[BioC] Fwd: Re: Installing Bioconductor packages on R 2.14.0 *without* administrator rights / from a script

[Joern Toedling]

Hello,

without touching upon any recent changes in biocLite, I would recommend 
the following simple way to install packages without administrator rights.

1. Create an environment variable called "R_LIBS" and point that a 
writeable directory where you want your packages to go to. For example 
in the ~/.bashrc set something like:
export R_LIBS="${HOME}/rpackages"
Syntax is bit different for other shells and I guess it's possible to do 
this under Windows as well.
2. Start up R and install packages using biocLite() or 
install.packages(). The directory defined in the variable "R_LIBS" will 
be the first entry returned by ".libPaths()"  (verify that) and thus 
used as default installation directory.

HTH,
Joern

On 11/29/2011 10:02 AM, andrea.grilli at ior.it wrote:
> Hi Firas,
> I had similar problems working in linux. If it's also your case, I 
> solved changing administrative privileges to paths were all packages 
> are installed:
> sudo chmod 777 -R /usr/lib/R
> sudo chmod 777 -R /usr/local/lib/R/site-library
>
> Maybe this is not the conventional way, but allows me to update all 
> libraries without creating a new personal folder each time R is 
> updated to a new version.
> Hope this help,
> Andrea
>
>
> ----- Messaggio inoltrato da stvjc at channing.harvard.edu -----
>     Data: Fri, 25 Nov 2011 11:27:50 -0500
>       Da: Vincent Carey <stvjc at channing.harvard.edu>
> Rispondi-A:Vincent Carey <stvjc at channing.harvard.edu>
>  Oggetto: Re: [BioC] Installing Bioconductor packages on R 2.14.0 
> *without* administrator rights / from a script
>        A: Firas Swidan <firas at biomatters.com>
>       Cc: bioconductor at r-project.org
>
> Are you sure this is specific to bioconductor installation?  Does
> install.packages() with a CRAN package selection work for you?  If it 
> does
> not, you should study the R installation and administration guide 
> available
> at R project manuals, and pose residual questions at r-help.
>
> Defining folders where packages can be installed can be accomplished with
> .libPaths() in the session.  Check the value of this, and add a writeable
> folder and try again once you have done so.  If you can make no progress
> with this advice, send the result of sessionInfo() and the attempted 
> values
> of .libPaths and perhaps more concrete advice can be given.  The details
> will depend on the specific version of windows you are using along with
> aspects of the security setup, which may not be readily reproducible
> outside your site.  But in general you should be able to install 
> libraries
> in personally writeable folders, without administrative privileges, you
> just have to set the parameters appropriately.  These are laid out in 
> some
> detail in the installation and administration manual.
>
>


-- 
Joern Toedling, PhD
Core Facility Bioinformatics
Institute of Molecular Biology gGmbH (IMB)
http://www.imb-mainz.de