[R] Odd timing behaviour in reading a file

From: Glenn Stone <Glenn.Stone_at_csiro.au>
Date: Thu 04 Aug 2005 - 13:36:20 EST


Hi all, please don't ask me why I tried this but.......

I have observed some odd behaviour in the time taken to read a file. I tried searching the archives without much success, but that could be me.

The first time I read a (60Mb) CSV file, takes a certain amount of time. The second time takes appreciably longer and the third and subsequent times very much shorter times. See below,

$ R2.1.1

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> system.time(temp <-

read.csv("Mapping50K_Xba240_annot.csv",header=TRUE, as.is=TRUE)) [1] 32.55 0.30 33.46 0.00 0.00
> system.time(temp <-

read.csv("Mapping50K_Xba240_annot.csv",header=TRUE, as.is=TRUE)) [1] 45.32 0.24 45.72 0.00 0.00
> system.time(temp <-

read.csv("Mapping50K_Xba240_annot.csv",header=TRUE, as.is=TRUE)) [1] 11.73 0.17 11.94 0.00 0.00
> system.time(temp <-

read.csv("Mapping50K_Xba240_annot.csv",header=TRUE, as.is=TRUE)) [1] 8.58 0.28 8.96 0.00 0.00
> system.time(temp <-

read.csv("Mapping50K_Xba240_annot.csv",header=TRUE, as.is=TRUE)) [1] 8.80 0.16 9.02 0.00 0.00

This is a relatively quiet opteron running redhat linux and using R2.1.1 The same pattern is repeatable, and occurs in R2.0.1 and on a Dell laptop running Windows XP.

I guess it is probably something to do with the garbage collector? Can anyone explain further? Particularly the first increase.

Thanks....

-- 
Glenn Stone
CSIRO Bioinformatics
http://www.bioinformatics.csiro.au

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Received on Thu Aug 04 13:40:38 2005

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