Macports pymc 2.0 test failures

gistfile1.txt

christoph-deils-macbook:tmp deil$ python2.6 -c 'import pymc; pymc.test()'
Running unit tests for pymc.tests
/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/pkgutil.py:186: ImportWarning: Not importing directory '/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/virtualenvwrapper': missing __init__.py
  file, filename, etc = imp.find_module(subname, path)
NumPy version 1.6.2
NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/numpy
Python version 2.6.8 (unknown, Apr 19 2012, 09:26:08) [GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.45)]
nose version 1.1.2
Plotting disabled
...S.S.....F.F..SS...........S.....S......S..............S....S.......S........S.....S..S......../opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pymc/distributions.py:2090: RuntimeWarning: divide by zero encountered in log
  return  np.sum(np.log(2.) + np.log(pymc.utils.normcdf((x-mu)*np.sqrt(tau)*alpha))) + normal_like(x,mu,tau)
....S........SSS....S..
======================================================================
FAIL: test (pymc.tests.test_container.test_Container)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pymc/tests/test_container.py", line 54, in test
    assert(D[1,i] is 1.)
AssertionError

======================================================================
FAIL: test_simple (pymc.tests.test_convergence.test_raftery_lewis)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pymc/tests/test_convergence.py", line 48, in test_simple
    assert(0.8 < (float(nprec)/kmind) / nmin < 1.2)
AssertionError

----------------------------------------------------------------------
Ran 116 tests in 13.725s

FAILED (SKIP=18, failures=2)








christoph-deils-macbook:tmp deil$ python2.7 -c 'import pymc; pymc.test()'
Running unit tests for pymc.tests
NumPy version 1.6.2
NumPy is installed in /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy
Python version 2.7.3 (default, Apr 18 2012, 21:11:11) [GCC 4.2.1 Compatible Apple Clang 3.1 (tags/Apple/clang-318.0.45)]
nose version 1.1.2
...........F.............E...........S..............S..............S....S.......S..............S..S......../opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/distributions.py:2090: RuntimeWarning: divide by zero encountered in log
  return  np.sum(np.log(2.) + np.log(pymc.utils.normcdf((x-mu)*np.sqrt(tau)*alpha))) + normal_like(x,mu,tau)
....S...F.....SS....EEEEEEE..
======================================================================
ERROR: test suite for <class 'pymc.tests.test_database.TestMySQL'>
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/suite.py", line 208, in run
    self.setUp()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/suite.py", line 291, in setUp
    self.setupContext(ancestor)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/suite.py", line 314, in setupContext
    try_run(context, names)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/nose/util.py", line 478, in try_run
    return func()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_database.py", line 165, in setUpClass
    dbmode='w')
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/MCMC.py", line 65, in __init__
    Sampler.__init__(self, input, db, name, calc_deviance=True, **kwds)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/Model.py", line 234, in __init__
    self._assign_database_backend(db)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/Model.py", line 421, in _assign_database_backend
    self.db = module.Database(**self._db_args)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/database/mysql.py", line 110, in __init__
    self.DB = MySQLdb.connect(user=self._user, passwd=self._passwd, host=self._host, port=self._port)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MySQLdb/__init__.py", line 81, in Connect
    return Connection(*args, **kwargs)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/MySQLdb/connections.py", line 187, in __init__
    super(Connection, self).__init__(*args, **kwargs2)
OperationalError: (2003, "Can't connect to MySQL server on 'www.freesql.org' (60)")

======================================================================
ERROR: test_draws (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 43, in test_draws
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_fmin (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 24, in test_fmin
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_fmin_cg (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 33, in test_fmin_cg
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_fmin_l_bfgs_b (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 27, in test_fmin_l_bfgs_b
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_fmin_ncg (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 30, in test_fmin_ncg
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_fmin_powell (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 36, in test_fmin_powell
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
ERROR: test_sig (pymc.tests.test_norm_approx.test_norm_approx)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_norm_approx.py", line 39, in test_sig
    N = NormApprox(model)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/NormalApproximation.py", line 483, in __init__
    raise ImportError, 'Scipy must be installed to use NormApprox and MAP.'
ImportError: Scipy must be installed to use NormApprox and MAP.

======================================================================
FAIL: test (pymc.tests.test_container.test_Container)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_container.py", line 54, in test
    assert(D[1,i] is 1.)
AssertionError

======================================================================
FAIL: test_random (pymc.tests.test_distributions.test_truncnorm)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pymc/tests/test_distributions.py", line 802, in test_random
    assert_almost_equal(r.mean(), truncnorm_expval(-1, .1, -20., 20.), 1)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/testing/utils.py", line 468, in assert_almost_equal
    raise AssertionError(msg)
AssertionError: 
Arrays are not almost equal to 1 decimals
 ACTUAL: -1.0683894166759134
 DESIRED: -0.99999999820581786

----------------------------------------------------------------------
Ran 135 tests in 101.543s

FAILED (SKIP=10, errors=8, failures=2)
Closing remaining open files: testresults/Disaster.hdf5... done