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user155695
Asked: 2014-09-16 03:45:36 +0800 CST

Upgrade R to 3.1.1 on ec2 via yum

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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?

amazon-ec2

2 Answers

  1. # 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
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  2. 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.

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