[R-sig-Fedora] Installing R on RedHat EL 5

Tue Nov 17 17:21:44 CET 2009

After registering with the RHN, su -c 'yum install R' worked fine.
I now have a working version of R:

> sessionInfo()
R version 2.9.2 (2009-08-24)
x86_64-redhat-linux-gnu

Marc, you mentioned there is a 2.10 available at

  http://koji.fedoraproject.org/koji/packageinfo?packageID=1230

Is there an easy way to install that or I'll have to wait until it makes
it to the RHEL repos.

Thank you again.
-Christos 

On Fri, 2009-11-13 at 17:47 -0500, Christos Hatzis wrote:
> 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
> >
> 
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> 
-- 
Christos Hatzis, Ph.D.
Nuvera Biosciences
Woburn, MA 01801