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 <myotis...@gmail.com> | > Subject: [R-sig-Debian] Installing and maintaining R on Ubuntu 9.04 - | > best practice | > To: r-sig-debian@r-project.org | > Message-ID: | > <2c75873c0906131453i791859c5k12f6e90d7bdfd...@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 | > | > | | _______________________________________________ | R-SIG-Debian mailing list | R-SIG-Debian@r-project.org | https://stat.ethz.ch/mailman/listinfo/r-sig-debian -- Three out of two people have difficulties with fractions. _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian