[R] Alternatives to merge for large data sets?

Adam D. I. Kramer adik at ilovebacon.org
Thu Sep 7 20:46:04 CEST 2006

On Thu, 7 Sep 2006, Prof Brian Ripley wrote:

> Which version of R?

Previously, 2.3.1.

> Please try 2.4.0 alpha, as it has a different and more efficient
> algorithm for the case of 1-1 matches.

I downloaded and installed R-latest, but got the same error message:

Error: cannot allocate vector of size 7301 Kb

...though at least the too-big size was larger this time.

My data set is not exactly 1-1; every item in "prof" may have one or more
matches in "pubbounds," though every item in "pubbounds" corrosponds only to
one "prof."


> On Wed, 6 Sep 2006, Adam D. I. Kramer wrote:
>> Hello,
>> I am trying to merge two very large data sets, via
>> pubbounds.prof <-
>> merge(x=pubbounds,y=prof,by.x="user",by.y="userid",all=TRUE,sort=FALSE)
>> which gives me an error of
>> Error: cannot allocate vector of size 2962 Kb
>> I am reasonably sure that this is correct syntax.
>> The trouble is that pubbounds and prof are large; they are data frames which
>> take up 70M and 11M respectively when saved as .Rdata files.
>> I understand from various archive searches that "merge can't handle that,"
>> because merge takes n^2 memory, which I do not have.
> Not really true (it has been changed since those days).  Of course, if you
> have multiple matches it must do so.
>> My question is whether there is an alternative to merge which would carry
>> out the process in a slower, iterative manner...or if I should just bite the
>> bullet, write.table, and use a perl script to do the job.
>> Thankful as always,
>> Adam D. I. Kramer
> -- 
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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