[BioC] Calculation times

[Jeff Gentry]

> I have recently upgraded my linux machine from R1.6.2/Bioconductor 1.1
> to R1.7/Bioconductor 1.2 and have found that the new version runs
> considerabley slower than the old version. So much so that I have a
> function to calculate fold change for an expression set that takes a few
> minutes to run in R1.6.2/BioC 1.1, but well over half an hour to run on
> the latest version. 

I'm not sure of all the how's and why's of what it affected, so do not
know if it would help out here - however there were some problems fixed in
R-1.7.0 (patched) which solved some problems which led to massive speed
problems.

You should make sure you are using an up to date R-1.7.0 (patched),
see: http://www.bioconductor.org/downloadingR.html for more information on
how to obtain it.  This is probably a good idea anyways, and very well
might solve your problem.