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Created February 6, 2014 11:13
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gensim errors on import of h5py and the neigbors module of sklearn
Raw
gistfile1.txt
Error compiling Cython file:
------------------------------------------------------------
...
(H5E_ARGS, H5E_BADTYPE): ValueError, # Invalid location in file
(H5E_REFERENCE, H5E_CANTINIT): ValueError, # Dereferencing invalid ref
}
cdef struct err_data_t:
H5E_error_t err
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:76:4: 'H5E_error_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct err_data_t:
H5E_error_t err
int n
cdef herr_t walk_cb(int n, H5E_error_t *desc, void *e):
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:79:5: 'herr_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
cdef struct err_data_t:
H5E_error_t err
int n
cdef herr_t walk_cb(int n, H5E_error_t *desc, void *e):
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:79:27: 'H5E_error_t' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
def unsilence_errors():
""" Re-enable HDF5's automatic error printing in this thread """
if H5Eset_auto(H5Eprint, stderr) < 0:
raise RuntimeError("Failed to enable automatic error printing")
cdef err_cookie set_error_handler(err_cookie handler):
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:141:5: 'err_cookie' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
def unsilence_errors():
""" Re-enable HDF5's automatic error printing in this thread """
if H5Eset_auto(H5Eprint, stderr) < 0:
raise RuntimeError("Failed to enable automatic error printing")
cdef err_cookie set_error_handler(err_cookie handler):
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:141:34: 'err_cookie' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
raise RuntimeError("Failed to enable automatic error printing")
cdef err_cookie set_error_handler(err_cookie handler):
# Note: exceptions here will be printed instead of raised.
cdef err_cookie old_handler
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:144:9: 'err_cookie' is not a type identifier
Error compiling Cython file:
------------------------------------------------------------
...
# and contributor agreement.
# Python-style minor error classes. If the minor error code matches an entry
# in this dict, the generated exception will be used.
_minor_table = {
H5E_SEEKERROR: IOError, # Seek failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:13:17: undeclared name not builtin: H5E_SEEKERROR
Error compiling Cython file:
------------------------------------------------------------
...
# Python-style minor error classes. If the minor error code matches an entry
# in this dict, the generated exception will be used.
_minor_table = {
H5E_SEEKERROR: IOError, # Seek failed
H5E_READERROR: IOError, # Read failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:14:17: undeclared name not builtin: H5E_READERROR
Error compiling Cython file:
------------------------------------------------------------
...
# Python-style minor error classes. If the minor error code matches an entry
# in this dict, the generated exception will be used.
_minor_table = {
H5E_SEEKERROR: IOError, # Seek failed
H5E_READERROR: IOError, # Read failed
H5E_WRITEERROR: IOError, # Write failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:15:18: undeclared name not builtin: H5E_WRITEERROR
Error compiling Cython file:
------------------------------------------------------------
...
# in this dict, the generated exception will be used.
_minor_table = {
H5E_SEEKERROR: IOError, # Seek failed
H5E_READERROR: IOError, # Read failed
H5E_WRITEERROR: IOError, # Write failed
H5E_CLOSEERROR: IOError, # Close failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:16:18: undeclared name not builtin: H5E_CLOSEERROR
Error compiling Cython file:
------------------------------------------------------------
...
_minor_table = {
H5E_SEEKERROR: IOError, # Seek failed
H5E_READERROR: IOError, # Read failed
H5E_WRITEERROR: IOError, # Write failed
H5E_CLOSEERROR: IOError, # Close failed
H5E_OVERFLOW: IOError, # Address overflowed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:17:16: undeclared name not builtin: H5E_OVERFLOW
Error compiling Cython file:
------------------------------------------------------------
...
H5E_SEEKERROR: IOError, # Seek failed
H5E_READERROR: IOError, # Read failed
H5E_WRITEERROR: IOError, # Write failed
H5E_CLOSEERROR: IOError, # Close failed
H5E_OVERFLOW: IOError, # Address overflowed
H5E_FCNTL: IOError, # File control (fcntl) failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:18:13: undeclared name not builtin: H5E_FCNTL
Error compiling Cython file:
------------------------------------------------------------
...
