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