Hi Francesc, On Wednesday 17 October 2007 05:00:41 am you wrote: > A Wednesday 17 October 2007, Darren Dale escrigué: > > [The next message has been sent to the list from an unsubscribed > > address. Please try to send mails here only if you are subscribed as > > it takes me some time to get aware of them and re-inject to the list]
I signed up for the mailing list this morning. > > 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? datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c .datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c .datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c .datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c datatype--> 1 datatype--> d datatype--> f datatype--> <---- Edatatype--> f <---- datatype--> d datatype--> s datatype--> 1 datatype--> c .datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c .datatype--> f datatype--> d datatype--> s datatype--> 1 datatype--> c > > 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. It could be something specific to gentoo then. I just tried removing the external ctypes package, and reinstalling python and pytables, to reproduce the original problem. I can't reproduce the errors, so I guess I should apologize for creating some noise. > > 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). I know, I'm the one who discovered the issue. The folks at gentoo created a patch for Numeric, so it will run and pass all the tests on a 64 bit machine with python-2.5. I guess it is still possible that there are some issues not addressed by the patch and not exposed by Numeric's tests. The manual does not indicate that Numeric is required for netcdf3. > The output of the attached > patch should provide more info. Also, please send the output for: > > python -c "import tables; tables.print_versions()" PyTables version: 2.0.1 HDF5 version: 1.6.5 NumPy version: 1.0.3.1 Zlib version: 1.2.3 LZO version: 2.02 (Oct 17 2005) BZIP2 version: 1.0.4 (20-Dec-2006) Python version: 2.5.1 (r251:54863, Oct 17 2007, 08:51:34) [GCC 4.2.2 (Gentoo 4.2.2 p1.0)] Platform: linux2-x86_64 Byte-ordering: little Darren ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Pytables-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pytables-users
