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

[Chris Evans]

I have changed the subject line to reflect a thread split.

Paul Johnson sent the following  at 02/08/12 18:39:

... much snipped that was continued in my last posting ...

> I'm not an unkind person, I'm not trying to insult you by ignoring
> the rest of your  message.  Lets fix one thing at a time.
>
> As for your complaint that nobody has written out all the details of
> why things work this way in Debian, well, I suppose you could be the
> one to write it all out :).  If you get a handle on how this works,
> you could post a blog explanation and we'd all benefit by being able
> to refer users to it.  That's how stuff gets done.

Agreed.  That way and by google and other search systems picking these
things up on archives of lists like these.  I'm happy to try to write
this up as a bloggish thing but one thing I've become very wary of is
such stuff cluttering up the internet long after the open source package
in question has moved on.  Nowadays I tend to use the time limited
searches in Google to restrict things to try to find out if things are
recent.  I might commit to trying to write an idiots' guide to running R
on Ubuntu and Debian and using update.packages() to keep
libraries/packages up to date ... but only if I feel confident that I'll
find time to keep it current.

>
> How did I learn about this packaging policy? I'm pretty sure I asked
> in this list, and was told the information is in the file that is
> distributed with the Debian package r-base-core,
> /usr/share/doc/r-base-core/changelog.Debian.gz,
>
> * debian/rules: Add R_LIBS setting to /etc/R/Renviron such that
> user-installed packages will be in /usr/local/lib/R/site-library,
> Debian packages will install into /usr/lib/R/site-library and the
> r-base-core and r-recommended packages will use the standard
> /usr/lib/R/library directory
>
>
> I know for sure from previous debates here that the Debian packagers
> expect you to use the packages they provide, and they don't think
> "ordinary" users should bother trying to compile packages.

OK.  Is that true packagers?  I've had that impression at times but at
other times it has also seemed that the packaging is designed to sit
alongside the CRAN repositories simply making it much easier to get the
bases of a minimal or a really nearly complete R system easily through
the Debian or Ubuntu upgrade systems. However, when I find I'm reading
things that way I find myself believing that update.packages() ought to
remain a non-deprecated option.

> That does not speak to the fact that you may not have access to an
> up-to-date repository for packages for your particular system.  John
> Nash pointed you at one that will work for you.

OK.  Let's see if I've got this right or wrong.  I think there are three 
repositories that a Ubuntu system can use to update R:
1) CRAN: challenging for raw installation but might be best way to do 
daily updates using update.packages() and believing that the majority of 
packages will give error messages explaining why that doesn't work when 
it doesn't (and to be fair, I think that Rgtk2 and rggobi do give such 
messages, I just haven't yet been able to spend time nailing down what I 
might have to do to get them what they want ... or to decided that 
that's not possible on Ubuntu 12.04)

2) the Debian/Ubuntu repositories that are linked with CRAN mirrors.  In 
my /etc/apt/sources.list these are:
    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/
These are much more likely than #1 to have all the dependencies already 
dealt with to provide a compiled library so you should (probably) never 
have to update other things in your system to get things working if you 
go this way.  However, they may not update as often as #1 and they may 
lack a few libraries that are in #1 (but if so, it may be because those 
libraries are a real challenge to compile for Debian/Ubuntu?)

3) Specific Ubuntu ppa repositories which John C Nash makes available at:
    https://launchpad.net/~marutter/+archive/rrutter
I'm not really very clearly how this differs markedly from #2 but it 
sounds as if it might update more often.

As I understand it, I would use update.packages() within R (sudo R) to 
update using #1 but #2 and #3 will update using synaptic or the Ubuntu 
package update system.  I am very unclear whether any of these systems 
is supposed to exclude or deprecate using the other.

OK.  Can people help clarify this?

Thanks again Paul and John,

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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