thanks Martin,
I've recompiled from source, but I get the same error.
It doesn't happen with R2.15.
I didn't notice the page on BioC devel: that's definitely a better solution. Thanks for highlighting it.
cheers,
Francesco


On 14 Jul 2012, at 18:30, Martin Morgan wrote:

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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---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
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