Installing R on Red Hat Enterprise Linux 6.6

Update:  Be sure to check out the next post in this series:  Securing R on Red Hat Enterprise Linux.

Some of my users need to be able to run the statistical programming language R on a few systems.  Typically, installing software in the RHN environment is a piece of cake, but here, I ran into some trouble which was surprisingly poorly documented in the Interwebs.

Basically, R is not in the standard RHN repository.  The instructions provided by CRAN (the Comprehensive R Archive Network) for installing R on Red Hat Enterprise Linux are given in a README file which is the only available resource in their “redhat” repository (http://cran.r-project.org/bin/linux/redhat/).  As one can plainly read, the instructions are quite simple:

2) Red Hat Enterprise Linux (RHEL)
CentOS
Scientific Linux
Oracle Linux
==================================

The Fedora RPMs for R have been ported to RHEL by the project Extra
Packages for Enterprise Linux (EPEL).

http://fedoraproject.org/wiki/EPEL

These RPMs are also compatible with distributions derived from RHEL.

To use the EPEL repository, it is sufficient to download and install
the appropriate “epel-release” RPM, as described in the EPEL FAQ:

https://fedoraproject.org/wiki/EPEL/FAQ#How_can_I_install_the_packages_from_the_EPEL_software_repository.3F

Then R can be installed as described above in the section on Fedora.

Unfortunately, adding the EPEL repository and attempting the command “yum install R” results in an error:

wget http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
yum localinstall epel-release-6-8.noarch.rpm
yum install R
...
--> Finished Dependency Resolution
Error: Package: R-core-devel-3.1.1-3.el6.x86_64 (epel)
           Requires: lapack-devel
Error: Package: R-core-devel-3.1.1-3.el6.x86_64 (epel) 
           Requires: blas-devel >= 3.0
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: texinfo-tex

Well that’s obnoxious.  Installing R from EPEL fails because neither the EPEL nor the RHN repositories have all of the prerequisite packages available.

Update:

Previously, I had instructed users to gather the missing packages above from the CentOS 6 repositories, but after doing a little digging, I found that the missing packages are in Red Hat’s rhel-6-server-optional-rpms.  Just head into the /etc/yum.repos.d/redhat.repo file and enable the repository by changing the appropriate “enabled = 0” line to “enabled = 1”:

vim /etc/yum.repos.d/redhat.repo

[rhel-6-server-optional-rpms]
...
enabled = 1

Now, executing yum install R will work as expected, and you’re on your way to happy end users.

Note:  User Fukamit below points us to the proper location for RHEL 6 Workstation users (it’s the rhel-6-workstation-optional-rpms repository), so if you’re running RHEL 6 Workstation, that’s the way to go.

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53 Responses to Installing R on Red Hat Enterprise Linux 6.6

  1. bytewiseoperator says:

    Thanks for the post. Just FYI for other readers:
    wget http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
    sudo yum localinstall epel-release-6-8.noarch.rpm
    sudo yum install R
    and two Y inputs later it installs. I guess the dependencies you wrote about have been resolved.

  2. Uzzal says:

    I also just wrote “yum install R” and two Y inputs later it installs!! But in this terminal window there was a Warning like

    “warning: rpmts_HdrFromFdno: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY
    Retrieving key from file:///etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6
    Importing GPG key 0x0608B895:
    Userid : EPEL (6)
    Package: epel-release-6-8.noarch (@/epel-release-6-8.noarch)
    From : /etc/pki/rpm-gpg/RPM-GPG-KEY-EPEL-6

    What’s this warning means?
    Is my R installation Successfull?

    • I believe that warning is simply informing you that your system automatically imported a GPG Key to use when determining that packages from the EPEL repository are legitimate. Unless you saw any other warnings or errors, you should be all set to use R!

