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

Also, as an aside, R should not have tried to write to
/usr/lib/R/site-library.  Via the file /etc/R/Renviron, we define the library
path.  You should see this in R:

R> .libPaths()
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"       "/usr/lib/R/library"           
R> 

and /usr/local/lib/R/site-library as the 1st directory in this path should be
the one being written too.   You can then make that very directory writeable
by you (my preference) or run the install step as root in R (more clumsy in
my book).

Dirk

New Rcpp master class for R and C++ integration is scheduled for 
San Francisco (Oct 8), more details / reg.info available at
http://www.revolutionanalytics.com/products/training/public/rcpp-master-class.php