[Biopython-dev] Test failure: write/read simple one-of locations.

[Peter Cock]

Hi all,

I noticed the following odd buildslave failure yesterday,
which was not reproducible (a retest passed), however
something very similar happened today (but again it
passed when repeated):

Failure on 6 December 2011, under Python 3.2
http://testing.open-bio.org/biopython/builders/Linux%20-%20Python%203.2/builds/291/steps/shell/logs/stdio

ERROR: test_oneof (test_SeqIO_features.FeatureWriting)
Features: write/read simple one-of locations.
...
ValueError: [one-of(0,3,6):21](+) versus [one-of(0,3,6):21](+):
SeqFeature(FeatureLocation(OneOfPosition(0, choices=[ExactPosition(0),
ExactPosition(3), ExactPosition(6)]), ExactPosition(21), strand=1),
type='CDS')
vs:
SeqFeature(FeatureLocation(OneOfPosition(44,
choices=[ExactPosition(0), ExactPosition(3), ExactPosition(6)]),
ExactPosition(21), strand=1), type='CDS')


Failure on 7 December 2011, under Python 3.1
http://testing.open-bio.org/biopython/builders/Linux%20-%20Python%203.1/builds/459/steps/shell/logs/stdio

ERROR: test_oneof (test_SeqIO_features.FeatureWriting)
Features: write/read simple one-of locations.
...
ValueError: [one-of(0,3,6):21](+) versus [one-of(0,3,6):21](+):
SeqFeature(FeatureLocation(OneOfPosition(0, choices=[ExactPosition(0),
ExactPosition(3), ExactPosition(6)]), ExactPosition(21), strand=1),
type='CDS')
vs:
SeqFeature(FeatureLocation(OneOfPosition(180,
choices=[ExactPosition(0), ExactPosition(3), ExactPosition(6)]),
ExactPosition(21), strand=1), type='CDS')


This is the same unit test, on the same machine, but
different revisions, different versions of Python, and also
slightly different output. This is an old machine, so it could
be a memory problem, or evidence of some subtle race
condition.

Has anyone else seen this error?

Peter