Installing and maintaining R on Ubuntu 9.04 -, best practice

I had an exchange of ideas on this with Dirk E. a couple of months ago. 
He can correct this if I state it wrongly, but
1) we agreed that using apt/Synaptic structure was best, but sometimes 
the packages are not available
2) also that using install.packages when there is a .deb can lead to 
some "confusion" (the package database on the
local system does not know about an R package installed from R)

We disagreed on whether a variant of install.packages (and related 
scripts) was worthwhile so that users could
ALWAYS use that version of install.packages and it would do the right 
thing and go to apt as needed. That is, one
can take the view that on Debian systems, one should always try the apt 
approach first. I feel that it is better to
offer a single gateway that then sorts things out behind the curtain. I 
prepared a reasonably effective
trial script that tested the concept. An issue is detecting the 
availability of an appropriate and viable .deb package
and returning proper information on success or failure to the user so 
they know how to proceed. Dirk had some
comments on the possible difficulties in doing that. He has more 
knowledge of Debian internals than I do.

As usual, the fly in the ointment is that folk who know how to prepare 
such a script clearly don't need it, while
those who need it don't have the expertise to prepare it. However, 
perhaps a small group of us could make an
attempt.  Or maybe someone has already done it for their own research group.

JN

Date: Sat, 13 Jun 2009 22:53:35 +0100
From: Graham Smith <myotisone at gmail.com>
Subject: [R-sig-Debian] Installing and maintaining R on Ubuntu 9.04 -
	best	practice
To: r-sig-debian at r-project.org
Message-ID:
	<2c75873c0906131453i791859c5k12f6e90d7bdfd02d at mail.gmail.com>
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Is there a best practice for installing and updating R on Ubuntu ?

I've had to clean install Ubuntu so I am starting from fresh.  I have
picked up various comments about ONLY using Synaptic OR only using
apt-get  OR only running update from inside R.

Being new to Ubuntu this is a bit confusing. Last time round I
installed  via Synaptic, but not all packages were available so
installed packages and run updates from R, but it was suggested this
bad practice. So before I start afresh, can anyone give me some
pointers on the best way of doing this.

Many thanks,

Graham