[R] Error: cannot allocate vector of size X.0 Mb

[Marc Schwartz]

On Sep 14, 2010, at 9:09 AM, John1983 wrote:

> 
> Hi,
> 
> I am working with a file (900MB in size) that has around 10 million records
> (in particular FASTQ records).
> I am able to read in the file as an object of BStringSet. When I start to
> manipulate the data, after almost 4 hours, I get the error message as Error:
> cannot allocate vector of size X.0 Mb (where X was once 160MB and then
> 180MB).
> 
> The R version used is 2.11.1. I am not sure how to check if this is 64-bit
> or not so that I can use >4GB of RAM. I typed 'version' at the R prompt and
> see this:
> platform       x86_64-unknown-linux-gnu                                   
> arch           x86_64                                                     
> os             linux-gnu                                                  
> system         x86_64, linux-gnu.
> Does this mean it is already a 64-bit version of R I use?
> 
> Please advice.

In an R session, see what the result of:

  .Machine$sizeof.pointer

gets you. 

If it returns 4, you are using 32 bit R and you will need to install 64 bit R.

If it returns 8, you are using 64 bit R.

The information above only tells us/you that you are running a 64 bit OS.

HTH,

Marc Schwartz