R help - Jun 2006 - Very slow read.table on Linux, compared to Win2000

Dear all,

I read.table a 17MB tabulator separated table with 483 variables(mostly numeric)
and 15000
observations into R. This takes a few seconds with R 2.3.1 on windows 2000, but
it takes
several minutes on my Linux machine. The linux machine is Ubuntu 6.06, 256 MR
RAM,
Athlon 1600 processor. The windows hardware is better (Pentium 4, 512 RAM), but
it
shouldn't make such a difference. 

The strange thing is that even doing something with the data(say a histogram of
a variable, or
transforming
integers into a factor)  takes really long time on the linux box and the
computer seems to work
extensively with the hard disk. 
Could this be caused by swapping ? Can I increase the memory allocated to R
somehow ?
I have checked the manual, but the memory options allowed for linux don't
seem to
help me (I may be doing it wrong, though ...)

The code I run:

TBO <-
read.table(file="TBO.dat",sep="\t",header=TRUE,dec=",");
# this takes forever
TBO$sexe<-factor(TBO$sexe,labels=c("man","vrouw"));   #
even this takes like 30 seconds, compared
to nothing on Win2000

I'd be grateful for any suggestions,

Regards,
David Vonka


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David Vonka (Netspar, Universiteit van Tilburg, room B-623)
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<davidek at zla-ryba.cz> writes:
> Dear all,
> 
> I read.table a 17MB tabulator separated table with 483 variables(mostly
numeric) and 15000
> observations into R. This takes a few seconds with R 2.3.1 on windows 2000,
but it takes
> several minutes on my Linux machine. The linux machine is Ubuntu 6.06, 256
MR RAM,
> Athlon 1600 processor. The windows hardware is better (Pentium 4, 512 RAM),
but it
> shouldn't make such a difference. 
> 
> The strange thing is that even doing something with the data(say a
histogram of a variable, or
> transforming
> integers into a factor)  takes really long time on the linux box and the
computer seems to work
> extensively with the hard disk. 
> Could this be caused by swapping ? Can I increase the memory allocated to R
somehow ?
> I have checked the manual, but the memory options allowed for linux
don't seem to
> help me (I may be doing it wrong, though ...)
> 
> The code I run:
> 
> TBO <-
read.table(file="TBO.dat",sep="\t",header=TRUE,dec=",");
# this takes forever
> TBO$sexe<-factor(TBO$sexe,labels=c("man","vrouw")); 
# even this takes like 30 seconds, compared
> to nothing on Win2000
> 
> I'd be grateful for any suggestions,
Almost surely, the fix is to insert more RAM chips. 256 MB leaves you
very little space for actual work these days, and a 17MB file will get
expanded to several times the original size during reading and data
manipulations. Using a lightweight window manager can help, but you
usually regret the switch for other reasons. 


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