[Rd] Problem with R >3.0.0

peter dalgaard pdalgd at gmail.com
Tue Aug 20 18:23:51 CEST 2013

On Aug 19, 2013, at 20:53 , Shelton, Samuel wrote:

> Dear R developer,
> I am an R user and am currently having a problem with versions of R >3.0.0. We build larger correlation matrices of >30000 with pairwise correlations made. We have been using a line of code
> simMat=bicor(datExpr1,use="p")

What is bicor()? From the WGCNA package? Perhaps the package is doing something incompatible with the long vector support in R 3.0.0. You need to report such queries to the maintainer. So far we have no evidence that the bug is in R itself, and you're not giving us anything reproducible to investigate.

> To build the similarity matrix with datExpr1 being a matrix with genes as columns (>30000) and rows being samples. This code works fine on an iMac running OSX 10.8.5 and using R 2.15.2 and the Rblas library. When I try to run the same code with R version 3.0.0 and 3.0.1 it only partially builds the matrix. It will return correlations for samples 1:11262 but from 11262:30000 the matrix is full of 0's.
> We would like to be able to use R 3.0.0 to allow us to build larger correlation matrices on our cluster but we can't use it at the moment due to this problem. My colleague has previously had a similar issue when using snow leopard and this was to do with a compatibility issue between snow leopard and the veclib. Has something changed in version 3.0.0 to give an incompatibility with the veclib?

This seems entirely speculative. Please stick to the facts.

Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

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