[Rd] Severe memory problem using split()
mtmorgan at fhcrc.org
Mon Jul 12 23:44:00 CEST 2010
On 07/12/2010 01:45 PM, cstrato wrote:
> Dear all,
> With great interest I followed the discussion:
> since I have currently a similar problem:
> In a new R session (using xterm) I am importing a simple table
> "Hu6800_ann.txt" which has a size of 754KB only:
>> ann <- read.delim("Hu6800_ann.txt")
>  7129 11
> When I call "object.size(ann)" the estimated memory used to store "ann"
> is already 2MB:
> 2034784 bytes
> Now I call "split()" and check the estimated memory used which turns out
> to be 3.3GB:
>> u2p <- split(ann[,"ProbesetID"],ann[,"UNIT_ID"])
> 3323768120 bytes
I guess things improve with stringsAsFactors=FALSE in read.delim?
> During the R session I am running "top" in another xterm and can see
> that the memory usage of R increases to about 550MB RSIZE.
> Now I do:
> 894056 bytes
> It takes about 3 minutes to complete this call and the memory usage of R
> increases to about 1.3GB RSIZE. Furthermore, during evaluation of this
> function the free RAM of my Mac decreases to less than 8MB free PhysMem,
> until it needs to swap memory. When finished, free PhysMem is 734MB but
> the size of R increased to 577MB RSIZE.
> Doing "split(ann[,"ProbesetID"],ann[,"UNIT_ID"],drop=TRUE)" did not
> change the object.size, only processing was faster and it did use less
> memory on my Mac.
> Do you have any idea what the reason for this behavior is?
> Why is the size of list "u2p" so large?
> Do I make any mistake?
> Here is my sessionInfo on a MacBook Pro with 2GB RAM:
> R version 2.11.1 (2010-05-31)
>  C
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> Best regards
> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
> V.i.e.n.n.a A.u.s.t.r.i.a
> e.m.a.i.l: cstrato at aon.at
> R-devel at r-project.org mailing list
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