  3. Fukamit says:

    The extra packages are available from the “RHEL Workstation Optional” channel.
    You can install them by enabling the repo as below:

    yum –enablerepo=rhel-6-workstation-optional-rpms lapack-devel blas-devel libicu-devel texinfo-tex

  4. Thanks bytewiseoperator, in the interests of saving time for other people there is a slight modification for Scientific Linux 7
    you need to use version 7

    wget http://www.mirrorservice.org/sites/dl.fedoraproject.org/pub/epel/7/x86_64/e/epel-release-7-5.noarch.rpm
    sudo yum localinstall epel-release-7-5.noarch.rpm
    sudo yum install R

  5. I hate this. None of these work because it keeps saying it does not update packages, but then it won’t delete it. In any case I still can’t install R.

  6. timdom says:

    I made the repository change in Red Hat Enterprise Linux Server release 7.1 with no luck?
    Any ideas? Thanks

    • Can you paste the output provided by yum when you attempt to install R?

      • timdom says:

        [root@localhost ~]# yum install R
        Loaded plugins: langpacks, product-id, subscription-manager
        rhel-7-server-optional-rpms
        rhel-7-server-rpms
        (1/2): rhel-7-server-optional-rpms/7Server/x86_64/primary_db
        (2/2): rhel-7-server-rpms/7Server/x86_64/primary_db
        (1/2): rhel-7-server-rpms/7Server/x86_64/updateinfo
        (2/2): rhel-7-server-optional-rpms/7Server/x86_64/updateinfo
        No package R available.
        Error: Nothing to do

      • You need the EPEL repository! Grab the RPM from https://fedoraproject.org/wiki/EPEL. Looks like you’re using RHEL 7, so the package you need to install to automatically configure the repository for your use is here.

      • timdom says:

        Thanks for your help!

  7. Mithilesh says:

    I have followed the above instructions:
    My error message during ‘yum install R’ phase is as under:

    –> Finished Dependency Resolution
    Error: Package: R-core-3.2.1-1.el6.x86_64 (epel-testing)
    Requires: libicuuc.so.42()(64bit)
    Error: Package: qpdf-libs-5.1.1-2.el6.x86_64 (epel)
    Requires: libpcre.so.0()(64bit)
    Error: Package: R-core-3.2.1-1.el6.x86_64 (epel-testing)
    Requires: libicui18n.so.42()(64bit)
    You could try using –skip-broken to work around the problem
    You could try running: rpm -Va –nofiles –nodigest

    • That’s odd – what do your repositories look like? Can you post the output of yum repolist? All of those files listed as required by the installation come from packages which are distributed from the default rhel-6-server-rpms repository. I can see that libicuuc.so.42 and libicui18n.so.42 both come from libicu-4.2.1-9.1.el6_2.i686, and libpcre.so.0 comes from pcre-7.8-6.el6.i686, both of which are present in rhel-6-server-rpms.

  8. Bill Ox says:

    I seem to be having the same problem as Mithilesh … clean EC2 server running RHEL-7; ran

    sudo su -c ‘rpm -Uvh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
    sudo yum update

    … then tried:
    sudo yum install R

    Runs into problems … installing R-core works fine but not R-devel.

    Get error message:

    –> Finished Dependency Resolution
    Error: Package: R-core-devel-3.2.1-1.el7.x86_64 (epel)
    Requires: blas-devel >= 3.0
    Error: Package: R-core-devel-3.2.1-1.el7.x86_64 (epel)
    Requires: lapack-devel
    Error: Package: R-core-devel-3.2.1-1.el7.x86_64 (epel)
    Requires: texinfo-tex
    You could try using –skip-broken to work around the problem
    You could try running: rpm -Va –nofiles –nodigest

    Any help very welcome! Thanks.

    • You need to enable the rhel-7-server-optional repository as described in the article (the article describes the process for RHEL 6, but it should be the same for RHEL 7 with the exception of replacing sixes with sevens in the instructions).

      • Bill Ox says:

        The file
        /etc/yum.repos.d/redhat.repo
        currently consists of:

        #
        # Certificate-Based Repositories
        # Managed by (rhsm) subscription-manager
        #
        # *** This file is auto-generated. Changes made here will be over-written. ***
        # *** Use “subscription-manager repo-override –help” if you wish to make changes. ***
        #
        # If this file is empty and this system is subscribed consider
        # a “yum repolist” to refresh available repos
        #

        Your article says add the lines

        [rhel-6-server-optional-rpms]

        enabled = 1

        Please could you be more explicit — what replaces ‘…’ ?
        Thanks!

