python-tables depends on missing dependency: libhdf5.so.6 in quantal

[Jason Moore]

python-tables depends on libhdf5 and makes a link to libhdf5.so.6, but when importing a freshly installed version of PyTables in 12.10 you get this error:

>> import tables
  File "/usr/local/lib/python2.7/dist-packages/tables/__init__.py", line 30, in <module>
    from tables.utilsExtension import getPyTablesVersion, getHDF5Version
ImportError: libhdf5.so.6: cannot open shared object file: No such file or directory

The version of python-tables in Quantal now has a dependency on libhdf5-7. libhdf5-7 only creates a file libhdf5.so.7, see http://packages.ubuntu.com/quantal/amd64/libhdf5-7/filelist

It seems that the binary file included in python-tables called utilsExtensions.so is looking for libhdf5.so.6 but it isn't there.

I used this symlink work around to get the package to work:

sudo ln -s /usr/lib/libhdf5.so.7.0.2 /usr/lib/libhdf5.so.6

which I copied from this similar octave bug: https://bugs.launchpad.net/ubuntu/+source/octave/+bug/1005243

Other info:

$ lsb_release -rd
Description: Ubuntu 12.10
Release: 12.10

[Jason Moore (moorepants)]

I just tried to reproduce the bug in a clean install of 12.10 on a different machine and was not able to.

I installed with:

$ apt-get install python-tables

and then tables imported fine. So I must have some issue associated with my machine which has a long history of installing/uninstalling pytables. Maybe I just have something corrupted.

[Antonio Valentino (a.valentino)]

I just checked the package control file and it is fine:

Depends: python-numpy (>= 1:1.6.1), python-numpy-abi9, python2.7, python (>= 2.7.1-0ubuntu2), python (<< 2.8), libbz2-1.0, libc6 (>= 2.14), libhdf5-7, liblzo2-2, python-numexpr (>= 1.4.1)

please check your APT sources, clean the APT cache and try to re-install python-tables

[jernej (jernej-makovsek)]

@Jason
tnx for posting the solution. I've upgraded recently to 12.10 from 12.04 and had the same problem.

[Julian Taylor (jtaylor)]

the "local" in here:
/usr/local/lib/python2.7/dist-packages/...
means you are not using the packaged pytables but an own install. The package does not have this issue.

If you really need an own install rebuilding it with the appropriate hdf -dev package installed should solve the issue.