Re: [Pytables-users] pytables: could not find the HDF5 runtime

[Anthony S. <sc...@gm...>]

Try leaving the pytables source dir and then running then running IPython.


On Mon, Dec 10, 2012 at 9:20 AM, Jennifer Flegg <jen...@ww...>wrote:

> Hi,
> I'm trying to install pytables and its proving difficult (using MAC OS
> 10.6.4).
> I have installed in "/usr/local/hdf5" and set the environment variable
> $HDF5_DIR to /usr/local/hdf5. When I run setup, I get a warning about
>  not being able to find the HDF5 runtime.
>
> ndmmac149:tables-2.4.0 jflegg$ sudo python setup.py install
>  --hdf5="/usr/local/hdf5"
> * Found numpy 1.6.1 package installed.
> * Found numexpr 2.0.1 package installed.
> * Found Cython 0.17.2 package installed.
> * Found HDF5 headers at ``/usr/local/hdf5/include``,
>  library at ``/usr/local/hdf5/lib``.
> .. WARNING:: Could not find the HDF5 runtime.
>    The HDF5 shared library was *not* found in the default library
>    paths. In case of runtime problems, please remember to install it.
> ld: library not found for -llzo2
> collect2: ld returned 1 exit status
> ld: library not found for -llzo2
> collect2: ld returned 1 exit status
> * Could not find LZO 2 headers and library; disabling support for it.
> ld: library not found for -llzo
> collect2: ld returned 1 exit status
> ld: library not found for -llzo
> collect2: ld returned 1 exit status
> * Could not find LZO 1 headers and library; disabling support for it.
> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``.
> running install
> running build
> running build_py
> creating build
> creating build/lib.macosx-10.5-i386-2.7
> creating build/lib.macosx-10.5-i386-2.7/tables
> copying tables/__init__.py -> build/lib.macosx-10.5-i386-2.7/tables
> copying tables/array.py -> build/lib.macosx-10.5-i386-2.7/tables
>
> When I import pytables in python, I get the following error message
>
> In [1]: import tables
> ---------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> /Users/jflegg/<ipython-input-1-389ecae14f10> in <module>()
> ----> 1 import tables
>
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-
> packages/tables/__init__.py in <module>()
>      28
>      29 # Necessary imports to get versions stored on the Pyrex extension
>
> ---> 30 from tables.utilsExtension import getPyTablesVersion,
> getHDF5Version
>      31
>      32
>
> ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/7.3
> /lib/python2.7/site-packages/tables/utilsExtension.so, 2):
> Symbol not found: _H5E_CALLBACK_g  Referenced from:
> /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-
> packages/tables/utilsExtension.so
>   Expected in: flat namespace
>  in /Library/Frameworks/Python.framework/Versions/7.3/lib/python2.7/site-
> packages/tables/utilsExtension.so
>
>
> Any help would be greatly appreciated.
> Jennifer
>
>
>
>
>
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