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Selecting columns from a HDFStore with a MultiIndex fails #3748

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hmgaudecker opened this issue Jun 3, 2013 · 16 comments · Fixed by #3749
Closed

Selecting columns from a HDFStore with a MultiIndex fails #3748

hmgaudecker opened this issue Jun 3, 2013 · 16 comments · Fixed by #3749
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@hmgaudecker
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Using the example from the docs here: http://pandas.pydata.org/pandas-docs/dev/io.html#storing-multi-index-dataframes but specifying the 'columns' in [1219] keyword when selecting:

store.select('df_mi', columns=['A', 'B'])

leads to the failure below. The original example works, as does selecting columns with a standard index. I'm on a fairly recent master (~1 week) and Python 3.3. Hope this is not expected and I did not miss an issue, I did search for a bit.

KeyError                                  Traceback (most recent call last)
<ipython-input-67-678a9c77d998> in <module>()
----> 1 store.select('df_mi', columns=['A', 'B'])

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, **kwargs)
    413             return TableIterator(func, nrows=s.nrows, start=start, stop=stop, chunksize=chunksize)
    414 
--> 415         return TableIterator(func, nrows=s.nrows, start=start, stop=stop).get_values()
    416 
    417     def select_as_coordinates(self, key, where=None, start=None, stop=None, **kwargs):

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/io/pytables.py in get_values(self)
    931 
    932     def get_values(self):
--> 933         return self.func(self.start, self.stop)
    934 
    935 

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/io/pytables.py in func(_start, _stop)
    408         # what we are actually going to do for a chunk
    409         def func(_start, _stop):
--> 410             return s.read(where=where, start=_start, stop=_stop, columns=columns, **kwargs)
    411 
    412         if iterator or chunksize is not None:

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/io/pytables.py in read(self, *args, **kwargs)
   3142     def read(self, *args, **kwargs):
   3143         df = super(AppendableMultiFrameTable, self).read(*args, **kwargs)
-> 3144         df.set_index(self.levels, inplace=True)
   3145         return df
   3146 

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/frame.py in set_index(self, keys, drop, append, inplace, verify_integrity)
   2795                 names.append(None)
   2796             else:
-> 2797                 level = frame[col].values
   2798                 names.append(col)
   2799                 if drop:

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/frame.py in __getitem__(self, key)
   1992         else:
   1993             # get column
-> 1994             return self._get_item_cache(key)
   1995 
   1996     def _getitem_slice(self, key):

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/generic.py in _get_item_cache(self, item)
    572             return cache[item]
    573         except Exception:
--> 574             values = self._data.get(item)
    575             res = self._box_item_values(item, values)
    576             cache[item] = res

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/internals.py in get(self, item)
   1646 
   1647     def get(self, item):
-> 1648         _, block = self._find_block(item)
   1649         return block.get(item)
   1650 

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/internals.py in _find_block(self, item)
   1773 
   1774     def _find_block(self, item):
-> 1775         self._check_have(item)
   1776         for i, block in enumerate(self.blocks):
   1777             if item in block:

/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas-0.12.0.dev_2bd1cf8-py3.3-linux-x86_64.egg/pandas/core/internals.py in _check_have(self, item)
   1780     def _check_have(self, item):
   1781         if item not in self.items:
-> 1782             raise KeyError('no item named %s' % com.pprint_thing(item))
   1783 
   1784     def reindex_axis(self, new_axis, method=None, axis=0, copy=True):

KeyError: 'no item named foo'
@jreback
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jreback commented Jun 3, 2013

this was a bug thanks for the report, should be in upcoming 0.11.1, was not handling this case

as a workaround, you can do:

store.select('df_mi', columns=['A', 'B','foo','bar'])

@jreback
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jreback commented Jun 3, 2013

also...what version of tables do you have installed?

