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

[Chris Evans]

John C Nash sent the following  at 01/08/12 15:30:

> The PPA for latest Ubuntu packages doesn't seem to be in the sources list.
>
> https://launchpad.net/~marutter/+archive/rrutter

Aha.  OK.  Fixed that.  That seems to have meant that cran, coda and 
spatial have now been updated (by apt-get update).  Interestingly, I'm 
still getting the comment that coda won't be updated even after that.  I 
suspect that means that the main cran repository has a version of coda 
even more recent than the one in rrutter.

> Also see the CRAN page (I've used the probability.ca mirror)
>
> http://probability.ca/cran/bin/linux/ubuntu/

I have and thought I was pretty compliant with that. Only thing I've not 
followed is the backports bit.

Many thanks,

C

>
> Best, JN
>
> On 08/01/2012 02:02 AM, Chris Evans wrote:
>> 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
*If I am writing from one of those roles, it will be clear. Otherwise*
*my views are my own and not representative of those institutions    *
If you have difficulty Emailing me on this address or getting a reply,
send again but cc to:       chris dot evans at nottshc dot nhs dot uk
and to:                     c dot evans at nottingham dot ac dot uk