pytables import

Asked by Konrad on 2011-05-26

Hello,

I'm having a hard time installing pytables on Ubuntu 11.04. After apt-get install, I go into python shell and "import tables" - the error stack below is what I get. I've tried multiple re-installs of pytables and hdf5 related packages... Any ideas?

Much appreciated,
Konrad

/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

Question information

Language:
English Edit question
Status:
Solved
For:
Ubuntu pytables Edit question
Assignee:
No assignee Edit question
Solved by:
David Fokkema
Solved:
2011-05-28
Last query:
2011-05-28
Last reply:
2011-05-28
mycae (mycae) said : #1

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

If you have not manually modified your hdf5 install, then this looks like a bug, and that the pytables package needs rebuilding (and probably patching). The native interface has changed, but the .so internal version number (soversion) was probably not changed.

Can you provide the output of :

apt-cache show libhdf5-serial-1.8.4
apt-cache show python-tables

Konrad (sosnowski-konrad) said : #2

Hi,

I have attempted to install tar ball pytables/hdf5 a while ago, had some problems, put that down, retried via Ubuntu Synaptic manager. Unfortunately I cannot recall the failure reason. I am a Linux novice hence please be gentle and :)

Here's the requested info, thanks for your help.

konrad@acerek:~ $ apt-cache show libhdf5-serial-1.8.4
Package: libhdf5-serial-1.8.4
Priority: optional
Section: universe/libs
Installed-Size: 4764
Maintainer: Ubuntu Developers <email address hidden>
Original-Maintainer: Debian GIS Project <email address hidden>
Architecture: amd64
Source: hdf5
Version: 1.8.4-patch1-2ubuntu3
Replaces: libhdf5-1.8.3
Provides: libhdf5-1.8, libhdf5-1.8.4
Depends: libc6 (>= 2.7), libgcc1 (>= 1:4.1.1), libgfortran3 (>= 4.3), libstdc++6 (>= 4.1.1), zlib1g (>= 1:1.1.4)
Conflicts: libhdf5-1.8, libhdf5-1.8.3, libhdf5-1.8.4
Filename: pool/universe/h/hdf5/libhdf5-serial-1.8.4_1.8.4-patch1-2ubuntu3_amd64.deb
Size: 1412452
MD5sum: 908b373fa72276fc038928aa28e8be67
SHA1: d38ee4a6a99bb8f027d7480b7cf3b2cd311ae09f
SHA256: 0886984d4d84f1c7183cb95f76b4e624fe4927360f4e234779ae2ae59a0564d8
Description: Hierarchical Data Format 5 (HDF5) - runtime files - serial version
 HDF5 is a file format and library for storing scientific data.
 HDF5 was designed and implemented to address the deficiencies of
 HDF4.x. It has a more powerful and flexible data model, supports
 files larger than 2 GB, and supports parallel I/O.
 .
 This package contains runtime files for serial platforms.
Homepage: http://hdfgroup.org/HDF5/
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu

konrad@acerek:~ $ apt-cache show python-tables
Package: python-tables
Priority: optional
Section: universe/python
Installed-Size: 4384
Maintainer: Ubuntu Developers <email address hidden>
Original-Maintainer: Wen Heping <email address hidden>
Architecture: amd64
Source: pytables
Version: 2.1.2-3.1build1
Depends: python (<< 2.8), python (>= 2.6), python-central (>= 0.6.11), python-numpy (>= 1:1.5.1), python-numpy (<< 1:1.6), libc6 (>= 2.4), libhdf5-serial-1.8.4 | libhdf5-1.8.4
Suggests: python-tables-doc, python-netcdf
Filename: pool/universe/p/pytables/python-tables_2.1.2-3.1build1_amd64.deb
Size: 874592
MD5sum: 1cb25c8d85f0cc64fbf1332caf8b32fe
SHA1: 563aaeace912f9f99d7bb7e714b35fda364dd6a4
SHA256: f3bd05c89963c45d036c8312eccadd5e1e4c2630fcbfdfdacf381a8ea09298dc
Description: hierarchical database for Python based on HDF5
 PyTables is a hierarchical database package designed to efficently
 manage very large amounts of data. PyTables is built on top of the
 HDF5 library and the NumPy package. It features an object-oriented
 interface that, combined with natural naming and C-code generated
 from Pyrex sources, makes it a fast, yet extremely easy to use tool
 for interactively save and retrieve large amounts of data.
 .
  - Compound types (records) can be used entirely from Python (i.e. it
    is not necessary to use C for taking advantage of them).
  - The tables are both enlargeable and compressible.
  - I/O is buffered, so you can get very fast I/O, specially with
    large tables.
  - Very easy to select data through the use of iterators over the
    rows in tables. Extended slicing is supported as well.
  - It supports the complete set of NumPy, Numeric and numarray objects.
Homepage: http://www.pytables.org
Python-Version: 2.6, 2.7
Bugs: https://bugs.launchpad.net/ubuntu/+filebug
Origin: Ubuntu

Best David Fokkema (dfokkema) said : #3

apt-get install liblzo2-2 solves it for me. I guess it should be listed as a dependency. The -dev package *is* listed as a build dependency. I'm not really sure why the missing symbol didn't seem to be lzo2 related.

Konrad (sosnowski-konrad) said : #4

Excellent, that was it. Many thanks!