nosetests -v sklearn/ giving errors on master

[devashishd12]

Versions used:

• Python 2.7.11
• Sklearn 0.18.dev0
• Scipy 0.16.1
• Numpy 1.10.2

Just to add, my master is up to date with upstream/master

Following is the traceback:

======================================================================
ERROR: sklearn.neighbors.tests.test_dist_metrics.TestMetrics.test_pickle('wminkowski', {'p': 1, 'w': array([ 0.31179588,  0.69634349,  0.37775184,  0.17960368])})
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/tests/test_dist_metrics.py", line 128, in check_pickle
    D2 = dm2.pairwise(self.X1)
  File "sklearn/neighbors/dist_metrics.pyx", line 390, in sklearn.neighbors.dist_metrics.DistanceMetric.pairwise (sklearn/neighbors/dist_metrics.c:5395)
    self.pdist(get_memview_DTYPE_2D(Xarr),
  File "sklearn/neighbors/dist_metrics.pyx", line 319, in sklearn.neighbors.dist_metrics.DistanceMetric.pdist (sklearn/neighbors/dist_metrics.c:4754)
    D[i1, i2] = self.dist(&X[i1, 0], &X[i2, 0], X.shape[1])
  File "sklearn/neighbors/dist_metrics.pyx", line 612, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.dist (sklearn/neighbors/dist_metrics.c:7880)
    return pow(self.rdist(x1, x2, size), 1. / self.p)
  File "sklearn/neighbors/dist_metrics.pyx", line 602, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.rdist (sklearn/neighbors/dist_metrics.c:7744)
    raise ValueError('WMinkowskiDistance dist: '
ValueError: WMinkowskiDistance dist: size of w does not match

======================================================================
ERROR: sklearn.neighbors.tests.test_dist_metrics.TestMetrics.test_pickle('wminkowski', {'p': 1.5, 'w': array([ 0.31179588,  0.69634349,  0.37775184,  0.17960368])})
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/tests/test_dist_metrics.py", line 128, in check_pickle
    D2 = dm2.pairwise(self.X1)
  File "sklearn/neighbors/dist_metrics.pyx", line 390, in sklearn.neighbors.dist_metrics.DistanceMetric.pairwise (sklearn/neighbors/dist_metrics.c:5395)
    self.pdist(get_memview_DTYPE_2D(Xarr),
  File "sklearn/neighbors/dist_metrics.pyx", line 319, in sklearn.neighbors.dist_metrics.DistanceMetric.pdist (sklearn/neighbors/dist_metrics.c:4754)
    D[i1, i2] = self.dist(&X[i1, 0], &X[i2, 0], X.shape[1])
  File "sklearn/neighbors/dist_metrics.pyx", line 612, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.dist (sklearn/neighbors/dist_metrics.c:7880)
    return pow(self.rdist(x1, x2, size), 1. / self.p)
  File "sklearn/neighbors/dist_metrics.pyx", line 602, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.rdist (sklearn/neighbors/dist_metrics.c:7744)
    raise ValueError('WMinkowskiDistance dist: '
ValueError: WMinkowskiDistance dist: size of w does not match

======================================================================
ERROR: sklearn.neighbors.tests.test_dist_metrics.TestMetrics.test_pickle('wminkowski', {'p': 3, 'w': array([ 0.31179588,  0.69634349,  0.37775184,  0.17960368])})
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/tests/test_dist_metrics.py", line 128, in check_pickle
    D2 = dm2.pairwise(self.X1)
  File "sklearn/neighbors/dist_metrics.pyx", line 390, in sklearn.neighbors.dist_metrics.DistanceMetric.pairwise (sklearn/neighbors/dist_metrics.c:5395)
    self.pdist(get_memview_DTYPE_2D(Xarr),
  File "sklearn/neighbors/dist_metrics.pyx", line 319, in sklearn.neighbors.dist_metrics.DistanceMetric.pdist (sklearn/neighbors/dist_metrics.c:4754)
    D[i1, i2] = self.dist(&X[i1, 0], &X[i2, 0], X.shape[1])
  File "sklearn/neighbors/dist_metrics.pyx", line 612, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.dist (sklearn/neighbors/dist_metrics.c:7880)
    return pow(self.rdist(x1, x2, size), 1. / self.p)
  File "sklearn/neighbors/dist_metrics.pyx", line 602, in sklearn.neighbors.dist_metrics.WMinkowskiDistance.rdist (sklearn/neighbors/dist_metrics.c:7744)
    raise ValueError('WMinkowskiDistance dist: '
ValueError: WMinkowskiDistance dist: size of w does not match

