[BioC] exomeCopy - no .Internal function 'cov' error

[Lescai, Francesco]

Hi there,
I was trying to update my code after updating the package exomeCopy, but I get an error from the exomeCopy function.

Error in var(lmfit$residuals) : there is no .Internal function 'cov'

In order to be 100% sure I've followed exactly the vignette code, loading the package data, and I get the very same error

> fit <- exomeCopy(rdata["chr1"],sample.name=exome.samples[3],X.names=c("bg","GC","GC.sq","width"),S=0:6,d=2)
Error in var(lmfit$residuals) : there is no .Internal function 'cov'

or if more than one chromosome
> fit.list <- lapply(samples,runExomeCopy,seqs)
Error in var(lmfit$residuals) : there is no .Internal function 'cov'

I'm using one of the R-devel versions - sessionInfo below

thanks very much,
Francesco


> sessionInfo()
R Under development (unstable) (2012-07-02 r59715)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multicore_0.1-7      exomeCopy_1.3.1      Rsamtools_1.9.18     Biostrings_2.25.6    GenomicRanges_1.9.28
[6] IRanges_1.15.17      BiocGenerics_0.3.0  

loaded via a namespace (and not attached):
 [1] MASS_7.3-19        RColorBrewer_1.0-5 bitops_1.0-4.1     colorspace_1.1-1   dichromat_1.2-4   
 [6] digest_0.5.2       ggplot2_0.9.1      grid_2.16.0        labeling_0.1       memoise_0.1       
[11] munsell_0.3        plyr_1.7.1         proto_0.3-9.2      reshape2_1.2.1     scales_0.2.1      
[16] stats4_2.16.0      stringr_0.6        tools_2.16.0       zlibbioc_1.3.0