[Bioperl-l] malloc errors while using Bio::SeqIO?

[Dave Messina]

Hi Rutger,
I ran your script on the same genbank file and, while I did not run out of
memory, I did see what appears to be a memory leak. Even when I manually
undef'd the reader and writer object every 1000 records, memory usage
continued to grow.

I can't quite figure out what's going on, though.

If I run a different program using SeqIO (the simple sequence converter from
the SeqIO HOWTO) on the same input file, I don't see this same runaway
growth.

Also, the problem seems a lot worse on perl 5.10 than on 5.8.8; on 5.8.8 the
sequence converter holds steady at about 12MB of real memory, whereas on
5.10 it grows, albeit slowly, for as long as the program is executing. When
I killed it about 20% of the way through the file, it was up to  about 44MB
of real memory.

Anyone else have a chance to look at this?


Dave