[R] Another big data size problem

Ernesto Jardim ernesto at ipimar.pt
Wed Jul 28 10:58:54 CEST 2004

On Wed, 2004-07-28 at 03:10, Federico Gherardini wrote:
> Hi all,
> I'm trying to read a 1220 * 20000 table in R but I'm having lot of problems. Basically what it happens is that R.bin starts eating all my memory until it gets about 90%. At that point it locks itself in a  uninterruptible sleep status (at least that's what top says) where it just sits there barely using the cpu at all but keeping its tons of memory. I've tried with read.table and scan but none of them did the trick. I've also tried some orrible hack like reading one line a time and gradually combining everything in a matrix using rbind... nope! It seems I can read up to 500 lines in a *decent* time but nothing more. The machine is a 3 GHz P4 with HT and 512 MB RAM running R-1.8.1. Will I have to write a little a C program myself to handle this thing or am I missing something?
> Thanks in advance for your help,
> fede


It looks like you're running linux !? if so it will be quite easy to
create a table in MySQL, upload all the data into the database and
access the data with RMySQL (it's _very_ fast). Probably there will be
some operations that you can do on MySQL instead of "eating" memory in



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