Thread: [Pytables-users] Problem using HDFStore in pandas on Windows 64-bit Anaconda CE

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[Pytables-users] Problem using HDFStore in pandas on Windows 64-bit Anaconda CE

From: Jon R. <row...@gm...> - 2013-02-15 09:29:38

Hi - apologies if this is a duplicate, I had an error sending the
first time and wasn't sure if it made it through.

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

After a little troubleshooting with the Anaconda/pandas lists, it's
been suggested that it might be a pytables issue (or at least some
kind of package mismatch causing pytables not to work).

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

Running the pytables self-test gives the following output:

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

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

Any help would be appreciated.

Thanks,
Jon

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

From: Anthony S. <sc...@gm...> - 2013-02-15 15:57:16

Hi Jon,

Unfortunately, I have no way of testing this out.  I will say that I have
had problems with HDF5 and Anaconda on windows before since they only ship
the static *.lib hdf5 libraries.  So it may be the case that the pandas ->
pytables / hdf5 interface hasn't been properly linked.  Barring someone on
this list who can test things out for you, you might try grabbing the
PyTables source from github and building it on top of your install of
Anaconda.  Sorry...

Be Well
Anthony


On Fri, Feb 15, 2013 at 3:29 AM, Jon Rowland <row...@gm...> wrote:

> Hi - apologies if this is a duplicate, I had an error sending the
> first time and wasn't sure if it made it through.
>
> I have an issue using pandas/HDFStore/pytables in the Anaconda CE
> distribution on Windows 64-bit.
>
> After a little troubleshooting with the Anaconda/pandas lists, it's
> been suggested that it might be a pytables issue (or at least some
> kind of package mismatch causing pytables not to work).
>
> I have a clean install of Anaconda 1.3.1 64-bit CE edition on a
> Windows 64-bit machine.
>
> Running the pytables self-test gives the following output:
>
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> 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
>
> Is this something I'm doing wrong or is there something wrong with the
> package?
>
> Any help would be appreciated.
>
> Thanks,
> Jon
>
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
> Pytables-users mailing list
> Pyt...@li...
> https://lists.sourceforge.net/lists/listinfo/pytables-users
>

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

From: Francesc A. <fa...@gm...> - 2013-02-15 16:12:52

Hi Jon and Anthony,

I can confirm that this is a package error of PyTables in Anaconda CE 64 
for Windows.  We have filed a ticket in Anaconda for fixing this.  Sorry 
for the inconveniences.

Francesc Alted

On 2/15/13 4:56 PM, Anthony Scopatz wrote:
> Hi Jon,
>
> Unfortunately, I have no way of testing this out.  I will say that I 
> have had problems with HDF5 and Anaconda on windows before since they 
> only ship the static *.lib hdf5 libraries.  So it may be the case that 
> the pandas -> pytables / hdf5 interface hasn't been properly linked. 
>  Barring someone on this list who can test things out for you, you 
> might try grabbing the PyTables source from github and building it on 
> top of your install of Anaconda.  Sorry...
>
> Be Well
> Anthony
>
>
> On Fri, Feb 15, 2013 at 3:29 AM, Jon Rowland <row...@gm... 
> <mailto:row...@gm...>> wrote:
>
>     Hi - apologies if this is a duplicate, I had an error sending the
>     first time and wasn't sure if it made it through.
>
>     I have an issue using pandas/HDFStore/pytables in the Anaconda CE
>     distribution on Windows 64-bit.
>
>     After a little troubleshooting with the Anaconda/pandas lists, it's
>     been suggested that it might be a pytables issue (or at least some
>     kind of package mismatch causing pytables not to work).
>
>     I have a clean install of Anaconda 1.3.1 64-bit CE edition on a
>     Windows 64-bit machine.
>
>     Running the pytables self-test gives the following output:
>
>     -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>     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
>
>     Is this something I'm doing wrong or is there something wrong with
>     the package?
>
>     Any help would be appreciated.
>
>     Thanks,
>     Jon
>
>     ------------------------------------------------------------------------------
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>
>
>
>
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-- 
Francesc Alted

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

From: Jon R. <row...@gm...> - 2013-02-15 17:13:04

Thanks for confirming - I'll keep an eye out for the fix.

On Fri, Feb 15, 2013 at 4:12 PM, Francesc Alted <fa...@gm...> wrote:
> Hi Jon and Anthony,
>
> I can confirm that this is a package error of PyTables in Anaconda CE 64
> for Windows.  We have filed a ticket in Anaconda for fixing this.  Sorry
> for the inconveniences.
>
> Francesc Alted
>
> On 2/15/13 4:56 PM, Anthony Scopatz wrote:
>> Hi Jon,
>>
>> Unfortunately, I have no way of testing this out.  I will say that I
>> have had problems with HDF5 and Anaconda on windows before since they
>> only ship the static *.lib hdf5 libraries.  So it may be the case that
>> the pandas -> pytables / hdf5 interface hasn't been properly linked.
>>  Barring someone on this list who can test things out for you, you
>> might try grabbing the PyTables source from github and building it on
>> top of your install of Anaconda.  Sorry...
>>
>> Be Well
>> Anthony
>>
>>
>> On Fri, Feb 15, 2013 at 3:29 AM, Jon Rowland <row...@gm...
>> <mailto:row...@gm...>> wrote:
>>
>>     Hi - apologies if this is a duplicate, I had an error sending the
>>     first time and wasn't sure if it made it through.
>>
>>     I have an issue using pandas/HDFStore/pytables in the Anaconda CE
>>     distribution on Windows 64-bit.
>>
>>     After a little troubleshooting with the Anaconda/pandas lists, it's
>>     been suggested that it might be a pytables issue (or at least some
>>     kind of package mismatch causing pytables not to work).
>>
>>     I have a clean install of Anaconda 1.3.1 64-bit CE edition on a
>>     Windows 64-bit machine.
>>
>>     Running the pytables self-test gives the following output:
>>
>>     -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
>>     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
>>
>>     Is this something I'm doing wrong or is there something wrong with
>>     the package?
>>
>>     Any help would be appreciated.
>>
>>     Thanks,
>>     Jon
>>
>>     ------------------------------------------------------------------------------
>>     Free Next-Gen Firewall Hardware Offer
>>     Buy your Sophos next-gen firewall before the end March 2013
>>     and get the hardware for free! Learn more.
>>     http://p.sf.net/sfu/sophos-d2d-feb
>>     _______________________________________________
>>     Pytables-users mailing list
>>     Pyt...@li...
>>     <mailto:Pyt...@li...>
>>     https://lists.sourceforge.net/lists/listinfo/pytables-users
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Free Next-Gen Firewall Hardware Offer
>> Buy your Sophos next-gen firewall before the end March 2013
>> and get the hardware for free! Learn more.
>> http://p.sf.net/sfu/sophos-d2d-feb
>>
>>
>> _______________________________________________
>> Pytables-users mailing list
>> Pyt...@li...
>> https://lists.sourceforge.net/lists/listinfo/pytables-users
>
>
> --
> Francesc Alted
>
>
> ------------------------------------------------------------------------------
> Free Next-Gen Firewall Hardware Offer
> Buy your Sophos next-gen firewall before the end March 2013
> and get the hardware for free! Learn more.
> http://p.sf.net/sfu/sophos-d2d-feb
> _______________________________________________
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