A Friday 18 March 2011 19:33:57 nicky van foreest escrigué:
> Hi Francesc,
>
> Thanks for your answer.
>
> On 17 March 2011 08:35, Francesc Alted <[email protected]> wrote:
> > A Wednesday 16 March 2011 22:34:11 nicky van foreest escrigué:
> >> Hi,
> >>
> >> While trying to install pytables on ubuntu I run into a strange
> >> (for me) problem. I followed the instructions in the README, and
> >> indeed with the PYTHONPATH with . I can run the test succesfully
> >> in ipython in ~/build/tables. However, if I run ipthon in another
> >> directory, e.g., ~/build/ and try to import pytables in another
> >> directory I get the error:
> >>
> >> ImportError: libhdf5-1.6.6.so.0: cannot open shared object file:
> >> No such file or directory
> >>
> >> Of course I ran sudo python setup.py install but to no avail.
> >
> > Is it possible that you already have stale files of previous
> > PyTables installations? If so, I'd suggest to clean up them.
> > Also, double check that the HDF5 lib/ dir is in your
> > LD_LIBRARY_PATH.
>
> I did this, but this did not work. Here is the output:
>
> $ pip install -U tables
> Downloading/unpacking tables
> Running setup.py egg_info for package tables
> * Found numpy 1.5.1 package installed.
> * Found HDF5 headers at ``/usr/include``, library at
> ``/usr/lib64``.
>
> So I set
>
> $ export LD_LIBRARY_PATH=/usr/lib64/
>
> running ipython then gives the following error:
>
> nicky@chuck:~/build$ ipython
> Python 2.6.5 (r265:79063, Apr 16 2010, 13:57:41)
> Type "copyright", "credits" or "license" for more information.
>
> IPython 0.10 -- An enhanced Interactive Python.
> ? -> Introduction and overview of IPython's features.
> %quickref -> Quick reference.
> help -> Python's own help system.
> object? -> Details about 'object'. ?object also works, ?? prints
> more.
>
> In [1]: import tables
> ---------------------------------------------------------------------
> ------ ImportError Traceback (most
> recent call last)
>
> /home/nicky/build/<ipython console> in <module>()
>
> /home/nicky/lib/python/tables/__init__.py in <module>()
> 54
> 55 # Necessary imports to get versions stored on the Pyrex
> extension
>
> ---> 56 from tables.utilsExtension import getPyTablesVersion,
> getHDF5Version 57
> 58 __version__ = getPyTablesVersion()
>
> ImportError: libhdf5-1.6.6.so.0: cannot open shared object file: No
> such file or directory
>
>
> This is kind of strange, at least for me.
>
> >> There is some other strange problem too. To install tables I used
> >> pip install -U tables. This comes a long way in the right
> >> direction, but fails to completely compile tables. For this it is
> >> necessary to enter the build/tables directory and run python
> >> setup.py install. Why is that?
> >
> > Can you attach the logs of the errors?
>
> Sure, Thanks again for your help.
I can see in your logs a couple of suspicious things:
"""
Removing /usr/local/lib/python2.6/dist-packages/tables-2.2.1.egg-info
error: /usr/local/lib/python2.6/dist-packages/tables-2.2.1.egg-info:
Permission denied
"""
Are you sure that you have writing permissions in /usr/local? I.e. make
sure that you are super-user before installing.
Another thing:
"""
building 'tables.linkExtension' extension
C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -
O2 -Wall -Wstrict-prototypes -fPIC
compile options: '-DNDEBUG=1 -DHAVE_BZ2_LIB=1 -Iblosc -
I/usr/local/lib/python2.6/dist-packages/numpy/core/include -
I/usr/include/python2.6 -c'
extra options: '-Isrc -DH5_USE_16_API'
gcc: tables/linkExtension.c
gcc: tables/linkExtension.c: No such file or directory
"""
I don't understand why you don't have the tables/linkExtension.c file.
I have double checked that it exists in
http://www.pytables.org/download/pytables-2.2.1/tables-2.2.1.tar.gz, so
why it does not in your case? At any rate, installing Cython can help
in regenerating the files locally.
HTH,
--
Francesc Alted
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