I am trying to get pytables-2.0.3 installed on Mac OS X 10.5.2. I note
that other people appear to have succeeded with this according to the
mailing list. I have HDF5 installed in $HOME/usr, and it passes all of
its selftests, so I don't think that the problem is there. This is
using the MacPython 2.5 distribution in /Library/Frameworks/...
I built pytables with "python setup.py build_ext --inplace
--hdf5=$HOME/usr --lflags="-L/$HOME/usr/lib -lz", because my HDF5 is in
a non-default location, and when I didn't build with "-lz", I got an
error about missing symbols when I did "import tables". With this
invocation, I can get pytables to build and import, but the test suite
fails with many HDF5 errors and eventually a bus error:
tables/filters.py:257: FiltersWarning: compression library ``lzo`` is
not availa
ble; using ``zlib`` instead
% (complib, default_complib), FiltersWarning )
HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5Adeprec.c line 159 in H5Acreate1(): not a type
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5A.c line 912 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
EHDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5Adeprec.c line 159 in H5Acreate1(): not a type
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5A.c line 912 in H5Awrite(): not an attribute
major: Invalid arguments to routine
minor: Inappropriate type
EHDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5Adeprec.c line 159 in H5Acreate1(): not a type
major: Invalid arguments to routine
minor: Inappropriate type
[...]
EHDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5Gdeprec.c line 293 in H5Gopen1(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 165 in H5G_loc(): invalid file ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5Adeprec.c line 208 in H5Aopen_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 241 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
#000: H5G.c line 699 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
Bus Error
Does anyone have any ideas about how to debug this problem? I had
difficulties getting HDF5 installed so that pytables would recognize it,
but I thought that I had done it correctly. Thanks for any help anyone
can give. Peace,
-Neil
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