[R-sig-Debian] Problem updating packages in 2.15.1 on Ubuntu 12.04

[Chris Evans]

The specific message is:
"Warning: package 'spatial' in library '/usr/lib/R/library' will not be 
updated"

and the number of libraries about which that's the complaint is now 
increasingly almost daily so clearly something is wrong.

I'm working on a laptop on which I do the recommended Ubuntu updates 
daily.  I done a standard installation of R 2.15.1 using synaptic with:

deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/
deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu precise/

in /etc/apt/sources.list and I added most of the optional packages that 
are packaged at that source.

I have been updating going into R through "sudo R" in my home directory 
and then using
"update.packages(instlib=.libPaths()[1],ask=FALSE)"

However, that gets these complaints about not updating.  I get the same 
message if I use:
"update.packages(ask=FALSE)"

I get the same if I use "su" rather than sudo and if I update as an 
ordinary user and if I point to a different mirror repository (I have 
been using Switzerland as Bristol seemed to be lagging behind 
Switzerland a lot).

I was doing to that without a personal library but tried updating as an 
ordinary user and created a personal library as prompted but that still 
gets the same but that means that my .libPaths() is now:

 > .libPaths()
[1] "/home/chris/R/i686-pc-linux-gnu-library/2.15"
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"

I think I've read and understood umpteen questions about the different 
ways of updating libraries on this list.  I would like to update to the 
latest library versions regularly (as 2.15.1 for Windoze in a VM box on 
this machine does fine).  Clearly I don't understand something and am 
doing something wrong.  Please can someone enlighten me?

Thanks in advance,

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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