      • Bill – if you had “rhel-6-server-optional-rpms” in your repository file, but you’re using RHEL 7, as your previous comment indicated, that would be the problem (Did you add “rhel-6-server-optional-rpms” yourself? It shouldn’t be in that file; you need to enable rhel-7-server-optional-rpms for RHEL 7).

        But, if you’re just going to use Ubuntu instead, then nevermind!

      • On RHEL the file to modify is /etc/yum.repos.d/redhat-rhui.repo … section [rhui-REGION-rhel-server-optional] and change enabled=0 to enabled=1. Voila.

      • If you are using Red Hat Update Infrastructure, then you are correct. If you are not using RHUI, the instructions I have provided are correct.

  9. Bill Ox says:

    Too bad – moved to Ubuntu, where everything just works out of the box.

  10. Am trying to enable the optional repos from RH and getting this message:
    [root@projecty yum.repos.d]# subscription-manager repos –enable rhel-6-server-optional-rpms
    Error: rhel-6-server-optional-rpms is not a valid repo ID. Use –list option to see valid repos.

    suggestions?

    • Well, the –enable option for the subscription-manager utility is only used by organizations which have locally-hosted content services (like Subscription Asset Manager). I don’t use the command in my organization; should you be using it in yours? The method I use to enable the rhel-6-server-optional-rpms repository is to simply modify the appropriate stanza in the /etc/yum.repos.d/redhat.repo file, as shown in the article. The stanza I modify appears on line 701 of that file, and I simply change the “enabled = 0” line (that’s line 710) to “enabled = 1”. Does that not work for you?

      • Here is what is in that file on my system:
        #
        # Red Hat Repositories
        # Managed by (rhsm) subscription-manager
        #

        that’s it. There are other files in that directory with repos, just not in that one.

      • Interesting – what’s the output of yum repolist? It looks like your system isn’t subscribed to RHN, at least not through Subscription Manager. Are you on RHN Classic, perhaps? I’d check to see if my RHN Classic machines are similar, but I don’t have any anymore.

  11. aima othman says:

    I had a same problem as above. already change enable=0 to enable=1 in both epel files in yum.repos.d

    but still having the same problem.

