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When I update my RHEL with yum update commend, it list all update packages, and after I hit Y for yes, got following response.

    Running rpm_check_debug
    Running Transaction Test
    Transaction Test Succeeded
    Running Transaction
    Warning: RPMDB altered outside of yum.
    Killed

Please help me to update my server.

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Someone or something killed yum. Take a look at your free memory, maybe you hit an OOM condition, and it's not scored well enough by the OOM killer. –  Chris Down Oct 29 '13 at 10:42
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1 Answer

This may not be a serious issue at all, see here:

The yum message "Warning: RPMDB altered outside of yum." [...] means some application has altered the rpm database (installed or removed a package) without going through the Yum APIs. This is almost always due to someone using rpm directly (Ie. rpm -ivh blah.rpm), but another possibility is an application built on top of the rpm APIs (Ie. smart, apt, zypp).

So it may have been something you did inadvertently, or some piece of software did. Hopefully it is not a big deal and can be resolved with:

yum clean all

Have a look at CLEAN OPTIONS in man yum to understand what that does. Basically it gets rid of any locally cached data to do with RPMDB; normally this is used to speed up transactions, so next time you run yum it will probably take a little bit longer because it needs to replace the (corrupted) data you just cleaned out.

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