R installation on RHEL

As of November 2017 Version 3.4.2-2 is available in RPMs from EPEL.

Binary package: R-3.4.2-2.el6.i686.rpm

Source package: R-3.4.2-2.el6.src.rpm

Introduction to GNU R on Linux Operating System - LinuxCareer's Documentation

R All Repositories

R-3.4.2-2.el6.i686.rpm EPEL

R-3.4.2-2.el6.x86_64.rpm EPEL

Requires

• R-devel = 3.4.2-2.el6
• R-java = 3.4.2-2.el6
• libRmath-devel = 3.4.2-2.el6

Install from Epel for RHEL6.x Howto

1. Download the latest epel-release rpm from

   http://dl.fedoraproject.org/pub/epel/6/i386/

2. Install epel-release rpm:

   # rpm -Uvh epel-release*rpm

3. Install R rpm package:

   # yum install R.x86_64

Typical errors during this installation involve missing libraries

Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
           Requires: blas-devel >= 3.0
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
       Requires: lapack-devel
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
       Requires: libicu-devel

See Install R on RedHat errors on dependencies that don't exist  for how to deal with this situation.  Summary

You suffered from missing libraries problem one way to solve them is to enable optional RPM repository.

repos --enable rhel-6-server-optional-rpms

For example:

subscription-manager repos --enable rhel-6-server-optional-rpms
1 local certificate has been deleted.
Repository 'rhel-6-server-optional-rpms' is enabled for this system.

Alternative is to download CENTOS RPMs using wget and yum local install use them

NEWS CONTENTS

• 20191020 : How to update a package in R? ( Oct 20, 2019 , stackoverflow.com )
• 20171206* Install R on RedHat errors on dependencies that don't exist ( Dec 06, 2017 , stackoverflow.com ) [Recommended]

Old News ;-)

[Oct 20, 2019] How to update a package in R?

Oct 20, 2019 | stackoverflow.com

Ask Question Asked 5 years, 8 months ago Active 10 months ago Viewed 23k times 23 4

---

Joshua Ulrich ,Jan 31, 2014 at 8:15

I would like to upgrade one R package to the newer version which is already available. I tried

update.packages(c("R2jags"))

but it does nothing! No output on console, no error, nothing. I used the same syntax as for install.packages but perhaps I'm doing something wrong. I have been looking at ?update.packages but I was not been able to figure out how it works, where to specify the package(s) etc. There is no example. I also tried to update the package using install.packages to "install" it again but that says "Warning: package 'R2jags' is in use and will not be installed" .

TMS ,Jan 30, 2014 at 16:47

You can't do this I'm afraid, well, not with update.packages() . You need to call install.packages("R2jags") instead.

You can't install R2jags in the current session because you have already loaded the current version into the session. If you need to, save any objects you can't easily recreate, and quit out of R. Then start a new R session, immediately run install.packages("R2jags") , then once finished, load the package and reload in any previously saved objects. You could try to unload the package with:

detach(package:R2jags, unload = TRUE)

but it is quite complex to do this cleanly unless the package cleans up after itself.

update.packages() exists to update all outdated packages in a stated library location. That library location is given by the first argument (if not supplied it works on all known library locations for the current R session). Hence you were asking it the update the packages in library location R2jags which is most unlikely to exist on your R installation.

amzu ,Jan 30, 2014 at 16:36

Additionally, you can install RStudio and update all packages by going to the Tools menu and selecting Check for Package Updates .

DJ6968 ,Dec 13, 2018 at 11:42

# The following two commands remove any previously installed H2O packages for R.
if ("package:h2o" %in% search()) { detach("package:h2o", unload=TRUE) }
if ("h2o" %in% rownames(installed.packages())) { remove.packages("h2o") }

# Next, we download packages that H2O depends on.
pkgs <- c("RCurl","jsonlite")
for (pkg in pkgs) {
if (! (pkg %in% rownames(installed.packages()))) { install.packages(pkg) }
}

# Now we download, install and initialize the H2O package for R.
install.packages("h2o", type="source", repos="http://h2o-release.s3.amazonaws.com/h2o/rel-xia/2/R")

# Finally, let's load H2O and start up an H2O cluster
library(h2o)`enter code here`
h2o.init()

[Dec 06, 2017] Install R on RedHat errors on dependencies that don't exist

Highly recommended!