    [bioinfo@bioinfo64-8 yum.repos.d]$ sudo yum install R
    Loaded plugins: fastestmirror, refresh-packagekit, security
    Setting up Install Process
    Loading mirror speeds from cached hostfile
    epel-testing/metalink | 2.4 kB 00:00
    epel-testing-debuginfo/metalink | 2.4 kB 00:00
    epel-testing-source/metalink | 2.4 kB 00:00
    * epel: http://ftp.kddilabs.jp
    * epel-debuginfo: http://ftp.kddilabs.jp
    * epel-source: kartolo.sby.datautama.net.id
    * epel-testing: kartolo.sby.datautama.net.id
    * epel-testing-debuginfo: kartolo.sby.datautama.net.id
    * epel-testing-source: kartolo.sby.datautama.net.id
    epel-testing | 4.4 kB 00:00
    epel-testing/primary_db | 424 kB 00:01
    epel-testing-debuginfo | 3.0 kB 00:00
    epel-testing-debuginfo/primary_db | 35 kB 00:00
    epel-testing-source | 3.7 kB 00:00
    epel-testing-source/primary_db | 88 kB 00:00
    Resolving Dependencies
    –> Running transaction check
    —> Package R.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: libRmath-devel = 3.2.1-2.el6 for package: R-3.2.1-2.el6.x86_64
    –> Processing Dependency: R-java = 3.2.1-2.el6 for package: R-3.2.1-2.el6.x86_64
    –> Processing Dependency: R-devel = 3.2.1-2.el6 for package: R-3.2.1-2.el6.x86_64
    –> Running transaction check
    —> Package R-devel.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: R-java-devel = 3.2.1-2.el6 for package: R-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: R-core-devel = 3.2.1-2.el6 for package: R-devel-3.2.1-2.el6.x86_64
    —> Package R-java.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: R-core = 3.2.1-2.el6 for package: R-java-3.2.1-2.el6.x86_64
    —> Package libRmath-devel.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: libRmath = 3.2.1-2.el6 for package: libRmath-devel-3.2.1-2.el6.x86_64
    –> Running transaction check
    —> Package R-core.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: tex(latex) for package: R-core-3.2.1-2.el6.x86_64
    –> Processing Dependency: tex(dvips) for package: R-core-3.2.1-2.el6.x86_64
    –> Processing Dependency: libtk8.5.so()(64bit) for package: R-core-3.2.1-2.el6.x86_64
    –> Processing Dependency: libtcl8.5.so()(64bit) for package: R-core-3.2.1-2.el6.x86_64
    —> Package R-core-devel.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: blas-devel >= 3.0 for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: xz-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: tk-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: texinfo-tex for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: tex(latex) for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: tcl-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: pcre-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: libicu-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: libX11-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: lapack-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    –> Processing Dependency: bzip2-devel for package: R-core-devel-3.2.1-2.el6.x86_64
    —> Package R-java-devel.x86_64 0:3.2.1-2.el6 will be installed
    –> Processing Dependency: java-devel for package: R-java-devel-3.2.1-2.el6.x86_64
    —> Package libRmath.x86_64 0:3.2.1-2.el6 will be installed
    –> Finished Dependency Resolution
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: libicu-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: bzip2-devel
    Error: Package: R-core-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: libtk8.5.so()(64bit)
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: xz-devel
    Error: Package: R-core-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: tex(dvips)
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: blas-devel >= 3.0
    Error: Package: R-core-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: tex(latex)
    Error: Package: R-core-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: libtcl8.5.so()(64bit)
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: lapack-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: pcre-devel
    Error: Package: R-java-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: java-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: tk-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: tex(latex)
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: libX11-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: tcl-devel
    Error: Package: R-core-devel-3.2.1-2.el6.x86_64 (epel-testing)
    Requires: texinfo-tex
    You could try using –skip-broken to work around the problem
    You could try running: rpm -Va –nofiles –nodigest

    [bioinfo@bioinfo64-8 yum.repos.d]$ ls
    epel.repo epel-testing.repo

    please advice. already two days try to solve this problem. huhuhuhu

    • Hey, did you get this resolved? I just found your comment in my spam filter! Sorry! If you’re on Red Hat Enterprise Linux, were you sure to enable the rhel-6-server-optional repository?

      Also, way later I looked back on this and saw that you appear to have added the wrong epel repositories (you have epel-testing and epel-source, not just epel, as I do). I hope you resolved the issue already, but for anyone else who finds this post because their output matches, that’s the problem.

  12. jamesmontalvo3 says:

    Thanks, this was a huge help. In trying to figure out how to make a script enable rhel-6-server-optional-rpms I found this https://access.redhat.com/solutions/265523. Instead of manually editing the /etc/yum.repos.d/redhat.repo file you can just do:

    subscription-manager repos –enable=rhel-6-server-optional-rpms

    Several of the above comments make reference to this capability, but I don’t think I saw a reference or this exact syntax.

  13. Tanmay says:

    Thanks for the article mate. I also ran into the same problem of dependencies. I tried to resolve as per your suggestion, but to my surprise when I went into the directory /etc/yum.repos.d, there was no redhat.repo file present.

    The only files present in my directory were: epel.repo, epel.repo.rpmsave, epel-testing.repo, rhel-source.repo.

    Going by the same logic, I changed enabled = 1 in all these files, but none of it helped. I would really appreciate your help in this regard. Thank you.

    • And you’re using Red Hat Enterprise Linux 6? Are you using Subscription Manager?

      • Tanmay says:

        Thanks for writing back. As you asked the output of ‘sudo subscription-manager status’ command is ‘-bash: subscription-manager: command not found’. So I feel you were right that it is RHN Classic. If that is the case, please let me know if there are other steps I could try to perform the installation. Thanks again and would feel great to see your inputs.

