[R-sig-Fedora] Scientific Linux

[(Ted Harding)]

On 30-Jun-2012 19:50:15 Marc Schwartz wrote:
> 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

Very many thanks, Marc! That is extremely helpful, in that it seems
to point to solutions for all thethings I was puzzled about!

Now to see how I get on ... (and, by the way, one reason for
Scientific Linux it that it has stuck with Gnome 2; and I have
strong reasons for avoiding Gnome 3 and the like).

All best wishes,
Ted.

-------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at wlandres.net>
Date: 30-Jun-2012  Time: 21:08:43
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