[R-sig-Debian] Installing and maintaining R on Ubuntu 9.04 -, best practice

[Dirk Eddelbuettel]

On 14 June 2009 at 09:23, John C Nash wrote:
| 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

There are no simple one-sentence summaries. I happen to think

a) that package management is a good thing (cf 15 years of Debian using tens
of thousands of packages, as well as 10 years of R/CRAN with now 1700
packages)

b) that we have no code right now that 'mixes' Debian's dpkg / apt-get and R'
install.packages(), both systems are independent of each other and may
trample on each other unless you're careful -- which is why we set R_LIBS in
Debian / Ubuntu to at least have non-overlapping archives

c) all this is _underdocumented_ and someone should just go to, say, the R
Wiki and start the 'best practices' document there so that we do not have to
re-hash it fifteen times over; the mailing list archives (esp of
r-sig-debian) have ample fodder of prior discussion
 
d) last and least importantly, that starting every discussion in the name of
the front-end is misleading -- I personally never use synaptic or aptitude
directly (I use wajig by Debian and R user/author Graham Williams of rattle
fame) so I don't see the point of always calling 'use synaptic'. 

| 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)

It all depends. See above. R_LIBS splits things so that 'R CMD INSTALL ...'
and remove will operate on /usr/local/lib/R/site-library leaving your apt /
dpkg managed packages alone.
 
| We disagreed on whether a variant of install.packages (and related 
| scripts) was worthwhile so that users could

I very much think it is both worthwhile, inevitable, and in need of
improvements.  With Debian offering ~ 100 packages and CRAN offering ~ 1700,
you inevitably end up mixing things,

| 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

Yes, sure, esp if the Debian-maintained packages is current.

| 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.

... and remains sceptical of the effectivenes of a simple script given that
the whole of the packaging infrastrucure is highly complex. That said, if you
(John) have time to design, develop, test, refine, ... such a script I'd be
the last person stopping you. 

Dirk



| 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>
| > Content-Type: text/plain; charset=UTF-8
| >
| > 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
| >
| >
| 
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