      • Ah, yeah, so I would advise migrating from RHN Classic to Subscription Manager. See the Red Hat Subscription Management documents, (this one in particular). Red Hat is going to terminate the RHN Classic service sometime soon, so you need to get moved over as you are able. In the meanwhile, if you want to try gaining access to the packages you need with RHN Classic, you might try following this article and enabling the “extras” channel through the RHN Classic administration web interface.

  14. GC says:

    Similar to Tanmay…I also changed enabled=1 in the epel.repo file.

    $ yum.repos.d]$ lsb_release -i -r
    Distributor ID: RedHatEnterpriseServer
    Release: 6.7

    $ cd /etc/yum.repos.d

    $ ls epel.repo epel-testing.repo packagekit-media.repo rhel-source.repo

  15. Charles says:

    Have been able to enabled the rhel-7-optional;
    but turn out to face another problem:
    Error: Multilib version problems found. This often means that the root
    cause is something else and multilib version checking is just
    pointing out that there is a problem. Eg.:

    1. You have an upgrade for gnome-settings-daemon which is missing some
    dependency that another package requires. Yum is trying to
    solve this by installing an older version of gnome-settings-daemon of the
    different architecture. If you exclude the bad architecture
    yum will tell you what the root cause is (which package
    requires what). You can try redoing the upgrade with
    –exclude gnome-settings-daemon.otherarch … this should give you an error
    message showing the root cause of the problem.

    2. You have multiple architectures of gnome-settings-daemon installed, but
    yum can only see an upgrade for one of those architectures.
    If you don’t want/need both architectures anymore then you
    can remove the one with the missing update and everything
    will work.

    3. You have duplicate versions of gnome-settings-daemon installed already.
    You can use “yum check” to get yum show these errors.

    …you can also use –setopt=protected_multilib=false to remove
    this checking, however this is almost never the correct thing to
    do as something else is very likely to go wrong (often causing
    much more problems).

    Protected multilib versions: gnome-settings-daemon-3.8.6.1-12.el7.i686 != gnome-settings-daemon-3.14.4-9.el7.x86_64

    Could you kindly advice on this?

    • Can you provide the yum command you used to generate this output? It looks like yum is trying to install gnome-settings-daemon-3.8.6.1-12.el7.i686 (which is a 32 bit package, as you can see by the i686 extension) but you already have a higher version of the x86_64 package installed (gnome-settings-daemon-3.14.4-9.el7.x86_64). So, yum informs you of this since it won’t install different versions of different architectures of the same package.

      For example: you can install packageA.version2.x86_64 and packageA.version2.i686, but yum will not let you install packageA.version2.x86_64 and packageA.version1.i686.

      I’m interested in why you’re getting this message when trying to install R; to my knowledge, gnome-settings-daemon isn’t required for R at all.

      • Charles says:

        Thanks for your reply.
        I just did the normal (sudo yum install R)
        I do not know if it is related, i changed the optional repo by this
        subscription-manager repo-override –repo=rhel-7-workstation-optional-rpms –add=enabled:1

