[Bioc-devel] biocLite Install Path

[Dan Tenenbaum]

Hi Dario,

On Thu, Oct 13, 2011 at 4:00 PM, Dario Strbenac
<D.Strbenac at garvan.org.au> wrote:
> Hello,
>
> It seems like the 'lib' argument is being ignored when it gets passed onto install.packages.
>
>> source("http://www.bioconductor.org/biocLite.R")
> BiocInstaller version 1.1.19 loaded, type ?biocLite for help
>> biocLite("GenomicFeatures", lib = "F:\\BIOC29")
> Installing package(s) into ‘C:/Users/dario/Documents/R/win64-library/2.11’
> (as ‘lib’ is unspecified)
> trying URL 'http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/BiocInstaller_1.1.28.zip'
> Content type 'application/zip' length 29003 bytes (28 Kb)
> opened URL
> downloaded 28 Kb
>
> package ‘BiocInstaller’ successfully unpacked and MD5 sums checked
>

Here, it's actually installing BiocInstaller, not GenomicFeatures.

BiocInstaller (which contains the biocLite() function) *does* pass
your lib argument to install.packages, which is why you see
GenomicFeatures there.

Dan


> ...             ...
>
>> sessionInfo()
> R version 2.14.0 alpha (2011-10-11 r57214)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252
> [3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.1.28
>
> loaded via a namespace (and not attached):
> [1] tools_2.14.0
>
> But when I look at F:\BIOC29, the packages are actually installed there.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
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