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[SOLVED] yum update reports duplicates and missing dependencies
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  1. #1
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    yum update reports duplicates and missing dependencies

    I have just gotten rid of Ubuntu in favor of Fedora, after more than ten years using Debian and Ubuntu. Most differences are pretty minimal but one big difference I haven't been able to master yet is the realm of rpm and yum.

    My kernel is 2.6.40-4.fc15.x86_64.

    Today, when running yum update I was greeted with a number of errors. I have no idea how to solve this or what caused it. I have tried searching for relevant solutions but haven't been able to find anything that describes the kind of issues I'm having.

    Output of yum check:
    Code:
    Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit
    glibc-2.14-5.x86_64 is a duplicate with glibc-2.14-4.x86_64
    glibc-common-2.14-5.x86_64 is a duplicate with glibc-common-2.14-4.x86_64
    1:perl-Module-Pluggable-3.90-160.fc15.noarch is a duplicate with 1:perl-Module-Pluggable-3.90-159.fc15.noarch
    1:perl-Module-Pluggable-3.90-160.fc15.noarch has missing requires of perl = ('4', '5.12.4', '160.fc15')
    1:perl-Pod-Escapes-1.04-160.fc15.noarch is a duplicate with 1:perl-Pod-Escapes-1.04-159.fc15.noarch
    1:perl-Pod-Escapes-1.04-160.fc15.noarch has missing requires of perl = ('4', '5.12.4', '160.fc15')
    1:perl-Pod-Simple-3.13-160.fc15.noarch is a duplicate with 1:perl-Pod-Simple-3.13-159.fc15.noarch
    1:perl-Pod-Simple-3.13-160.fc15.noarch has missing requires of perl = ('4', '5.12.4', '160.fc15')
    I have also attached the output of yum update, which I believe is more verbose on the sources, et.c.

    I'm afraid that if I just start forcing removal of packages I'll render my system useless. If anyone can help me or point me in the right direction I'd be very thankful.
    Attached Files Attached Files

  2. #2
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    Re: yum update reports duplicates and missing dependencies

    Take a look at the yum package-cleanup utility (cli) there is a --cleandupes option.

    I had a failed pre-upgrade once and had to spend some time manually deleting duplicates working through the package-cleanup list.
    ======
    Doug G
    ======

  3. #3
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    Re: yum update reports duplicates and missing dependencies

    I ran package-cleanup --cleandupes but it suggested that I remove 75 packages, of which I could identify quite many as very important. I didn't go through with it.

    However, it gave me a list of 5 packages for "Removing":

    Code:
    Removing:
     glibc                        x86_64      2.14-4                            @updates              12 M
     glibc-common                 x86_64      2.14-4                            @updates             113 M
     perl-Module-Pluggable        noarch      1:3.90-159.fc15                   @updates              30 k
     perl-Pod-Escapes             noarch      1:1.04-159.fc15                   @updates              21 k
     perl-Pod-Simple              noarch      1:3.13-159.fc15                   @updates             465 k
    Is it safe (more or less) to remove them? Which tool should I use to do that? Would a normal yum update work afterwards?

    Edit:
    One of the duplicates is glibc. It suggests removing glibc.x86_64, AND removing glibc.i686 as "Removing for dependencies". I guess it would wreak havoc on my system if glibc was missing. How do I specify which of the glibc-duplicates should be removed? I should stick with the x86_64 one I guess. Lot's of guessing here. :P
    Last edited by Kristoffer; 14th August 2011 at 09:02 AM. Reason: glibc stuff

  4. #4
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    Re: yum update reports duplicates and missing dependencies

    try

    yum cleanup

    and than yum update

    what shows yum repolist?
    FC15, 4GB mem, Dell Studio 17 laptop

  5. #5
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    Re: yum update reports duplicates and missing dependencies

    Quote Originally Posted by MysticalDice
    yum cleanup
    and than yum update
    what shows yum repolist?
    Code:
    [root@bastet ~]# yum clean all; yum update
    Loaded plugins: fastestmirror, langpacks, presto, refresh-packagekit
    Cleaning repos: Dropbox fedora google-chrome google-earth rpmfusion-free rpmfusion-free-updates rpmfusion-nonfree
                  : rpmfusion-nonfree-updates updates
    I don't know it it's relevant, but the output of package-cleanup --cleandupes command only lists packages from the @fedora and @updates repositories.

