[Bioperl-l] bioperl-network warnings when loading the DIP dataset

Florin Iucha florin at iucha.net
Sun Oct 1 20:24:03 EDT 2006


On Sun, Oct 01, 2006 at 05:56:39PM -0400, Brian Osborne wrote:
> I'm not seeing any segmentation fault using the same file you're using as
> input (dip20060402.mif). I'm assuming you don't see this error when you use
> smaller files as input, like those in the t/data directory.

The t/data files are fine.

Also the largest file (full_2_psi1.xml) from release 2006-09-19 of the
MINT [1] database does not produce the crash.  It has a new warning, however:

   Can't call method "text" on an undefined value at
   /usr/local/share/perl/5.8.8/Bio/Network/IO/psi.pm line 290.

> When I watch the script in top I see Perl using about 135Mb (RSIZE) right
> before the script exits. How much memory do you use?

"ps ux" tells me VSZ = 272788 and RSZ = 254992. This is on x86-64 with
64 bit perl.  The box has 2 GB of physical memory so these numbers
don't seem to be a concern.

> Thank you for the note, and in the future write to bioperl-l since there may
> be others who are interested in hearing about what you've encountered.

Do'h! You have the list address loud and clear in three places, but I got
your contact info from the AUTHORS.  Will use the proper channel from now
on!

Thanks,
florin

[1] ftp://mint.bio.uniroma2.it/pub/release/psi1/

-- 
If we wish to count lines of code, we should not regard them as lines
produced but as lines spent.                       -- Edsger Dijkstra
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