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'ClosureScope' object has no attribute 'scope_class' #35

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shakthimaan opened this issue Oct 1, 2015 · 13 comments
Closed

'ClosureScope' object has no attribute 'scope_class' #35

shakthimaan opened this issue Oct 1, 2015 · 13 comments

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@shakthimaan
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Trying to install pomegranate (c8a246b) using 'sudo python setup.py install' on Ubuntu 14.10 with Python 2.7.10 and Anaconda 2.3.0. Using gcc and g++ versions 4.9.1.

guest@foo ~/installs/python/pomegranate (master) $ sudo python setup.py install
Compiling pomegranate/utils.pyx because it changed.
Compiling pomegranate/hmm.pyx because it changed.
Compiling pomegranate/FactorGraph.pyx because it changed.
Compiling pomegranate/base.pyx because it changed.
Compiling pomegranate/distributions.pyx because it changed.
Compiling pomegranate/BayesianNetwork.pyx because it changed.
Compiling pomegranate/fsm.pyx because it changed.
Compiling pomegranate/gmm.pyx because it changed.
Cythonizing pomegranate/BayesianNetwork.pyx
Cythonizing pomegranate/FactorGraph.pyx
Cythonizing pomegranate/base.pyx
Cythonizing pomegranate/distributions.pyx
Cythonizing pomegranate/fsm.pyx
warning: pomegranate/fsm.pyx:124:37: Index should be typed for more efficient access
Cythonizing pomegranate/gmm.pyx
Cythonizing pomegranate/hmm.pyx

Error compiling Cython file:
------------------------------------------------------------
...

        if verbose:
            print( "Total Training Improvement: {}".format( improvement ) )
        return improvement

    cdef double _train_baum_welch(self, list sequences, double stop_threshold, 
     ^
------------------------------------------------------------

pomegranate/hmm.pyx:2168:6: closures inside cdef functions not yet supported

Error compiling Cython file:
------------------------------------------------------------
...
                iteration += 1
                last_log_probability_sum = trained_log_probability_sum

                memset( expected_transitions, 0, m*m*sizeof(double) )

                parallel( delayed( self._baum_welch_summarize, check_pickle=False )(
                                                                      ^
------------------------------------------------------------

pomegranate/hmm.pyx:2213:71: Compiler crash in CreateClosureClasses

ModuleNode.body = StatListNode(hmm.pyx:7:0)
StatListNode.stats[23] = StatListNode(hmm.pyx:79:5)
StatListNode.stats[0] = CClassDefNode(hmm.pyx:79:5,
    as_name = u'HiddenMarkovModel',
    base_class_module = u'',
    base_class_name = u'Model',
    class_name = u'HiddenMarkovModel',
    doc = u'\n\tRepresents a Hidden Markov Model.\n\t',
    module_name = u'',
    visibility = u'private')
CClassDefNode.body = StatListNode(hmm.pyx:80:1)
StatListNode.stats[36] = CFuncDefNode(hmm.pyx:2168:6,
    args = [...]/11,
    doc = u'\n\t\tGiven a list of sequences, perform Baum-Welch iterative re-estimation on\n\t\tthe model parameters.\n\t\t\n\t\tIterates until the log of the "score" (total likelihood of all \n\t\tsequences) changes by less than stop_threshold. Returns the final log\n\t\tscore.\n\t\t\n\t\tAlways trains for at least min_iterations.\n\t\t',
    modifiers = [...]/0,
    needs_closure = True,
    visibility = u'private')
CFuncDefNode.body = StatListNode(hmm.pyx:2172:2,
    is_terminator = True)
StatListNode.stats[5] = WithStatNode(hmm.pyx:2201:7)
WithStatNode.body = TryFinallyStatNode(hmm.pyx:2201:7,
    preserve_exception = 1)
TryFinallyStatNode.body = TryExceptStatNode(hmm.pyx:2201:7,
    has_default_clause = 1)
TryExceptStatNode.body = StatListNode(hmm.pyx:2201:7)
StatListNode.stats[1] = StatListNode(hmm.pyx:2202:3)
StatListNode.stats[2] = WhileStatNode(hmm.pyx:2205:3)
WhileStatNode.body = StatListNode(hmm.pyx:2206:4)
StatListNode.stats[4] = ExprStatNode(hmm.pyx:2213:12)
ExprStatNode.expr = SimpleCallNode(hmm.pyx:2213:12,
    analysed = True,
    is_temp = 1,
    use_managed_ref = True)
SimpleCallNode.arg_tuple = TupleNode(hmm.pyx:2213:12,
    is_sequence_constructor = 1,
    is_temp = 1,
    result_is_used = True,
    use_managed_ref = True)
TupleNode.args[0] = GeneratorExpressionNode(hmm.pyx:2213:71,
    genexpr_name = u'genexpr4',
    is_temp = 1,
    name = u'genexpr',
    needs_closure = True,
    needs_self_code = True,
    pymethdef_cname = u'__pyx_mdef_11pomegranate_3hmm_17HiddenMarkovModel_17_train_baum_welch_1genexpr',
    result_is_used = True,
    use_managed_ref = True)