======================================================================
ERROR: sklearn.neighbors.tests.test_dist_metrics.TestMetrics.test_pickle('seuclidean', {'V': array([ 0.22741463,  0.25435648,  0.05802916,  0.43441663])})
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/tests/test_dist_metrics.py", line 128, in check_pickle
    D2 = dm2.pairwise(self.X1)
  File "sklearn/neighbors/dist_metrics.pyx", line 390, in sklearn.neighbors.dist_metrics.DistanceMetric.pairwise (sklearn/neighbors/dist_metrics.c:5395)
    self.pdist(get_memview_DTYPE_2D(Xarr),
  File "sklearn/neighbors/dist_metrics.pyx", line 319, in sklearn.neighbors.dist_metrics.DistanceMetric.pdist (sklearn/neighbors/dist_metrics.c:4754)
    D[i1, i2] = self.dist(&X[i1, 0], &X[i2, 0], X.shape[1])
  File "sklearn/neighbors/dist_metrics.pyx", line 464, in sklearn.neighbors.dist_metrics.SEuclideanDistance.dist (sklearn/neighbors/dist_metrics.c:6384)
    return sqrt(self.rdist(x1, x2, size))
  File "sklearn/neighbors/dist_metrics.pyx", line 454, in sklearn.neighbors.dist_metrics.SEuclideanDistance.rdist (sklearn/neighbors/dist_metrics.c:6239)
    raise ValueError('SEuclidean dist: size of V does not match')
ValueError: SEuclidean dist: size of V does not match

======================================================================
ERROR: sklearn.neighbors.tests.test_dist_metrics.TestMetrics.test_pickle('mahalanobis', {'VI': array([[ 0.80314541,  0.98494408,  0.59389881,  1.16113843],
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/tests/test_dist_metrics.py", line 128, in check_pickle
    D2 = dm2.pairwise(self.X1)
  File "sklearn/neighbors/dist_metrics.pyx", line 390, in sklearn.neighbors.dist_metrics.DistanceMetric.pairwise (sklearn/neighbors/dist_metrics.c:5395)
    self.pdist(get_memview_DTYPE_2D(Xarr),
  File "sklearn/neighbors/dist_metrics.pyx", line 319, in sklearn.neighbors.dist_metrics.DistanceMetric.pdist (sklearn/neighbors/dist_metrics.c:4754)
    D[i1, i2] = self.dist(&X[i1, 0], &X[i2, 0], X.shape[1])
  File "sklearn/neighbors/dist_metrics.pyx", line 682, in sklearn.neighbors.dist_metrics.MahalanobisDistance.dist (sklearn/neighbors/dist_metrics.c:8708)
  File "sklearn/neighbors/dist_metrics.pyx", line 664, in sklearn.neighbors.dist_metrics.MahalanobisDistance.rdist (sklearn/neighbors/dist_metrics.c:8521)
    ITYPE_t size) nogil except -1:
ValueError: Mahalanobis dist: size of V does not match

----------------------------------------------------------------------
Ran 6811 tests in 216.465s

FAILED (SKIP=14, errors=5)

[raghavrv]

Thats strange. Travis/Appveyor doesn't report any errors right? Which OS are you using?

