Centos 6 yum update - Packages skipped because of dependency problems

Question

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?

Thanks! I agree with them. But some of the links above are not available,there are many other sites you can download the "epel" repo: 1 [http://mirrors.yun-idc.com/epel](http://mirrors.yun-idc.com/epel) and 2 [http://mirrors.hustunique.com/epel](http://mirrors.hustunique.com/epel) then you can choose the right version according to the platform. — Eric, Dec 17 '13 at 06:45

score 3 · Accepted Answer · edited Jul 17 '22 at 08:33

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

rpm -qa |grep epel

then you may get this

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

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

yum update

Thats all.

score 2 · Answer 2 · edited Jan 27 '12 at 00:43

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.

edited Jan 27 '12 at 00:43

Mark Henderson

68,316
31
175
255

answered Jan 26 '12 at 23:26

Ed Moxley

21
1

The `yum clean all` was the missing step. Thanks. – Gareth Jun 27 '12 at 12:06

Brian Layman · Answer 3 · 2015-09-11T00:01:03.210

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.

score 1 · Answer 4 · answered Nov 18 '11 at 14:49

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

answered Nov 18 '11 at 14:49

Anarko_Bizounours

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I have done this and updated my repo but I still get the same dependency issues. – Scott Nov 18 '11 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. – Anarko_Bizounours Nov 18 '11 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` http://pastebin.com/RPYpUyE6 – Scott Nov 18 '11 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)[http://serverfault.com/questions/62026/how-to-know-from-which-yum-repository-a-package-has-been-installed/324857] – Martian Nov 18 '11 at 15:20
What Martian said, it may be a packages conflict between epel5 and 6. try desinstalling them, and reinstall them using epel6 – Anarko_Bizounours Nov 22 '11 at 14:36

score 0 · Answer 5 · answered Nov 18 '11 at 14:15

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

Centos 6 yum update - Packages skipped because of dependency problems

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