@hmgaudecker
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Master from last Friday, on top of an Anaconda Python 3.3 environment

In [15]: tables.__version__

Out[15]: '3.0.0rc2'

@jreback
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jreback commented Jun 3, 2013

what happens when you do:

nosetests pandas/io/tests/test_pytables.py

@hmgaudecker
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Nothing pretty... Probably should have checked before, but I never was so sure about how to run Pandas' test suite. So that's something I learned now!

(Output below truncated due to Github limit)

$ nosetests pandas/io/tests/test_pytables.py -v
test_append (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_append_diff_item_order (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_append_frame_column_oriented (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_append_hierarchical (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_append_misc (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_append_raise (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_append_some_nans (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_append_to_multiple (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_append_with_data_columns (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_append_with_strings (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_big_put_frame (pandas.io.tests.test_pytables.TestHDFStore) ... SKIP: no big put frame
test_big_table2_frame (pandas.io.tests.test_pytables.TestHDFStore) ... SKIP: no big table2 frame
test_big_table_frame (pandas.io.tests.test_pytables.TestHDFStore) ... SKIP: no big table frame
test_big_table_panel (pandas.io.tests.test_pytables.TestHDFStore) ... SKIP: no big table panel
test_can_serialize_dates (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_contains (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_conv_read_write (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_coordinates (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_copy (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_create_table_index (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_empty_series_frame (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_factory_fun (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_fixed_offset_tz (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_float_index (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_flush (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_frame (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_frame_select (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_get (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_getattr (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_index_types (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_keys (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_legacy_0_10_read (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_legacy_read (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_legacy_table_read (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_legacy_table_write (pandas.io.tests.test_pytables.TestHDFStore) ... SKIP
test_long (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_longpanel (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test using ndim tables in new ways ... FAIL
test_overwrite_node (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_panel_select (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_put (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_put_compression (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_put_compression_blosc (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_put_integer (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_put_mixed_type (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_put_string_index (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_pytables_native_read (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_read_column (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_remove (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_remove_crit (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_remove_where (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_reopen_handle (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_repr (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_select (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_select_as_multiple (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_select_dtypes (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_select_filter_corner (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_select_iterator (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_select_with_many_inputs (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_series (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_sparse_frame (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_sparse_panel (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_sparse_series (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_sparse_with_compression (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_start_stop (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_store_datetime_fractional_secs (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_store_datetime_mixed (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_store_hierarchical (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_store_index_name (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_store_mixed (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_store_series_name (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_string_select (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_table_append_with_timezones (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_table_index_incompatible_dtypes (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_table_mixed_dtypes (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_table_values_dtypes_roundtrip (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_terms (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_timeseries_preepoch (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_timezones (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_tseries_indices_frame (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_tseries_indices_series (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_tuple_index (pandas.io.tests.test_pytables.TestHDFStore) ... ok
test_unicode_index (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_unimplemented_dtypes_table_columns (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_versioning (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_wide (pandas.io.tests.test_pytables.TestHDFStore) ... ERROR
test_wide_table (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL
test_wide_table_dups (pandas.io.tests.test_pytables.TestHDFStore) ... FAIL

======================================================================
ERROR: test_append_some_nans (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 465, in test_append_some_nans
    store.append('df1', df[10:])
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 610, in append
    self._write_to_group(key, value, table=True, append=True, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2740, in write
    min_itemsize=min_itemsize, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2474, in create_axes
    raise e
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2469, in create_axes
    **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1231, in set_atom
    self.set_atom_string(block, existing_col, min_itemsize, nan_rep)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1272, in set_atom_string
    if eci > itemsize:
TypeError: unorderable types: NoneType() > int()

======================================================================
ERROR: test_append_to_multiple (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2225, in test_append_to_multiple
    tm.assert_frame_equal(result, expected)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 238, in assert_frame_equal
    check_less_precise=check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 197, in assert_series_equal
    assert_almost_equal(left.values, right.values, check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 139, in assert_almost_equal
    assert_almost_equal(a[i], b[i], check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 135, in assert_almost_equal
    if np.array_equal(a, b):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numpy/core/numeric.py", line 2120, in array_equal
    return bool(equal(a1,a2).all())
AttributeError: 'NotImplementedType' object has no attribute 'all'