[devashishd12]

Actually now I'm getting a different set of errors after pulling upstream. I'm using ubuntu 14.04. Now I'm getting 86 errors and 9 failures! Can't tell what's happening here..... It's just my system right?
Here's a part of the traceback if this helps:

    from sklearn import svm, grid_search, datasets
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.grid_search.GridSearchCV[0]>", line 1, in <module>
        from sklearn import svm, grid_search, datasets
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/__init__.py", line 13, in <module>
        from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/classes.py", line 6, in <module>
        from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/grid_search.py", line 714, in sklearn.grid_search.GridSearchCV
Failed example:
    iris = datasets.load_iris()
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.grid_search.GridSearchCV[1]>", line 1, in <module>
        iris = datasets.load_iris()
    NameError: name 'datasets' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/grid_search.py", line 716, in sklearn.grid_search.GridSearchCV
Failed example:
    svr = svm.SVC()
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.grid_search.GridSearchCV[3]>", line 1, in <module>
        svr = svm.SVC()
    NameError: name 'svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/grid_search.py", line 717, in sklearn.grid_search.GridSearchCV
Failed example:
    clf = grid_search.GridSearchCV(svr, parameters)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.grid_search.GridSearchCV[4]>", line 1, in <module>
        clf = grid_search.GridSearchCV(svr, parameters)
    NameError: name 'grid_search' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/grid_search.py", line 718, in sklearn.grid_search.GridSearchCV
Failed example:
    clf.fit(iris.data, iris.target)
                                # doctest: +NORMALIZE_WHITESPACE +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.grid_search.GridSearchCV[5]>", line 1, in <module>
        clf.fit(iris.data, iris.target)
    NameError: name 'clf' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1bb56c8>.getvalue()))


======================================================================
FAIL: Doctest: sklearn.metrics.classification.hinge_loss
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for sklearn.metrics.classification.hinge_loss
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1607, in hinge_loss

----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1660, in sklearn.metrics.classification.hinge_loss
Failed example:
    from sklearn import svm
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[0]>", line 1, in <module>
        from sklearn import svm
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/__init__.py", line 13, in <module>
        from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/classes.py", line 6, in <module>
        from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1664, in sklearn.metrics.classification.hinge_loss
Failed example:
    est = svm.LinearSVC(random_state=0)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[4]>", line 1, in <module>
        est = svm.LinearSVC(random_state=0)
    NameError: name 'svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1665, in sklearn.metrics.classification.hinge_loss
Failed example:
    est.fit(X, y)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[5]>", line 1, in <module>
        est.fit(X, y)
    NameError: name 'est' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1670, in sklearn.metrics.classification.hinge_loss
Failed example:
    pred_decision = est.decision_function([[-2], [3], [0.5]])
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[6]>", line 1, in <module>
        pred_decision = est.decision_function([[-2], [3], [0.5]])
    NameError: name 'est' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1671, in sklearn.metrics.classification.hinge_loss
Failed example:
    pred_decision  # doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[7]>", line 1, in <module>
        pred_decision  # doctest: +ELLIPSIS
    NameError: name 'pred_decision' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1673, in sklearn.metrics.classification.hinge_loss
Failed example:
    hinge_loss([-1, 1, 1], pred_decision)  # doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[8]>", line 1, in <module>
        hinge_loss([-1, 1, 1], pred_decision)  # doctest: +ELLIPSIS
    NameError: name 'pred_decision' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1681, in sklearn.metrics.classification.hinge_loss
Failed example:
    est = svm.LinearSVC()
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[12]>", line 1, in <module>
        est = svm.LinearSVC()
    NameError: name 'svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1682, in sklearn.metrics.classification.hinge_loss
Failed example:
    est.fit(X, Y)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[13]>", line 1, in <module>
        est.fit(X, Y)
    NameError: name 'est' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1687, in sklearn.metrics.classification.hinge_loss
Failed example:
    pred_decision = est.decision_function([[-1], [2], [3]])
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[14]>", line 1, in <module>
        pred_decision = est.decision_function([[-1], [2], [3]])
    NameError: name 'est' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/classification.py", line 1689, in sklearn.metrics.classification.hinge_loss
Failed example:
    hinge_loss(y_true, pred_decision, labels)  #doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.classification.hinge_loss[16]>", line 1, in <module>
        hinge_loss(y_true, pred_decision, labels)  #doctest: +ELLIPSIS
    NameError: name 'pred_decision' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1bb5f38>.getvalue()))


