[Biopython-dev] Test failures on Jython 2.5.1

[Peter]

On Mon, May 17, 2010 at 8:37 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> Hi all (especially Eric),
>
> I've just run the test suite with Jython 2.5.1 and this found some new
> problems. Most of these are XML related from Bio.Phylo
>
> ...
>
> There are also a couple of SeqIO related problems with large files:
>
> ERROR: test_SeqIO
> OutOfMemoryError: java.lang.OutOfMemoryError: Java heap space
> ERROR: Write and read back Human_contigs.embl
> OutOfMemoryError: java.lang.OutOfMemoryError: Java heap space
>
> Example Tests/EMBL/Human_contigs.embl is causing the problem.
> This is a sequence of length 958952, but the file doesn't actually
> hold the sequence so we use an UnknownSeq object. The two
> out of heap space error are both from trying to create a string of
> 958952 "N" characters. I'll have a look at this - we can probably
> avoid it in the test.

Fixed on the trunk. Once we have moved to using string equality
for Seq objects comparing two UnknownSeq objects can be
handled much more cleanly (without the memory overhead of
the naive approach of building the strings).

Peter