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    Re: yum update reports duplicates and missing dependencies


  7. #7
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    Re: yum update reports duplicates and missing dependencies

    So, I used yumex to remove the oldest version of the conflicting packages. yumex, like package-cleanup, listed a lot of depending packages to remove. However they were mostly i686 so I figured - what the heck, I'll go ahead and remove the lot. I don't need my machine for work until tomorrow morning anyway, plenty of time for a re-install.

    Everything went fine. I ran a yum update that finished without problems.

    A big thank you to everyone that pointed me in the right direction!

    Cheers!

  8. #8
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    Re: yum update reports duplicates and missing dependencies

    A couple of months ago I also ran into this problem after upgrading my fedora.

    I also tried the package-cleanup utilitly and it started removing required libs rendering my workstation unworkable. Luckely I could reinstall fedora not deleting my home partition.

    Yesterday the same problem occured and I fixed it removing the older version of the duplicate.

    For example:
    I got these duplicates:
    oxygen-icon-theme-4.8.3-1.fc16.noarch is a duplicate with oxygen-icon-theme-4.8.2-1.fc16.noarch
    sane-backends-libs-1.0.22-10.fc16.i686 is a duplicate with sane-backends-libs-1.0.22-8.fc16.i686

    What I did is I used the 'yum remove sane-backends-libs-1.0.22-8.fc16.i686' and afterwards a yum update.

    Everything is nog working fine.

    J

  9. #9
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    Re: yum update reports duplicates and missing dependencies

    In the future, you might consider using this instead:

    package-cleanup --dupes

    This will list any duplicates, but do nothing about it. Then, if you're worried about something such as glibc, you can try this:

    yum list installed glibc

    This will tell you exactly what you have installed, so that you can tell yum which version or versions to remove.
    Registered Linux user #470359 and permanently recovered BOFH.

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

  10. #10
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    Re: yum update reports duplicates and missing dependencies

    I just updated to Fedora 17 and cannot run yum update because of a whole bunch of errors.

    package-cleanup -- orphans finds a whole bunch of F16 packages still present on my machine, the same packages that yum update is complaining about.

    How do I take the package list generated by package-cleanup and feed it to a yum process to eliminate all the problem packages ?

    Thanks

  11. #11
    Yellowman Guest

    Re: yum update reports duplicates and missing dependencies

    Quote Originally Posted by me2
    I just updated to Fedora 17 and cannot run yum update because of a whole bunch of errors.

    package-cleanup -- orphans finds a whole bunch of F16 packages still present on my machine, the same packages that yum update is complaining about.

    How do I take the package list generated by package-cleanup and feed it to a yum process to eliminate all the problem packages ?

    Thanks
    Try this instead

    Code:
    su
    yum distro-sync

  12. #12
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    Re: yum update reports duplicates and missing dependencies

    Quote Originally Posted by josipj
    A couple of months ago I also ran into this problem after upgrading my fedora.

    I also tried the package-cleanup utilitly and it started removing required libs rendering my workstation unworkable. Luckely I could reinstall fedora not deleting my home partition.

    Yesterday the same problem occured and I fixed it removing the older version of the duplicate.

    For example:
    I got these duplicates:
    oxygen-icon-theme-4.8.3-1.fc16.noarch is a duplicate with oxygen-icon-theme-4.8.2-1.fc16.noarch
    sane-backends-libs-1.0.22-10.fc16.i686 is a duplicate with sane-backends-libs-1.0.22-8.fc16.i686

    What I did is I used the 'yum remove sane-backends-libs-1.0.22-8.fc16.i686' and afterwards a yum update.

    Everything is nog working fine.

    J
    If there is only file then you can do it manually. I have 384 no. of such files. What to now??

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