======================================================================
FAIL: Doctest: sklearn.metrics.scorer.make_scorer
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for sklearn.metrics.scorer.make_scorer
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/scorer.py", line 249, in make_scorer

----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/scorer.py", line 297, in sklearn.metrics.scorer.make_scorer
Failed example:
    from sklearn.svm import LinearSVC
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.scorer.make_scorer[4]>", line 1, in <module>
        from sklearn.svm import LinearSVC
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/__init__.py", line 13, in <module>
        from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/classes.py", line 6, in <module>
        from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/metrics/scorer.py", line 298, in sklearn.metrics.scorer.make_scorer
Failed example:
    grid = GridSearchCV(LinearSVC(), param_grid={'C': [1, 10]},
                        scoring=ftwo_scorer)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.metrics.scorer.make_scorer[5]>", line 1, in <module>
        grid = GridSearchCV(LinearSVC(), param_grid={'C': [1, 10]},
    NameError: name 'LinearSVC' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1b52f38>.getvalue()))


======================================================================
FAIL: Doctest: sklearn.pipeline.Pipeline
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for sklearn.pipeline.Pipeline
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 28, in Pipeline

----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 58, in sklearn.pipeline.Pipeline
Failed example:
    from sklearn import svm
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[0]>", line 1, in <module>
        from sklearn import svm
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/__init__.py", line 13, in <module>
        from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/classes.py", line 6, in <module>
        from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 60, in sklearn.pipeline.Pipeline
Failed example:
    from sklearn.feature_selection import SelectKBest
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[2]>", line 1, in <module>
        from sklearn.feature_selection import SelectKBest
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 61, in sklearn.pipeline.Pipeline
Failed example:
    from sklearn.feature_selection import f_regression
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[3]>", line 1, in <module>
        from sklearn.feature_selection import f_regression
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 67, in sklearn.pipeline.Pipeline
Failed example:
    anova_filter = SelectKBest(f_regression, k=5)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[6]>", line 1, in <module>
        anova_filter = SelectKBest(f_regression, k=5)
    NameError: name 'SelectKBest' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 68, in sklearn.pipeline.Pipeline
Failed example:
    clf = svm.SVC(kernel='linear')
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[7]>", line 1, in <module>
        clf = svm.SVC(kernel='linear')
    NameError: name 'svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 69, in sklearn.pipeline.Pipeline
Failed example:
    anova_svm = Pipeline([('anova', anova_filter), ('svc', clf)])
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[8]>", line 1, in <module>
        anova_svm = Pipeline([('anova', anova_filter), ('svc', clf)])
    NameError: name 'anova_filter' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 73, in sklearn.pipeline.Pipeline
Failed example:
    anova_svm.set_params(anova__k=10, svc__C=.1).fit(X, y)
                                                 # doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[9]>", line 1, in <module>
        anova_svm.set_params(anova__k=10, svc__C=.1).fit(X, y)
    NameError: name 'anova_svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 76, in sklearn.pipeline.Pipeline
Failed example:
    prediction = anova_svm.predict(X)
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[10]>", line 1, in <module>
        prediction = anova_svm.predict(X)
    NameError: name 'anova_svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 77, in sklearn.pipeline.Pipeline
Failed example:
    anova_svm.score(X, y)                        # doctest: +ELLIPSIS
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[11]>", line 1, in <module>
        anova_svm.score(X, y)                        # doctest: +ELLIPSIS
    NameError: name 'anova_svm' is not defined
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 80, in sklearn.pipeline.Pipeline
Failed example:
    anova_svm.named_steps['anova'].get_support()
    # doctest: +NORMALIZE_WHITESPACE
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.Pipeline[12]>", line 1, in <module>
        anova_svm.named_steps['anova'].get_support()
    NameError: name 'anova_svm' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1b06c68>.getvalue()))


