Cannot install python package tables

Question

[root@e06e8f90e201 optimus]# pip install tables
Collecting tables
  Downloading tables-3.2.3.1.tar.gz (7.1MB)
    100% |################################| 7.1MB 120kB/s 
    Complete output from command python setup.py egg_info:
    /usr/bin/ld: cannot find -lhdf5
    collect2: error: ld returned 1 exit status
    * Using Python 2.7.5 (default, Nov 20 2015, 02:00:19)
    * USE_PKGCONFIG: True
    .. ERROR:: Could not find a local HDF5 installation.
       You may need to explicitly state where your local HDF5 headers and
       library can be found by setting the ``HDF5_DIR`` environment
       variable or by using the ``--hdf5`` command-line option.

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-SvZePF/tables/

Has anyone got any idea what this means? I have not explicitly/knowningly installed tables before, so maybe it does not exist on my local pc?

Anthon · Accepted Answer · 2016-08-08 06:05:35Z

2

From the blurp on tables on PyPI:

PyTables is built on top of the HDF5 library ...

Therefore you have to have the libhdf5.[so/a] library installed, which is also mentioned in the prerequisites.

On Debian (or derived) systems you should be able to install with your package manager:

apt-get install libhdf5-dev

( on yum based systems search with something like yum --enablerepo=epel provides \*/libhdf5.so).

answered Aug 8, 2016 at 6:05

Anthon

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