[BioC] Repository for Bioconductor annotation packages
hpages at fhcrc.org
Sat Jul 15 22:43:04 CEST 2006
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.
> biocLite installs in the R library directory on the server.
This is what it does by default. But you can specify your own library
directory with the 'lib' arg:
> 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...
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