A Wednesday 17 October 2007, Darren Dale escrigué:
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> -----------------------------------------------------------------
>
> Hello,
>
> (I am not subscribed to the mailing list, please include my email if
> you respond to this post.)
>
> I just wanted to report my experience installing pytables-2.0.1. I'm
> running
> gentoo linux on a 64bit amd machine, with gcc-4.2.2. The ebuild I
> used is
> attached, if anyone is interested.
>
> The first time I built and tested pytables-2, tables.test() reported
> one error:
>
> =====================================================================
>= ERROR: None (tables.netcdf3.tests.test_netcdf3.NetCDFFileTestCase2)
> ---------------------------------------------------------------------
>- Traceback (most recent call last):
> File "/usr/lib64/python2.5/site-packages/tables/tests/common.py",
> line 247,
> in newmethod
> return oldmethod(self, *args, **kwargs)
>
> File
> "/usr/lib64/python2.5/site-packages/tables/netcdf3/tests/test_netcdf3
>.py", line 168, in test_h5tonc
> nobjects, nbytes = f.nctoh5(self.filenc)
> File
> "/usr/lib64/python2.5/site-packages/tables/netcdf3/__init__.py", line
> 478, in nctoh5
> var =
> self.createVariable(varname,datatype,ncvar.dimensions,least_significa
>nt_digit=lsd,filters=filters) File
> "/usr/lib64/python2.5/site-packages/tables/netcdf3/__init__.py", line
> 294, in createVariable
> var =
> NetCDFVariable(varname,self,datatype,dimensions,least_significant_dig
>it=least_significant_digit,expectedsize=expectedsize,filters=filters)
> File "/usr/lib64/python2.5/site-packages/tables/netcdf3/__init__.py",
> line
> 581, in __init__
> raise ValueError, 'datatype must be one
> of %s'%_netcdftype_dict.keys()
> ValueError: datatype must be one of
> ['c', 'd', 'f', 'i', 'F', 'l', '1', 's', 'D']
>
> ---------------------------------------------------------------------
Mmm, I'm curious about which datatype should be causing this. Can you
try applying the attached patch and send me the output?
> When I ran tables.test(heavy=True), I got 661 errors, almost all
> looked something like this:
>
> =====================================================================
>= ERROR: Testing ``((lbound < c_time64) & (c_time64 <= rbound)) |
> ((c_extra+1) >
> 0)``. [#L506]
> ---------------------------------------------------------------------
>- Traceback (most recent call last):
>
> File
> "/usr/lib64/python2.5/site-packages/tables/tests/test_queries.py",
> line
> 253, in setUp
> fill_table(table, self.shape, self.nrows)
>
> File
> "/usr/lib64/python2.5/site-packages/tables/tests/test_queries.py",
> line
> 183, in fill_table
> row[ncolname] = row[colname] = coldata
> File "tableExtension.pyx", line 1290, in
> tableExtension.Row.__setitem__
> File "tableExtension.pyx", line 128, in
> tableExtension.getNestedFieldCache
> File "utilsExtension.pyx", line 328, in
> utilsExtension.getNestedField ValueError: field named c_int16 not
> found.
>
> ---------------------------------------------------------------------
>-
>
>
> I installed ctypes-1.0.2, which took care of 660 of the failures.
> Should a ctypes version be listed in the manual as a prerequisite?
I've never seen this error before (and normally run PyTables on 64-bit
Linux machines, but under SuSe, not Gentoo), and as far as I know,
there should be no dependency on ctypes at all. Sorry but I'm puzzled
here.
> Is the netcdf error a known pytables bug, or is it maybe a
> configuration issue on my end?
I don't know. The NetCDF module still relies on having a proper
installation of Numeric, and I know that Numeric has issues in 64-bit
machines (specially when using Python 2.5). The output of the attached
patch should provide more info. Also, please send the output for:
python -c "import tables; tables.print_versions()"
Cheers,
--
>0,0< Francesc Altet http://www.carabos.com/
V V Cárabos Coop. V. Enjoy Data
"-"
Index: tables/netcdf3/__init__.py
===================================================================
--- tables/netcdf3/__init__.py (revision 3256)
+++ tables/netcdf3/__init__.py (working copy)
@@ -577,6 +577,7 @@
"""
def __init__(self, varname, NetCDFFile, datatype, dimensions, least_significant_digit=None,expectedsize=1000,filters=None):
+ print "datatype-->", datatype
if datatype not in _netcdftype_dict.keys():
raise ValueError, 'datatype must be one of %s'%_netcdftype_dict.keys()
self._NetCDF_parent = NetCDFFile
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