[R] help about the dist() error message

Thomas Lumley tlumley at u.washington.edu
Wed Apr 16 20:32:18 CEST 2003

On Wed, 16 Apr 2003, Meng Xue wrote:

> hello,
> I have a problem when call dist() of package mva on a large data
> set. The following error message are obtained when I use dist()
> on m, a two dimensional data set with the size 100,000. It seems
> that the length of vector out of bound, since when I compute
> dist on small data set(10,000), it works well. but for large
> data set, it   exit with the message "negative length vector are
> not allowed" .

With 100,000 points there are 50 billion pairwise distances, which would
take at least 400 Gb of memory.  It probably wouldn't even fit on your
disk, let alone in memory.

You need to work out why you want the pairwise distances and decide what
you can do instead.


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