R devel - Feb 2012 - capture.output() is trying to allocate 17179869182.6 Gb on my not so big data.frame

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

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

-- 
Herv? Pag?s

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

On 02/07/2012 04:08 PM, Herv? Pag?s 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
>

-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793
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