Not sure if my problems are with PyTables; but, any guidance would be great.
I am installing PyTables on new Ubuntu install.
1) Attempt to build PyTables as instructed in readme appears successful. The
following are warnings that I presume to be okay.
gcc: tables/linkExtension.c
tables/linkExtension.c: In function
‘__pyx_pf_6tables_13linkExtension_12ExternalLink_1_g_open’:
tables/linkExtension.c:1824: warning: passing argument 4 of
‘H5Lunpack_elink_val’ from incompatible pointer type
/usr/local/hdf5/include/H5Lpublic.h:193: note: expected ‘const char **’ but
argument is of type ‘char **’
tables/linkExtension.c:1824: warning: passing argument 5 of
‘H5Lunpack_elink_val’ from incompatible pointer type
/usr/local/hdf5/include/H5Lpublic.h:193: note: expected ‘const char **’ but
argument is of type ‘char **’
tables/linkExtension.c: At top level:
/home/chauveinc/.local/lib/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1532:
warning: ‘_import_array’ defined but not used
2) Run tables.test() which produces version info and a stack smashing error
-
Versions meet reqs. Can anyone help with what the error may indicate?
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
PyTables version: 2.2.1
HDF5 version: 1.8.4
NumPy version: 1.6.0b2
Numexpr version: 1.4.2 (not using Intel's VML/MKL)
Zlib version: 1.2.3.3 (in Python interpreter)
Blosc version: 1.1.2 (2010-11-04)
Cython version: 0.14.1
Python version: 2.6.5 (r265:79063, Apr 16 2010, 13:09:56)
[GCC 4.4.3]
Platform: linux2-i686
Byte-ordering: little
Detected cores: 1
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
Performing only a light (yet comprehensive) subset of the test suite.
If you want a more complete test, try passing the --heavy flag to this
script
(or set the 'heavy' parameter in case you are using tables.test() call).
The whole suite will take more than 2 minutes to complete on a relatively
modern CPU and around 150 MB of main memory.
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
tables/filters.py:264: FiltersWarning: compression library ``bzip2`` is not
available; using ``zlib`` instead
% (complib, default_complib), FiltersWarning )
tables/filters.py:264: FiltersWarning: compression library ``lzo`` is not
available; using ``zlib`` instead
% (complib, default_complib), FiltersWarning )
*** stack smashing detected ***: /usr/bin/python terminated
3) I run setup;py install and run anyway. PyTables work in ipython for my
application; but, in the eclipse IDE, the import tables results in
File "/usr/local/lib/python2.6/dist-packages/tables/__init__.py", line 63,
in <module>
from tables.utilsExtension import getPyTablesVersion, getHDF5Version
File "definitions.pxd", line 138, in init tables.utilsExtension
(tables/utilsExtension.c:9078)
ValueError: numpy.dtype has the wrong size, try recompiling
It working in ipython and eclipse is a surprise as the same intrepeter is
being used. What is the best way to track the differences between the two?
There are seemingly two separate questions; but, any help would be very much
appreciated.
Thanks,
Todd
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