H5E_WRITEERROR: IOError, # Write failed
H5E_CLOSEERROR: IOError, # Close failed
H5E_OVERFLOW: IOError, # Address overflowed
H5E_FCNTL: IOError, # File control (fcntl) failed
H5E_FILEEXISTS: IOError, # File already exists
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:20:18: undeclared name not builtin: H5E_FILEEXISTS
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CLOSEERROR: IOError, # Close failed
H5E_OVERFLOW: IOError, # Address overflowed
H5E_FCNTL: IOError, # File control (fcntl) failed
H5E_FILEEXISTS: IOError, # File already exists
H5E_FILEOPEN: IOError, # File already open
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:21:16: undeclared name not builtin: H5E_FILEOPEN
Error compiling Cython file:
------------------------------------------------------------
...
H5E_OVERFLOW: IOError, # Address overflowed
H5E_FCNTL: IOError, # File control (fcntl) failed
H5E_FILEEXISTS: IOError, # File already exists
H5E_FILEOPEN: IOError, # File already open
H5E_CANTCREATE: IOError, # Unable to create file
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:22:18: undeclared name not builtin: H5E_CANTCREATE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_FCNTL: IOError, # File control (fcntl) failed
H5E_FILEEXISTS: IOError, # File already exists
H5E_FILEOPEN: IOError, # File already open
H5E_CANTCREATE: IOError, # Unable to create file
H5E_CANTOPENFILE: IOError, # Unable to open file
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:23:20: undeclared name not builtin: H5E_CANTOPENFILE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_FILEEXISTS: IOError, # File already exists
H5E_FILEOPEN: IOError, # File already open
H5E_CANTCREATE: IOError, # Unable to create file
H5E_CANTOPENFILE: IOError, # Unable to open file
H5E_CANTCLOSEFILE: IOError, # Unable to close file
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:24:21: undeclared name not builtin: H5E_CANTCLOSEFILE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_FILEEXISTS: IOError, # File already exists
H5E_FILEOPEN: IOError, # File already open
H5E_CANTCREATE: IOError, # Unable to create file
H5E_CANTOPENFILE: IOError, # Unable to open file
H5E_CANTCLOSEFILE: IOError, # Unable to close file
H5E_NOTHDF5: IOError, # Not an HDF5 file
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:25:15: undeclared name not builtin: H5E_NOTHDF5
Error compiling Cython file:
------------------------------------------------------------
...
H5E_FILEOPEN: IOError, # File already open
H5E_CANTCREATE: IOError, # Unable to create file
H5E_CANTOPENFILE: IOError, # Unable to open file
H5E_CANTCLOSEFILE: IOError, # Unable to close file
H5E_NOTHDF5: IOError, # Not an HDF5 file
H5E_BADFILE: ValueError, # Bad file ID accessed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:26:15: undeclared name not builtin: H5E_BADFILE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CANTCREATE: IOError, # Unable to create file
H5E_CANTOPENFILE: IOError, # Unable to open file
H5E_CANTCLOSEFILE: IOError, # Unable to close file
H5E_NOTHDF5: IOError, # Not an HDF5 file
H5E_BADFILE: ValueError, # Bad file ID accessed
H5E_TRUNCATED: IOError, # File has been truncated
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:27:17: undeclared name not builtin: H5E_TRUNCATED
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CANTOPENFILE: IOError, # Unable to open file
H5E_CANTCLOSEFILE: IOError, # Unable to close file
H5E_NOTHDF5: IOError, # Not an HDF5 file
H5E_BADFILE: ValueError, # Bad file ID accessed
H5E_TRUNCATED: IOError, # File has been truncated
H5E_MOUNT: IOError, # File mount error
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:28:13: undeclared name not builtin: H5E_MOUNT
Error compiling Cython file:
------------------------------------------------------------
...
