[BioC] R hangs when applying johnson.all.pairs.sp (in library RBGL) to some graphs

Seth Falcon sfalcon at fhcrc.org
Sat Jun 3 16:13:41 CEST 2006

Hi Dan,

Sorry for the delay in response.  You need to subscribe to post to the
list and our list moderator was unavailable to check the queue...

"Dan Bebber" <dan.bebber at plants.ox.ac.uk> writes:
> Hello,
> when I apply johnson.all.pairs.sp to certain graphs, R hangs.
> The R window can still be resized, minimized etc. and the "stop current 
> computation" button can be pressed (though nothing happens).
> The computation can be interrupted by attempting to close R, then pressing 
> "cancel" when the "save workspace" dialogue opens. However, R then becomes 
> unstable and shuts down without warning.
> The error also causes R to shut down occassionally.
> I have this problem with 2 of 35 graphs I am analysing.

Can you provide some details about the two graphs that cause the
hanging behavior?  Also, how long did you let things "hang"?
Computing all pairs shortest paths can be computationally intensive
for larger graphs.  One possibility is that everything is working ok,
but the calculation is taking longer than you would like.

> I can provide an example of a test graph if anyone would be kind enough to 
> test this on their system.

That would be great. 


+ seth

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