Re: [pystatsmodels] Problem using HDFStore in pandas on Windows 64-bit Anaconda CE

[Jeff Reback]

try

import tables

tables.test()

and report the results (this tests the Pytables suite which HDFStore uses)

you have an installation issue of some kind

maybe a version conflict with HDF5 somewhere

hopefully that will report the issue 

On Feb 14, 2013, at 4:44 PM, Jon <rowla...@gmail.com> wrote:

Hi,

I have an issue using pandas/HDF in the Anaconda CE distribution on Windows 64-bit.

I asked on the Anaconda list and they suggested that it may either be a pandas or pytables issue, so I'm wondering if anyone has see it before.

I have a clean install of Anaconda 1.3.1 64-bit CE edition on a Windows 64-bit machine.

I'm trying to do some basic work with pandas and HD5Store, but even the basics don't seem to be working.

For example the following causes an error:

import pandas as pd; s = pd.HD5Store('store.h5')

I have the same code working on the Anaconda 1.3.0 64-bit CE edition on a Mac fine. I've tried this on a second Windows machine and get the same error.

Is this something I'm doing wrong or is there something wrong with the package?

Interestingly, running the command again in the same session seems to work without an error.

The full output is below.

Thanks,

Jon

Python 2.7.3 |AnacondaCE 1.3.1 (64-bit)| (default, Jan  7 2013, 09:47:12)

.1500 64 bit (AMD64)]

Type "copyright", "credits" or "license" for more information.

IPython 0.13.1 -- An enhanced Interactive Python.

?         -> Introduction and overview of IPython's features.

%quickref -> Quick reference.

help      -> Python's own help system.

object?   -> Details about 'object', use 'object??' for extra details.

In [1]: import pandas as pd

In [2]: s = pd.HDFStore('store.hd5')

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:

  #000: ..\..\src\H5A.c line 241 in H5Acreate2(): not a type

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:

  #000: ..\..\src\H5A.c line 920 in H5Awrite(): not an attribute

    major: Invalid arguments to routine

    minor: Inappropriate type

---------------------------------------------------------------------------

HDF5ExtError                              Traceback (most recent call last)

<ipython-input-2-b95a41da7899> in <module>()

----> 1 s = pd.HDFStore('store.hd5')

C:\Anaconda\lib\site-packages\pandas\io\pytables.pyc in __init__(self, path, mod

e, complevel, complib, fletcher32)

    205         self.fletcher32 = fletcher32

    206         self.filters = None

--> 207         self.open(mode=mode, warn=False)

    208

    209     @property

C:\Anaconda\lib\site-packages\pandas\io\pytables.pyc in open(self, mode, warn)

    298

    299         try:

--> 300             self.handle = h5_open(self.path, self.mode)

    301         except IOError, e:  # pragma: no cover

    302             if 'can not be written' in str(e):

C:\Anaconda\lib\site-packages\pandas\io\pytables.pyc in h5_open(path, mode)

    119 def h5_open(path, mode):

    120     tables = _tables()

--> 121     return tables.openFile(path, mode)

    122

    123

C:\Anaconda\lib\site-packages\tables\file.pyc in openFile(filename, mode, title,

 rootUEP, filters, **kwargs)

    228             return filehandle

    229     # Finally, create the File instance, and return it

--> 230     return File(filename, mode, title, rootUEP, filters, **kwargs)

    231

    232

C:\Anaconda\lib\site-packages\tables\file.pyc in __init__(self, filename, mode,

title, rootUEP, filters, **kwargs)

    533         # Complete the creation of the root node

    534         # (see the explanation in ``RootGroup.__init__()``.

--> 535         root._g_postInitHook()

    536

    537         # Save the PyTables format version for this file.

C:\Anaconda\lib\site-packages\tables\group.pyc in _g_postInitHook(self)

    223                 setAttr = self._v_attrs._g__setattr

    224                 # Set the title, class and version attributes.

--> 225                 setAttr('TITLE', self._v_new_title)

    226                 setAttr('CLASS', self._c_classId)

    227                 setAttr('VERSION', self._v_version)

C:\Anaconda\lib\site-packages\tables\attributeset.pyc in _g__setattr(self, name,

 value)

    384                 value = stvalue[()]

    385

--> 386         self._g_setAttr(self._v_node, name, stvalue)

    387

    388         # New attribute or value. Introduce it into the local

C:\Anaconda\lib\site-packages\tables\hdf5Extension.pyd in tables.hdf5Extension.A

ttributeSet._g_setAttr (tables\hdf5Extension.c:4064)()

HDF5ExtError: Can't set attribute 'TITLE' in node:

 / (RootGroup) ''.

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[Jon]

Thanks Jeff.

I get a header that looks like this:

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

PyTables version:  2.4.0

HDF5 version:      1.8.9

NumPy version:     1.6.2

Numexpr version:   2.0.1 (not using Intel's VML/MKL)

Zlib version:      1.2.3 (in Python interpreter)

Blosc version:     1.1.3 (2010-11-16)

Cython version:    0.17.4

Python version:    2.7.3 |AnacondaCE 1.3.1 (64-bit)| (default, Jan  7 2013, 09:47:12) [MSC v.1500 64 bit (AMD64)]

Byte-ordering:     little

Detected cores:    4

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

Then I get a *lot* of output to standard error - pages and pages of it - that looks something like this:

C:\Anaconda\lib\site-packages\tables\filters.py:253: FiltersWarning: compression library ``bzip2`` is not available; using ``zlib`` instead

  % (complib, default_complib), FiltersWarning )

C:\Anaconda\lib\site-packages\tables\filters.py:253: FiltersWarning: compression library ``lzo`` is not available; using ``zlib`` instead

  % (complib, default_complib), FiltersWarning )

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:

  #000: ..\..\src\H5A.c line 241 in H5Acreate2(): not a type

    major: Invalid arguments to routine

    minor: Inappropriate type

HDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:

  #000: ..\..\src\H5A.c line 920 in H5Awrite(): not an attribute

    major: Invalid arguments to routine

    minor: Inappropriate type

EHDF5-DIAG: Error detected in HDF5 (1.8.9) thread 0:

  #000: ..\..\src\H5A.c line 241 in H5Acreate2(): not a type

    major: Invalid arguments to routine

    minor: Inappropriate type

Thanks,

Jon

[Jeff Reback]

can u post to

mailto:pytable...@lists.sourceforge.net

they know much more about the HDF5 libraries

Jeff 

[Jon]

Just to follow up - this has been confirmed as a packaging problem in Anaconda, which they are looking to fix.

Thanks for the help, Jon

On Thursday, February 14, 2013 10:39:46 PM UTC, Jeff Reback wrote:

can u post to

mailto:pyt...@lists.sourceforge.net

[Jeff Reback]

np