[BioC] Cannot allocate vector of size xxxxxxkb

[Dermot Morris]

Brooks, Anthony B <anthony.brooks at ...> writes:

> 
> Hi Guys,
> 
> I know this question has been asked many times before, but all the
> "solutions" I try seem to fail.
> 
> I have a Dell Optiplex, 2 X 3.4Ghz Dual Core Processor with 4Gb of RAM
> running windows XP Professional.
> 
> I am trying to read in a measly 16 HG-U133 Plus2.0 arrays using the
> following script.
> 
> celnames <- choose.files(caption="Choose CEL file(s)")
> 
> celnames <- sort(celnames)
> 
> Data <- ReadAffy(filenames=celnames)
> 
> However, I get the "Cannot allocate vector of size" error.
> 
> I have tried adding the --max-mem-size=2Gb tag onto my shortcut.
> 
> Using memory.limit(size=4000) 
> 
> The thing is I've used the same PC to analyse 27 arrays before, so I'm
> not sure what's chanaged. I'm shut down as many applications running on
> my system as possible.
> 
> Is there an idiot's guide on how to get R to use more memory anywhere?
> 
> Thanks in advance
> 
> Tony
> 
Hi Tony,

You first need to make sure Windows can use the extra memory bu inserting 
a /3Gb switch You can do this by editing boot.ini file according to the 
procedure outlined in http://support.microsoft.com/kb/823440/

My boot.ini under Windows XP PRO looks like this:

[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(2)\WINDOWS
[operating systems]

multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="1. Microsoft Windows XP 
Professional" /fastdetect multi(0)disk(0)rdisk(0)partition(2)\WINDOWS="2. /3GB 
Microsoft Windows XP Professional" /fastdetect /3GB multi(0)disk(0)rdisk(0)
partition(2)\WINDOWS="3. /3GB /USERVA 3072 Microsoft Windows XP 
Professional" /fastdetect /3GB /USERVA=3072

Note: Option and 3 are broadly similar you only need one of them.

This can be very risky as if you don't do it correctly you won't be able to re-
boot computer so make sure you know what you are doing or get someone who does.

Regards,

Dermot



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