[BioC] Repository for Bioconductor annotation packages

[Herve Pages]

Daniel Gatti wrote:
> Daniel Gatti wrote:
>
>  >> O/S: Linux
>  >> arch : i686
>  >> R version : 2.2.1
>  >>
>  >> I'm using the install.packages() command to install Bioconductor
>  >> libraries to my home directory.  I can install functional packages like
>  >> "safe" and "GOstats". But when I try to install annotation packages, it
>  >> tells me that it can't find them in given repository.  I'm using
>  >> repos="http://www.bioconductor.org".  What repository should I use for
>  >> the annotation packages?
>  >>
>  >> install.packages("hgu133a", lib = "~/Rlib",
>  >> repos="http://www.bioconductor.org")
>
>  >It's easier to use biocLite() instead.
>  >
>  >source("http://www.bioconductor.org/biocLite.R")
>  >biocLite("hgu133a")
>
> biocLite installs in the R library directory on the server.

Hi Daniel,

This is what it does by default. But you can specify your own library
directory with the 'lib' arg:
  > source('http://bioconductor.org/biocLite.R')
  > biocLite('Biobase', lib='my_lib_dir')
In fact, all the arguments that can be used with the install.packages()
function can also be used with biocLite().
I don't think this is documented on the Bioconductor website. It probably
should (and will be soon). Sorry for that...

Best,

H.

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Hervé Pagès
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