======================================================================
ERROR: test_append_with_strings (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 635, in test_append_with_strings
    store.append('s1', wp2)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 610, in append
    self._write_to_group(key, value, table=True, append=True, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2761, in write
    a.validate_and_set(table, append)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1065, in validate_and_set
    self.validate_col()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1084, in validate_col
    % (itemsize,self.cname, c.itemsize))
ValueError: Trying to store a string with len [28] in [minor_axis] column but
this column has a limit of [20]!
Consider using min_itemsize to preset the sizes on these columns

======================================================================
ERROR: test_contains (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 177, in test_contains
    store['b'] = tm.makeDataFrame()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_conv_read_write (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 108, in test_conv_read_write
    assert_series_equal(o, roundtrip('series',o))
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 105, in roundtrip
    return read_hdf(self.path, key)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 168, in read_hdf
    return f(store)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 164, in <lambda>
    f = lambda store: store.select(key, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 407, in select
    return TableIterator(func, nrows=s.nrows, start=start, stop=stop).get_values()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 901, in __init__
    self.stop  = min(self.nrows,stop)
TypeError: unorderable types: NoneType() < NoneType()

======================================================================
ERROR: test_copy (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2455, in test_copy
    do_copy()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2452, in do_copy
    safe_close(tstore)
UnboundLocalError: local variable 'tstore' referenced before assignment

======================================================================
ERROR: test_create_table_index (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 859, in test_create_table_index
    store.create_table_index('p5', columns=['major_axis'])
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 686, in create_table_index
    raise Exception("PyTables >= 2.3 is required for table indexing")
Exception: PyTables >= 2.3 is required for table indexing

======================================================================
ERROR: test_empty_series_frame (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1627, in test_empty_series_frame
    self._check_roundtrip(df1, tm.assert_frame_equal)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2327, in _check_roundtrip
    store['obj'] = obj
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_factory_fun (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 89, in test_factory_fun
    tbl['a'] = tm.makeDataFrame()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_getattr (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 257, in test_getattr
    store['df'] = df
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_keys (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 132, in test_keys
    store['b'] = tm.makeStringSeries()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1855, in write
    self.write_index('index', obj.index)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_legacy_0_10_read (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2410, in test_legacy_0_10_read
    store.select(k)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 397, in select
    s = self._create_storer(group)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 792, in _create_storer
    if 'table' not in pt:
TypeError: Type str doesn't support the buffer API

======================================================================
ERROR: test_legacy_read (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2375, in test_legacy_read
    store['a']
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 238, in __getitem__
    return self.get(key)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 371, in get
    return self._read_group(group)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 876, in _read_group
    s = self._create_storer(group)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 792, in _create_storer
    if 'table' not in pt:
TypeError: Type str doesn't support the buffer API

======================================================================
ERROR: test_legacy_table_read (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2386, in test_legacy_table_read
    store.select('df1')
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 397, in select
    s = self._create_storer(group)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 792, in _create_storer
    if 'table' not in pt:
TypeError: Type str doesn't support the buffer API

