[R] Error in vector("integer", length) : vector size cannot be NA

[Petr Savicky]

On Wed, Dec 08, 2010 at 08:12:34PM -0800, mathijsdevaan wrote:
> 
> Hello,
> 
> I have uploaded a csv file that looks like this:
> 
> > gc
>          alpha_id     beta_id
> 1       142053       1
> 2         9454       1
> 3       295618       2
> 4        42691       2
> 5       389224       3
> 6         9455       3
> 
> The alpha_id contains 310660 unique values and the beta_id contains 17431
> unique values. The number of rows adds up to more than 1.3 million. Now I
> want to convert this list of observations into a matrix with alpha_id in the
> first row and beta_id in the first column (or vice versa) and a count in the
> cells. So this would be an option M = as.matrix( table(gc) ). However, I
> keep getting this error message:
> 
> Error in vector("integer", length) : vector size cannot be NA
> In addition: Warning messages:
> 1: In pd * (as.integer(cat) - 1L) : NAs produced by integer overflow
> 2: In pd * nl : NAs produced by integer overflow
> 
> There is no missing data in my file, so I don't know what's wrong. Can you
> please help me? Thanks!

The number of entries in the table is 310660*17431. Using integer
type, this is 310660*17431*4 bytes, which is 20.17 GB. This probably
does not fit into RAM. Function table() produces a full matrix, not
a sparse one, even if there are empty cells.

Petr Savicky.