Failure of "import tables"

[Boris]

Binary package hint: python-tables

>>> import tables
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/tables/__init__.py", line 76, in <module>
    from tables.file import File, openFile, copyFile
  File "/usr/lib/python2.7/dist-packages/tables/file.py", line 43, in <module>
    from tables import hdf5Extension
ImportError: /usr/lib/python2.7/dist-packages/tables/hdf5Extension.so: undefined symbol: H5T_STD_U8BE_g

ProblemType: Bug
DistroRelease: Ubuntu 11.04
Package: python-tables 2.1.2-3.1build1
ProcVersionSignature: Ubuntu 2.6.38-7.38-generic 2.6.38
Uname: Linux 2.6.38-7-generic x86_64
Architecture: amd64
Date: Tue Mar 22 14:56:03 2011
InstallationMedia: Ubuntu 11.04 "Natty Narwhal" - Alpha amd64 (20110302)
ProcEnviron:
 LANGUAGE=en_US:en
 PATH=(custom, no user)
 LANG=en_US.UTF-8
 SHELL=/bin/bash
SourcePackage: pytables
UpgradeStatus: Upgraded to natty on 2011-03-22 (0 days ago)

[Michele Mattioni (mattions)]

I add aldo my report, 'cause I have another callback, however I think it's all related...

mattions@triton:~$ python
Python 2.7.1+ (r271:86832, Apr 11 2011, 18:13:53)
[GCC 4.5.2] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/mattions/Work/progs/pytables/lib/python2.6/site-packages/tables/__init__.py", line 84, in <module>
    from tables.file import File, openFile, copyFile
  File "/home/mattions/Work/progs/pytables/lib/python2.6/site-packages/tables/file.py", line 58, in <module>
    from tables import hdf5Extension
ImportError: /home/mattions/Work/progs/pytables/lib/python2.6/site-packages/tables/hdf5Extension.so: undefined symbol: H5E_CALLBACK_g

[Michele Mattioni (mattions)]

Ignore my report.

I just found out that it was an old installation of pytables, imported in my bashrc!

[Reinis Ivanovs (dabas)]

I get this error too. Just did apt-get install python-tables, and the library can't be imported.

[Konrad (sosnowski-konrad)]

Hi, slightly different stack trace, also on Ubuntu 11.04 - any ideas? Tried multiple re-installs of pytables and hdf5 related packages...

/usr/lib/python2.7/dist-packages/tables/__init__.py in <module>()
     74 # Import the user classes from the proper modules

     75 from tables.exceptions import *
---> 76 from tables.file import File, openFile, copyFile
     77 from tables.node import Node
     78 from tables.group import Group

/usr/lib/python2.7/dist-packages/tables/file.py in <module>()
     41
     42 import tables.misc.proxydict
---> 43 from tables import hdf5Extension
     44 from tables import utilsExtension
     45 from tables import parameters

ImportError: /usr/lib/python2.7/dist-packages/tables/hdf5Extension.so: undefined symbol: H5T_STD_U8BE_g

[David Fokkema (dfokkema)]

Answered question #159188. You can do:

sudo apt-get install liblzo2-2

and the problem is solved. Thus, this needs to be a dependency.

[Brett (this-is-spam-mail)]

I was having the same problem and David Fokkema's suggestion worked. Thanks!!

[Christof Buchbender (ascurion)]

For me this solved the issue as well. Thanks also from me!