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I'm trying to keep my offsite backup server up to date so I've run an update and I'm getting dependency issues. I haven't got a clue how to continue. Below is the output from from YUM.

[root@localhost philosophy-admin]# yum update --skip-broken
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
 * Webmin: webmin.mirror.somersettechsolutions.co.uk
 * base: mirror.mhd.uk.as44574.net
 * epel: mirror.bytemark.co.uk
 * extras: mirror.mhd.uk.as44574.net
 * updates: mirror.mhd.uk.as44574.net
Setting up Update Process
Resolving Dependencies
--> Running transaction check
---> Package TurboGears2.noarch 0:2.1-0.1.b2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: TurboGears2-2.1-0.1.b2.el5.noarch
---> Package iotop.noarch 0:0.4.1-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: iotop-0.4.1-2.el5.noarch
---> Package python-babel.noarch 0:0.9.5-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-babel-0.9.5-2.el5.noarch
---> Package python-beaker.noarch 0:1.5.4-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-beaker-1.5.4-1.el5.noarch
---> Package python-ethtool.x86_64 0:0.6-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-ethtool-0.6-2.el5.x86_64
---> Package python-markdown.noarch 0:2.0.3-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-markdown-2.0.3-1.el5.noarch
--> Processing Dependency: python-elementtree for package: python-markdown-2.0.3-1.el5.noarch
---> Package python-nose.noarch 0:0.11.3-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-nose-0.11.3-2.el5.noarch
---> Package python-paramiko.noarch 0:1.7.6-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-paramiko-1.7.6-1.el5.noarch
---> Package python-psycopg2.x86_64 0:2.0.14-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-psycopg2-2.0.14-1.el5.x86_64
--> Processing Dependency: libpq.so.4()(64bit) for package: python-psycopg2-2.0.14-1.el5.x86_64
---> Package python-pygments.noarch 0:1.4-3.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-pygments-1.4-3.el5.noarch
--> Processing Dependency: python-imaging for package: python-pygments-1.4-3.el5.noarch
---> Package python-pylons.noarch 0:0.9.7-4.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-pylons-0.9.7-4.el5.noarch
--> Processing Dependency: python-decorator3 for package: python-pylons-0.9.7-4.el5.noarch
---> Package python-repoze-tm2.noarch 0:1.0-0.6.a5.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-tm2-1.0-0.6.a5.el5.noarch
---> Package python-repoze-who.noarch 0:1.0.18-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-who-1.0.18-2.el5.noarch
---> Package python-repoze-who-testutil.noarch 0:1.0-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-who-testutil-1.0-1.el5.noarch
---> Package python-routes.noarch 0:1.12.1-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-routes-1.12.1-1.el5.noarch
---> Package python-turbojson.noarch 0:1.2.1-9.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-turbojson-1.2.1-9.el5.noarch
---> Package python-webhelpers.noarch 0:1.0-0.2.b7.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-webhelpers-1.0-0.2.b7.el5.noarch
---> Package python-webob.noarch 0:0.9.8-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-webob-0.9.8-2.el5.noarch
--> Running transaction check
---> Package TurboGears2.noarch 0:2.1-0.1.b2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: TurboGears2-2.1-0.1.b2.el5.noarch
---> Package iotop.noarch 0:0.4.1-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: iotop-0.4.1-2.el5.noarch
---> Package python-babel.noarch 0:0.9.5-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-babel-0.9.5-2.el5.noarch
---> Package python-beaker.noarch 0:1.5.4-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-beaker-1.5.4-1.el5.noarch
---> Package python-decorator3.noarch 0:3.1.2-2.el5.1 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-decorator3-3.1.2-2.el5.1.noarch
---> Package python-ethtool.x86_64 0:0.6-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-ethtool-0.6-2.el5.x86_64
---> Package python-imaging.x86_64 0:1.1.6-19.el6 set to be updated
---> Package python-markdown.noarch 0:2.0.3-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-markdown-2.0.3-1.el5.noarch
--> Processing Dependency: python-elementtree for package: python-markdown-2.0.3-1.el5.noarch
---> Package python-nose.noarch 0:0.11.3-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-nose-0.11.3-2.el5.noarch
---> Package python-paramiko.noarch 0:1.7.6-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-paramiko-1.7.6-1.el5.noarch
---> Package python-psycopg2.x86_64 0:2.0.14-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-psycopg2-2.0.14-1.el5.x86_64
--> Processing Dependency: libpq.so.4()(64bit) for package: python-psycopg2-2.0.14-1.el5.x86_64
---> Package python-pygments.noarch 0:1.4-3.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-pygments-1.4-3.el5.noarch
---> Package python-pylons.noarch 0:0.9.7-4.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-pylons-0.9.7-4.el5.noarch
---> Package python-repoze-tm2.noarch 0:1.0-0.6.a5.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-tm2-1.0-0.6.a5.el5.noarch
---> Package python-repoze-who.noarch 0:1.0.18-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-who-1.0.18-2.el5.noarch
---> Package python-repoze-who-testutil.noarch 0:1.0-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-repoze-who-testutil-1.0-1.el5.noarch
---> Package python-routes.noarch 0:1.12.1-1.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-routes-1.12.1-1.el5.noarch
---> Package python-turbojson.noarch 0:1.2.1-9.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-turbojson-1.2.1-9.el5.noarch
---> Package python-webhelpers.noarch 0:1.0-0.2.b7.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-webhelpers-1.0-0.2.b7.el5.noarch
---> Package python-webob.noarch 0:0.9.8-2.el5 set to be updated
--> Processing Dependency: python(abi) = 2.4 for package: python-webob-0.9.8-2.el5.noarch
--> Finished Dependency Resolution

