[BioC] R crashing, updating

Seth Falcon sfalcon at fhcrc.org
Wed Apr 12 00:32:45 CEST 2006

Hi Tarun,

I don't think you will like my answers...

"Tarun Nayar" <tnayar at bcgsc.ca> writes:
> 1. When I 
>> ReadAffy(widget=T) for over about 20 HGU133aplus2 chips, I get the
> following message:
> Error: cannot allocate vector of size 232872 Kb
> In addition: Warning messages:
> 1: Reached total allocation of 1500Mb: see help(memory.size) 
> 2: Reached total allocation of 1500Mb: see help(memory.size)
> I'm running Windows XP, 2Gb Ram, 3Ghz. Surely, I should be able to
> analyze more than 20 chips at a time with this system (?) I've already
> upped my memory.limit...

It looks like R has indeed reached 1.5Gb and on a Windows system w/
2Gb RAM, I wouldn't expect to be able to access much more than that.

> Is there a cheaper way to create an Affy batch?

We are working on bounded memory algorithms, but they are not
available yet.  Until then, obtaining a Linux system with lots of RAM
will be the most efficient approach.

> 2. When I want to update to the next version of R, how do I avoid having
> to re-install all of the Bioconductor packages I already have installed
> on my current version? At the moment, when I re-install, I can't load
> any of the prior packages...

Because of changes in R, you will need to reinstall Bioconductor

Each Bioc release is targeted towards a particular R release.  Bioc
1.7 goes with R 2.2.x.  The upcoming Bioc 1.8 (to be released ~May 1)
is what you will want to use with the about to be released R-2.3.x


+ seth

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