Compiler crash traceback from this point on:
  File "Visitor.py", line 170, in Cython.Compiler.Visitor.TreeVisitor._visit (Cython/Compiler/Visitor.c:4287)
  File "/usr/lib/python2.7/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 2364, in visit_LambdaNode
    self.create_class_from_scope(node.def_node, self.module_scope, node)
  File "/usr/lib/python2.7/dist-packages/Cython/Compiler/ParseTreeTransforms.py", line 2342, in create_class_from_scope
    type=cscope.scope_class.type,
AttributeError: 'ClosureScope' object has no attribute 'scope_class'
Traceback (most recent call last):
  File "setup.py", line 36, in <module>
    extensions = cythonize( extensions )
  File "/usr/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 798, in cythonize
    cythonize_one(*args[1:])
  File "/usr/lib/python2.7/dist-packages/Cython/Build/Dependencies.py", line 915, in cythonize_one
    raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: pomegranate/hmm.pyx
@jmschrei
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jmschrei commented Oct 2, 2015

What is your cython version?

@shakthimaan
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Cython version 0.20.2

@jmschrei
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jmschrei commented Oct 9, 2015

Upgrade to 0.23 and let me know if this fixes the issue.

@jmschrei
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Were you able to get this to work?

@shakthimaan
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I manually installed Cython 0.23.4. It compiles and installs fine, but, when I try to import, I get the following warnings:

>>> from pomegranate import *

In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:2138:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:8636:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:8636:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:10203:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:10203:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12494:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12494:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12568:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12568:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12811:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12811:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:13285:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:13285:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:15347:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:15347:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:9093:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:9093:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:10660:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:10660:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:12951:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:12951:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13025:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13025:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13268:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13268:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13742:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13742:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:15804:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:15804:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_pf_11pomegranate_3fsm_18FiniteStateMachine_10to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:4097:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:8861:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:8861:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:10428:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:10428:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12719:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12719:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12793:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12793:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13036:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13036:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13510:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13510:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:15572:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:15572:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:2099:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:2100:31: warning: variable ‘__pyx_f_11pomegranate_5utils_pair_lse’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils_pair_lse)(double, double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_pf_11pomegranate_3gmm_19GeneralMixtureModel_10to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:4706:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:8423:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:8423:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:9990:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:9990:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12281:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12281:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12355:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12355:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12598:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12598:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13072:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13072:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:15134:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:15134:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^

>>> 

@jmschrei
Copy link
Owner

Yeah this is fine, it normally produces a lot of warnings. As long as it doesn't crash. You can run the unit tests by running nosetests -s -v if you cloned the github repo, and that should ensure it's working on your computer.

@jmschrei
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Owner

You should also get that warning the first time you import. Are you getting it on later imports?

@shakthimaan
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Author

I tried it the second time, and now I get:

$ python
Python 2.7.10 |Anaconda 2.3.0 (64-bit)| (default, May 28 2015, 17:02:03) 
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org
>>> from pomegranate import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/shakthi/installs/python/anaconda/lib/python2.7/site-packages/pomegranate/__init__.py", line 38, in <module>
    from .hmm import *
ImportError: /home/shakthi/installs/python/anaconda/lib/python2.7/site-packages/pomegranate/hmm.so: undefined symbol: PyFPE_jbuf
>>> 

$ python
Python 2.7.10 |Anaconda 2.3.0 (64-bit)| (default, May 28 2015, 17:02:03)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
Anaconda is brought to you by Continuum Analytics.
Please check out: http://continuum.io/thanks and https://binstar.org

from pomegranate import *
Traceback (most recent call last):
File "", line 1, in
File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/pomegranate/init.py", line 38, in
from .hmm import *
ImportError: /home/guest/installs/python/anaconda/lib/python2.7/site-packages/pomegranate/hmm.so: undefined symbol: PyFPE_jbuf

