Hey Todd, 2011/4/21, Todd Matthews <mtoddmatth...@gmail.com>: > 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
Yes, I think these warnings are expected. > 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 'stack smashing'? Wow, never seen something like that. I presume this could be related with a different NumPy version used. See later. > > 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? Based of the "numpy.dtype has the wrong size" error, I'd say that you have two different NumPy installations. Please double check that you are using the same NumPy library in both ipython and eclipse environments. > There are seemingly two separate questions; but, any help would be very much > appreciated. Hope this helps, -- Francesc Alted ------------------------------------------------------------------------------ Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
