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

Dave Messina David.Messina at sbc.su.se
Sat Aug 9 07:04:04 EDT 2008

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

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?


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