Re: [Rd] capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame

From: Martin Morgan <mtmorgan_at_fhcrc.org>
Date: Tue, 07 Feb 2012 19:31:41 -0800

On 02/07/2012 04:08 PM, Hervé Pagès wrote:
> Hi,
>
> This is what I get with recent R devel on a 64-bit Ubuntu laptop:
>
> > mydf <- data.frame(a=1:2080, b=1001:2040, c=letters, d=LETTERS,
> e=1:1040)
> > mydf_in_a_character_vector <- capture.output(mydf)
> Error in print.default(m, ..., quote = quote, right = right) :
> cannot allocate memory block of size 17179869182.6 Gb

The error is thrown inside src/main/printarray.c:425

		Rprintf("%*s%s", R_print.gap, "",
			EncodeString(x[i + j * r], w[j], quote, right));

where the array w is the result of an unPROTECTed allocation earlier in the function, and a garbage collection triggered in MatrixRowLabel (in this case; allocation also occurs in MatrixColLabel, Rprintf). PROTECTion seems to have been implemented in the file assuming that the only allocations are at the head of the function; the return in the _PRINT_DEAL_c_eq_0 macro makes it difficult to balance the protection stack, and R_alloc seems to be a better solution anyway. diff attached.

Martin Morgan

>
> I get something similar with R 2.14.1.
>
> Cheers,
> H.
>
> > sessionInfo()
> R Under development (unstable) (2012-01-16 r58124)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>

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