I am making some tentative steps into using Linux (Mandriva at the moment) and notice that not all the Linux binaries on CRAN are the latest release. As R (plus Grass) will be key programs for me on Linux, is there a preferred Linux distribution that people in the R communiuty use? Many thanks, Graham [[alternative HTML version deleted]]
On Sun, 19 Feb 2006, Graham Smith wrote:> I am making some tentative steps into using Linux (Mandriva at the moment) > and notice that not all the Linux binaries on CRAN are the latest release. > > As R (plus Grass) will be key programs for me on Linux, is there a preferred > Linux distribution that people in the R communiuty use?There are a fair number of distributions out there, and often users find that even though they have installed an R binary, they cannot successfully install R contributed packages because their build train is incomplete, and/or they lack development components. Building R from source on modern Linux distributions is not difficult, and will let you check whether you can install R contributed packages with C, C++, or Fortran source code. Essentially the same concerns apply to GRASS, and particularly to the software GRASS depends on, crucially GDAL/OGR. While learning to install from source may seem challenging, it is worth doing especially when you would like to work using several linked applications. The R-GRASS interface is developed on RHEL4, I believe a lead GRASS developer also uses RHEL, but others use Mandriva and many more Debian, Ubuntu, and so on. If you'd like a taster, Quantian (0.7.9.1) has GRASS 6.0.1, GDAL 1.2.6, and r-base 2.2.0 (none the latest releases, but perhaps enough to try out). If in doubt about a distribution, consider what support resources are close to you. "gmail.com" isn't very informative, but many organisationa and universities do have Linux policies, and choosing a distribution that maximises the chances to being able to talk to someone using the same distribution is sensible, even if it isn't the one you though of first. Chapter 2 of http://cran.r-project.org/doc/manuals/R-admin.html is helpful reading if you decide to install from source.> > Many thanks, > > Graham > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html >-- Roger Bivand Economic Geography Section, Department of Economics, Norwegian School of Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: Roger.Bivand at nhh.no
Graham,
On 19 February 2006 at 15:59, Graham Smith wrote:
| I am making some tentative steps into using Linux (Mandriva at the moment)
| and notice that not all the Linux binaries on CRAN are the latest release.
|
| As R (plus Grass) will be key programs for me on Linux, is there a preferred
| Linux distribution that people in the R communiuty use?
Picking your preferred distribution is a fairly complex undertaking that will
invariably reflect a lot of your personal preferences. Just like we may all
pick a different desk, chair or desk lamp for our work environment, we also
often end up with different computing choices. [1]
That said, if you are looking for R and Grass pre-built you could consider
either Debian, or the Ubuntu/Kubuntu derivatives. We work fairly hard at
keeping the packages in Debian timely, and you'd get R and some 50 or so
CRAN
packages already prebuilt and ready to use, as well as goodies like ESS,
Ggobi and more. Likewise, my personal Quantian project may well be unique in
containing all that plus essentially all of CRAN and BioConductor (and lots
more) in a single DVD.
But at the end of the day you need to decide what you are comfortable with
installing and administrating. If you have friends or colleagues that use a
particular flavour then that may be reason enough to go with that flavour.
Finally, R and Grass don't care and you can always carry your scripts over
to
another variant.
Hth, Dirk
[1] Provided they all run an Emacs flavour and ESS. Just kidding.
--
Hell, there are no rules here - we're trying to accomplish something.
-- Thomas A. Edison
Em Dom 19 Fev 2006 20:49, Dirk Eddelbuettel escreveu:> Likewise, my personal Quantian project may well be > unique in containing all that plus essentially all of CRAN and BioConductor > (and lots more) in a single DVD.Quantian is a great job. I have appreciated it a lot. However, Linux is far more flexible than the large number of distributions. They are good starting points. The real power is that you can become (at least partially) independent of distributions by compiling software by your own, extending and upgrading far beyond the support teams go. For instance, I am using rigth now an old Conectiva 10 in which packaged R was version 1.9 and no upgrades were published by support. My current R installation is version 2.2.1. It compiled and runs smoothly. :-) Not to mention some other 50+ pieces of software that did not exist in the original distribution. Regards, -- Alexandre Santos Aguiar, MD
On Sunday 19 February 2006 10:59, Graham Smith wrote:> I am making some tentative steps into using Linux (Mandriva at the moment) > and notice that not all the Linux binaries on CRAN are the latest release. > > As R (plus Grass) will be key programs for me on Linux, is there a > preferred Linux distribution that people in the R communiuty use? > > Many thanks, > > Graham > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.htmlAs others stated, much depends on what you're comfortable using on a long-term basis and that can depend on several things. With Linux, I gravitated towards Gentoo simply because the "portage" system made updating very easy. You could also look into FreeBSD (http://www.freebsd.org). It's a mature, very well put together operating system (also my personal choice), and the R port is usually kept up to date. Best of luck, jon
Here we use Scientific Linux Distribution 4.2 (https://www.scientificlinux.org/ ), that is based on RHEL4. In this platform we both have R(2.2.1.) and GRASS(6.0.2) working. Graham Smith wrote:>I am making some tentative steps into using Linux (Mandriva at the moment) >and notice that not all the Linux binaries on CRAN are the latest release. > >As R (plus Grass) will be key programs for me on Linux, is there a preferred >Linux distribution that people in the R communiuty use? > >Many thanks, > >Graham > > [[alternative HTML version deleted]] > >______________________________________________ >R-help at stat.math.ethz.ch mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html > > >
Thanks to everyone on this. Iyt ha sgiven me some useful insights into the> different options. I am going to try Ubuntu for the time being and see how I > get on. Probably revewing the situatin once I understand a bit more about > how Linux works.Graham [[alternative HTML version deleted]]
I thought I'd add my vote for Gentoo, which has been my distro of choice for some time (although Slackware is very good as well, and teaches you a lot about *NIX in general). The main advantage of gentoo is that updating is very easy using the portage system (as pointed out by jon butchar), but unlike other distributions which have packages which are compiled for generic x86 architechtures, you get one that is custom compiled to your architechture and with the options you want compiled in (throught the USE flags). This is the point that Alexandre Santos Aguiar was making. Its a little more complicated to install the say Ubuntu where you just drop the disc in the CD-ROM and point and click you way through, but the documentation is second to none, and is extremly detailed. In addition the forums are really useful as well (although you may want to use Google to search them as the default search engine isn't that brilliant). If you were to go with this option then I would recommend writing your own script for installing packages (again from source). An example of one that I have written can be found at http://slack.ser.man.ac.uk/progs/R/scripts/install.genetics.R This way all the packages are installed from source and custom compiled as well. HTH's Neil -- "Religion is the work of the Devil" - Anon Email - nshephard at gmail.com / neilshep at cyllene.uwa.edu.au Website - http://slack.ser.man.ac.uk/ Blog - http://slack---line.blogspot.com/ Flickr - http://www.flickr.com/photos/slackline/