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

[Martin Morgan]

On 07/14/2012 09:08 AM, Lescai, Francesco wrote:
> 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

One answer is that, to use R-devel, specify type="source" when 
installing packages, e.g.,

   biocLite('exomeCopy', type='source')

This may require that you have additional operating system specific 
tools installed, as described here http://r.research.att.com/tools/.

An alternative, consistent with Bioc builds, is to use R-2.15.1 for 
devel, as described at http://bioconductor.org/developers/useDevel/.

R is now on a yearly release cycle. As a consequence both release and 
devel versions of Bioconductor are currently built using R-2.15.1 
(Bioc-devel will switch to R-devel after our next release, some time in 
September / October). R-devel has re-organized the location of some 
.Internal functions, so the R-2.15.1 built packages are not compatible.

Martin

>
> 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
>
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