======================================================================
FAIL: Doctest: sklearn.pipeline.make_union
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for sklearn.pipeline.make_union
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 550, in make_union

----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 559, in sklearn.pipeline.make_union
Failed example:
    from sklearn.decomposition import PCA, TruncatedSVD
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.make_union[0]>", line 1, in <module>
        from sklearn.decomposition import PCA, TruncatedSVD
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/decomposition/__init__.py", line 11, in <module>
        from .sparse_pca import SparsePCA, MiniBatchSparsePCA
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/decomposition/sparse_pca.py", line 9, in <module>
        from ..linear_model import ridge_regression
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/pipeline.py", line 560, in sklearn.pipeline.make_union
Failed example:
    make_union(PCA(), TruncatedSVD())    # doctest: +NORMALIZE_WHITESPACE
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.pipeline.make_union[1]>", line 1, in <module>
        make_union(PCA(), TruncatedSVD())    # doctest: +NORMALIZE_WHITESPACE
    NameError: name 'PCA' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1b06f38>.getvalue()))


======================================================================
FAIL: Doctest: sklearn.utils.validation.has_fit_parameter
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 2226, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for sklearn.utils.validation.has_fit_parameter
  File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/utils/validation.py", line 578, in has_fit_parameter

----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/utils/validation.py", line 583, in sklearn.utils.validation.has_fit_parameter
Failed example:
    from sklearn.svm import SVC
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.utils.validation.has_fit_parameter[0]>", line 1, in <module>
        from sklearn.svm import SVC
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/__init__.py", line 13, in <module>
        from .classes import SVC, NuSVC, SVR, NuSVR, OneClassSVM, LinearSVC, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/svm/classes.py", line 6, in <module>
        from ..linear_model.base import LinearClassifierMixin, SparseCoefMixin, \
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/__init__.py", line 23, in <module>
        from .stochastic_gradient import SGDClassifier, SGDRegressor
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/linear_model/stochastic_gradient.py", line 16, in <module>
        from ..feature_selection.from_model import _LearntSelectorMixin
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/__init__.py", line 25, in <module>
        from .mutual_info_ import mutual_info_regression, mutual_info_classif
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/feature_selection/mutual_info_.py", line 11, in <module>
        from ..neighbors import NearestNeighbors
      File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/__init__.py", line 8, in <module>
        from .dist_metrics import DistanceMetric
    ImportError: /home/devashish/EXPERIMENTATION/scikit-learn/sklearn/neighbors/dist_metrics.so: undefined symbol: PyFPE_jbuf
----------------------------------------------------------------------
File "/home/devashish/EXPERIMENTATION/scikit-learn/sklearn/utils/validation.py", line 584, in sklearn.utils.validation.has_fit_parameter
Failed example:
    has_fit_parameter(SVC(), "sample_weight")
Exception raised:
    Traceback (most recent call last):
      File "/home/devashish/miniconda/lib/python2.7/doctest.py", line 1315, in __run
        compileflags, 1) in test.globs
      File "<doctest sklearn.utils.validation.has_fit_parameter[1]>", line 1, in <module>
        has_fit_parameter(SVC(), "sample_weight")
    NameError: name 'SVC' is not defined

>>  raise self.failureException(self.format_failure(<StringIO.StringIO instance at 0x7f52b1ab47e8>.getvalue()))


----------------------------------------------------------------------
Ran 220 tests in 0.811s

FAILED (errors=86, failures=9)

[devashishd12]

This is what happened when I tried to compile dist_metrics.pyx:

In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1761:0,
                 from /usr/include/python2.7/numpy/ndarrayobject.h:17,
                 from /usr/include/python2.7/numpy/arrayobject.h:4,
                 from dist_metrics.c:242:
/usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
dist_metrics.c:245:25: fatal error: arrayobject.h: No such file or directory
 #include "arrayobject.h"
                         ^
compilation terminated.

[raghavrv]

Try a make clean?

[devashishd12]

Typing just make worked. Thanks a lot for the help! Although it still baffles me how this started failing suddenly.