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....@cbs.dk Priv: pda...@gmail.com ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
