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Question

alvas

Asked: 2014-10-28 00:28:01 +0800 CST2014-10-28 00:28:01 +0800 CST 2014-10-28 00:28:01 +0800 CST

How to install scipy with pip3?

772

I am trying to install scipy for python3.x and I am trying to install it with pip3

sudo pip3 install scipy

But I have the following errors:

Downloading/unpacking scipy
  Running setup.py (path:/tmp/pip_build_root/scipy/setup.py) egg_info for package scipy

    warning: no previously-included files matching '*_subr_*.f' found under directory 'scipy/linalg/src/id_dist/src'
    no previously-included directories found matching 'scipy/special/tests/data/boost'
    no previously-included directories found matching 'scipy/special/tests/data/gsl'
    no previously-included directories found matching 'doc/build'
    no previously-included directories found matching 'doc/source/generated'
    warning: no previously-included files matching '*.pyc' found anywhere in distribution
    warning: no previously-included files matching '*~' found anywhere in distribution
    warning: no previously-included files matching '*.bak' found anywhere in distribution
    warning: no previously-included files matching '*.swp' found anywhere in distribution
    warning: no previously-included files matching '*.pyo' found anywhere in distribution
Installing collected packages: scipy
  Running setup.py install for scipy
    blas_opt_info:
    blas_mkl_info:
      libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    openblas_info:
      libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib/atlas-base', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    atlas_blas_info:
      libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib/atlas-base', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    blas_info:
      FOUND:
        language = f77
        library_dirs = ['/usr/lib']
        libraries = ['blas']

      FOUND:
        language = f77
        library_dirs = ['/usr/lib']
        libraries = ['blas']
        define_macros = [('NO_ATLAS_INFO', 1)]

    lapack_opt_info:
    openblas_lapack_info:
      libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    lapack_mkl_info:
    mkl_info:
      libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

      NOT AVAILABLE

    atlas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas-base
      libraries lapack_atlas not found in /usr/lib/atlas-base
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib
      libraries lapack_atlas not found in /usr/lib
      libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_threads_info'>
      NOT AVAILABLE

    atlas_info:
      libraries f77blas,cblas,atlas not found in /usr/local/lib
      libraries lapack_atlas not found in /usr/local/lib
      libraries f77blas,cblas,atlas not found in /usr/lib/atlas-base
      libraries lapack_atlas not found in /usr/lib/atlas-base
      libraries f77blas,cblas,atlas not found in /usr/lib
      libraries lapack_atlas not found in /usr/lib
      libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu
      libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu
    <class 'numpy.distutils.system_info.atlas_info'>
      NOT AVAILABLE

    lapack_info:
      libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE

    lapack_src_info:
      NOT AVAILABLE

    /usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1526: 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__)
    /usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1432: 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__)
    /usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1443: 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__)
    /usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1446: 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__)
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip_build_root/scipy/setup.py", line 237, in <module>
        setup_package()
      File "/tmp/pip_build_root/scipy/setup.py", line 234, in setup_package
        setup(**metadata)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/core.py", line 135, in setup
        config = configuration()
      File "/tmp/pip_build_root/scipy/setup.py", line 173, in configuration
        config.add_subpackage('scipy')
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/setup.py", line 13, in configuration
        config.add_subpackage('interpolate')
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage
        caller_level = 2)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage
        caller_level = caller_level + 1)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/interpolate/setup.py", line 11, in configuration
        lapack_opt = get_info('lapack_opt', notfound_action=2)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py", line 356, in get_info
        return cl().get_info(notfound_action)
      File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py", line 514, in get_info
        raise self.notfounderror(self.notfounderror.__doc__)
    numpy.distutils.system_info.LapackNotFoundError:
        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.
    Complete output from command /usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-w234i8a7-record/install-record.txt --single-version-externally-managed --compile:
    blas_opt_info:

blas_mkl_info:

  libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



openblas_info:

  libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



atlas_blas_threads_info:

Setting PTATLAS=ATLAS

  libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib/atlas-base', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



atlas_blas_info:

  libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib/atlas-base', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



blas_info:

  FOUND:

    language = f77

    library_dirs = ['/usr/lib']

    libraries = ['blas']



  FOUND:

    language = f77

    library_dirs = ['/usr/lib']

    libraries = ['blas']

    define_macros = [('NO_ATLAS_INFO', 1)]



lapack_opt_info:

openblas_lapack_info:

  libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



lapack_mkl_info:

mkl_info:

  libraries mkl,vml,guide not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



  NOT AVAILABLE



atlas_threads_info:

