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:[email protected]]
Sent: Friday, November 13, 2009 4:41 PM
To: [email protected]
Cc: [email protected]
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
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