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

[Kasper Daniel Hansen]

I am not fully up to date on the 64 bit windows issue, but I would  
assume that the CRAN build is done for a 32 bit system. If that is  
the case you need to recompile it - perhaps do a little search to see  
if someone else has already done it.

If you have such a big machine, why are you running windows on it :)

/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
>
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