Setting PTATLAS=ATLAS

  libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib

  libraries lapack_atlas not found in /usr/local/lib

  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/atlas-base

  libraries lapack_atlas not found in /usr/lib/atlas-base

  libraries ptf77blas,ptcblas,atlas not found in /usr/lib

  libraries lapack_atlas not found in /usr/lib

  libraries ptf77blas,ptcblas,atlas not found in /usr/lib/x86_64-linux-gnu

  libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu

<class 'numpy.distutils.system_info.atlas_threads_info'>

  NOT AVAILABLE



atlas_info:

  libraries f77blas,cblas,atlas not found in /usr/local/lib

  libraries lapack_atlas not found in /usr/local/lib

  libraries f77blas,cblas,atlas not found in /usr/lib/atlas-base

  libraries lapack_atlas not found in /usr/lib/atlas-base

  libraries f77blas,cblas,atlas not found in /usr/lib

  libraries lapack_atlas not found in /usr/lib

  libraries f77blas,cblas,atlas not found in /usr/lib/x86_64-linux-gnu

  libraries lapack_atlas not found in /usr/lib/x86_64-linux-gnu

<class 'numpy.distutils.system_info.atlas_info'>

  NOT AVAILABLE



lapack_info:

  libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']

  NOT AVAILABLE



lapack_src_info:

  NOT AVAILABLE



/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1526: 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__)

/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1432: 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__)

/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1443: 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__)

/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py:1446: 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__)

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/tmp/pip_build_root/scipy/setup.py", line 237, in <module>

    setup_package()

  File "/tmp/pip_build_root/scipy/setup.py", line 234, in setup_package

    setup(**metadata)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/core.py", line 135, in setup

    config = configuration()

  File "/tmp/pip_build_root/scipy/setup.py", line 173, in configuration

    config.add_subpackage('scipy')

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

    caller_level = 2)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

    caller_level = caller_level + 1)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/setup.py", line 13, in configuration

    config.add_subpackage('interpolate')

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 966, in add_subpackage

    caller_level = 2)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 935, in get_subpackage

    caller_level = caller_level + 1)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/misc_util.py", line 872, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/interpolate/setup.py", line 11, in configuration

    lapack_opt = get_info('lapack_opt', notfound_action=2)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py", line 356, in get_info

    return cl().get_info(notfound_action)

  File "/usr/local/lib/python3.4/dist-packages/numpy/distutils/system_info.py", line 514, in get_info

    raise self.notfounderror(self.notfounderror.__doc__)

numpy.distutils.system_info.LapackNotFoundError:

    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.

----------------------------------------
Cleaning up...
Command /usr/bin/python3 -c "import setuptools, tokenize;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(getattr(tokenize, 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-w234i8a7-record/install-record.txt --single-version-externally-managed --compile failed with error code 1 in /tmp/pip_build_root/scipy
Storing debug log for failure in /home/alvas/.pip/pip.log

How do I install scipy with pip3? If there isn't any solution with pip3, how else can i install scipy for python3.x?

1 Answers

Voted

Oli · Answer 1 · 2014-10-28T00:46:54+08:00

It's telling you exactly what you need to do: install all those build dependencies.

Before I get there, I've said a few times before that I generally don't recommend people use pip (or pip3) to install packages into their global Python install. Both pip and apt-get are completely oblivious to each other. Files can be unduly overwritten or removed and because much of your operating system depends on your Python environment working, messing with it isn't a good idea.

So I would recommend either using a virtualenv (where you keep everything separate from the system) or only using repository-deployed packages.

That said, the technical reason you can't install is because SciPy needs to compile a load of stuff and it has external dependencies for a lot of that. These need to be fulfilled. You could do this manually (by reading the error) or in this case where there is a repo version, you could ask Apt to install the build dependencies:

sudo apt-get build-dep python3-scipy

And that will install a metric butt-load of packages. Note that some of these will probably be things you've already wedged in with pip. I'm seeing a lot of numpy stuff. Beware.

And you'd still need to go through a similar process if you're building in a virtualenv but I would recommend against using apt to fulfil your dependencies because you'll probably have differing versions of dependencies. That's not a healthy build recipe.

In short, using the repo version is easiest.

You could also try

sudo apt-get install python3-scipy

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