Collecting scipy
  Using cached scipy-1.7.1-cp39-cp39-macosx_10_9_x86_64.whl (32.8 MB)
Collecting numba
  Downloading numba-0.54.0-cp39-cp39-macosx_10_14_x86_64.whl (2.2 MB)
     |████████████████████████████████| 2.2 MB 6.5 MB/s 
Collecting Cython
  Using cached Cython-0.29.24-cp39-cp39-macosx_10_9_x86_64.whl (1.9 MB)
Collecting numpy
  Using cached numpy-1.21.2-cp39-cp39-macosx_10_9_x86_64.whl (17.0 MB)
Collecting joblib
  Using cached joblib-1.0.1-py3-none-any.whl (303 kB)
Collecting numpy
  Using cached numpy-1.20.3-cp39-cp39-macosx_10_9_x86_64.whl (16.1 MB)
Requirement already satisfied: setuptools in ./python3.9/site-packages (from numba->tslearn) (57.4.0)
Collecting llvmlite<0.38,>=0.37.0rc1
  Downloading llvmlite-0.37.0-cp39-cp39-macosx_10_9_x86_64.whl (19.1 MB)
     |████████████████████████████████| 19.1 MB 10.4 MB/s 
Collecting threadpoolctl>=2.0.0
  Using cached threadpoolctl-2.2.0-py3-none-any.whl (12 kB)
Building wheels for collected packages: tslearn
  Building wheel for tslearn (PEP 517) ... done
  Created wheel for tslearn: filename=tslearn-0.5.2-cp39-cp39-macosx_11_0_x86_64.whl size=453841 sha256=61509e3465a305d68cf80d79cb2bce6e65b79df2ac44801e313619dce6c46570
  Stored in directory: /Users/xxxx/Library/Caches/pip/wheels/0b/54/14/f3e83b35c37ecd2c38ab5cce1d6954421e3f22b20b41447401
Successfully built tslearn
Installing collected packages: numpy, threadpoolctl, scipy, llvmlite, joblib, scikit-learn, numba, Cython, tslearn
Successfully installed Cython-0.29.24 joblib-1.0.1 llvmlite-0.37.0 numba-0.54.0 numpy-1.20.3 scikit-learn-0.24.2 scipy-1.7.1 threadpoolctl-2.2.0 tslearn-0.5.2


$ pip list

Package       Version
------------- -------
Cython        0.29.24
joblib        1.0.1
llvmlite      0.37.0
numba         0.54.0
numpy         1.20.3
pip           21.2.3
scikit-learn  0.24.2
scipy         1.7.1
setuptools    57.4.0
threadpoolctl 2.2.0
tslearn       0.5.2