[Pytables-users] bug in pytables/hdf

[russ <ru...@ag...>]

Hello, I'm working with pytables 0.9.1 on windows 2000 and seem to have 
discovered a bug somewhere in the works.  Essentially I have a table 
with two columns, "mmid" and "mmidn", and pytables can't read the 
"mmidn" column.  Following is a short program that demonstrates the 
problem, and following that is the output of the program.  The problem 
seems to be in the naming; changing "mmidn" to "abcd" fixes the 
problem.  Similarly, changing the pair to "abc" and "abcd" recreates the 
problem.  Any help would be appreciated.
Thanks, -Russ
ru...@ag...
--------------------------------------------------------------------------------
import sys,os
import tables as hdf

class Consolidatedtable(hdf.IsDescription):
    mmid = hdf.Int32Col(pos=4)
    mmidn = hdf.Int32Col(pos=5)
fname='tmp.h5'
print 'pytables version:', hdf.__version__

print 'writing', fname
h5 = hdf.openFile(fname, mode='w', title='bwdata')
t=h5.createTable('/','q',Consolidatedtable,'data',expectedrows=10000)
r=t.row
r['mmid']=0
r['mmidn']=0
r.append()
h5.close()


print 'reading'
h5=hdf.openFile(fname)
print 'this works:', h5.root.q['mmid']
print 'this does not:', h5.root.q['mmidn']


--------------------------------------------------------------------------------
program output:

$ /d/py/test_mmidn.py
pytables version: 0.9.1
writing tmp.h5
reading
this works: [0]
this does not:HDF5-DIAG: Error detected in HDF5 library version: 
1.6.3-patch thr
ead 0.  Back trace follows.
  #000: D:\hdf5\src\H5Tcompound.c line 327 in H5Tinsert(): unable to 
insert memb
er
    major(13): Datatype interface
    minor(45): Unable to insert object
  #001: D:\hdf5\src\H5Tcompound.c line 418 in H5T_insert(): member 
overlaps with
 another member
    major(13): Datatype interface
    minor(45): Unable to insert object

Traceback (most recent call last):
  File "d:/util/mypython.py", line 15, in ?
    execfile(sys.argv[0])
  File "d:/py/test_mmidn.py", line 24, in ?
    print 'this does not:', h5.root.q['mmidn']
  File "D:\Python23\lib\site-packages\tables\Table.py", line 778, in 
__getitem__

    return self.read(field=key)
  File "D:\Python23\lib\site-packages\tables\Table.py", line 592, in read
    return self._read(start, stop, step, field, coords)
  File "D:\Python23\lib\site-packages\tables\Table.py", line 731, in _read
    self._read_field_name(result, start, stop, step, field)
  File "hdf5Extension.pyx", line 1831, in 
hdf5Extension.Table._read_field_name
RuntimeError: Problems reading table column.