Issue with scipy install on windows

python numpy scipy scikit-learn
13,176

On Windows, you can run into problems if installing scipy using pip. If you're running anaconda, you can try what was suggested in the comments:

conda install scipy

Or you can try downloading a Windows version of the latest scipy from here:

Unofficial Windows Binaries for Python Extension Packages by Christoph Gohlke, Laboratory for Fluorescence Dynamics, University of California, Irvine

And then using pip to install the downloaded .whl file.

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13,176
swamoch
Author by

swamoch

Updated on June 15, 2022

Comments

  • swamoch
    swamoch almost 2 years

    I had previously install scipy, numpy and then scikit-learn which were all working fine. Today, I updated all my libraries with a pip install. numpy and scikit-learn updated to the latest versions, but scipy had a compile issue and was rolled back.

    When I try 

    from sklearn.ensemble import RandomForestClassifier

    I get

    ImportError: No module named 'format'

    I tried to resolve this, but it didn't work for me.

    So, I uninstalled scipy, so that I can reinstall without any errors. I am unable to do this.

    Failed building wheel for scipy when i try pip install scipy

    this is the trace:

    Collecting scipy
  Using cached scipy-0.16.0.tar.gz
Building wheels for collected packages: scipy
  Running setup.py bdist_wheel for scipy
  Complete output from command c:\users\xxx\anaconda3\python.exe -c "import setuptools;__file__='C:\\Users\\xxx\\AppData\\Local\\Temp\\pip-build-fqlt6je0\\scipy\\setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" bdist_wheel -d C:\Users\xxx\AppData\Local\Temp\tmpnacedj77pip-wheel-:
  lapack_opt_info:
  openblas_lapack_info:
    libraries openblas not found in ['c:\\users\\xxx\\anaconda3\\lib', 'C:\\', 'c:\\users\\xxx\\anaconda3\\libs']
    NOT AVAILABLE

  lapack_mkl_info:
  mkl_info:
    libraries mkl_lapack95_lp64,mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,libiomp5md,libifportmd not found in []
    NOT AVAILABLE

    NOT AVAILABLE

  atlas_3_10_threads_info:
  Setting PTATLAS=ATLAS
    libraries tatlas,tatlas not found in c:\users\xxx\anaconda3\lib
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
    libraries tatlas,tatlas not found in C:\
    libraries lapack_atlas not found in C:\
    libraries tatlas,tatlas not found in c:\users\xxx\anaconda3\libs
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
  <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
    NOT AVAILABLE

  atlas_3_10_info:
    libraries satlas,satlas not found in c:\users\xxx\anaconda3\lib
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
    libraries satlas,satlas not found in C:\
    libraries lapack_atlas not found in C:\
    libraries satlas,satlas not found in c:\users\xxx\anaconda3\libs
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
  <class 'numpy.distutils.system_info.atlas_3_10_info'>
    NOT AVAILABLE

  atlas_threads_info:
  Setting PTATLAS=ATLAS
    libraries ptf77blas,ptcblas,atlas not found in c:\users\xxx\anaconda3\lib
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
    libraries ptf77blas,ptcblas,atlas not found in C:\
    libraries lapack_atlas not found in C:\
    libraries ptf77blas,ptcblas,atlas not found in c:\users\xxx\anaconda3\libs
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
  <class 'numpy.distutils.system_info.atlas_threads_info'>
    NOT AVAILABLE

  atlas_info:
    libraries f77blas,cblas,atlas not found in c:\users\xxx\anaconda3\lib
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
    libraries f77blas,cblas,atlas not found in C:\
    libraries lapack_atlas not found in C:\
    libraries f77blas,cblas,atlas not found in c:\users\xxx\anaconda3\libs
    libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
  <class 'numpy.distutils.system_info.atlas_info'>
    NOT AVAILABLE

  lapack_info:
    libraries lapack not found in ['c:\\users\\xxx\\anaconda3\\lib', 'C:\\', 'c:\\users\\xxx\\anaconda3\\libs']
    NOT AVAILABLE

  lapack_src_info:
    NOT AVAILABLE

    NOT AVAILABLE

  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/lib/intel64 is invalid.
    warnings.warn('Specified path %s is invalid.' % d)
  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/compiler/lib/intel64 is invalid.
    warnings.warn('Specified path %s is invalid.' % d)
  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/include is invalid.
    warnings.warn('Specified path %s is invalid.' % d)
  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1505: 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.
    warnings.warn(AtlasNotFoundError.__doc__)
  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1516: 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.
    warnings.warn(LapackNotFoundError.__doc__)
  c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1519: 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.
    warnings.warn(LapackSrcNotFoundError.__doc__)
  Running from scipy source directory.
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 253, in <module>
      setup_package()
    File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 250, in setup_package
      setup(**metadata)
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\core.py", line 135, in setup
      config = configuration()
    File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 175, in configuration
      config.add_subpackage('scipy')
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 966, in add_subpackage
      caller_level = 2)
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 935, in get_subpackage
      caller_level = caller_level + 1)
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 872, in _get_configuration_from_setup_py
      config = setup_module.configuration(*args)
    File "scipy\setup.py", line 15, in configuration
      config.add_subpackage('linalg')
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 966, in add_subpackage
      caller_level = 2)
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 935, in get_subpackage
      caller_level = caller_level + 1)
    File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 872, in _get_configuration_from_setup_py
      config = setup_module.configuration(*args)
    File "scipy\linalg\setup.py", line 19, in configuration
      raise NotFoundError('no lapack/blas resources found')
  numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