======================================================================
ERROR: test_long (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1757, in test_long
    self._check_roundtrip(wp.to_frame(), _check)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2327, in _check_roundtrip
    store['obj'] = obj
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_overwrite_node (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1768, in test_overwrite_node
    store['a'] = tm.makeTimeDataFrame()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_panel_select (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2029, in test_panel_select
    result = store.select('wp', [crit1, crit2])
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 407, in select
    return TableIterator(func, nrows=s.nrows, start=start, stop=stop).get_values()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 921, in get_values
    return self.func(self.start, self.stop)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 402, in func
    return s.read(where=where, start=_start, stop=_stop, columns=columns, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2631, in read
    if not self.read_axes(where=where, **kwargs):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2301, in read_axes
    values = self.selection.select()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 3403, in select
    return self.table.table.readWhere(self.condition, start=self.start, stop=self.stop)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/table.py", line 1522, in read_where
    self._where(condition, condvars, start, stop, step)]
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/table.py", line 1484, in _where
    compiled = self._compile_condition(condition, condvars)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/table.py", line 1358, in _compile_condition
    compiled = compile_condition(condition, typemap, indexedcols)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/conditions.py", line 419, in compile_condition
    func = NumExpr(expr, signature)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numexpr-2.1-py3.3-linux-x86_64.egg/numexpr/necompiler.py", line 559, in NumExpr
    precompile(ex, signature, context)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numexpr-2.1-py3.3-linux-x86_64.egg/numexpr/necompiler.py", line 511, in precompile
    constants_order, constants = getConstants(ast)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numexpr-2.1-py3.3-linux-x86_64.egg/numexpr/necompiler.py", line 294, in getConstants
    for a in constants_order]
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numexpr-2.1-py3.3-linux-x86_64.egg/numexpr/necompiler.py", line 294, in <listcomp>
    for a in constants_order]
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numexpr-2.1-py3.3-linux-x86_64.egg/numexpr/necompiler.py", line 284, in convertConstantToKind
    return kind_to_type[kind](x)
TypeError: string argument without an encoding

======================================================================
ERROR: test_put (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 278, in test_put
    store['b'] = df[:10]
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_put_mixed_type (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 374, in test_put_mixed_type
    store.put('df',df)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_put_string_index (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 309, in test_put_string_index
    store['a'] = s
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1855, in write
    self.write_index('index', obj.index)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_read_column (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2147, in test_read_column
    tm.assert_almost_equal(result.values, df2['string'].values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 139, in assert_almost_equal
    assert_almost_equal(a[i], b[i], check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 135, in assert_almost_equal
    if np.array_equal(a, b):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numpy/core/numeric.py", line 2120, in array_equal
    return bool(equal(a1,a2).all())
AttributeError: 'NotImplementedType' object has no attribute 'all'

======================================================================
ERROR: test_remove (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1256, in test_remove
    store['b'] = df
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_remove_where (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1288, in test_remove_where
    crit1 = Term('index', '>', 'foo')
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 3218, in __init__
    raise ValueError("an inequality condition cannot have multiple values [%s]" % str(self))
ValueError: an inequality condition cannot have multiple values [field->index,op->>,value->foo]

======================================================================
ERROR: test_repr (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 145, in test_repr
    store['b'] = tm.makeStringSeries()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1855, in write
    self.write_index('index', obj.index)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_select (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1816, in test_select
    store.put('wp2', wp, table=False)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 2019, in write
    return super(PanelStorer, self).write(obj, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1998, in write
    self.write_index('axis%d' % i, ax)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

======================================================================
ERROR: test_select_as_multiple (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2268, in test_select_as_multiple
    tm.assert_frame_equal(result, expected)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 238, in assert_frame_equal
    check_less_precise=check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 197, in assert_series_equal
    assert_almost_equal(left.values, right.values, check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 139, in assert_almost_equal
    assert_almost_equal(a[i], b[i], check_less_precise)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/util/testing.py", line 135, in assert_almost_equal
    if np.array_equal(a, b):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/numpy/core/numeric.py", line 2120, in array_equal
    return bool(equal(a1,a2).all())
AttributeError: 'NotImplementedType' object has no attribute 'all'

======================================================================
ERROR: test_series (pandas.io.tests.test_pytables.TestHDFStore)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 1456, in test_series
    self._check_roundtrip(s, tm.assert_series_equal)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/tests/test_pytables.py", line 2327, in _check_roundtrip
    store['obj'] = obj
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 241, in __setitem__
    self.put(key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 536, in put
    self._write_to_group(key, value, table=table, append=append, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 871, in _write_to_group
    s.write(obj = value, append=append, complib=complib, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1855, in write
    self.write_index('index', obj.index)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1635, in write_index
    self.write_array(key, converted.values)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/pandas/io/pytables.py", line 1807, in write_array
    self._handle.createArray(self.group, key, value)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/_past.py", line 35, in oldfunc
    return obj(*args, **kwargs)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/file.py", line 892, in create_array
    obj=obj, title=title, byteorder=byteorder)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 187, in __init__
    byteorder, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/node.py", line 266, in __init__
    self._v_objectid = self._g_create()
  File "/home/xxx/anaconda/envs/py33/lib/python3.3/site-packages/tables/array.py", line 204, in _g_create
    raise TypeError("Array objects cannot currently deal with void, "
TypeError: Array objects cannot currently deal with void, unicode or object arrays