H5E_NOTHDF5: IOError, # Not an HDF5 file
H5E_BADFILE: ValueError, # Bad file ID accessed
H5E_TRUNCATED: IOError, # File has been truncated
H5E_MOUNT: IOError, # File mount error
H5E_NOFILTER: IOError, # Requested filter is not available
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:30:16: undeclared name not builtin: H5E_NOFILTER
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADFILE: ValueError, # Bad file ID accessed
H5E_TRUNCATED: IOError, # File has been truncated
H5E_MOUNT: IOError, # File mount error
H5E_NOFILTER: IOError, # Requested filter is not available
H5E_CALLBACK: IOError, # Callback failed
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:31:16: undeclared name not builtin: H5E_CALLBACK
Error compiling Cython file:
------------------------------------------------------------
...
H5E_TRUNCATED: IOError, # File has been truncated
H5E_MOUNT: IOError, # File mount error
H5E_NOFILTER: IOError, # Requested filter is not available
H5E_CALLBACK: IOError, # Callback failed
H5E_CANAPPLY: IOError, # Error from filter 'can apply' callback
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:32:16: undeclared name not builtin: H5E_CANAPPLY
Error compiling Cython file:
------------------------------------------------------------
...
H5E_MOUNT: IOError, # File mount error
H5E_NOFILTER: IOError, # Requested filter is not available
H5E_CALLBACK: IOError, # Callback failed
H5E_CANAPPLY: IOError, # Error from filter 'can apply' callback
H5E_SETLOCAL: IOError, # Error from filter 'set local' callback
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:33:16: undeclared name not builtin: H5E_SETLOCAL
Error compiling Cython file:
------------------------------------------------------------
...
H5E_NOFILTER: IOError, # Requested filter is not available
H5E_CALLBACK: IOError, # Callback failed
H5E_CANAPPLY: IOError, # Error from filter 'can apply' callback
H5E_SETLOCAL: IOError, # Error from filter 'set local' callback
H5E_NOENCODER: IOError, # Filter present but encoding disabled
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:34:17: undeclared name not builtin: H5E_NOENCODER
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CALLBACK: IOError, # Callback failed
H5E_CANAPPLY: IOError, # Error from filter 'can apply' callback
H5E_SETLOCAL: IOError, # Error from filter 'set local' callback
H5E_NOENCODER: IOError, # Filter present but encoding disabled
H5E_BADATOM: ValueError, # Unable to find atom information (already closed?)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:36:15: undeclared name not builtin: H5E_BADATOM
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CANAPPLY: IOError, # Error from filter 'can apply' callback
H5E_SETLOCAL: IOError, # Error from filter 'set local' callback
H5E_NOENCODER: IOError, # Filter present but encoding disabled
H5E_BADATOM: ValueError, # Unable to find atom information (already closed?)
H5E_BADGROUP: ValueError, # Unable to find ID group information
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:37:16: undeclared name not builtin: H5E_BADGROUP
Error compiling Cython file:
------------------------------------------------------------
...
H5E_SETLOCAL: IOError, # Error from filter 'set local' callback
H5E_NOENCODER: IOError, # Filter present but encoding disabled
H5E_BADATOM: ValueError, # Unable to find atom information (already closed?)
H5E_BADGROUP: ValueError, # Unable to find ID group information
H5E_BADSELECT: ValueError, # Invalid selection (hyperslabs)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:38:17: undeclared name not builtin: H5E_BADSELECT
Error compiling Cython file:
------------------------------------------------------------
...
H5E_NOENCODER: IOError, # Filter present but encoding disabled
H5E_BADATOM: ValueError, # Unable to find atom information (already closed?)
H5E_BADGROUP: ValueError, # Unable to find ID group information
H5E_BADSELECT: ValueError, # Invalid selection (hyperslabs)
H5E_UNINITIALIZED: ValueError, # Information is uinitialized
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:39:21: undeclared name not builtin: H5E_UNINITIALIZED
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADATOM: ValueError, # Unable to find atom information (already closed?)