Dec 06, 2017 | stackoverflow.com

Jon ,Jul 11, 2014 at 23:55

I have installed R before on a machine running RedHat EL6.5, but I recently had a problem installing new packages (i.e. install.packages()). Since I couldn't find a solution to this, I tried reinstalling R using:

sudo yum remove R

and

sudo yum install R

But now I get:

....
---> Package R-core-devel.x86_64 0:3.1.0-5.el6 will be installed
--> Processing Dependency: blas-devel >= 3.0 for package: R-core-devel-3.1.0-5.el6.x86_64
--> Processing Dependency: libicu-devel for package: R-core-devel-3.1.0-5.el6.x86_64
--> Processing Dependency: lapack-devel for package: R-core-devel-3.1.0-5.el6.x86_64
---> Package xz-devel.x86_64 0:4.999.9-0.3.beta.20091007git.el6 will be installed
--> Finished Dependency Resolution
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
           Requires: blas-devel >= 3.0
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
       Requires: lapack-devel
Error: Package: R-core-devel-3.1.0-5.el6.x86_64 (epel)
       Requires: libicu-devel
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

I already checked, and blas-devel is installed, but the newest version is 0.2.8. Checked using:

yum info openblas-devel.x86_64

Any thoughts as to what is going wrong? Thanks.

Scott Ritchie ,Jul 12, 2014 at 0:31

A cursory search of blas-devel in google shows that the latest version is at least version 3.2. You probably used to have an older version of R installed, and the newer version depends on a version of BLAS not available in RedHat? – Scott Ritchie Jul 12 '14 at 0:31

bdemarest ,Jul 12, 2014 at 0:31

Can solve this by sudo yum install lapack-devel , etc.. until the errors stop. – bdemarest Jul 12 '14 at 0:31

Jon ,Jul 14, 2014 at 4:08

sudo yum install lapack-devel does not work. Returns: No package lapack-devel available. Scott - you are right that blas-devel is not available in yum. What is the best way to fix this? – Jon Jul 14 '14 at 4:08

Owen ,Aug 27, 2014 at 18:33

I had the same issue. Not sure why these packages are missing from RHEL's repos, but they are in CentOS 6.5, so the follow solution works, if you want to keep things in the package paradigm:

wget http://mirror.centos.org/centos/6/os/x86_64/Packages/lapack-devel-3.2.1-4.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/blas-devel-3.2.1-4.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/texinfo-tex-4.13a-8.el6.x86_64.rpm
wget http://mirror.centos.org/centos/6/os/x86_64/Packages/libicu-devel-4.2.1-9.1.el6_2.x86_64.rpm
sudo yum localinstall *.rpm

cheers

---

UPDATE: Leon's answer is better -- see below.

DavidJ ,Mar 23, 2015 at 19:50

When installing texinfo-tex-5.1-4.el7.x86_654, it complains about requiring tex(epsd.tex), but I've no idea which package supplies that. This is on RHEL7, obviously (and using CentOS7 packages). – DavidJ Mar 23 '15 at 19:50

Owen ,Mar 24, 2015 at 21:07

Are you trying to install using rpm or yum? yum should attempt to resolve dependencies. – Owen Mar 24 '15 at 21:07

DavidJ ,Mar 25, 2015 at 14:18

It was yum complaining. Adding the analogous CentOS repo to /etc/yum.repos.d temporarily and then installing just the missing dependencies, then removing it and installing R fixed the issue. It is apparently a issue/bug with the RHEL package dependencies. I had to be careful to ensure the all other packages came from the RHEL repos, not CentOS, hence not a good idea to install R itself when the CentOS repo is active. – DavidJ Mar 25 '15 at 14:18

Owen ,Mar 26, 2015 at 4:49

Glad you figured it out. When I stumbled on this last year I was also surprised that the Centos repos seemed more complete than RHEL. – Owen Mar 26 '15 at 4:49

Dave X ,May 28, 2015 at 19:33

They are in the RHEL optional RPMs. See Leon's answer. – Dave X May 28 '15 at 19:33

Leon ,May 21, 2015 at 18:38

Do the following:

1. vim /etc/yum.repos.d/redhat.repo
2. Change enabled = 0 in [rhel-6-server-optional-rpms] section of the file to enabled=1
3. yum install R

DONE!

I think I should give reference to the site of solution:

https://bluehatrecord.wordpress.com/2014/10/13/installing-r-on-red-hat-enterprise-linux-6-5/

Dave X ,May 28, 2015 at 19:31

Works for RHEL7 with [rhel-7-server-optional-rpms] change too. – Dave X May 28 '15 at 19:31

Jon ,Aug 4, 2014 at 4:49

The best solution I could come up with was to install from source. This worked and was not too bad. However, now it isn't in my package manager.