Packages skipped because of dependency problems:
    TurboGears2-2.1-0.1.b2.el5.noarch from epel
    iotop-0.4.1-2.el5.noarch from epel
    python-babel-0.9.5-2.el5.noarch from epel
    python-beaker-1.5.4-1.el5.noarch from epel
    python-decorator3-3.1.2-2.el5.1.noarch from epel
    python-ethtool-0.6-2.el5.x86_64 from epel
    python-imaging-1.1.6-19.el6.x86_64 from base
    python-markdown-2.0.3-1.el5.noarch from epel
    python-nose-0.11.3-2.el5.noarch from epel
    python-paramiko-1.7.6-1.el5.noarch from epel
    python-psycopg2-2.0.14-1.el5.x86_64 from epel
    python-pygments-1.4-3.el5.noarch from epel
    python-pylons-0.9.7-4.el5.noarch from epel
    python-repoze-tm2-1.0-0.6.a5.el5.noarch from epel
    python-repoze-who-1.0.18-2.el5.noarch from epel
    python-repoze-who-testutil-1.0-1.el5.noarch from epel
    python-routes-1.12.1-1.el5.noarch from epel
    python-turbojson-1.2.1-9.el5.noarch from epel
    python-webhelpers-1.0-0.2.b7.el5.noarch from epel
    python-webob-0.9.8-2.el5.noarch from epel

How do I sort out these dependency issues?

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5 Answers 5

3

I got the same problem with you when I using linode vps centos 6 template. To solve the problem, do this:

  1. rpm -qa |grep epel

    then you may get this

    epel-release-5-4.noarch

  2. yum remove epel-release-5-4.noarch

  3. Install version 6 epel

    for i386:

    rpm -Uvh http://download.fedora.redhat.com/pub/epel/6/i386/epel-release-6-5.noarch.rpm
    

    for x86_64:

    rpm -Uvh http://download.fedora.redhat.com/pub/epel/6/x86_64/epel-release-6-5.noarch.rpm
    
  4. yum update

Thats all.

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2

I saw the same dependency problems after mistakenly installing epel-release-5.4 on a CentOS 6 system, removing it then installing epel-release-6.5. Running yum clean all solved the problem.

1
  • The yum clean all was the missing step. Thanks.
    – Gareth
    Jun 27, 2012 at 12:06
2

I had the same error and had realized how my mistake happened, repaired the issue, but still got the error. I'd basically already done everything on this thread as well, but the problem persisted. I've fixed it now and wanted to share my solution.

Symptom: El5 versions attempt to install on CentOS 6 and are listed under rpm -qa

Original Cause: When installing the EPEL repository (or any other), the wrong version is installed for the OS.

Attempted Solution: Uninstall wrong repo install correct repo

Final Solution: Even though the correct version is installed, the cache directory still contained the el5 info. In order to correct this, after you uninstall wrong repo install correct repo, you must the delete cached repo information with this line:

rm -Rf /var/cache/yum/x86_64/6/epel*

Please edit that line to be specific to your version or simply delete everything under the yum directory.

1

You must update your epel repo, because like Martian said, you use EL5 repo rather than EL6

Try this manipulation to update your repo :

# wget http://ftp.riken.jp/Linux/fedora/epel/RPM-GPG-KEY-EPEL-6
# rpm --import RPM-GPG-KEY-EPEL-6 
# rm -f RPM-GPG-KEY-EPEL-6

Normally this would fix your problem

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  • I have done this and updated my repo but I still get the same dependency issues.
    – Scott
    Nov 18, 2011 at 15:02
  • 1
    did you update centos from 5.6 to 6.0? It's pretty weird that you've got problem dependencies... Try removing all your repos, and reinstall them for 6.0. Nov 18, 2011 at 15:05
  • No this was a fresh install centos 6.0. How do I go about removing repos? here is the latest export on yum update pastebin.com/RPYpUyE6
    – Scott
    Nov 18, 2011 at 15:07
  • If you still have missing deps may be some packages from epel5 repos were already installed and you may need to remove those. To find out which are from where have a look (here)[serverfault.com/questions/62026/…
    – Martian
    Nov 18, 2011 at 15:20
  • What Martian said, it may be a packages conflict between epel5 and 6. try desinstalling them, and reinstall them using epel6 Nov 22, 2011 at 14:36
0

$TITLE says it is CentOS 6 while yum update complains about el5 packages. Looks like epel repo for RHEL5 is used instead of for RHEL6.

You need to update epel-release first if present or get one if missing. Simply run following and then try yum update again:

wget "http://download.fedoraproject.org/pub/epel/6/i386/epel-release-6-5.noarch.rpm"
sudo yum update ./epel-release-6-5.noarch.rpm

Further Reading:

2
  • changed to download the x86_64 version rather than the i386. When trying to install it fails with this error: warning: rpmts_HdrFromFdno: Header V3 RSA/SHA256 Signature, key ID 0608b895: NOKEY Public key for epel-release-6-5.noarch.rpm is not installed
    – Scott
    Nov 18, 2011 at 14:30
  • I think rather than sudo yum update, using rpm -uvh is a better way to update the depot. Nov 18, 2011 at 14:46

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