H5E_BADGROUP: ValueError, # Unable to find ID group information
H5E_BADSELECT: ValueError, # Invalid selection (hyperslabs)
H5E_UNINITIALIZED: ValueError, # Information is uinitialized
H5E_UNSUPPORTED: NotImplementedError, # Feature is unsupported
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:40:19: undeclared name not builtin: H5E_UNSUPPORTED
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADGROUP: ValueError, # Unable to find ID group information
H5E_BADSELECT: ValueError, # Invalid selection (hyperslabs)
H5E_UNINITIALIZED: ValueError, # Information is uinitialized
H5E_UNSUPPORTED: NotImplementedError, # Feature is unsupported
H5E_NOTFOUND: KeyError, # Object not found
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:42:16: undeclared name not builtin: H5E_NOTFOUND
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADSELECT: ValueError, # Invalid selection (hyperslabs)
H5E_UNINITIALIZED: ValueError, # Information is uinitialized
H5E_UNSUPPORTED: NotImplementedError, # Feature is unsupported
H5E_NOTFOUND: KeyError, # Object not found
H5E_CANTINSERT: ValueError, # Unable to insert object
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:43:18: undeclared name not builtin: H5E_CANTINSERT
Error compiling Cython file:
------------------------------------------------------------
...
H5E_UNSUPPORTED: NotImplementedError, # Feature is unsupported
H5E_NOTFOUND: KeyError, # Object not found
H5E_CANTINSERT: ValueError, # Unable to insert object
H5E_BADTYPE: TypeError, # Inappropriate type
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:45:15: undeclared name not builtin: H5E_BADTYPE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_NOTFOUND: KeyError, # Object not found
H5E_CANTINSERT: ValueError, # Unable to insert object
H5E_BADTYPE: TypeError, # Inappropriate type
H5E_BADRANGE: ValueError, # Out of range
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:46:16: undeclared name not builtin: H5E_BADRANGE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_NOTFOUND: KeyError, # Object not found
H5E_CANTINSERT: ValueError, # Unable to insert object
H5E_BADTYPE: TypeError, # Inappropriate type
H5E_BADRANGE: ValueError, # Out of range
H5E_BADVALUE: ValueError, # Bad value
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:47:16: undeclared name not builtin: H5E_BADVALUE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADTYPE: TypeError, # Inappropriate type
H5E_BADRANGE: ValueError, # Out of range
H5E_BADVALUE: ValueError, # Bad value
H5E_EXISTS: ValueError, # Object already exists
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:49:14: undeclared name not builtin: H5E_EXISTS
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADTYPE: TypeError, # Inappropriate type
H5E_BADRANGE: ValueError, # Out of range
H5E_BADVALUE: ValueError, # Bad value
H5E_EXISTS: ValueError, # Object already exists
H5E_ALREADYEXISTS: ValueError, # Object already exists, part II
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:50:21: undeclared name not builtin: H5E_ALREADYEXISTS
Error compiling Cython file:
------------------------------------------------------------
...
H5E_BADRANGE: ValueError, # Out of range
H5E_BADVALUE: ValueError, # Bad value
H5E_EXISTS: ValueError, # Object already exists
H5E_ALREADYEXISTS: ValueError, # Object already exists, part II
H5E_CANTCONVERT: TypeError, # Can't convert datatypes
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:51:19: undeclared name not builtin: H5E_CANTCONVERT
Error compiling Cython file:
------------------------------------------------------------
...
H5E_EXISTS: ValueError, # Object already exists
H5E_ALREADYEXISTS: ValueError, # Object already exists, part II
H5E_CANTCONVERT: TypeError, # Can't convert datatypes
H5E_CANTDELETE: KeyError, # Can't delete message
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:53:18: undeclared name not builtin: H5E_CANTDELETE
Error compiling Cython file:
------------------------------------------------------------
...
H5E_ALREADYEXISTS: ValueError, # Object already exists, part II
H5E_CANTCONVERT: TypeError, # Can't convert datatypes
H5E_CANTDELETE: KeyError, # Can't delete message
H5E_CANTOPENOBJ: KeyError,
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:55:19: undeclared name not builtin: H5E_CANTOPENOBJ
Error compiling Cython file:
------------------------------------------------------------
...
H5E_CANTDELETE: KeyError, # Can't delete message
H5E_CANTOPENOBJ: KeyError,
H5E_CANTMOVE: ValueError, # Can't move a link
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:57:16: undeclared name not builtin: H5E_CANTMOVE
Error compiling Cython file:
------------------------------------------------------------
...
