[Biopython-dev] curious error from HMM unit test

Peter biopython at maubp.freeserve.co.uk
Mon Jan 17 16:37:03 UTC 2011

On Mon, Jan 17, 2011 at 4:17 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
> It could have been an exotic bug in Jython (or its interactions with the
> JVM) where the JIT or garbage collector is removing local variables too
> early. I don't see how you could provide a "fix" for it in Biopython, since
> k definitely exists at that point in the loop in any valid Python and Jython
> almost always handles it correctly.

Good point - maybe that is the most likely explanation.

> Maybe you could seed the RNG at the start of the unit test to ensure the
> same paths are always taken?

We could do, but as part of that I'd want to increase the test coverage
to ensure most of the HMM code is actually covered in the single non-
stochastic run. As no-one is actively looking after it, so I'd rather not
touch the tests.


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