Skip to content

Best 64-bit Linux distro for R?

11 messages · Krzysztof Sakrejda, Shige Song, Stavros Macrakis +4 more

Krzysztof Sakrejda
# 
I'm running R on the current version of Gentoo and had no trouble building the complete system required.  The only problem is that the current version in portage (stable) is 2.7.2. 

I would be curious to hear what insightful responses you get.

Best,

Krzysztof

Sent via BlackBerry by AT&T

-----Original Message-----
From: Stavros Macrakis <macrakis at alum.mit.edu>

Date: Sun, 8 Feb 2009 17:27:10 
To: <r-help at r-project.org>
Subject: [R] Best 64-bit Linux distro for R?


The R FAQ is very helpful about installing R on various Linuxes, but doesn't
seem to discuss the advantages of one distribution over another.  I am new
to Linux (though not to Unix!), and would appreciate some guidance from
those with experience.

I plan to set up a headless Linux x86 server for the sole purpose of running
64-bit R. Are there reasons to prefer some Linux distributions over others?
I have no preference between binary and source distributions of R, as along
as they are complete, up-to-date, easy to install, and easy to update.

I would be accessing the server through my Windows desktop using Emacs/ESS.
What is the recommended way to display plots on the desktop? An X server? A
display Postscript server? Something else?

My data come out of a DBMS; do some Linux distributions have better ODBC
drivers than others?

Thanks,

            -s


______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Dirk Eddelbuettel
#
On 8 February 2009 at 17:27, Stavros Macrakis wrote:
| The R FAQ is very helpful about installing R on various Linuxes, but doesn't
| seem to discuss the advantages of one distribution over another.  I am new
| to Linux (though not to Unix!), and would appreciate some guidance from
| those with experience.
| 
| I plan to set up a headless Linux x86 server for the sole purpose of running
| 64-bit R. Are there reasons to prefer some Linux distributions over others?
| I have no preference between binary and source distributions of R, as along
| as they are complete, up-to-date, easy to install, and easy to update.
| 
| I would be accessing the server through my Windows desktop using Emacs/ESS.
| What is the recommended way to display plots on the desktop? An X server? A
| display Postscript server? Something else?
| 
| My data come out of a DBMS; do some Linux distributions have better ODBC
| drivers than others?

Good question, and while it in general may depend on your preferences and
tastes, there are some things that make the Ubuntu amd64 _server_ flavour
appealing for your situation:

- it is meant for servers, so no extra desktop apps or processes

- Ubuntu amd64 has support via CRAN's binary set of R packages, ie you get 
  a pre-built R 2.8.1 without any extra work

- additional goodies such as ESS, littler, ... available via CRAN as well 
  in updated packages

- you still have the usual 20,000+ Ubuntu packages, including iodbc and
  unixodbc and number of related packages:
    edd at joe:~$ apt-cache search odbc| wc -l
    101
    edd at joe:~$

It so happens that I just installed another compute server at work on Friday.
I had a cdrom handy with Ubuntu 8.04 for amd64/server -- the install was done
in a few minutes, as was the on-line upgrade to Ubuntu 8.10.  All in under
300 packages were installed as I chose a lean default.  You can probably
achieve the same using Debian's install cdroms. Your mileage may vary but a
number of us have been happy with this.  And to connect, I use Cygwin's x11
server which got updated recently and have no issues.

Hth, Dirk
Dirk Eddelbuettel
#
On 8 February 2009 at 18:35, Stavros Macrakis wrote:
| Thanks for your help!
| 
| You mention amd64 -- I didn't realize that AMD and Intel were different for
| this purpose.  I will actually be installing on a VM on top of an Intel
| box.  Does that change things?

No. And they are not different. It's just how the names evolved. These days,
you want the the so-called 'amd64' flavour on both Intel and Amd.

You probably find the precise details at Wikipedia and other places, but in a
nutshell, Intel gambled big on their Itanium iniative ('ia64') of chips and
... lost to AMD with their simpler line of 'amd64' design which Intel
eventually started to emulate / copy. To differentiate the then-different
chips of AMD from Intels Itanium ia64 line, the 'amd64' name was
introduced.  These days ia64 is ancient history and "we're all amd64 users".

By the way, if you decide to go with Ubuntu or Debian, the r-sig-debian list
is there to help.

Hth, Dirk
M. Edward (Ed) Borasky
#
On Sun, Feb 8, 2009 at 3:54 PM, Dirk Eddelbuettel <edd at debian.org> wrote:
You will also see the "amd64" architecture referred to by the name
"x86_64". It is yet another name for the same architecture. As far as
the choice of distro is concerned, I've had total success with R on
all the major distros on my 64-bit machine. But I would definitely
give the nod to a Debian-based distro like Ubuntu because of the large
existing base of R packages in the Debian / Ubuntu repositories.
Girish A.R.
# 
So, does that mean I can install Ubuntu 64-bit "amd64" server edition
on a machine that has Intel Xeon processor without much of a problem?

Thanks,
-Girish
On Feb 9, 5:33?am, "M. Edward (Ed) Borasky" <zzn... at gmail.com> wrote:
Dirk Eddelbuettel
#
On 8 February 2009 at 18:29, Girish A.R. wrote:
| So, does that mean I can install Ubuntu 64-bit "amd64" server edition
| on a machine that has Intel Xeon processor without much of a problem?

Yes it should work. You have a choice of 32bit and 64bit OS for these.
Background details are at http://en.wikipedia.org/wiki/Amd64 

Dirk
Girish A.R.
# 
Thanks, All!

-Girish
On Feb 9, 7:49?am, Dirk Eddelbuettel <e... at debian.org> wrote:
Neil Shephard
#
KMSL wrote:
The latest _stable_ version (in terms of Gentoo's testing and release
policy, NOT R's) is 2.7.2 as you note, but dev-lang/R-2.8.1 is already in
portage (I usually request a version bump in Bugzilla when a new version of
R or ESS is released).

I have no problems running R-2.8.1 (although I am on ARCH="x86"), and I have
system-wide set ACCEPT_KEYWORDS="~x86" so I always get the unstable versions
installed (and duly report back on bugs I encounter with R and other
packages).

If you don't want to go to testing on your system you can install the newer
version of R by adding the relevant entry to
/etc/portage/package.keywords...

echo 'dev-lan/R' >> /etc/portage/package.keywords
emerge -uDNa dev-lang/R

Besides which its easy to bump the version in a local overlay yourself, but
I shan't digress further,

Neil