[R] memory failure in adonis function (permanova)

[Gavin Simpson]

On Tue, 2010-03-16 at 17:12 +0100, Paloma Ruiz wrote:
> Dear all,
> 
> I am trying to get a PERMANOVA with quite large data set. I am reading a lot
> about this question, but I do not get the answer about it. Although I know
> that the R function is adonis () (vegan package), it does not work:
> 
> adonis(Pha.env~SPha, data=Pha, permutations=10)
> 
> The error message:
>  Error: cannot allocate vector of size 334.2 Mb
> In addition: Warning messages:
> 1: In vegdist(lhs, method = method, ...) :
>   Reached total allocation of 1535Mb: see help(memory.size)
> 2: In vegdist(lhs, method = method, ...) :
>   Reached total allocation of 1535Mb: see help(memory.size)
> 3: In vegdist(lhs, method = method, ...) :
>   Reached total allocation of 1535Mb: see help(memory.size)
> 4: In vegdist(lhs, method = method, ...) :
>   Reached total allocation of 1535Mb: see help(memory.size)
> 
> When I have received this message from R usually it is due to an incorrect
> introduction of the function elements (i.e., memory message errors).
> However, I've just checked my matrix (Pha.env is a data.frame with num or
> int variables, and, Pha is a data.frame with factor variables) and the
> length of matrices is the same. I know that I'm wrong somewhere specifying
> the matrices in adonis(), but I can't fix it.

That error is coming from the calculation of the dissimilarity matrix
and you've exhausted the 1.5GB of (allocated) RAM on your system. How
many samples (rows) are you trying that on?

G

> 
> Thanks in advance,
> 
> Paloma
> 
> 	[[alternative HTML version deleted]]
> 
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