Reading large files in R

-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch 
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of 
Adaikalavan Ramasamy
Sent: Monday, August 08, 2005 12:02 PM
To: Jean-Pierre Gattuso
Cc: r-help at stat.math.ethz.ch
Subject: Re: [R] Reading large files in R

From Note section of help("read.delim") :

     'read.table' is not the right tool for reading large matrices,
     especially those with many columns: it is designed to read _data
     frames_ which may have columns of very different classes. Use
     'scan' instead.

So I am not sure why you used 'scan', then converted it to a 
data frame.

1) Can provide an sample of the data that you are trying to read in.
2) How much memory does your machine has ?
3) Try reading in the first few lines using the nmax argument in scan.

Regards, Adai



On Mon, 2005-08-08 at 12:50 -0600, Jean-Pierre Gattuso wrote:

Dear R-listers:

I am trying to work with a big (262 Mb) file but apparently 

reach a  

memory limit using R on a MacOSX as well as on a unix machine.

This is the script:

 > type=list(a=0,b=0,c=0)
 > tmp <- scan(file="coastal_gebco_sandS_blend.txt", what=type,  

sep="\t", quote="\"", dec=".", skip=1, na.strings="-99", 

nmax=13669628)

Read 13669627 records

 > gebco <- data.frame(tmp)

Error: cannot allocate vector of size 106793 Kb


Even tmp does not seem right:

 > summary(tmp)

Error: recursive default argument reference


Do you have any suggestion?

Thanks,
Jean-Pierre Gattuso