[R-sig-Fedora] Scientific Linux

[Marc Schwartz]

On Jun 30, 2012, at 1:25 PM, Ted Harding wrote:

> Greetings!
> 
> I have just signed up to r-sig-fedora because I have
> installed Scientific Linux 6.2 (my first Red Hat based
> Linux since over 10 years ago ... ). I'm trying this for
> basically 2 reasons: first, I expect CERN and FermiLab
> should do a good job of maintaining their distribution,
> and in particular to take care of its compatibility with
> scientific software; second, because it still has Gnome 2 ...
> 
> I installed it off the Live DVD from the Scientific Linux
> website, and this went very smoothly. However, it does not
> of course come in the first instance with any special
> scientific software (in in particular not with R).
> 
> For extra packages it has been suggested to me to use EPEL
> (Extra Packages for Enterprise Linux, not specifically for
> Scientific Linux). And there are the CRAN repositories, of
> course.
> 
> I am now wondering -- and somewhat puzzled -- as to how best
> to move forward. At some stage in exploring my installation
> (and I cannot now recall how I got there) an information
> panel came up which said that it was not possible to add
> further package sources to the list of software sources!
> 
> So, for instance, it would seem not to be possible to
> add a CRAN mirror.
> 
> So it looks as though one may be stuck with downloading
> what one wants, package by package, and installing it by
> hand (and not getting automatic updates etc.)
> 
> Any comments, please? Red Hat has changed a lot since I
> last installed it (RH 7.1 in 2001; I have more recently
> been installing Debian), and I'm not familiar with the
> current way of running things (and, in particular, with
> the intermingling of Gnome and KDE things).
> 
> With thanks,
> Ted.

Hi Ted,

Since SL 6 is based upon RHEL 6, you can use the EPEL to install R once you have added the EPEL repos to your "yum" configuration. 'yum' in the means for installing, upgrading and removing default Linux packages. It is the parallel in a sense for 'apt' on Debian based distros.

If you have not yet done so, there are instructions here:

  http://fedoraproject.org/wiki/EPEL

for installing the EPEL yum repo configurations for 6 series distros. Once you have done that, you can use:

  yum install R

as root or via sudo from the CLI. That will install R with base and recommended packages.

You do want to use yum to install SL/EPEL based RPMs, as it will resolve package dependencies as you install things, much like install.packages(..., dependencies = TRUE). So you should not have to download individual RPMs and use 'rpm' from the CLI.

You will not be able to add CRAN mirrors to the yum based installation process and unlike Debian distros, largely thanks to Dirk I believe, the EPEL/Fedora based repos will not have a large selection of R CRAN packages to install from binaries. So you will need to continue to use install.packages() from within R as a root user.

I have not used Fedora since F10 a little over 3 years ago, since moving to OSX. I was using GNOME at the time and not KDE, so had little need for KDE based apps. That being said, my recollection is that they could co-exist, provided that you had the requisite libraries for both DEs installed. I don't know what the current state of affairs is with GNOME 3, though have taken note of the infighting in the community relative to developments with GNOME, Unity, etc.

I hope that this is helpful to get you going.

Regards,

Marc Schwartz