Gensim problem or pip problem?

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Indra Lukmana

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Apr 11, 2014, 9:17:49 AM4/11/14
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Greetings

i was installing gensim on ubuntu, i used 'pip install --upgrade gensim'. The gensim installed normally, but then the pip program tried to install scipy (which resulted in the following outcome). i tried importing gensim on python shell and there are no error shown, i think it is a problem in pip? (is it right). Do i need to worry about something here?

pip install --upgrade gensimRequirement already up-to-date: gensim in /usr/local/lib/python2.7/dist-packages
  Downloading scipy-0.13.3.tar.gz (10.7MB): 10.7MB downloaded
  Running 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'
    no previously-included directories found matching '*/__pycache__'
    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
  Found existing installation: scipy 0.12.0
    Uninstalling scipy:
      Successfully uninstalled 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
    
    atlas_blas_threads_info:
    Setting PTATLAS=ATLAS
      libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/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', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1504: 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__)
    blas_info:
      libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/x86_64-linux-gnu']
      NOT AVAILABLE
    
    /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1513: UserWarning:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
      warnings.warn(BlasNotFoundError.__doc__)
    blas_src_info:
      NOT AVAILABLE
    
    /usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:
        Blas (http://www.netlib.org/blas/) sources not found.
        Directories to search for the sources can be specified in the
        numpy/distutils/site.cfg file (section [blas_src]) or by setting
        the BLAS_SRC environment variable.
      warnings.warn(BlasSrcNotFoundError.__doc__)
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip_build_root/scipy/setup.py", line 230, in <module>
        setup_package()
      File "/tmp/pip_build_root/scipy/setup.py", line 227, in setup_package
        setup(**metadata)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup
        config = configuration()
      File "/tmp/pip_build_root/scipy/setup.py", line 170, in configuration
        config.add_subpackage('scipy')
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
        caller_level = 2)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
        caller_level = caller_level + 1)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/setup.py", line 12, in configuration
        config.add_subpackage('integrate')
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage
        caller_level = 2)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
        caller_level = caller_level + 1)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
        config = setup_module.configuration(*args)
      File "scipy/integrate/setup.py", line 12, in configuration
        blas_opt = get_info('blas_opt',notfound_action=2)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 348, in get_info
        return cl().get_info(notfound_action)
      File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 507, in get_info
        raise self.notfounderror(self.notfounderror.__doc__)
    numpy.distutils.system_info.BlasNotFoundError:
        Blas (http://www.netlib.org/blas/) libraries not found.
        Directories to search for the libraries can be specified in the
        numpy/distutils/site.cfg file (section [blas]) or by setting
        the BLAS environment variable.
    Complete output from command /usr/bin/python -c "import setuptools;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-XRmxO9-record/install-record.txt --single-version-externally-managed:
    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



atlas_blas_threads_info:

Setting PTATLAS=ATLAS

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

  NOT AVAILABLE



/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1504: 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__)

blas_info:

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

  NOT AVAILABLE



/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1513: UserWarning:

    Blas (http://www.netlib.org/blas/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [blas]) or by setting

    the BLAS environment variable.

  warnings.warn(BlasNotFoundError.__doc__)

blas_src_info:

  NOT AVAILABLE



/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py:1516: UserWarning:

    Blas (http://www.netlib.org/blas/) sources not found.

    Directories to search for the sources can be specified in the

    numpy/distutils/site.cfg file (section [blas_src]) or by setting

    the BLAS_SRC environment variable.

  warnings.warn(BlasSrcNotFoundError.__doc__)

Traceback (most recent call last):

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

  File "/tmp/pip_build_root/scipy/setup.py", line 230, in <module>

    setup_package()

  File "/tmp/pip_build_root/scipy/setup.py", line 227, in setup_package

    setup(**metadata)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/core.py", line 152, in setup

    config = configuration()

  File "/tmp/pip_build_root/scipy/setup.py", line 170, in configuration

    config.add_subpackage('scipy')

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage

    caller_level = 2)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage

    caller_level = caller_level + 1)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/setup.py", line 12, in configuration

    config.add_subpackage('integrate')

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 1003, in add_subpackage

    caller_level = 2)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage

    caller_level = caller_level + 1)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py

    config = setup_module.configuration(*args)

  File "scipy/integrate/setup.py", line 12, in configuration

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

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 348, in get_info

    return cl().get_info(notfound_action)

  File "/usr/lib/python2.7/dist-packages/numpy/distutils/system_info.py", line 507, in get_info

    raise self.notfounderror(self.notfounderror.__doc__)

numpy.distutils.system_info.BlasNotFoundError:

    Blas (http://www.netlib.org/blas/) libraries not found.

    Directories to search for the libraries can be specified in the

    numpy/distutils/site.cfg file (section [blas]) or by setting

    the BLAS environment variable.

----------------------------------------
  Rolling back uninstall of scipy
Cleaning up...
Command /usr/bin/python -c "import setuptools;__file__='/tmp/pip_build_root/scipy/setup.py';exec(compile(open(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" install --record /tmp/pip-XRmxO9-record/install-record.txt --single-version-externally-managed failed with error code 1 in /tmp/pip_build_root/scipy
Storing complete log in /root/.pip/pip.log



Christopher Corley

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Apr 11, 2014, 11:20:44 AM4/11/14
to gensim
You should look up how to install a BLAS library (there should be
several to choose from) on Ubuntu. Then installing scipy should work.

Chris.

Excerpts from Indra Lukmana's message of 2014-04-11 08:17:49 -0500:
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