# "Fudge" table to accomodate annoying inconsistencies in HDF5's use
# of the minor error codes. If a (major, minor) entry appears here,
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:64:14: undeclared name not builtin: H5E_CACHE
Error compiling Cython file:
------------------------------------------------------------
...
# "Fudge" table to accomodate annoying inconsistencies in HDF5's use
# of the minor error codes. If a (major, minor) entry appears here,
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:65:17: undeclared name not builtin: H5E_RESOURCE
Error compiling Cython file:
------------------------------------------------------------
...
# "Fudge" table to accomodate annoying inconsistencies in HDF5's use
# of the minor error codes. If a (major, minor) entry appears here,
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:65:31: undeclared name not builtin: H5E_CANTINIT
Error compiling Cython file:
------------------------------------------------------------
...
# of the minor error codes. If a (major, minor) entry appears here,
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:66:17: undeclared name not builtin: H5E_INTERNAL
Error compiling Cython file:
------------------------------------------------------------
...
# of the minor error codes. If a (major, minor) entry appears here,
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:66:32: undeclared name not builtin: H5E_SYSERRSTR
Error compiling Cython file:
------------------------------------------------------------
...
# it will override any entry in the minor error table.
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
(H5E_DATATYPE, H5E_CANTINIT): TypeError, # No conversion path
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:67:17: undeclared name not builtin: H5E_DATATYPE
Error compiling Cython file:
------------------------------------------------------------
...
_exact_table = {
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
(H5E_DATATYPE, H5E_CANTINIT): TypeError, # No conversion path
(H5E_DATASET, H5E_CANTINIT): ValueError, # bad param for dataset setup
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:68:16: undeclared name not builtin: H5E_DATASET
Error compiling Cython file:
------------------------------------------------------------
...
(H5E_CACHE, H5E_BADVALUE): IOError, # obj create w/o write intent 1.8
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
(H5E_DATATYPE, H5E_CANTINIT): TypeError, # No conversion path
(H5E_DATASET, H5E_CANTINIT): ValueError, # bad param for dataset setup
(H5E_ARGS, H5E_CANTINIT): TypeError, # Illegal operation on object
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:69:13: undeclared name not builtin: H5E_ARGS
Error compiling Cython file:
------------------------------------------------------------
...
(H5E_RESOURCE, H5E_CANTINIT): IOError, # obj create w/o write intent 1.6
(H5E_INTERNAL, H5E_SYSERRSTR): IOError, # e.g. wrong file permissions
(H5E_DATATYPE, H5E_CANTINIT): TypeError, # No conversion path
(H5E_DATASET, H5E_CANTINIT): ValueError, # bad param for dataset setup
(H5E_ARGS, H5E_CANTINIT): TypeError, # Illegal operation on object
(H5E_SYM, H5E_CANTINIT): ValueError, # Object already exists/1.8
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:70:12: undeclared name not builtin: H5E_SYM
Error compiling Cython file:
------------------------------------------------------------
...
(H5E_DATATYPE, H5E_CANTINIT): TypeError, # No conversion path
(H5E_DATASET, H5E_CANTINIT): ValueError, # bad param for dataset setup
(H5E_ARGS, H5E_CANTINIT): TypeError, # Illegal operation on object
(H5E_SYM, H5E_CANTINIT): ValueError, # Object already exists/1.8
(H5E_ARGS, H5E_BADTYPE): ValueError, # Invalid location in file
(H5E_REFERENCE, H5E_CANTINIT): ValueError, # Dereferencing invalid ref
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:72:18: undeclared name not builtin: H5E_REFERENCE
Error compiling Cython file:
------------------------------------------------------------
...
cdef char *mn_desc = NULL
cdef char *desc = NULL
err.n = -1
if H5Ewalk(H5E_WALK_UPWARD, walk_cb, &err) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:97:14: undeclared name not builtin: H5Ewalk
Error compiling Cython file:
------------------------------------------------------------
...
cdef char *mn_desc = NULL
cdef char *desc = NULL
err.n = -1
if H5Ewalk(H5E_WALK_UPWARD, walk_cb, &err) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:97:30: undeclared name not builtin: H5E_WALK_UPWARD
Error compiling Cython file:
------------------------------------------------------------
...
