[BioC] memory.limit

[James W. MacDonald]

Hi Dimitriy,

Dmitriy Scvortsov wrote:
> Hi guys
>
>   I am trying to load dataset of 50 cel files using   ReadAffy in my machine
>
>
> It runs win XP and I'm using R Version 2.3.1
>
> Each  cel file is about 13 mb  so estimated memory usage is at most 800 mb
> I have 2G available
>   

Well, that estimate doesn't take into account the amount of copying that 
goes on, nor does it account for Window's inability to return large 
blocks of memory that have already been used. It is not hard at all to 
burn through 2 Gb of RAM with 50 U133plus2 chips. I think you could 
probably process this many on say, Linux, but not on Windows. You are 
better off trying justRMA(), which is much more memory friendly.
> I have requested memory limit  2G by   memory.limit(size=2048  ) command,
> but  I keep getting 
>
> Error message "Error: cannot allocate vector of size 518671 Kb"    which is
> less than default 1G.
>   

This error doesn't concern the total amount of memory that has been 
allocated, but the amount of RAM that R is requesting for the current 
operation.
> When I am trying to check amount of memory available  by
>
>   
>> memory.size(max =T)
>>     
>
>   
>> [1] 546152448
>>     
>
> Can anybody explain  me what's going on here , and  how to make it work ?
>   

Not sure about that one, unless you are running some other process that 
is sucking up a bunch of RAM. Anyway, the fix is to use justRMA(), or 
boot Linux. You can get Quantian and boot directly off a CD to see if 
Linux will work for you, if you are interested.

HTH,

Jim


> Thank you
>
>
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