Unable to install sklearn when building docker image

Question

When I try to install sklearn (scikit-learn) when building a docker image, it fails.

These are the processed lines of the Dockerfile:

FROM amancevice/pandas:0.25.0-alpine

RUN apk update
RUN apk add build-base
RUN apk add gcc musl-dev libc-dev util-linux-dev linux-headers python3-dev postgresql-libs postgresql-dev git libffi-dev libmemcached-dev zlib-dev ca-certificates zlib-dev jpeg-dev freetype-dev libpng

RUN pip3 install --upgrade pip
RUN pip3 install scikit-learn

Everything goes smoothly, right until the last line. There, it first of all takes forever, then an error occurs. This is the log:

Step 6/13 : RUN pip3 install scikit-learn
 ---> Running in 154f28d1d6db
Collecting scikit-learn
  Downloading scikit-learn-0.23.1.tar.gz (7.2 MB)
  Installing build dependencies: started
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-wy0vmutb/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.28.5' 'numpy==1.13.3; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation == '"'"'CPython'"'"'' 'numpy==1.14.0; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation != '"'"'CPython'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'scipy>=0.19.1'
       cwd: None
  Complete output (173 lines):
  Ignoring numpy: markers 'python_version == "3.6" and platform_system != "AIX" and platform_python_implementation == "CPython"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6" and platform_system != "AIX" and platform_python_implementation != "CPython"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.8" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.8" and platform_system == "AIX"' don't match your environment

This is just some text to avoid the error It looks like your post is mostly code; please add some more details..

  Collecting setuptools
    Downloading setuptools-47.1.1-py3-none-any.whl (583 kB)
  Collecting wheel
    Downloading wheel-0.34.2-py2.py3-none-any.whl (26 kB)
  Collecting Cython>=0.28.5
    Downloading Cython-0.29.19-py2.py3-none-any.whl (971 kB)
  Collecting numpy==1.14.5
    Downloading numpy-1.14.5.zip (4.9 MB)
  Collecting scipy>=0.19.1
    Downloading scipy-1.4.1.tar.gz (24.6 MB)
    Installing build dependencies: started
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: still running...
    Installing build dependencies: finished with status 'done'
    Getting requirements to build wheel: started
    Getting requirements to build wheel: finished with status 'done'
      Preparing wheel metadata: started
      Preparing wheel metadata: finished with status 'error'
      ERROR: Command errored out with exit status 1:
       command: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpam7hu__p
           cwd: /tmp/pip-install-r5ojdgp_/scipy
      Complete output (137 lines):
      lapack_opt_info:
      lapack_mkl_info:
      customize UnixCCompiler
        libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE

      openblas_lapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE

      openblas_clapack_info:
      customize UnixCCompiler
      customize UnixCCompiler
        libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE

      atlas_3_10_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries tatlas,tatlas not found in /usr/lib/
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
        NOT AVAILABLE

      atlas_3_10_info:
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries satlas,satlas not found in /usr/lib/
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_3_10_info'>
        NOT AVAILABLE

      atlas_threads_info:
      Setting PTATLAS=ATLAS
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_threads_info'>
        NOT AVAILABLE

      atlas_info:
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/local/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib
      customize UnixCCompiler
        libraries f77blas,cblas,atlas not found in /usr/lib/
      customize UnixCCompiler
        libraries lapack_atlas not found in /usr/lib/
      <class 'numpy.distutils.system_info.atlas_info'>
        NOT AVAILABLE

      lapack_info:
      customize UnixCCompiler
        libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
        NOT AVAILABLE

      lapack_src_info:
        NOT AVAILABLE

        NOT AVAILABLE

      setup.py:420: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-lva1a_hp'), proceeding with generating Cython sources and expanding templates
        ' '.join(sys.argv[1:])))
      Running from scipy source directory.
      /tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624: UserWarning:
          Atlas (http://math-atlas.sourceforge.net/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [atlas]) or by setting
          the ATLAS environment variable.
        self.calc_info()
      /tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624: UserWarning:
          Lapack (http://www.netlib.org/lapack/) libraries not found.
          Directories to search for the libraries can be specified in the
          numpy/distutils/site.cfg file (section [lapack]) or by setting
          the LAPACK environment variable.
        self.calc_info()
      /tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/numpy/distutils/system_info.py:624: UserWarning:
          Lapack (http://www.netlib.org/lapack/) sources not found.
          Directories to search for the sources can be specified in the
          numpy/distutils/site.cfg file (section [lapack_src]) or by setting
          the LAPACK_SRC environment variable.
        self.calc_info()
      Traceback (most recent call last):
        File "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
          main()
        File "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
          json_out['return_val'] = hook(**hook_input['kwargs'])
        File "/usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py", line 133, in prepare_metadata_for_build_wheel
          return hook(metadata_directory, config_settings)
        File "/tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 158, in prepare_metadata_for_build_wheel
          self.run_setup()
        File "/tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 250, in run_setup
          self).run_setup(setup_script=setup_script)
        File "/tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/setuptools/build_meta.py", line 143, in run_setup
          exec(compile(code, __file__, 'exec'), locals())
        File "setup.py", line 540, in <module>
          setup_package()
        File "setup.py", line 536, in setup_package
          setup(**metadata)
        File "/tmp/pip-build-env-ru46tr0i/overlay/lib/python3.7/site-packages/numpy/distutils/core.py", line 135, in setup
          config = configuration()
        File "setup.py", line 435, in configuration
          raise NotFoundError(msg)
      numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpam7hu__p Check the logs for full command output.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3.7 /usr/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-wy0vmutb/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- setuptools wheel 'Cython>=0.28.5' 'numpy==1.13.3; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation == '"'"'CPython'"'"'' 'numpy==1.14.0; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"' and platform_python_implementation != '"'"'CPython'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'scipy>=0.19.1' Check the logs for full command output.
The command '/bin/sh -c pip3 install scikit-learn' returned a non-zero code: 1

Answer 1

I have the same problem. This guy was using python 3.7 and I'm using 3.8 Python Version should not be the problem here.

Try to use other Docker image such as slim ones.

FROM python:3.8-slim
...

References here: Installing python numpy module inside python alpine docker

Answer 2

Try to downgrade your Python version, because Scikit Learn don't support Python 3.9 yet.