R SIG Debian - Aug 2012 - Problem updating packages in 2.15.1 on Ubuntu 12.04

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

The PPA for latest Ubuntu packages doesn't seem to be in the sources list.

https://launchpad.net/~marutter/+archive/rrutter

Also see the CRAN page (I've used the probability.ca mirror)

http://probability.ca/cran/bin/linux/ubuntu/

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
> 
> 
>

On Wed, Aug 1, 2012 at 1:02 AM, Chris Evans <chrishold at psyctc.org>
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.
>
Yes, the something wrong is the system administrator :)

Please remember that you have a choice of installing R packages from
the R repositories using install.packages (or update.packages). That
downloads source code, compiles and installs. Generally, on Debian, it
will install to /usr/local/lib/R/site-library.  But you may also
install them as Debian packages that have been built on somebody
else's system and wrapped up for your usage.  Those generally install
into /usr/lib/R/site-library.  As you know, R is provided with a set
of recommended packages, and when you install r-base-core, it brings
with it those recommended packages, which have names like:

r-cran-boot
r-cran-cairodevice

Since you don't give the full output of update.packages(), I can only
guess what is going wrong.  But I'm almost certain this is it.

You have the R spatial package installed from a debian package:

Check the spatial package like so:

$ dpkg -l | grep spatial
ii  r-cran-spatial                               7.3-3-1
             GNU R package for spatial statistics

$ dpkg -L r-cran-spatial

Now, if you are inside R and you run

$ install.packages("spatial", dep=T)

or

$ update.packages()

your system notices you already have a copy of spatial in
/usr/lib/site-library (from the deb package).  But you told your R to
download and compile the new version, and do it "the R way".
However, your system does not have all of the tools (compilers and
shared libraries) required to build the package.  If we could see the
full output from your failed effort, I believe that would be obvious.

So, either you need to get the right repository specified in
/etc/apt/sources.list.d so that you can update the R packages with a
Debian package manager (such as apt-get or synaptic), or you need to
install a lot of compilers and other tools need to build your own
packages.

Or do both, and then have competing versions of the spatial library on
your system.  That can make research very exciting! Its like Forest
Gump said, "life is like a box of chocolates. You never know what
you'll get."
> 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).
>
A result of the fact you lack the development tools required to
compile the R packages.

> 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
>
> _______________________________________________
> R-SIG-Debian mailing list
> R-SIG-Debian at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-debian


-- 
Paul E. Johnson
Professor, Political Science    Assoc. Director
1541 Lilac Lane, Room 504     Center for Research Methods
University of Kansas               University of Kansas
http://pj.freefaculty.org            http://quant.ku.edu