Error message specific to limma employed using R 2.15.2

Question

I recently updated R, and code I had written using the limma package before now returns an error.

The code was

classes = c(rep('Phenotype1',), rep('Phenotype 2',))
classes= as.factor(classes)
design=model.matrix(~classes-1)
colnames(design)=levels(classes) 
fit1= lmFit(exset, design)
cm=makeContrasts(Phenotype 1 - Phenotype 2, levels=design)
fit2= contrasts.fit(fit1,cm) 
fit3= eBayes(fit2)

With the new version of R, the following command

fit2= contrasts.fit(fit1,cm)

returns this error message...

Error in .Call("La_chol", as.matrix(x), PACKAGE = "base") : 
Incorrect number of arguments (1), expecting 2 for 'La_chol'

Answer 1

limma is a package from the BioConductor project, and each version of R has an associated version of BioConductor. If you updated R without updating your BioConductor packages (including limma), there might be some incompatibilities. Are you sure you're using the latest version of limma and BioConductor?