[Biopython-dev] biopython-1.51 test log, sage inclusion

[Peter]

On Mon, Aug 17, 2009 at 10:25 PM, Marshall Hampton<mhampton at d.umn.edu> wrote:
>
> After copying the Tests folder from the source to my site-packages
> directory, most of the errors go away,

Well that does suggest some sort of path issue, but moving the
test directory around that isn't a very good solution.

> except for the one mentioned above and this one:

Assuming the "one mentioned above" was the EMBOSS one, fine.

> ERROR: test_SeqIO_online
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>  File "run_tests.py", line 248, in runTest
>    suite = unittest.TestLoader().loadTestsFromName(name)
>  File "/Users/mh/sagestuff/sage-4.1/local/lib/python/unittest.py", line 576,
> in loadTestsFromName
>    module = __import__('.'.join(parts_copy))
>  File "test_SeqIO_online.py", line 62, in <module>
>    record = SeqIO.read(handle, format) # checks there is exactly one record
>  File
> "/Users/mh/sagestuff/sage-4.1/local/lib/python2.6/site-packages/Bio/SeqIO/__init__.py",
> line 485, in read
>    raise ValueError("No records found in handle")
> ValueError: No records found in handle
>
> ...not sure what the problem might be with that.

That is an online test using the NCBI's web services. This could
be a transient failure due to the network.

Peter