  ----------------------------------------
  Failed building wheel for scipy
Failed to build scipy
Installing collected packages: scipy
  Running setup.py install for scipy
    Complete output from command c:\users\xxx\anaconda3\python.exe -c "import setuptools, tokenize;__file__='C:\\Users\\xxx\\AppData\\Local\\Temp\\pip-build-fqlt6je0\\scipy\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\xxx\AppData\Local\Temp\pip-garwperl-record\install-record.txt --single-version-externally-managed --compile:
    lapack_opt_info:
    openblas_lapack_info:
      libraries openblas not found in ['c:\\users\\xxx\\anaconda3\\lib', 'C:\\', 'c:\\users\\xxx\\anaconda3\\libs']
      NOT AVAILABLE

    lapack_mkl_info:
    mkl_info:
      libraries mkl_lapack95_lp64,mkl_blas95_lp64,mkl_intel_lp64,mkl_intel_thread,mkl_core,libiomp5md,libifportmd not found in []
      NOT AVAILABLE

      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
      libraries tatlas,tatlas not found in c:\users\xxx\anaconda3\lib
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
      libraries tatlas,tatlas not found in C:\
      libraries lapack_atlas not found in C:\
      libraries tatlas,tatlas not found in c:\users\xxx\anaconda3\libs
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
      libraries satlas,satlas not found in c:\users\xxx\anaconda3\lib
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
      libraries satlas,satlas not found in C:\
      libraries lapack_atlas not found in C:\
      libraries satlas,satlas not found in c:\users\xxx\anaconda3\libs
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in c:\users\xxx\anaconda3\lib
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
      libraries ptf77blas,ptcblas,atlas not found in C:\
      libraries lapack_atlas not found in C:\
      libraries ptf77blas,ptcblas,atlas not found in c:\users\xxx\anaconda3\libs
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
      libraries f77blas,cblas,atlas not found in c:\users\xxx\anaconda3\lib
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\lib
      libraries f77blas,cblas,atlas not found in C:\
      libraries lapack_atlas not found in C:\
      libraries f77blas,cblas,atlas not found in c:\users\xxx\anaconda3\libs
      libraries lapack_atlas not found in c:\users\xxx\anaconda3\libs
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    lapack_info:
      libraries lapack not found in ['c:\\users\\xxx\\anaconda3\\lib', 'C:\\', 'c:\\users\\xxx\\anaconda3\\libs']
      NOT AVAILABLE

    lapack_src_info:
      NOT AVAILABLE

      NOT AVAILABLE

    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/lib/intel64 is invalid.
      warnings.warn('Specified path %s is invalid.' % d)
    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/compiler/lib/intel64 is invalid.
      warnings.warn('Specified path %s is invalid.' % d)
    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:594: UserWarning: Specified path C:/Program Files (x86)/Intel/Composer XE/mkl/include is invalid.
      warnings.warn('Specified path %s is invalid.' % d)
    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1505: 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.
      warnings.warn(AtlasNotFoundError.__doc__)
    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1516: 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.
      warnings.warn(LapackNotFoundError.__doc__)
    c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\system_info.py:1519: 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.
      warnings.warn(LapackSrcNotFoundError.__doc__)
    Running from scipy source directory.
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 253, in <module>
        setup_package()
      File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 250, in setup_package
        setup(**metadata)
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\core.py", line 135, in setup
        config = configuration()
      File "C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy\setup.py", line 175, in configuration
        config.add_subpackage('scipy')
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy\setup.py", line 15, in configuration
        config.add_subpackage('linalg')
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "c:\users\xxx\anaconda3\lib\site-packages\numpy\distutils\misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy\linalg\setup.py", line 19, in configuration
        raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    ----------------------------------------
Command "c:\users\xxx\anaconda3\python.exe -c "import setuptools, tokenize;__file__='C:\\Users\\xxx\\AppData\\Local\\Temp\\pip-build-fqlt6je0\\scipy\\setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record C:\Users\xxx\AppData\Local\Temp\pip-garwperl-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\xxx\AppData\Local\Temp\pip-build-fqlt6je0\scipy

    I see that libraries blas and lapack are missing. Is there a simpler way to resolve my error than having to make from the installers. I would have to get BLAS, LAPACK, ATLAS for this.

    Any inputs as to why I faced this issue, did the library files get deleted when i tried to update?

    Thanks!

  • swamoch
    swamoch over 8 years
    I tried conda install, I keep running into issues like: ImportError: cannot import name 'check_arrays'

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