[R-sig-Debian] update.packages() as ordinary user, /usr/lib/R/site-library is not writable

[Chris Evans]

I am moving from windoze on a Dell laptop to Debian but I seem to have 
hit a snag for R.  I managed to find the information to point an 
/etc/apt/sources.list entry at my local CRAN repository and have 
installed R 2.13.1 for squeeze from the Bristol UK repository.

I  installed a number of the additional R packages using synaptic which 
reported no errors but when I run my first update.packages() as an 
ordinary user I get this:


The downloaded packages are in
	‘/tmp/Rtmp9LYziU/downloaded_packages’
Warning in install.packages(update[instlib == l, "Package"], l, 
contriburl = contriburl,  :
   'lib = "/usr/lib/R/library"' is not writable
Error in install.packages(update[instlib == l, "Package"], l, contriburl 
= contriburl,  :
   unable to install packages
In addition: Warning messages:
1: In install.packages(update[instlib == l, "Package"], l, contriburl = 
contriburl,  :
   installation of package 'rgl' had non-zero exit status
2: In install.packages(update[instlib == l, "Package"], l, contriburl = 
contriburl,  :
   installation of package 'XML' had non-zero exit status

Although all the compilations have run through, presumably with errors 
for rgl and XML, clearly the "not writable" status of /usr/lib/R/library 
has genuinely prevented the update.

I thought I'd seen strong advice here recently against updating 
libraries as root so I'm intrigued about this.  Can someone advise me 
what I should do?

Thanks in advance and huge thanks to all who do the porting to Debian 
and generally make R so good.

Chris

-- 
Chris Evans <chris at psyctc.org> Skype: chris-psyctc
Consultant Psychiatrist in Psychotherapy, Notts. PDD network;
Professor, Psychotherapy, Nottingham University
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