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

Christos Hatzis christos.hatzis at nuverabio.com
Tue Nov 17 20:51:43 CET 2009 

Thanks for all your help, Marc.

This is like a new ecosystem for me, living in the Windows world for too
many years, but will eventually feel like home.  My memories on Unix are
from the Apollo/Domain systems and the Cray-1 and X-MP systems back in grad
school.  Linux is nothing like that, but then again Windows 3.0 was the name
of the game back then. It is really amazing the sophistication and volume of
Linux resources that are available out there. 

-Christos

-----Original Message-----
From: r-sig-fedora-bounces at r-project.org
[mailto:r-sig-fedora-bounces at r-project.org] On Behalf Of Marc Schwartz
Sent: Tuesday, November 17, 2009 11:54 AM
To: Marc Schwartz
Cc: r-sig-fedora at r-project.org; chatzis-rhel at nuverabio.com
Subject: Re: [R-sig-Fedora] Installing R on RedHat EL 5

Sorry, correction on the command below:

   su -c "yum --enablerepo=epel-testing update R"

Time for more coffee...

Marc

On Nov 17, 2009, at 10:47 AM, Marc Schwartz wrote:

> Hi Christos,
>
> The R 2.10.0 RPMs will be in the EPEL testing repo until the so- 
> called Bodhi system has sufficient positive Karma to move them to  
> release. You can see the current status here:
>
>  https://admin.fedoraproject.org/updates/EL-5/FEDORA-EPEL-2009-0809
>
> If you have the EPEL yum repo configuration set up to support the  
> EPEL testing repo, which I believe is the case by default, you just  
> need to enable that repo, as it should be disabled by default.
>
> Bear in mind that if you are in a production environment, this is a  
> testing release and may have problems as with any pre-release  
> software. Those problems at this point are more likely in the RPM  
> packaging of R, rather than in R itself. I am also presuming that  
> the EPEL package is of 2.10.0 initial release and not of a  
> subsequent patch release, if you tend to use them (I do on OSX).
>
> Thus, if you elect to proceed, you should be able to use:
>
> su -c "--enablerepo=epel-testing yum update R"
>
> You may want to use the 'yum repolist' command again just to be sure  
> of the correct name for the EPEL testing repo, which would be in the  
> output of that command.
>
> If you do decide to proceed, I would recommend that after some  
> testing, you return to Bodhi to offer your comments and a bump in  
> Karma if you do not identify any problems. Getting sufficient Karma  
> is required to move the application to a stable release repo and is  
> part of the peer review process for Fedora/RHEL-EPEL RPMs.
>
> HTH,
>
> Marc
>
>
> On Nov 17, 2009, at 10:21 AM, Christos Hatzis wrote:
>
>> 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
>>>>
>>>
>>> _______________________________________________
>>> R-SIG-Fedora mailing list
>>> R-SIG-Fedora at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>>>
>> -- 
>> Christos Hatzis, Ph.D.
>> Nuvera Biosciences
>> Woburn, MA 01801
>>
>
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> R-SIG-Fedora at r-project.org
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