Linux Distribution Choice

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Linux Distribution Choice

Graham Smith
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

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Re: Linux Distribution Choice

Roger Bivand
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]]
>
> ______________________________________________
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>

--
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: [hidden email]

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Roger Bivand
Department of Economics
NHH Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Linux Distribution Choice

Dirk Eddelbuettel
In reply to this post by Graham Smith

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

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Re: Linux Distribution Choice

Alexandre Aguiar
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

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Re: Linux Distribution Choice

PaulJohnson32gmail
Fedora Core Linux is our preference here. The Fedora Extras system
keeps R (and just about everything else we need) up to date.  Much of
the Linux kernel and gcc development that goes on in the RedHat
company makes its way to Fedora more quickly than it does to other
distributions.

But the Debian-based distributions are nice too, don't take this as an
insult to them.

--
Paul E. Johnson
Professor, Political Science
1541 Lilac Lane, Room 504
University of Kansas

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Re: Linux Distribution Choice

jon butchar
In reply to this post by Graham Smith
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]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html

As 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

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Re: Linux Distribution Choice

Kenneth Cabrera
In reply to this post by Graham Smith
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]]
>
>______________________________________________
>[hidden email] mailing list
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>  
>

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Re: Linux Distribution Choice

Detlef Steuer
In reply to this post by Dirk Eddelbuettel
On Sun, 19 Feb 2006 17:49:42 -0600
Dirk Eddelbuettel <[hidden email]> wrote:

>
> 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.

I can only second Dirk's advise: his Quantian project is just great. But if you have coworkers around who already are specialized in one of the distros you can more than probably use their experience to get a quick start.
Shameless self plug: From version 10.0 on there is even a yast repository for the SuSe an OpenSuse kind of linux :-)
(http://fawn.unibw-hamburg.de/~steuer/SL-10.0-OSS, soon on CRAN)

Have fun (and get the work done),
Detlef



>
> 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
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Linux Distribution Choice

Graham Smith
In reply to this post by Graham Smith
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

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Re: Linux Distribution Choice

Ulises M. Alvarez
Ubuntu is a good choice : )

First, I will recommend you to take a look at:
http://ubuntuguide.org/

Specially...
http://ubuntuguide.org/#extrarepositories

It is slightly out of date, but still is useful.

Once you are done with that, installing R is quit simple. From a
terminal -available from the menus in your panel-, type:

$ sudo aptitude install r-base r-base-core r-base-html r-recommended
r-doc-pdf

And that's it!


On the other hand, if you want to install from the source, you may try
from a terminal the following:

$ sudo apt-get build-dep r-base
(A lot of *.deb's here)

$ sudo aptitude install checkinstall

Once you are done with that, get and unpack the R-source (once again on
a terminal):

$ wget -c http://cran.us.r-project.org/src/base/R-2/R-2.2.1.tar.gz
$ tar -xzf R-2.2.1.tar.gz
$ cd R-2.2.1
$ ./configure && make && make check
(You may like to see the results of 'make check' to asses that
everything went fine)

Finally:

$ sudo checkinstall
(You may enter some info here or leave the defaults)

And that's it!

Whatever you choose, I strongly recommend to run:
$ sudo apt-get build-dep r-base

So you can install, and build, additional packages from CRAN. You may
cut and paste the terminal commands, just be sure to omit the '$' symbol.

Graham Smith wrote:

> 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]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

--
U.M.A.
http://sophie.fata.unam.mx/

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Re: Linux Distribution Choice

Dirk Eddelbuettel

Ulises,

Thanks for the helpful post but allow me to add one or two corrections:

On 20 February 2006 at 11:40, Ulises M. Alvarez wrote:
| Ubuntu is a good choice : )
|
| First, I will recommend you to take a look at:
| http://ubuntuguide.org/
|
| Specially...
| http://ubuntuguide.org/#extrarepositories
|
| It is slightly out of date, but still is useful.
|
| Once you are done with that, installing R is quit simple. From a
| terminal -available from the menus in your panel-, type:
|
| $ sudo aptitude install r-base r-base-core r-base-html r-recommended
| r-doc-pdf
|
| And that's it!

The key here is the archive you point to.

Ubuntu freezes every six months, so 5.10 does "by design" not have R 2.2.0
and 2.2.1 which were released after 5.10.  See the R FAQ for the address of
the Debian stable backport (and our thanks to Chris Steigies for building
them); once you add the line to /etc/apt/sources.list you even get current
packages so that

        $ apt-get install r-base

can do its work. aptitude, wajig, ... and dozen other frontends then will as
well, of course. The r-base meta package should imply all the one you listed
above.  This ought to work on Ubutu as well as was discussed on r-help last
week.  It may fail if and when Debian's and Ubuntu's libraries diverge.

| On the other hand, if you want to install from the source, you may try
| from a terminal the following:
|
| $ sudo apt-get build-dep r-base
| (A lot of *.deb's here)

Actually, 'apt-get install r-base-dev' should do the trick and was designed
by Doug for just that.

| $ sudo aptitude install checkinstall
|
| Once you are done with that, get and unpack the R-source (once again on
| a terminal):
|
| $ wget -c http://cran.us.r-project.org/src/base/R-2/R-2.2.1.tar.gz
| $ tar -xzf R-2.2.1.tar.gz
| $ cd R-2.2.1
| $ ./configure && make && make check
| (You may like to see the results of 'make check' to asses that
| everything went fine)

Configuring that way omits a lot of little goodies we have in the Debian
package. I'd go with the prebuild ones, or locally rebuild from Debian
sources.

| Finally:
|
| $ sudo checkinstall
| (You may enter some info here or leave the defaults)
|
| And that's it!
|
| Whatever you choose, I strongly recommend to run:
| $ sudo apt-get build-dep r-base

Again, 'r-base-dev' should cover that.

| So you can install, and build, additional packages from CRAN. You may

Or just use the 50-some existing ones in Debian and (K)Ubuntu. Do a

        $ apt-cache rdepends r-base-core

to see all the packages depending on r-base-core, which includes all CRAN,
Omegahat, ... packages we currently have.  

Dirk

| cut and paste the terminal commands, just be sure to omit the '$' symbol.
|
| Graham Smith wrote:
| > 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]]
| >
| > ______________________________________________
| > [hidden email] mailing list
| > https://stat.ethz.ch/mailman/listinfo/r-help
| > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
| >
|
| --
| U.M.A.
| http://sophie.fata.unam.mx/
|
| ______________________________________________
| [hidden email] mailing list
| https://stat.ethz.ch/mailman/listinfo/r-help
| PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

--
Hell, there are no rules here - we're trying to accomplish something.
                                                  -- Thomas A. Edison

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Re: Linux Distribution Choice

nshephard
In reply to this post by Graham Smith
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 - [hidden email] / [hidden email]

Website - http://slack.ser.man.ac.uk/
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