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

From: Hervé Pagès <hpages_at_fhcrc.org>
Date: Wed, 08 Feb 2012 17:36:18 -0800

Thanks Martin. H.

On 02/08/2012 12:55 AM, Martin Maechler wrote:
>>>>>> Martin Morgan<mtmorgan@fhcrc.org>
>>>>>> on Tue, 7 Feb 2012 19:31:41 -0800 writes:
>
> > 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.
>
> yes, I think so too.
>
> > diff attached.
>
> I'm testing that and will commit.. if things seem fine.
> Martin Maechler
>
> > 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 x external: printarray.c.diff
> > text/x-patch, u [Click mouse-2 to display text]
> > ______________________________________________ R-devel_at_r-project.org
> > mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
>

-- 
Hervé Pagès

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

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Received on Thu 09 Feb 2012 - 01:38:10 GMT

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