Installing R on RedHat EL 5

sessionInfo()

Marc,

It seems that the RHEL is there and is active.  I'd rather stay with RHEL
since I do have purchased support.
I have started the process of registering the system with RHN so I will try
to see if system updates will solve the problem.  Will report back.

Thanks again.
-Christos

-----Original Message-----
From: Marc Schwartz [mailto:marc_schwartz at me.com] 
Sent: Friday, November 13, 2009 4:41 PM
To: christos.hatzis at nuverabio.com
Cc: r-sig-fedora at r-project.org
Subject: Re: [R-sig-Fedora] Installing R on RedHat EL 5

Hmmm....that would suggest that yum is not picking up the default RHEL  
repos for some reason, as it would seem logical that those files would  
be there as opposed to the EPEL. Typically, yum will get any  
dependencies from all enabled and accessible repos.

As RHEL's repos for their binary RPMs are only available to folks who  
have paid for support, I am not sure how to best assist in getting the  
yum repo config RPM so that you can install or re-install it to  
confirm that the RHEL repo is configured and active.

One thing that you can check is to use:

   yum repolist

which should show you the current list of configured repos on your  
system and whether or not they are enabled. I suppose that it is  
possible that either the main RHEL binary repo is not configured on  
your system, it is not enabled or perhaps your system is being  
prevented from accessing it. You may have to run that command as 'root'.

An alternative, which has some risk, is to use the CentOS yum repos,  
which are supposed to be binary compatible with RHEL. The risk is that  
if you are in fact paying for RHEL support to RH, I would be hesitant  
to mix and match, if there is any risk of complications in the support  
contract.

Not having the 'devel' versions of the various RPMs will at some point  
cause you problems when installing source packages from CRAN.

A lot of the important details here are going to be dependent upon how  
you installed RHEL and whether or not there is a paid support contract  
in place for your installation.  If you have a SysAdmin that installed  
RHEL for you, he or she would be of help in resolving this.

HTH,

Marc

On Nov 13, 2009, at 2:52 PM, Christos Hatzis wrote:

The installation seems to have gone through ok, but this is what I am
getting at the end:

--> Finished Dependency Resolution
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
 --> Missing Dependency: libX11-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
 --> Missing Dependency: pcre-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
 --> Missing Dependency: tk-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
R-devel-2.9.2-1.el5.x86_64 from epel has depsolving problems
 --> Missing Dependency: tcl-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: tcl-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: tk-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: pcre-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)
Error: Missing Dependency: libX11-devel is needed by package
R-devel-2.9.2-1.el5.x86_64 (epel)

Do I need to install other tools before running
su -c 'yum install R'?

Thanks again.
-Christos

On Fri, 2009-11-13 at 15:11 -0500, Marc Schwartz wrote:

On Nov 13, 2009, at 1:59 PM, Christos Hatzis wrote:

Hi,

I am totally new to Linux and trying to install R and related
tools.  I
downloaded the rpm files for el4/x86_64 from the CRAN repository and
tried to run rpm but it did not go through complaining about
dependencies.

Do all the listed rpm files need to be installed?  What is the order
in
which these need to be installed?

I appreciate any help with this or any suggestions for alternate  
ways
for installing pre-compiled versions of R and the packages in RHL.

Thanks.
-Christos Hatzis

The easiest way is to use the EPEL, which is a yum repository for  
RHEL
and CentOS.

There is more information here:

  http://fedoraproject.org/wiki/EPEL

with the key steps here in the FAQ:

  http://fedoraproject.org/wiki/EPEL/FAQ#howtouse

If you are on 64 bit RHEL, you will need to replace the 'i386' in the
first command's path with 'x86_64':

  su -c 'rpm -Uvh

http://download.fedora.redhat.com/pub/epel/5/x86_64/epel-release-5-3.noarch 

.
rpm'

Then replace 'foo' in the second command with 'R', which will install
R and any other dependencies that you may require:

  su -c 'yum install R'

Note that the latest version available appears to be 2.9.2 and I
suspect that this is due to the imminent release of Fedora 12, which
is presumably consuming Tom Callaway and others at the moment.

HTH,

Marc Schwartz

-- 
Christos Hatzis, Ph.D.
Nuvera Biosciences
Woburn, MA 01801