[BioC] Memory Issue under WinXP x64 (64 bit Windows XP)

[Carleton Garrett]

Francois, Kasper

Thanks for the info and your insights. I've been looking into setting up the 
computer to dual boot in Windows/Linux in order to run 'R' without the 
Windows constraints. (Sorry about missing the point in the Windows FAQ).

Regards

Carl Garrett


----- Original Message ----- 
From: "Kasper Daniel Hansen" <khansen at stat.Berkeley.EDU>
To: "Carleton Garrett" <ctgarret at hsc.vcu.edu>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Thursday, May 18, 2006 5:25 PM
Subject: Re: [BioC] Memory Issue under WinXP x64 (64 bit Windows XP)


> Actually in the R for Windows FAQ (which you of course consulted  before 
> sending your email), it says under 8.1
> "Note that building under Windows 64 is not supported as no suitable 
> compiler is available"
>
> This means you need to switch OS if you want R to use the many GB of 
> memory you have.
>
> /Kasper
>
> On May 18, 2006, at 2:01 PM, Carleton Garrett wrote:
>
>> Hi
>>
>> I'm currently running Bioconductor version 2.2.0 under Windows XP x64
>> with 16 Gb RAM and Virtual Memory upto 100 Gb.
>>
>> In trying to combine 67 Affy u133a and 67 Affy u133a_2 cel files I am
>> able to form the initial affy batches using read.affybatch() but get a
>> memory allocation error (below) when I try to combine them with the
>> 'combineAffyBatch()' function
>>
>> Error: cannot allocate vector of size 280,470 Kb
>>
>> Attempts to increase memory size within 'R' are only partly  successful.
>> Attempting to increase the memory to 16 Gb (16000 Mb) through using  the
>> following command
>>
>> memory.limit(size=16000)
>>
>> produces the error
>>
>> Error in memory.size(size) : don't be silly! : your machine has a 4 Gb
>> limit [not true according to the OS].
>>
>> Reducing the number of cel files in the two initial affy batches to 16
>> each (but not 33 each) did allow the combined affy batch to be created
>> so the combneAffyBatch() function appears to work on this platform.
>>
>> Two questions:
>>
>> 1)   Does the binary version 2.2.0 of R for Windows have a built-in
>> memory limit of 4 Gb? - and if so, is there a way to circumvent  this 
>> limit?
>>
>> 2)   Is there anything peculiar about the combineAffyBatch() function
>> that makes it use memory inefficiently?
>>
>>     I raise the above question because even when the number of cel  files
>> was reduced to 33 u133a and 33 u133a_2 there was a memory allocation
>> error when I ran combineAffyBatch() that was the same as with the 67 +
>> 67 cel files (ie, "Error: cannot allocate vector of size 280,470 Kb")
>> and yet the memory.limit() was ~4.2 Gb and the memory.size() was only
>> ~1.4 Gb in a machine with 16 Gb RAM.
>>
>> Any suggestions welcomed.
>>
>> Carl Garrett
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/ 
>> gmane.science.biology.informatics.conductor
>
>
>