I tried with sudo:

$ sudo python
[sudo] password for guest: 
Python 2.7.8 (default, Oct 20 2014, 15:05:19) 
[GCC 4.9.1] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from pomegranate import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.7/dist-packages/pomegranate/__init__.py", line 38, in <module>
    from .hmm import *
  File "pomegranate/hmm.pyx", line 1, in init pomegranate.hmm (pomegranate/hmm.c:53535)
  File "pomegranate/base.pyx", line 10, in init pomegranate.base (pomegranate/base.c:22782)
ImportError: No module named networkx

@jmschrei
Copy link
Owner

Can you try deleting the pomegranate folder from your site packages folder (or wherever your PYTHON_PATH is), and the associated egg folder, and trying a fresh install? Please try:

git clone https://github.com/jmschrei/pomegranate
cd pomegranate
python setup.py install
nosetests -s -v

Let me know if that works.

@shakthimaan
Copy link
Author

$ nosetests -s -v

warning: pomegranate/hmm.pyx:634:23: Index should be typed for more efficient access
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:2508:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:2509:31: warning: variable ‘__pyx_f_11pomegranate_5utils_pair_lse’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils_pair_lse)(double, double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_pf_11pomegranate_3hmm_17HiddenMarkovModel_16is_infinite’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:7198:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong((__pyx_v_self->finite == 0)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 314; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:7198:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_f_11pomegranate_3hmm_17HiddenMarkovModel__train_baum_welch’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:25249:5: warning: ‘return’ with no value, in function returning non-void [-Wreturn-type]
     return;
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_pf_11pomegranate_3hmm_17HiddenMarkovModel_54to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:30673:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:36984:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:36984:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:38551:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:38551:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:40842:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:40842:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:40916:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:40916:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:41159:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:41159:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:41633:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:41633:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:43695:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:43695:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:258:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:259:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_f_11pomegranate_3hmm_17HiddenMarkovModel__sample’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:15932:58: warning: ‘__pyx_v_k’ may be used uninitialized in this function [-Wmaybe-uninitialized]
       __pyx_t_4 = __Pyx_PyInt_From_int((__pyx_v_out_edges[__pyx_v_k])); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 907; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
                                                          ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_pf_11pomegranate_3hmm_17HiddenMarkovModel_50train’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:24961:13: warning: ‘__pyx_v_improvement’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_t_1 = PyFloat_FromDouble(__pyx_v_improvement); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1969; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
             ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c: In function ‘__pyx_f_11pomegranate_3hmm_17HiddenMarkovModel__train_baum_welch’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:25994:11: warning: ‘__pyx_v_trained_log_probability_sum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   __pyx_r = (__pyx_v_trained_log_probability_sum - __pyx_v_initial_log_probability_sum);
           ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:25994:11: warning: ‘__pyx_v_initial_log_probability_sum’ may be used uninitialized in this function [-Wmaybe-uninitialized]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:2113:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_pf_11pomegranate_4base_5State_8is_silent’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:3238:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_t_1); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 85; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:3238:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_pf_11pomegranate_4base_5Model_2__str__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:4450:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:10345:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:10345:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:11912:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:11912:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14203:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14203:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14277:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14277:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14520:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14520:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14994:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:14994:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:17056:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:17056:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/base.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:2354:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:2355:31: warning: variable ‘__pyx_f_11pomegranate_5utils_pair_lse’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils_pair_lse)(double, double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_11pomegranate_13distributions_12Distribution_30to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:5758:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_3 = __Pyx_PyBool_FromLong(__pyx_v_self->frozen); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 211; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:5758:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_11pomegranate_13distributions_12Distribution_6frozen___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:6323:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_v_self->frozen); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 12; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:6323:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_11pomegranate_13distributions_20DiscreteDistribution_8equals’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:18081:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(Py_False);
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:18154:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(Py_False);
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:18345:7: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
       __Pyx_INCREF(Py_False);
       ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:18369:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(Py_True);
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_11pomegranate_13distributions_19MixtureDistribution_2__str__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:25993:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_11pomegranate_13distributions_33IndependentComponentsDistribution_2__str__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:29587:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_gb_11pomegranate_13distributions_27ConditionalProbabilityTable_7__str___2generator’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:34541:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_gb_11pomegranate_13distributions_21JointProbabilityTable_7__str___2generator3’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:38102:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:43602:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:43602:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:45169:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:45169:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47460:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47460:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47534:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47534:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47777:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:47777:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:48251:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:48251:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:50313:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:50313:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/distributions.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/utils.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/utils.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/utils.c:259:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
