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Issue with scipy install on windows

Tags:

python

numpy

scipy

scikit-learn

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!

like image 300
swamoch Avatar asked Sep 11 '15 19:09

swamoch

People also ask

How do I install SciPy on Windows 10?

Type and run pip install scipy in the command prompt. This will use the Python Package index, and install the core SciPy packages on your computer. You can also install other core packages like Numpy and Matplotlib by using the pip install numpy and pip install matplotlib commands.

Does Python 3.10 support SciPy?

I suppose this is caused because Scipy has no Python 3.10 support (yet), so trying to install it with that Python should fail somewhere. Consider using a lower Python version, or use Anaconda (like a user suggested).

Can I install SciPy with pip?

Method 1: Using pip to install Scipy Package Follow the below steps to install the Scipy package on macOS using pip: Step 1: Install the latest Python3 in MacOS. Step 2: Check if pip3 and python3 are correctly installed. Step 3: Upgrade your pip to avoid errors during installation.

1 Answers

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.

like image 102
IVlad Avatar answered Oct 20 '22 01:10

IVlad
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