Hello, As it says in the installation documentation of PyTables that one should mail the developers with any strange errors that pytables would produce so that they can be fixed in future releases, here is my story: I simply installed pytables using easy_install which completed successfully but the when executing the tests, I get an error. Any help greatly appreciated ! Here is my bash transcript:
[sincl...@sv-17-019 ~]$ sudo yum install python-setuptools-devel [...] [sincl...@sv-17-019 ~]$ sudo yum install hdf5-static [...] [sincl...@sv-17-019 ~]$ sudo easy_install tables Searching for tables Reading http://pypi.python.org/simple/tables/ Reading http://www.pytables.org/ Best match: tables 2.1.2 Downloading http://www.pytables.org/download/stable/tables-2.1.2.tar.gz Processing tables-2.1.2.tar.gz Running tables-2.1.2/setup.py -q bdist_egg --dist-dir /tmp/easy_install-yA50jO/tables-2.1.2/egg-dist-tmp-vai72S * Found numpy 1.3.0 package installed. * Found HDF5 headers at ``/usr/include``, library at ``/usr/lib64``. * Could not find LZO 2 headers and library; disabling support for it. * Could not find LZO 1 headers and library; disabling support for it. * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib64``. warning: no previously-included files matching '*' found under directory 'doc/xml' /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5ARRAY.c:4: /usr/include/python2.6/pyconfig-64.h:1019:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/H5public.h:44, from /usr/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5ARRAY.c:1: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5ARRAY.c:4: /usr/include/python2.6/pyconfig-64.h:1028:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/H5public.h:44, from /usr/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5ARRAY.c:1: /usr/include/features.h:160:1: warning: this is the location of the previous definition /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used tables/utilsExtension.c: In function ‘__pyx_f_6tables_14utilsExtension_AtomToHDF5Type’: tables/utilsExtension.c:2451: warning: ‘__pyx_v_tid’ may be used uninitialized in this function tables/utilsExtension.c: In function ‘__pyx_f_6tables_14utilsExtension_enumToHDF5’: tables/utilsExtension.c:2309: warning: ‘__pyx_exc_lineno’ may be used uninitialized in this function tables/utilsExtension.c: In function ‘__pyx_f_6tables_14utilsExtension_loadEnum’: tables/utilsExtension.c:2650: warning: ‘__pyx_r’ may be used uninitialized in this function tables/utilsExtension.c:2696: warning: ‘__pyx_exc_lineno’ may be used uninitialized in this function tables/hdf5Extension.c: In function ‘__pyx_f_6tables_13hdf5Extension_5Array__readArray’: tables/hdf5Extension.c:4441: warning: ‘__pyx_v_extdim’ may be used uninitialized in this function In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5VLARRAY.c:3: /usr/include/python2.6/pyconfig-64.h:1019:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/H5public.h:44, from /usr/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5VLARRAY.c:1: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5VLARRAY.c:3: /usr/include/python2.6/pyconfig-64.h:1028:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/H5public.h:44, from /usr/include/hdf5.h:24, from src/H5ATTR.h:19, from src/H5VLARRAY.c:1: /usr/include/features.h:160:1: warning: this is the location of the previous definition /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5TB-opt.c:36: /usr/include/python2.6/pyconfig-64.h:1019:1: warning: "_POSIX_C_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from src/H5TB-opt.c:31: /usr/include/features.h:158:1: warning: this is the location of the previous definition In file included from /usr/include/python2.6/pyconfig.h:6, from /usr/include/python2.6/Python.h:8, from src/utils.h:1, from src/H5TB-opt.c:36: /usr/include/python2.6/pyconfig-64.h:1028:1: warning: "_XOPEN_SOURCE" redefined In file included from /usr/include/stdlib.h:25, from src/H5TB-opt.c:31: /usr/include/features.h:160:1: warning: this is the location of the previous definition src/H5TB-opt.c: In function ‘H5TBOread_elements’: src/H5TB-opt.c:300: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type /usr/include/H5Spublic.h:128: note: expected ‘const hsize_t *’ but argument is of type ‘const hsize_t **’ src/H5TB-opt.c: In function ‘H5TBOwrite_elements’: src/H5TB-opt.c:509: warning: passing argument 4 of ‘H5Sselect_elements’ from incompatible pointer type /usr/include/H5Spublic.h:128: note: expected ‘const hsize_t *’ but argument is of type ‘const hsize_t **’ src/H5TB-opt.c: At top level: /usr/lib64/python2.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:968: warning: ‘_import_array’ defined but not used zip_safe flag not set; analyzing archive contents... /usr/lib/python2.6/site-packages/setuptools/command/bdist_egg.py:422: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal symbols = dict.fromkeys(iter_symbols(code)) tables.tests.common: module references __file__ Adding tables 2.1.2 to easy-install.pth file Installing ptrepack script to /usr/bin Installing ptdump script to /usr/bin Installing nctoh5 script to /usr/bin Installed /usr/lib/python2.6/site-packages/tables-2.1.2-py2.6-linux-x86_64.egg Processing dependencies for tables Finished processing dependencies for tables [sincl...@sv-17-019 ~]$ [sincl...@sv-17-019 ~]$ [sincl...@sv-17-019 ~]$ [sincl...@sv-17-019 ~]$ [sincl...@sv-17-019 ~]$ python Python 2.6.2 (r262:71600, Jan 25 2010, 18:46:47) [GCC 4.4.2 20091222 (Red Hat 4.4.2-20)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import tables >>> tables.test() -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= PyTables version: 2.1.2 HDF5 version: 1.8.3 NumPy version: 1.3.0 Zlib version: 1.2.3 BZIP2 version: 1.0.5 (10-Dec-2007) Python version: 2.6.2 (r262:71600, Jan 25 2010, 18:46:47) [GCC 4.4.2 20091222 (Red Hat 4.4.2-20)] Platform: linux2-x86_64 Byte-ordering: little -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 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 80 MB of main memory. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Skipping Numeric test suite. Skipping numarray test suite. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= /usr/lib/python2.6/site-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/filters.py:258: FiltersWarning: compression library ``lzo`` is not available; using ``zlib`` instead % (complib, default_complib), FiltersWarning ) ...............................................................................................................................................................................................................................................................................................................................................................................................................F..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... ====================================================================== FAIL: None (tables.tests.test_basics.OldFlavorTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/usr/lib/python2.6/site-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/tests/common.py", line 248, in newmethod return oldmethod(self, *args, **kwargs) File "/usr/lib/python2.6/site-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/tests/test_basics.py", line 2202, in test self.assert_(common.allequal(node_data, data, new_flavor)) AssertionError ---------------------------------------------------------------------- Ran 6517 tests in 34.251s FAILED (failures=1) >>> ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