cdef char *mn_desc = NULL
cdef char *desc = NULL
err.n = -1
if H5Ewalk(H5E_WALK_UPWARD, walk_cb, &err) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:97:39: Cannot convert '<error>' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef char *mn_desc = NULL
cdef char *desc = NULL
err.n = -1
if H5Ewalk(H5E_WALK_UPWARD, walk_cb, &err) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:97:41: Cannot convert 'err_data_t *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
desc = err.err.desc
if desc is NULL:
raise RuntimeError("Failed to extract detailed error description")
try:
mj_desc = H5Eget_major(err.err.maj_num)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:111:30: undeclared name not builtin: H5Eget_major
Error compiling Cython file:
------------------------------------------------------------
...
desc = err.err.desc
if desc is NULL:
raise RuntimeError("Failed to extract detailed error description")
try:
mj_desc = H5Eget_major(err.err.maj_num)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:111:30: Obtaining 'char *' from temporary Python value
Error compiling Cython file:
------------------------------------------------------------
...
if desc is NULL:
raise RuntimeError("Failed to extract detailed error description")
try:
mj_desc = H5Eget_major(err.err.maj_num)
mn_desc = H5Eget_minor(err.err.min_num)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:112:30: undeclared name not builtin: H5Eget_minor
Error compiling Cython file:
------------------------------------------------------------
...
if desc is NULL:
raise RuntimeError("Failed to extract detailed error description")
try:
mj_desc = H5Eget_major(err.err.maj_num)
mn_desc = H5Eget_minor(err.err.min_num)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:112:30: Obtaining 'char *' from temporary Python value
Error compiling Cython file:
------------------------------------------------------------
...
msg = ("%s (%s: %s)" % (desc.decode('utf-8'),
mj_desc.decode('utf-8'),
mn_desc.decode('utf-8')) ).encode('utf-8')
finally:
free(mj_desc)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:120:12: undeclared name not builtin: free
Error compiling Cython file:
------------------------------------------------------------
...
finally:
free(mj_desc)
free(mn_desc)
# HDF5 forbids freeing "desc"
PyErr_SetString(eclass, msg)
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:124:19: undeclared name not builtin: PyErr_SetString
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "stdio.h":
void *stderr
def silence_errors():
""" Disable HDF5's automatic error printing in this thread """
if H5Eset_auto(NULL, NULL) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:133:18: undeclared name not builtin: H5Eset_auto
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "stdio.h":
void *stderr
def silence_errors():
""" Disable HDF5's automatic error printing in this thread """
if H5Eset_auto(NULL, NULL) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:133:19: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef extern from "stdio.h":
void *stderr
def silence_errors():
""" Disable HDF5's automatic error printing in this thread """
if H5Eset_auto(NULL, NULL) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:133:25: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
if H5Eset_auto(NULL, NULL) < 0:
raise RuntimeError("Failed to disable automatic error printing")
def unsilence_errors():
""" Re-enable HDF5's automatic error printing in this thread """
if H5Eset_auto(H5Eprint, stderr) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:138:27: undeclared name not builtin: H5Eprint
Error compiling Cython file:
------------------------------------------------------------
...
if H5Eset_auto(NULL, NULL) < 0:
raise RuntimeError("Failed to disable automatic error printing")
def unsilence_errors():
""" Re-enable HDF5's automatic error printing in this thread """
if H5Eset_auto(H5Eprint, stderr) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:138:35: Cannot convert 'void *' to Python object
Error compiling Cython file:
------------------------------------------------------------
...
cdef err_cookie set_error_handler(err_cookie handler):
# Note: exceptions here will be printed instead of raised.
cdef err_cookie old_handler
if H5Eget_auto(&old_handler.func, &old_handler.data) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:146:18: undeclared name not builtin: H5Eget_auto
Error compiling Cython file:
------------------------------------------------------------
...
cdef err_cookie set_error_handler(err_cookie handler):
# Note: exceptions here will be printed instead of raised.
cdef err_cookie old_handler
if H5Eget_auto(&old_handler.func, &old_handler.data) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:146:19: Cannot take address of Python variable
Error compiling Cython file:
------------------------------------------------------------
...
cdef err_cookie set_error_handler(err_cookie handler):
# Note: exceptions here will be printed instead of raised.
cdef err_cookie old_handler
if H5Eget_auto(&old_handler.func, &old_handler.data) < 0:
^
------------------------------------------------------------
/Library/Python/2.7/site-packages/h5py/_errors.pyx:146:38: Cannot take address of Python variable
clang: warning: argument unused during compilation: '-mno-fused-madd'
/Users/bayerj/.pyxbld/temp.macosx-10.8-intel-2.7/pyrex/h5py/_errors.c:1:2: error: #error Do not use this file, it is the result of a failed Cython compilation.