Failure: ImportError (Building module pomegranate.hmm failed: ['ImportError: No module named joblib\n']) ... ERROR
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:2134:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:8404:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:8404:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:9971:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:9971:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12262:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12262:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12336:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12336:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12579:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:12579:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:13053:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:13053:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:15115:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:15115:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/BayesianNetwork.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:9081:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:9081:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:10648:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:10648:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:12939:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:12939:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13013:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13013:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13256:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13256:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13730:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:13730:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:15792:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:15792:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/FactorGraph.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_pf_11pomegranate_3fsm_18FiniteStateMachine_10to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:4093:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:8857:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:8857:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:10424:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:10424:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12715:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12715:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12789:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:12789:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13032:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13032:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13506:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:13506:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:15568:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:15568:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/fsm.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1804:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:257:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/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 " \
  ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:2096:31: warning: variable ‘__pyx_f_11pomegranate_5utils__log’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils__log)(double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:2097:31: warning: variable ‘__pyx_f_11pomegranate_5utils_pair_lse’ declared ‘inline’
 static CYTHON_INLINE double (*__pyx_f_11pomegranate_5utils_pair_lse)(double, double); /*proto*/
                               ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_pf_11pomegranate_3gmm_19GeneralMixtureModel_18to_json’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:5123:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __Pyx_INCREF(((PyObject *)((PyObject*)(&PyString_Type))));
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_pf_15View_dot_MemoryView_5array_7memview___get__’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:8840:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 220; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:8840:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_is_slice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:10407:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
         __pyx_t_7 = __Pyx_PyBool_FromLong(__pyx_v_self->dtype_is_object); if (unlikely(!__pyx_t_7)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 385; __pyx_clineno = __LINE__; goto __pyx_L4_error;}
         ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:10407:9: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_16is_c_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12698:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'C', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 579; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12698:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview___pyx_pf_15View_dot_MemoryView_10memoryview_18is_f_contig’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12772:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_1 = __Pyx_PyBool_FromLong(__pyx_memviewslice_is_contig(__pyx_v_mslice, 'F', __pyx_v_self->view.ndim)); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 585; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:12772:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_new’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13015:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 614; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13015:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘_unellipsify’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13489:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
     __pyx_t_4 = __Pyx_PyBool_FromLong(__pyx_v_have_slices); if (unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 654; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
     ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:13489:5: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: In function ‘__pyx_memoryview_fromslice’:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:15551:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   __pyx_t_2 = __Pyx_PyBool_FromLong(__pyx_v_dtype_is_object); if (unlikely(!__pyx_t_2)) {__pyx_filename = __pyx_f[2]; __pyx_lineno = 970; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
   ^
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:15551:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:26:0,
                 from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:257:
/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c: At top level:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1629:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
In file included from /home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/ufuncobject.h:317:0,
                 from /home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/gmm.c:258:
/home/guest/installs/python/anaconda/lib/python2.7/site-packages/numpy/core/include/numpy/__ufunc_api.h:241:1: warning: ‘_import_umath’ defined but not used [-Wunused-function]
 _import_umath(void)
 ^
tests.test_bayes_net.test_guest ... ok
tests.test_bayes_net.test_guest_monty ... ok
tests.test_bayes_net.test_monty ... ok
tests.test_bayes_net.test_imputation ... ok
tests.test_bayes_net.test_numpy_imputation ... ok
tests.test_bayes_net.test_raise_error ... ok
tests.test_distributions.test_normal ... ok
tests.test_distributions.test_uniform ... ok
tests.test_distributions.test_discrete ... ok
tests.test_distributions.test_lognormal ... ok
tests.test_distributions.test_gamma ... ok
tests.test_distributions.test_exponential ... ok
tests.test_distributions.test_gaussian_kernel ... ok
tests.test_distributions.test_triangular_kernel ... ok
tests.test_distributions.test_uniform_kernel ... ok
tests.test_distributions.test_mixture ... ok
tests.test_distributions.test_independent ... ok
tests.test_distributions.test_conditional ... ok
tests.test_distributions.test_monty ... ok
tests.test_fsm.test_nickles ... ok
tests.test_fsm.test_dimes ... ok
tests.test_fsm.test_quarter ... ok
tests.test_fsm.test_invalid ... Exception SyntaxError: SyntaxError('No edges leaving state 10 with key 25',) in 'pomegranate.fsm.FiniteStateMachine._step' ignored
Exception SyntaxError: SyntaxError('No edges leaving state 25 with key 25',) in 'pomegranate.fsm.FiniteStateMachine._step' ignored
ok
tests.test_gmm.test_multivariate_gmm_log_probability ... ok
tests.test_gmm.test_multivariate_gmm_posterior ... ok
tests.test_gmm.test_multivariate_gmm_maximum_a_posteriori ... ok
tests.test_gmm.test_multivariate_gmm_train ... Improvement: 9.61890274923
Improvement: 0.28826350545
Improvement: 0.118696228416
Improvement: 0.842658494989
Improvement: 3.69827255551
Improvement: 0.675616560885
Improvement: 6.75775905989e-06
ok
tests.test_gmm.test_multivariate_gmm_train_iterations ... ok
ERROR
tests.test_huge_monty_hall.test_monty ... ok
tests.test_huge_monty_hall.test_friend ... ok
tests.test_huge_monty_hall.test_remaining ... ok
tests.test_huge_monty_hall.test_prize ... ok
ERROR
tests.test_titanic.test_network ... ok
tests.test_titanic.test_guest ... ok

