Upgrade R to 3.1.1 on ec2 via yum

Question

I have an ec2 instance with an older version (3.0.2) of R that I'm trying to update to the latest (3.1.1). This is not available in the default yum repo, but is available under EPEL.

The installed version is 3.0.2:

[hadoop@ip-172-31-19-15 ~]$ yum list R-core
Loaded plugins: priorities, update-motd, upgrade-helper
970 packages excluded due to repository priority protections
Installed Packages
R-core.x86_64                                                                                  3.0.2-1.17.amzn1                                                                                   @amzn-main
Available Packages
R-core.i686                                                                                    3.0.2-1.17.amzn1                                                                                   amzn-main

These are the repos

[hadoop@ip-172-31-19-15 ~]$ yum repolist
Loaded plugins: priorities, update-motd, upgrade-helper
970 packages excluded due to repository priority protections
repo id                                                                             repo name                                                                                                     status
!amzn-main/latest                                                                   amzn-main-Base                                                                                                     4,801
!amzn-updates/latest                                                                amzn-updates-Base                                                                                                  1,497
epel/x86_64                                                                         Extra Packages for Enterprise Linux 6 - x86_64                                                                10,139+970
repolist: 16,437

Specifying the epel repo, I can see version 3.1.1, it is also listed here

sudo yum --disablerepo="*" --enablerepo="epel" list R-core
Loaded plugins: priorities, update-motd, upgrade-helper
Installed Packages
R-core.x86_64                                                                                  3.0.2-1.17.amzn1                                                                                   @amzn-main
Available Packages
R-core.i686                                                                                    3.1.1-3.el6                                                                                        epel      
R-core.x86_64                                                                                  3.1.1-3.el6

However when I try to install using sudo yum --disablerepo="*" --enablerepo="epel" install R-core I get the following errors:

--> Finished Dependency Resolution
Error: Package: R-java-3.1.1-3.el6.x86_64 (epel)
           Requires: java-1.5.0-gcj
Error: Package: R-core-devel-3.1.1-3.el6.x86_64 (epel)
           Requires: libicu-devel
Error: Package: R-core-devel-3.1.1-3.el6.x86_64 (epel)
           Requires: tcl-devel
Error: Package: R-core-devel-3.1.1-3.el6.x86_64 (epel)
           Requires: tk-devel
Error: Package: R-core-3.1.1-3.el6.x86_64 (epel)
           Requires: libicuuc.so.42()(64bit)
Error: Package: R-core-3.1.1-3.el6.x86_64 (epel)
           Requires: xdg-utils
Error: Package: R-core-3.1.1-3.el6.x86_64 (epel)
           Requires: libicui18n.so.42()(64bit)
Error: Package: R-core-3.1.1-3.el6.x86_64 (epel)
           Requires: libtcl8.5.so()(64bit)
Error: Package: R-core-3.1.1-3.el6.x86_64 (epel)
           Requires: libtk8.5.so()(64bit)
 You could try using --skip-broken to work around the problem
 You could try running: rpm -Va --nofiles --nodigest

Presumably this is caused by disabling * repo and only enabling epel which could prevent some dependencies being found, I had to do otherwise it'd only find 3.0.2 from amzn_main.

What is the correct command I should use to install 3.1.1 from the epel repo?

score 1 · Answer 1 · answered Sep 15 '14 at 12:07

# yum install yum-priorities

Need to add a priority to all the repos set up. Go to /etc/yum.repos.d and edit all the files and add priority

The lower the number the more important it is – so the EPEL ones are the lowest.

Example:

[epel]
name=Extra Packages for Enterprise Linux 6 - $basearch
#baseurl=http://download.fedoraproject.org/pub/epel/6/$basearch
mirrorlist=https://mirrors.fedoraproject.org/metalink?repo=epel-6&arch=$basearch
failovermethod=priority
enabled=1
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
priority=10

score 0 · Answer 2 · answered Sep 15 '14 at 13:28

0

EPEL is not compatible with Amazon Linux. It used to be, back in the very early days when Amazon Linux looked more like CentOS, but it is too different now.

answered Sep 15 '14 at 13:28

Michael Hampton

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Interesting, as the AWS documentation still advises how to enable EPEL : http://docs.aws.amazon.com/AWSEC2/latest/UserGuide/add-repositories.html – user155695 Sep 15 '14 at 14:10
Yes, it does. Unfortunately it's wrong. – Michael Hampton Sep 15 '14 at 15:32

Upgrade R to 3.1.1 on ec2 via yum

2 Answers2