Problems install SciPy

Question

I'm having an absolute nightmare installing SciPy. I have it working on anaconda but that interpreter doesn't have my other libs.

Using this command python -m pip install scipy produces the error:

Collecting scipy
  Using cached scipy-0.19.0.zip
Installing collected packages: scipy
  Running setup.py install for scipy ... error
    Complete output from command C:\Python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\loba3\\appdata\\local\\temp\\pip-build-9_n1ir\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record c:\users\loba3\appdata\local\temp\pip-vxgx6l-record\install-record.txt --single-version-externally-managed --compile:

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install scipy`   (last SciPy release on PyPI)


    lapack_opt_info:
    openblas_lapack_info:
      libraries openblas not found in ['C:\\Python27\\lib', 'C:\\', 'C:\\Python27\\libs']
      NOT AVAILABLE

    lapack_mkl_info:
      libraries mkl_rt not found in ['C:\\Python27\\lib', 'C:\\', 'C:\\Python27\\libs']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    C:\Python27\lib\site-packages\numpy\distutils\system_info.py:639: UserWarning: Specified path C:\projects\numpy-wheels\windows-wheel-builder\atlas-builds\atlas-3.10.1-sse2-32\lib is invalid.
      warnings.warn('Specified path %s is invalid.' % d)
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1532: 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__)
    lapack_info:
      libraries lapack not found in ['C:\\Python27\\lib', 'C:\\', 'C:\\Python27\\libs']
      NOT AVAILABLE

    C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1543: 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__)
    lapack_src_info:
      NOT AVAILABLE

    C:\Python27\lib\site-packages\numpy\distutils\system_info.py:1546: 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__)
      NOT AVAILABLE

    Running from scipy source directory.
    non-existing path in 'scipy\\integrate': 'quadpack.h'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "c:\users\loba3\appdata\local\temp\pip-build-9_n1ir\scipy\setup.py", line 416, in <module>
        setup_package()
      File "c:\users\loba3\appdata\local\temp\pip-build-9_n1ir\scipy\setup.py", line 412, in setup_package
        setup(**metadata)
      File "C:\Python27\lib\site-packages\numpy\distutils\core.py", line 135, in setup
        config = configuration()
      File "c:\users\loba3\appdata\local\temp\pip-build-9_n1ir\scipy\setup.py", line 336, in configuration
        config.add_subpackage('scipy')
      File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 1000, in add_subpackage
        caller_level = 2)
      File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 969, in get_subpackage
        caller_level = caller_level + 1)
      File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 906, 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:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 1000, in add_subpackage
        caller_level = 2)
      File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 969, in get_subpackage
        caller_level = caller_level + 1)
      File "C:\Python27\lib\site-packages\numpy\distutils\misc_util.py", line 906, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy\linalg\setup.py", line 20, in configuration
        raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    ----------------------------------------
Command "C:\Python27\python.exe -u -c "import setuptools, tokenize;__file__='c:\\users\\loba3\\appdata\\local\\temp\\pip-build-9_n1ir\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record c:\users\loba3\appdata\local\temp\pip-vxgx6l-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in c:\users\loba3\appdata\local\temp\pip-build-9_n1ir\scipy\

Similary installing with: pip3 install scipy Produces:

C:\Users\loba3>pip3 install scipy
Collecting scipy
  Using cached scipy-0.19.0.zip
Building wheels for collected packages: scipy
  Running setup.py bdist_wheel for scipy ... error
  Complete output from command c:\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\loba3\\AppData\\Local\\Temp\\pip-build-0xe2tade\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d C:\Users\loba3\AppData\Local\Temp\tmppxe32c39pip-wheel- --python-tag cp36:
  lapack_opt_info:
  lapack_mkl_info:
    libraries mkl_rt not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
    NOT AVAILABLE

  openblas_lapack_info:
    libraries openblas not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
    NOT AVAILABLE

  atlas_3_10_threads_info:
  Setting PTATLAS=ATLAS
  c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:1051: UserWarning: Specified path C:\projects\numpy-wheels\windows-wheel-builder\atlas-builds\atlas-3.10.1-sse2-32\lib is invalid.
    pre_dirs = system_info.get_paths(self, section, key)
  <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
    NOT AVAILABLE

  atlas_3_10_info:
  <class 'numpy.distutils.system_info.atlas_3_10_info'>
    NOT AVAILABLE

  atlas_threads_info:
  Setting PTATLAS=ATLAS
  <class 'numpy.distutils.system_info.atlas_threads_info'>
    NOT AVAILABLE

  atlas_info:
  <class 'numpy.distutils.system_info.atlas_info'>
    NOT AVAILABLE

  c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
  lapack_info:
    libraries lapack not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
    NOT AVAILABLE

  c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
  lapack_src_info:
    NOT AVAILABLE

  c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
    NOT AVAILABLE

  Running from scipy source directory.
  non-existing path in 'scipy\\integrate': 'quadpack.h'
  Traceback (most recent call last):
    File "<string>", line 1, in <module>
    File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 416, in <module>
      setup_package()
    File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 412, in setup_package
      setup(**metadata)
    File "c:\python36-32\lib\site-packages\numpy\distutils\core.py", line 135, in setup
      config = configuration()
    File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 336, in configuration
      config.add_subpackage('scipy')
    File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage
      caller_level = 2)
    File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage
      caller_level = caller_level + 1)
    File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 907, 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:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage
      caller_level = 2)
    File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage
      caller_level = caller_level + 1)
    File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 907, in _get_configuration_from_setup_py
      config = setup_module.configuration(*args)
    File "scipy\linalg\setup.py", line 20, in configuration
      raise NotFoundError('no lapack/blas resources found')
  numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

  ----------------------------------------
  Failed building wheel for scipy
  Running setup.py clean for scipy
  Complete output from command c:\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\loba3\\AppData\\Local\\Temp\\pip-build-0xe2tade\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:

  `setup.py clean` is not supported, use one of the following instead:

    - `git clean -xdf` (cleans all files)
    - `git clean -Xdf` (cleans all versioned files, doesn't touch
                        files that aren't checked into the git repo)

  Add `--force` to your command to use it anyway if you must (unsupported).