  16. Charles says:

    Sorry i should have posted the earlier log files together

    –> Running transaction check
    —> Package gmp-devel.x86_64 1:5.1.1-5.el7 will be updated
    —> Package gmp-devel.x86_64 1:6.0.0-12.el7_1 will be an update
    —> Package libtasn1-devel.x86_64 0:3.3-3.el7 will be updated
    —> Package libtasn1-devel.x86_64 0:3.8-2.el7 will be an update
    —> Package nettle-devel.x86_64 0:2.7.1-4.el7 will be installed
    –> Processing Conflict: vte-profile-0.38.3-2.el7.x86_64 conflicts vte3 Restarting Dependency Resolution with new changes.
    –> Running transaction check
    —> Package gnome-settings-daemon-updates.x86_64 0:3.8.6.1-12.el7 will be an update
    —> Package vte3.x86_64 0:0.34.6-3.el7 will be updated
    —> Package vte3.x86_64 0:0.36.4-1.el7 will be an update
    –> Processing Conflict: systemd-219-19.el7.x86_64 conflicts initscripts Restarting Dependency Resolution with new changes.
    –> Running transaction check
    —> Package initscripts.x86_64 0:9.49.17-1.el7 will be updated
    —> Package initscripts.x86_64 0:9.49.30-1.el7 will be an update
    –> Processing Conflict: systemd-219-19.el7.x86_64 conflicts dracut Restarting Dependency Resolution with new changes.
    –> Running transaction check
    —> Package dracut.x86_64 0:033-161.el7 will be updated
    –> Processing Dependency: dracut = 033-161.el7 for package: dracut-network-033-161.el7.x86_64
    –> Processing Dependency: dracut = 033-161.el7 for package: dracut-config-rescue-033-161.el7.x86_64
    —> Package dracut.x86_64 0:033-360.el7_2 will be an update
    –> Running transaction check
    —> Package dracut-config-rescue.x86_64 0:033-161.el7 will be updated
    —> Package dracut-config-rescue.x86_64 0:033-360.el7_2 will be an update
    —> Package dracut-network.x86_64 0:033-161.el7 will be updated
    —> Package dracut-network.x86_64 0:033-360.el7_2 will be an update
    –> Finished Dependency Resolution
    Error: Multilib version problems found. This often means that the root
    cause is something else and multilib version checking is just
    pointing out that there is a problem. Eg.:

    1. You have an upgrade for gnome-settings-daemon which is missing some
    dependency that another package requires. Yum is trying to
    solve this by installing an older version of gnome-settings-daemon of the
    different architecture. If you exclude the bad architecture
    yum will tell you what the root cause is (which package
    requires what). You can try redoing the upgrade with
    –exclude gnome-settings-daemon.otherarch … this should give you an error
    message showing the root cause of the problem.

    2. You have multiple architectures of gnome-settings-daemon installed, but
    yum can only see an upgrade for one of those architectures.
    If you don’t want/need both architectures anymore then you
    can remove the one with the missing update and everything
    will work.

    3. You have duplicate versions of gnome-settings-daemon installed already.
    You can use “yum check” to get yum show these errors.

    …you can also use –setopt=protected_multilib=false to remove
    this checking, however this is almost never the correct thing to
    do as something else is very likely to go wrong (often causing
    much more problems).

    Protected multilib versions: gnome-settings-daemon-3.8.6.1-12.el7.i686 != gnome-settings-daemon-3.14.4-9.el7.x86_64

  17. JJY says:

    Hi there, thank you for the post! I was able to successfully installed R on CentOS 6.7, but I was having trouble installing any package. I kept getting the following error messages:

    /usr/lib64/R/bin/R:line 8:uname:command not found

    /usr/lib64/R/bin/R:line 143:exec:sh: not found

    Any suggestion/insight will be much appreciated!

    • That is pretty weird. Are you executing the R command from a user context with an extremely limited PATH variable? It seems to be unable to find very basic commands (uname and sh, both located in /bin).

      Can you show me the command you are executing which generates that error output (and maybe the commands you used to install R and leading up to the problematic command)?

  18. manisword says:

    Hi,
    I’m unable to install R. It is Red Hat Linux version 6.6(Santiago)
    I tried yum install r-base, for which it show no package found.
    I also tried sudo yum localinstall epel-release-7-5.noarch.rpm, for which it says
    “Cannot open: epel-release-7-5.noarch.rpm. Skipping.
    Nothing to do”
    I also, did try installing R by copying the set up files, unzipping them and ./configure. It threw error saying f77 compiler not found.

    Can you help me with a way to install a simple version of R?

  19. LiYouyou says:

    This is very helpful.
    There is a tip.
    If you met some problem about “Error: Cannot retrieve metalink for repository: epel. Please verify its path and try again” at the second step “yum install R”, you could check this https://stackoverflow.com/questions/26734777/yum-error-cannot-retrieve-metalink-for-repository-epel-please-verify-its-path/27901957#27901957?newreg=3f4a4e2acb324109856373eca434f18f.

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