Recommended Links

Softpanorama Recommended

Top articles

[Dec 06, 2017] Install R on RedHat errors on dependencies that don't exist Published on Dec 06, 2017 | stackoverflow.com

Sites

• How-to install R on CentOS
• Installing R on Red Hat Enterprise Linux 6.6 Engineering Walden

Etc

Society

Groupthink : Two Party System as Polyarchy : Corruption of Regulators : Bureaucracies : Understanding Micromanagers and Control Freaks : Toxic Managers :   Harvard Mafia : Diplomatic Communication : Surviving a Bad Performance Review : Insufficient Retirement Funds as Immanent Problem of Neoliberal Regime : PseudoScience : Who Rules America : Neoliberalism  : The Iron Law of Oligarchy : Libertarian Philosophy

Quotes

War and Peace : Skeptical Finance : John Kenneth Galbraith :Talleyrand : Oscar Wilde : Otto Von Bismarck : Keynes : George Carlin : Skeptics : Propaganda  : SE quotes : Language Design and Programming Quotes : Random IT-related quotes :  Somerset Maugham : Marcus Aurelius : Kurt Vonnegut : Eric Hoffer : Winston Churchill : Napoleon Bonaparte : Ambrose Bierce :  Bernard Shaw : Mark Twain Quotes

Bulletin:

Vol 25, No.12 (December, 2013) Rational Fools vs. Efficient Crooks The efficient markets hypothesis : Political Skeptic Bulletin, 2013 : Unemployment Bulletin, 2010 :  Vol 23, No.10 (October, 2011) An observation about corporate security departments : Slightly Skeptical Euromaydan Chronicles, June 2014 : Greenspan legacy bulletin, 2008 : Vol 25, No.10 (October, 2013) Cryptolocker Trojan (Win32/Crilock.A) : Vol 25, No.08 (August, 2013) Cloud providers as intelligence collection hubs : Financial Humor Bulletin, 2010 : Inequality Bulletin, 2009 : Financial Humor Bulletin, 2008 : Copyleft Problems Bulletin, 2004 : Financial Humor Bulletin, 2011 : Energy Bulletin, 2010 : Malware Protection Bulletin, 2010 : Vol 26, No.1 (January, 2013) Object-Oriented Cult : Political Skeptic Bulletin, 2011 : Vol 23, No.11 (November, 2011) Softpanorama classification of sysadmin horror stories : Vol 25, No.05 (May, 2013) Corporate bullshit as a communication method  : Vol 25, No.06 (June, 2013) A Note on the Relationship of Brooks Law and Conway Law

History:

Fifty glorious years (1950-2000): the triumph of the US computer engineering : Donald Knuth : TAoCP and its Influence of Computer Science : Richard Stallman : Linus Torvalds  : Larry Wall  : John K. Ousterhout : CTSS : Multix OS Unix History : Unix shell history : VI editor : History of pipes concept : Solaris : MS DOS :  Programming Languages History : PL/1 : Simula 67 : C : History of GCC development :  Scripting Languages : Perl history   : OS History : Mail : DNS : SSH : CPU Instruction Sets : SPARC systems 1987-2006 : Norton Commander : Norton Utilities : Norton Ghost : Frontpage history : Malware Defense History : GNU Screen : OSS early history

Classic books:

The Peter Principle : Parkinson Law : 1984 : The Mythical Man-Month :  How to Solve It by George Polya : The Art of Computer Programming : The Elements of Programming Style : The Unix Hater’s Handbook : The Jargon file : The True Believer : Programming Pearls : The Good Soldier Svejk : The Power Elite

Most popular humor pages:

Manifest of the Softpanorama IT Slacker Society : Ten Commandments of the IT Slackers Society : Computer Humor Collection : BSD Logo Story : The Cuckoo's Egg : IT Slang : C++ Humor : ARE YOU A BBS ADDICT? : The Perl Purity Test : Object oriented programmers of all nations : Financial Humor : Financial Humor Bulletin, 2008 : Financial Humor Bulletin, 2010 : The Most Comprehensive Collection of Editor-related Humor : Programming Language Humor : Goldman Sachs related humor : Greenspan humor : C Humor : Scripting Humor : Real Programmers Humor : Web Humor : GPL-related Humor : OFM Humor : Politically Incorrect Humor : IDS Humor : "Linux Sucks" Humor : Russian Musical Humor : Best Russian Programmer Humor : Microsoft plans to buy Catholic Church : Richard Stallman Related Humor : Admin Humor : Perl-related Humor : Linus Torvalds Related humor : PseudoScience Related Humor : Networking Humor : Shell Humor : Financial Humor Bulletin, 2011 : Financial Humor Bulletin, 2012 : Financial Humor Bulletin, 2013 : Java Humor : Software Engineering Humor : Sun Solaris Related Humor : Education Humor : IBM Humor : Assembler-related Humor : VIM Humor : Computer Viruses Humor : Bright tomorrow is rescheduled to a day after tomorrow : Classic Computer Humor

The Last but not Least Technology is dominated by two types of people: those who understand what they do not manage and those who manage what they do not understand ~Archibald Putt. Ph.D

The statements, views and opinions presented on this web page are those of the author (or referenced source) and are not endorsed by, nor do they necessarily reflect, the opinions of the Softpanorama society. We do not warrant the correctness of the information provided or its fitness for any purpose. The site uses AdSense so you need to be aware of Google privacy policy. You you do not want to be tracked by Google please disable Javascript for this site. This site is perfectly usable without Javascript.

Last modified: October, 20, 2019