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

[andrea.grilli at ior.it]

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.

On Thu, Nov 24, 2011 at 9:32 PM, Firas Swidan <firas at biomatters.com> wrote:

> Hi,
>
> I used to be able to install Bioconductor packages from a script *without*
> having administrator rights (e.g., on Windows) by specifying the library
> location to where the packages are to be installed.
>
> However, with the new R (2.14.0) and Bioconductor releases, the command
>
>
>
> source("http://bioconductor.org/biocLite.R")
>
>
>
> would fail without administrator rights, because it tries to install
> packages to directories that require administrator rights.
>
> I checked the file biocLite.R and located the line where this problematic
> install happens (install.packages("BiocInstaller", repos=a["BioCsoft",
> "URL"]))
>
>
> Is there a safe way to avoid the requirement for administrator rights? I
> know that I could modify the above command and add a library location
> argument, but is that safe?
>
> In particular I am wondering why the r-script was modified to require the
> administrator right?
>
> Thanks,
> Firas.