----------------------------------------------------------------------
Ran 88 tests in 3.562s

FAILED (SKIP=5, errors=40, failures=15)

@jreback
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jreback commented Jun 3, 2013

ok....just found this out myself!

(as pytables JUST (like yesterday) came out officially for py3k; problem is that everything is stored as bytes,
so have to decode on deserialization......fix soon!

@jreback
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jreback commented Jun 4, 2013

I have opened an issue for this #3750, and am working to get it in the 0.11.1 release. The version you have 'works' as long as you don't use a where clauses (pretty useless I know)....but having some issues with getting this to work. So you are going to be pretty limited until we fix this, either use 2.7 or wait a bit; should have this fixed pretty soon (the python 3 issues). The issue that you raises here is fixed as well. @hmgaudecker thanks for the report

@jreback
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jreback commented Jun 5, 2013

if you are adventurous, pls give this PR a shot: #3762
(also prob want to use PyTables, 3.0.0), should work on 3.3 (still debugging 3.2)

@jreback
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jreback commented Jun 6, 2013

@hmgaudecker I merged into master....all py3k should work now.....(and numpy >=1.6.1)

pls give me a try and let me know...thanks

@hmgaudecker
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Works for me, thanks a lot!!!

@jreback
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jreback commented Jun 7, 2013

great!

do let me know if you find anything...this is pretty new

also....didn't REALLY test actually saving a hdf in py3 and then reading in py2, I think it should work
(the reverse works just fine)

@WellSys
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WellSys commented Aug 10, 2013

I'm duplicating this on Gholke's Pytables downloaded today (8/10/13) , and producing the following error: Array objects cannot currently deal with void, unicode or object arrays.

This thread reads like this was to have been fixed by now and I'm wondering if any of you could point me at binary Pytables install set for Windows 7 64-bit Python 3.3.

Thx.

@jreback
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jreback commented Aug 10, 2013

u r using pandas 0.12?
u need PyTables 3.0.0 as u r using py3

show me the code u r using as well

@WellSys
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WellSys commented Aug 12, 2013

pandas 0.11 -- Is pandas 0.12 required now?
tables 3.0.0

Here's the code :

import pandas as pd
frame = pd.read_csv('ex1.csv')
store = pd.HDFStore('mydata.h5')
''' The following line causes the error '''
store['obj1'] = frame
store['obj1_col'] = frame['a']
print("\n frame via store using HDF5 format = \n", store)
print("\n Page 142, Binary Data Formats: Using HDF5 Format, cont'd")
print("\n frame via store['obj1'] = \n", store['obj1'])

This is ex1.csv:

a b c d message
1 2 3 4 hello
5 6 7 8 world
9 10 11 12 foo

This is from Python for Data Analysis, page 141 on my Nook for PC version, chapter 6, Binary Data Formats, Using HDF5 Format.

I had this snippet tested Saturday morning and then it not only stopped, but my eclipse stopped finding builtins like print() and could not bring up the debugger to duplicate the error message. So, I can't duplicate this problem right now but I thought I would pass this along for your consideration. Thanks for your interest.

@jreback
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jreback commented Aug 12, 2013

yes 0.12 is required if on py 3k with pytables 3.0.0

if not on py3k then < 0.12 is ok

@jreback
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jreback commented Aug 12, 2013

I am going to put a note in the docs about this
pytables 3.0.0 came out after 0.11

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