[SciPy-User] ImportError for clapack and flapack

Jonathan Bruck jdt.bruck@gmail....
Sat Jan 19 21:52:45 CST 2013


Hi Scipy Users,

I have installed numpy and scipy into a virtualenv using pip but I have
import errors in the linalg libraries that prevent me from continuing to
make SimpleCV work.

running numpy.test() prints out no big messages like this.
running scipy.test() prints out the following.

In particular it is the import errors that are causing me problems.

I am using Ubuntu 12.10 64-bit on my laptop, and I prepared for this
installation by using "sudo apt-get build-dep numpy scipy" (along with
plenty of other installs).

Thanks in advance
Regards,
Jonathan

======================================================================
ERROR: Failure: ImportError
(/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/interpolate/__init__.py",
line 154, in <module>
    from rbf import Rbf
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/interpolate/rbf.py",
line 49, in <module>
    from scipy import linalg
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 15, in <module>
    from scipy.linalg import clapack
ImportError:
/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/clapack.so:
undefined symbol: clapack_sgesv

======================================================================
ERROR: Failure: ImportError
(/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/__init__.py",
line 148, in <module>
    import clapack
ImportError:
/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/lib/lapack/clapack.so:
undefined symbol: clapack_sgesv

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: test_common.test_pade_trivial
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_common.py",
line 9, in test_pade_trivial
    nump, denomp = pade([1.0], 0)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/common.py",
line 371, in pade
    from scipy import linalg
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: test_common.test_pade_4term_exp
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_common.py",
line 18, in test_pade_4term_exp
    nump, denomp = pade(an, 0)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/common.py",
line 371, in pade
    from scipy import linalg
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/__init__.py",
line 146, in <module>
    from _root import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/_root.py",
line 17, in <module>
    import nonlin
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/optimize/nonlin.py",
line 116, in <module>
    from scipy.linalg import norm, solve, inv, qr, svd, lstsq, LinAlgError
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/signal/__init__.py",
line 218, in <module>
    from cont2discrete import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/signal/cont2discrete.py",
line 9, in <module>
    from scipy import linalg
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/__init__.py",
line 90, in <module>
    from isolve import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/__init__.py",
line 6, in <module>
    from lgmres import lgmres
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/lgmres.py",
line 5, in <module>
    from scipy.linalg import get_blas_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/tests/test_base.py",
line 34, in <module>
    from scipy.sparse.linalg import splu
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/__init__.py",
line 90, in <module>
    from isolve import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/__init__.py",
line 6, in <module>
    from lgmres import lgmres
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/sparse/linalg/isolve/lgmres.py",
line 5, in <module>
    from scipy.linalg import get_blas_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
ERROR: Failure: ImportError (cannot import name flapack)
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/loader.py",
line 390, in loadTestsFromName
    addr.filename, addr.module)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 39, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/importer.py",
line 86, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/stats/__init__.py",
line 321, in <module>
    from stats import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/stats/stats.py",
line 194, in <module>
    import scipy.linalg as linalg
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/__init__.py",
line 133, in <module>
    from basic import *
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/basic.py",
line 12, in <module>
    from lapack import get_lapack_funcs
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/linalg/lapack.py",
line 14, in <module>
    from scipy.linalg import flapack
ImportError: cannot import name flapack

======================================================================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py",
line 52, in tst_fromimage
    assert_(img.min() >= imin)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py",
line 34, in assert_
    raise AssertionError(msg)
AssertionError

======================================================================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py",
line 52, in tst_fromimage
    assert_(img.min() >= imin)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py",
line 34, in assert_
    raise AssertionError(msg)
AssertionError

======================================================================
FAIL: Test generator for parametric tests
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/misc/tests/test_pilutil.py",
line 52, in tst_fromimage
    assert_(img.min() >= imin)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py",
line 34, in assert_
    raise AssertionError(msg)
AssertionError

======================================================================
FAIL: test_io.test_imread
----------------------------------------------------------------------
Traceback (most recent call last):
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/nose/case.py",
line 197, in runTest
    self.test(*self.arg)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/decorators.py",
line 146, in skipper_func
    return f(*args, **kwargs)
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/scipy/ndimage/tests/test_io.py",
line 16, in test_imread
    assert_array_equal(img.shape, (300, 420, 3))
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py",
line 707, in assert_array_equal
    verbose=verbose, header='Arrays are not equal')
  File
"/home/jonathan/.virtualenvs/py27/local/lib/python2.7/site-packages/numpy/testing/utils.py",
line 600, in assert_array_compare
    raise AssertionError(msg)
AssertionError:
Arrays are not equal

(shapes (0,), (3,) mismatch)
 x: array([], dtype=float64)
 y: array([300, 420,   3])

----------------------------------------------------------------------
Ran 2446 tests in 24.397s

FAILED (KNOWNFAIL=7, SKIP=7, errors=10, failures=4)
Out[2]: <nose.result.TextTestResult run=2446 errors=10 failures=4>


-- 
There are no passengers on Spaceship Earth.  We are all crew.

Jonathan Bruck
E: jdt.bruck@gmail.com
Mob: 0421188951
Bachelor of Engineering (Mechanical, Biomedical), Bachelor of Medical
Science
--
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