#error Do not use this file, it is the result of a failed Cython compilation.
^
1 error generated.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Library/Python/2.7/site-packages/h5py/__init__.py", line 10, in <module>
from h5py import _errors
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 431, in load_module
language_level=self.language_level)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 209, in load_module
inplace=build_inplace, language_level=language_level)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 186, in build_module
reload_support=pyxargs.reload_support)
File "/Library/Python/2.7/site-packages/pyximport/pyxbuild.py", line 104, in pyx_to_dll
dist.run_commands()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/Library/Python/2.7/site-packages/Cython/Distutils/build_ext.py", line 163, in run
_build_ext.build_ext.run(self)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/Library/Python/2.7/site-packages/Cython/Distutils/build_ext.py", line 171, in build_extensions
self.build_extension(ext)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension
depends=ext.depends)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/ccompiler.py", line 624, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/unixccompiler.py", line 180, in _compile
raise CompileError, msg
ImportError: Building module h5py._errors failed: ["CompileError: command 'clang' failed with exit status 1\n"]
Raw
gistfile2.txt
clang: warning: argument unused during compilation: '-mno-fused-madd'
In file included from /Users/bayerj/.pyxbld/temp.macosx-10.8-intel-2.7/pyrex/sklearn/neighbors/dist_metrics.c:340:
In file included from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/arrayobject.h:4:
In file included from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarrayobject.h:17:
In file included from /Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/ndarraytypes.h:1736:
/Library/Python/2.7/site-packages/numpy-1.8.0.dev_dff8c94_20130602-py2.7-macosx-10.8-intel.egg/numpy/core/include/numpy/npy_deprecated_api.h:11:2: warning: #warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
^
/Users/bayerj/.pyxbld/temp.macosx-10.8-intel-2.7/pyrex/sklearn/neighbors/dist_metrics.c:343:10: fatal error: 'arrayobject.h' file not found
#include "arrayobject.h"
^
1 warning and 1 error generated.
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/Users/bayerj/devel/scikit-learn/sklearn/neighbors/__init__.py", line 6, in <module>
from .ball_tree import BallTree
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 431, in load_module
language_level=self.language_level)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 210, in load_module
mod = imp.load_dynamic(name, so_path)
File "dist_metrics.pxd", line 48, in init sklearn.neighbors.ball_tree (/Users/bayerj/.pyxbld/temp.macosx-10.8-intel-2.7/pyrex/sklearn/neighbors/ball_tree.c:35770)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 431, in load_module
language_level=self.language_level)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 209, in load_module
inplace=build_inplace, language_level=language_level)
File "/Library/Python/2.7/site-packages/pyximport/pyximport.py", line 186, in build_module
reload_support=pyxargs.reload_support)
File "/Library/Python/2.7/site-packages/pyximport/pyxbuild.py", line 104, in pyx_to_dll
dist.run_commands()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/Library/Python/2.7/site-packages/Cython/Distutils/build_ext.py", line 163, in run
_build_ext.build_ext.run(self)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 340, in run
self.build_extensions()
File "/Library/Python/2.7/site-packages/Cython/Distutils/build_ext.py", line 171, in build_extensions
self.build_extension(ext)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/command/build_ext.py", line 499, in build_extension
depends=ext.depends)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/ccompiler.py", line 624, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/unixccompiler.py", line 180, in _compile
raise CompileError, msg
ImportError: Building module sklearn.neighbors.ball_tree failed: ['ImportError: Building module sklearn.neighbors.dist_metrics failed: ["CompileError: command \'clang\' failed with exit status 1\\n"]\n']
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