======================================================================
ERROR: Failure: ImportError (Building module pomegranate.hmm failed: ['ImportError: No module named joblib\n'])
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/home/guest/installs/python/pomegranate/pomegranate/__init__.py", line 38, in <module>
    from .hmm import *
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/pyximport/pyximport.py", line 431, in load_module
    language_level=self.language_level)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/pyximport/pyximport.py", line 210, in load_module
    mod = imp.load_dynamic(name, so_path)
  File "pomegranate/hmm.pyx", line 32, in init pomegranate.hmm (/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:49487)
    from joblib import Parallel
ImportError: Building module pomegranate.hmm failed: ['ImportError: No module named joblib\n']

======================================================================
ERROR: test suite for <module 'tests.test_hmm_training' from '/home/guest/installs/python/pomegranate/tests/test_hmm_training.py'>
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 209, in run
    self.setUp()
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp
    self.setupContext(ancestor)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext
    try_run(context, names)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
    return func()
  File "/home/guest/installs/python/pomegranate/tests/test_hmm_training.py", line 49, in setup
    model.add_transition( model.start, m1, 0.9 )
  File "pomegranate/hmm.pyx", line 206, in pomegranate.hmm.HiddenMarkovModel.add_transition (/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:5371)
    self.graph.add_edge(a, b, weight=log(probability),
NameError: name 'log' is not defined

======================================================================
ERROR: test suite for <module 'tests.test_profile_hmm' from '/home/guest/installs/python/pomegranate/tests/test_profile_hmm.py'>
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 209, in run
    self.setUp()
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 292, in setUp
    self.setupContext(ancestor)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/suite.py", line 315, in setupContext
    try_run(context, names)
  File "/home/guest/installs/python/anaconda/lib/python2.7/site-packages/nose/util.py", line 471, in try_run
    return func()
  File "/home/guest/installs/python/pomegranate/tests/test_profile_hmm.py", line 47, in setup
    model.add_transition( model.start, m1, 0.9 )
  File "pomegranate/hmm.pyx", line 206, in pomegranate.hmm.HiddenMarkovModel.add_transition (/home/guest/.pyxbld/temp.linux-x86_64-2.7/pyrex/pomegranate/hmm.c:5371)
    self.graph.add_edge(a, b, weight=log(probability),
NameError: name 'log' is not defined

----------------------------------------------------------------------
Ran 35 tests in 76.330s

FAILED (errors=3)

Importing from the Python interpreter also stops at 'cannot find joblib'.

@jmschrei
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Owner

Oh. Can you run conda install joblib? =) I may have forgot to mention it in a requirements section somewhere. Version 0.9.0b4 should be the best.

@shakthimaan
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Author

Yup. After running "conda install joblib", running "from pomegranate import *" in the Python interpreter worked. Thanks!

@jmschrei
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Awesome! I'll close the issue then.

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