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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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4 Answers

up vote 3 down vote accepted

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 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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Thank you, fixed mine too. – Eddsstudio Jan 30 at 9:49
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up vote 1 down vote

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. – Brady 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 pastebin.com/RPYpUyE6 – Brady 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)[serverfault.com/questions/62026/… – 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
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up vote 0 down vote

$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:

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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 – Brady Nov 18 '11 at 14:30
I think rather than sudo yum update, using rpm -uvh is a better way to update the depot. – Anarko_Bizounours Nov 18 '11 at 14:46
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up vote 0 down vote

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.

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