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I'm used to Yum on CentOS 5 being a total pig and breaking every other week, but until now I've always been able to fix the problem by simply running:

yum clean all

And then updating normally.

Not working today. I did a lot of googling, and another common piece of advice was to disable fastmirror, tried that too, still to no avail. Here is the error I'm getting:

# yum update
addons                                                                               |  951 B     00:00     
addons/primary                                                                       |  204 B     00:00     
base                                                                                 | 2.1 kB     00:00     
base/primary_db                                                                      | 2.2 MB     00:00     
extras                                                                               | 2.1 kB     00:00     
extras/primary_db                                                                    | 244 kB     00:00     
spacewalk-client-tools                                                               | 1.9 kB     00:00     
spacewalk-client-tools/primary_db                                                    |  15 kB     00:00     
updates                                                                              | 1.9 kB     00:00     
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.heanet.ie/pub/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.as29550.net/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.melbourne.co.uk/sites/ftp.centos.org/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.ellogroup.com/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.netrino.co.uk/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.coreix.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.krystal.co.uk/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.ukfast.co.uk/sites/ftp.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://anorien.csc.warwick.ac.uk/mirrors/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.ox.ac.uk/sites/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.bytemark.co.uk/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.nluug.nl/ftp/pub/os/Linux/distr/CentOS/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.denit.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.oxilion.nl/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.tudelft.nl/centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.widexs.nl/ftp/pub/os/Linux/distr/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.nl.leaseweb.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.supportex.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://centos.mirror.evertje.net/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://nl.mirror.eurid.eu/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.heanet.ie/pub/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.as29550.net/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.melbourne.co.uk/sites/ftp.centos.org/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.ellogroup.com/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.netrino.co.uk/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.coreix.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.krystal.co.uk/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.ukfast.co.uk/sites/ftp.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://anorien.csc.warwick.ac.uk/mirrors/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.ox.ac.uk/sites/mirror.centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.bytemark.co.uk/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.nluug.nl/ftp/pub/os/Linux/distr/CentOS/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.denit.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.oxilion.nl/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://ftp.tudelft.nl/centos.org/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.widexs.nl/ftp/pub/os/Linux/distr/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirror.nl.leaseweb.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://mirrors.supportex.net/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://centos.mirror.evertje.net/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
updates/primary_db                                                                   | 603 kB     00:00     
http://nl.mirror.eurid.eu/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2: [Errno -1] Metadata file does not match checksum
Trying other mirror.
Error: failure: repodata/primary.sqlite.bz2 from updates: [Errno 256] No more mirrors to try.
#

Is it possible that every yum mirror being tried has a dead sqlite package? Is there a way to tell yum to ignore sqlite and just update the rest? I tried --skip-broken, but it still errored out with the identical error.

CentOS is so broken these days :(

Bart.

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I should also mention that this is happening on all our CentOS 5 servers, not just one. –  Bart B Jun 9 '11 at 15:32
1  
Nothing wrong with the mirrors, i just tested a couple of them and they work as expected. –  fpmurphy1 Jun 9 '11 at 15:41
    
its not the sqlite package its, the repo meta data file being downloaded which is in sqlite format. For some reason it seems yum can't match the check sum. Did you do "yum clean all"? –  Hameedullah Khan Jun 9 '11 at 16:32
    
As it says in my question, I tried all the usual hacks to get yum to behaving, including a yum clean all. –  Bart B Jun 10 '11 at 12:54
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3 Answers

I checked http://nl.mirror.eurid.eu/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2 and the mirror looks OK.

To check I manually pulled down the file:

wget http://nl.mirror.eurid.eu/centos/5.6/updates/x86_64/repodata/primary.sqlite.bz2

Run sha1sum on it:

$ sha1sum primary.sqlite.bz2 
0c3f80f4063c9e64c000c5e6f1e5bda0a0623822  primary.sqlite.bz2

$ bzip2 -d primary.sqlite.bz2
$ sha1sum primary.sqlite 
adda574a8d795705b80d6c2003947c1ae2797f5f  primary.sqlite

and checked these values against the values listed in http://nl.mirror.eurid.eu/centos/5.6/updates/x86_64/repodata/repomd.xml

<data type="primary_db"><location href="repodata/primary.sqlite.bz2"/>
  <checksum type="sha">0c3f80f4063c9e64c000c5e6f1e5bda0a0623822</checksum>
  <timestamp>1307575563</timestamp>
  <open-checksum type="sha">adda574a8d795705b80d6c2003947c1ae2797f5f</open-checksum>
  <database_version>10</database_version>
</data>

Try a yum clean all and check that the files in /var/cache/yum/... in the same manner.

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http_caching=none in yum.conf then give it a try

Reference: http://plone.lucidsolutions.co.nz/linux/rpm/yum-metadata-file-does-not-match-checksum

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Whilst this may theoretically answer the question, it would be preferable to include the essential parts of the answer here, and provide the link for reference. –  Scott Pack Nov 9 '12 at 20:00
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up vote 0 down vote accepted

It seems the simple answer was to wait a day and try again.

Since nothing changed on my end since yesterday, the CentOS peeps mush have fixed some kind of bug on their end.

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