[R] limit of cmdscale function

Kawashima, Masayuki kawasima.m at jp.fujitsu.com
Thu Nov 6 05:50:49 CET 2014


We have a few questions regarding the use of the "isoMDS" function.

When we run "isoMDS" function using 60,000 x 60,000 data matrix, 
we get the following error message:

cmdscale(d, k) : invalid value of 'n'
Calls: isoMDS -> cmdscale

We checked the source code of "cmdscale" and found the following limitation:
## we need to handle nxn internally in dblcen
if(is.na(n) || n > 46340) stop("invalid value of 'n'")

1. This cmdscale limitation ('n > 46340') is due to the limitation of BLAS and LAPACK variables(int4) which can only handle '2^31-1' amount of data?

2. Is there any workaround to run isoMDS using large data (i.e. greater than 46340)?
   We would like to run isoMDS using a maximum of 150,000x150,000 data matrix.

Best regards

Masayuki Kawashima
Email: kawasima.m �� jp.fujitsu.com

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