  ----------------------------------------
  Failed cleaning build dir for scipy
Failed to build scipy
Installing collected packages: scipy
  Running setup.py install for scipy ... error
    Complete output from command c:\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\loba3\\AppData\\Local\\Temp\\pip-build-0xe2tade\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\loba3\AppData\Local\Temp\pip-xbbmy91e-record\install-record.txt --single-version-externally-managed --compile:

    Note: if you need reliable uninstall behavior, then install
    with pip instead of using `setup.py install`:

      - `pip install .`       (from a git repo or downloaded source
                               release)
      - `pip install scipy`   (last SciPy release on PyPI)


    lapack_opt_info:
    lapack_mkl_info:
      libraries mkl_rt not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
      NOT AVAILABLE

    openblas_lapack_info:
      libraries openblas not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
      NOT AVAILABLE

    atlas_3_10_threads_info:
    Setting PTATLAS=ATLAS
    c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:1051: UserWarning: Specified path C:\projects\numpy-wheels\windows-wheel-builder\atlas-builds\atlas-3.10.1-sse2-32\lib is invalid.
      pre_dirs = system_info.get_paths(self, section, key)
    <class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
      NOT AVAILABLE

    atlas_3_10_info:
    <class 'numpy.distutils.system_info.atlas_3_10_info'>
      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
    lapack_info:
      libraries lapack not found in ['c:\\python36-32\\lib', 'C:\\', 'c:\\python36-32\\libs']
      NOT AVAILABLE

    c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
    lapack_src_info:
      NOT AVAILABLE

    c:\python36-32\lib\site-packages\numpy\distutils\system_info.py:572: 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()
      NOT AVAILABLE

    Running from scipy source directory.
    non-existing path in 'scipy\\integrate': 'quadpack.h'
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 416, in <module>
        setup_package()
      File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 412, in setup_package
        setup(**metadata)
      File "c:\python36-32\lib\site-packages\numpy\distutils\core.py", line 135, in setup
        config = configuration()
      File "C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\setup.py", line 336, in configuration
        config.add_subpackage('scipy')
      File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage
        caller_level = 2)
      File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage
        caller_level = caller_level + 1)
      File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 907, 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:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 1001, in add_subpackage
        caller_level = 2)
      File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 970, in get_subpackage
        caller_level = caller_level + 1)
      File "c:\python36-32\lib\site-packages\numpy\distutils\misc_util.py", line 907, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy\linalg\setup.py", line 20, in configuration
        raise NotFoundError('no lapack/blas resources found')
    numpy.distutils.system_info.NotFoundError: no lapack/blas resources found

    ----------------------------------------
Command "c:\python36-32\python.exe -u -c "import setuptools, tokenize;__file__='C:\\Users\\loba3\\AppData\\Local\\Temp\\pip-build-0xe2tade\\scipy\\setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record C:\Users\loba3\AppData\Local\Temp\pip-xbbmy91e-record\install-record.txt --single-version-externally-managed --compile" failed with error code 1 in C:\Users\loba3\AppData\Local\Temp\pip-build-0xe2tade\scipy\

I have also tried to install numpy+mlk

C:\Python27\toinstall>python -m pip install numpy-1.11.3+mkl-cp27-cp27m-win_amd64.whl
numpy-1.11.3+mkl-cp27-cp27m-win_amd64.whl is not a supported wheel on this platform.

But it wont let me install

From this post I have installed minGW and added it to my path. Install SciPy still throws the error.

Please help me

EDIT: I'm running on a 64bit system. python 2.7 however the same errors show when I try and install in python 3.6

EDIT: WTF I tried the 32 bit version scipy‑0.19.0‑cp27‑cp27m‑win32.whl and it worked..... but when I got to system in windows it says I have a 64 bit system

Answer 1

Just to add to the list:

I was having the same issue working on an old Python 2.7 project which required scipy==0.17.1. Installing scipy via conda does work, but I needed a "pure" pip installation from a requirements file.

After an hour of searching for a solution, it turns out the latest scipy version (scipy 1.1.0 in my case) installs without issue using pip on windows 10 (and works for my project..).

Answer 2

This is probably because your pip is old. Upgrade pip and try to install scipy again.

pip install --upgrade pip
pip install scipy

Answer 3

As installing scipy package requires a lot of other dependencies to be installed beforehand for it to install as you can read here mentioned on scipy site.

To address your problem:

Method1:

Using pre-built scipy libraries from Christoph Gohlke site

To install .whl file all you is pip

pip install PATH_TO_whl_FILE and it's done.

Method2:

You can simply use Anaconda which comes with lots of scientific libraries including scipy, matplotlib etc.. all you can ever need

Answer 4

one alternative of pip is to use conda, so you can try :

conda install -c anaconda scipy=0.19.0

But normally you should be able to install directly from pip

python -m pip install --upgrade pip
pip install scipy

you can find more information here : https://www.scipy.org/install.html

Answer 5

Don't compile Scipy on Windows, just use a precompiled wheel. You can find it, along with many other precompiled packages for Windows, here: http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy

Also, please try not to use Python 2.7, it's not getting any younger. Use Python 3.