Broken YUM
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  1. #1
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    Question Broken YUM

    For some reason, yum is broken (F17 desktop) and gives an error about a bad DB.
    Since yum is how updates etc are fixed, how do I go about fixing (delete/reinstall etc) yum

    ---------- Post added at 03:58 PM ---------- Previous post was at 01:23 PM ----------

    Now I am by the failed system, this is what I get.

    error: rpmdb: BDB0113 Thread/process 721/3077977920 failed: BDB1507 Thread died in Berkeley DB library
    error: db5 error(-30973) from dbenv->failchk: BDB0087 DB_RUNRECOVERY: Fatal error, run database recovery
    error: cannot open Packages index using db5 - (-30973)
    error: cannot open Packages database in /var/lib/rpm
    CRITICAL:yum.main:
    This is what I find in /var/lib/rpm.
    [root@jan rpm]# ls
    Basenames __db.002 Group Obsoletename Requirename Triggername
    Conflictname __db.003 Installtid Packages Sha1header
    __db.001 Dirnames Name Providename Sigmd5
    Last edited by griffinmt; 5th November 2012 at 10:00 PM.
    Martyn Griffin

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    Re: Broken YUM

    rm -f /var/lib/rpm/__db*

    rpm --rebuilddb
    Note the double underscore the first command before the "db*". All that should be run as root user

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    Re: Broken YUM

    With Linux, man is your friend. Specifically this:

    man yum

    Run this as root:

    yum clean rpmdb

    That should clean up your database. If you still have trouble:

    yum clean all

    may be needed, but try cleaning just the DB first; no need to use a bigger hammer than you need.
    Registered Linux user #470359 and permanently recovered BOFH.

    Any advice in this post is worth exactly what you paid for it.

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    Re: Broken YUM

    I tried the clean options but I got the same results. Tomorrow I will delete the __db files then try it again. Thanks
    Martyn Griffin

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    Re: Broken YUM

    I guess
    Code:
    yum makecache
    doesnt have an effect either, right?
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    Re: Broken YUM

    I'll try the makecache tomorrow too.
    Thanks.
    Martyn Griffin

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    Re: Broken YUM

    I ran into it this morning, also. Found out it exists since F15 (see: <https://bugzilla.redhat.com/show_bug.cgi?id=739492>) Bug description is almost exact match, why the hell the bug was closed in F16?

    @Marko: Lepa hvala za nasvet, prijatelj!

    I followed nice advice from Marko, killed some files as he instructs. All my previous attempts were kicks in the darkness.

    rm -f /var/lib/rpm/__db*

    Then I issued:

    rpm --rebuilddb

    And:

    yum clean all (to be sure everything really cleans up)

    Finally:

    yum makecache

    And for test, I ran:

    yum --skip-broken (as always!)

    and it worked! Well, I lost 6 hours for this to learn the hard way.

    On my way through darkness, I went even looking back in my /var/log/yum.log. There was nothing wrong. According to it, I've installed/updated during last days (bigones & notables):
    - latest available kernel until now (3.6.6.1, x86_64, nothing special added to it),
    - KDE 4.9.2
    - yumex 3.0.9 (irrelevant, I always run yum from terminal),
    - yum-langpacks 0.3.0-3.fc17,
    - createrepo_c-libs-0.1.11-1.fc17.x86_64,
    - os-prober-1.56-1.fc17.x86_64,
    - wine-1.5.16-1.fc17.x86_64,
    - perl-core-5.14.3-217.fc17.x86_64,
    - my yum --version gives this output:
    Code:
    3.4.3
      Installed: rpm-4.9.1.3-7.fc17.x86_64 at 2012-07-03 13:20
      Built    : Fedora Project at 2012-05-07 10:05
      Committed: Panu Matilainen <pmatilai at redhat.com> at 2012-05-07
    
      Installed: yum-3.4.3-29.fc17.noarch at 2012-09-08 14:39
      Built    : Fedora Project at 2012-08-28 14:32
      Committed: Zdenek Pavlas <zpavlas at redhat.com> at 2012-08-28
    
      Installed: yum-plugin-aliases-1.1.31-4.fc17.noarch at 2012-07-03 19:58
      Built    : Fedora Project at 2012-01-26 20:48
      Committed: James Antill <jamesfedora at project.org> at 2012-01-26
    
      Installed: yum-plugin-fastestmirror-1.1.31-4.fc17.noarch at 2012-07-03 19:53
      Built    : Fedora Project at 2012-01-26 20:48
      Committed: James Antill <jamesfedora at project.org> at 2012-01-26
    The incriminated version of RPM from the bug above was 4.9.1.1-1at opening in F15 and 4.9.1.1-3 at closing in F16.
    I normally run su in Konsole, as one thread (i7 allows me 8 independent threads). It would interesting which version of yum/rpm Griffin has.

    If somebody wants my yum.log, I backed it up a copy before rebuilding databases.

  8. #8
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    Re: Broken YUM

    Worked for me! Thanks @jozze

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