Hi Karl

Are you using Ubuntu? I just looked at my installation and see the same four libs. I wonder if this is due to initially installing R from the official Ubuntu repos and then updating R (to the current version) using the CRAN repos?

Just a thought.

Best

Iain



________________________________
 From: Martin Morgan <mtmorgan@fhcrc.org>
To: Karl Brand <k.brand@erasmusmc.nl> 
Cc: bioconductor@r-project.org 
Sent: Wednesday, 23 November 2011, 17:39
Subject: Re: [BioC] package ‘DAVIDQuery’ is not available (for R version 2.14.0)

On 11/23/2011 08:34 AM, Karl Brand wrote:
>
> Esteemed BioC UseRs and Devs,
>
> I'm trying (and failing) to install the BioC package "DAVIDQuery". There
> must be a simple way to solve this issue, but my googling failed to
> solve this issue.
>
> Within (ESS/Emacs) R --vanilla i tried:
>
>  > install.packages("DAVIDQuery", dependencies=TRUE)
> Installing package(s) into
> ‘/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13’
> (as ‘lib’ is unspecified)
> --- Please select a CRAN mirror for use in this session ---
> Loading Tcl/Tk interface ... done
> Warning message:
> In getDependencies(pkgs, dependencies, available, lib) :
> package ‘DAVIDQuery’ is not available (for R version 2.14.0)

DAVIDQuery is a Bioconductor package, but it sounds like you're choosing 
a 'CRAN' archive. The recommended installation process is

   source("http://bioconductor.org/biocLite.R")
   biocLite("DAVIDQuery")


>  >
>
> This makes me wonder if i need to specify a different library (path). If
> so, which one?
>
>  > .libPaths()
> [1] "/home/kbrand/R/x86_64-pc-linux-gnu-library/2.13"
> [2] "/usr/local/lib/R/site-library"
> [3] "/usr/lib/R/site-library"
> [4] "/usr/lib/R/library"

That there are four is due to someone / thing other than R; see ?Startup 
for hints on how these libraries are identified.

Martin

>
> (This is a bigger area of ignorance for me - why has R set up four
> separate libraries by default? Where some require use of sudo to
> install/update packages, whilst others do not? And what are the
> implications when it comes time to upgrade to the next version of R? I
> have obtained some advice on this before -
> https://stat.ethz.ch/pipermail/ess-help/2011-September/007120.html - but
> have failed to implement this given my focus on just using R, neglecting
> its proper maintenance, and all round inexperience with linux).
>
> I'd really appreciate responses on getting "DAVIDQuery" running on my
> currently installed R 2.14.0 (as well as any tips on 'good practice'
> when it comes to R library management on linux (ubuntu)).
>
> Sincerely,
>
> Karl
>
>  > sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_DK.UTF-8" LC_COLLATE=en_AU.UTF-8
> [5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] tcltk_2.14.0 tools_2.14.0
>  >
>


-- 
Computational Biology
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