F18 How to resolve yum file conflict.
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  1. #1
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    Exclamation F18 How to resolve yum file conflict.

    This is really holding me up. I need to install zend-server-ce, however i'm having an issue that I cannot seem to get around.

    To narrow it down a little. Here's the specific issue.

    Code:
    Downloading Packages:
    Running Transaction Check
    Running Transaction Test
    
    
    Transaction Check Error:
      file /usr/lib64 from install of liboci8-zend-11.2.0.2-1.x86_64 conflicts with file from package filesystem-3.1-2.fc18.x86_64
    
    Error Summary
    -------------
    The "Error Summary" contains nothing. Is there a way I can resolve this and get zend-ce installed? Where can I go from here? I've never dealt with a conflict like this.

    Thank you in advance for your time.

  2. #2
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    Re: F18 How to resolve yum file conflict.

    No, here's the specific issue:

    This rpm package was prepared by someone without adequate technical understanding of creating rpm packages. It is certainly not an official Fedora rpm package.

    The problem: This package is trying to "take ownership" of /usr/lib64, and thus everything installed into and under it. Well, /usr/lib64 is already owned by the Fedora package "filesystem", an essential and crucial OS package.

  3. #3
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    Re: F18 How to resolve yum file conflict.

    Some posts suggest that the error is a bug in the package. Others suggest this fix:

    Add the --replacefiles option to rpm, e.g:

    sudo rpm -i --replacefiles downloaded_file_name.rpm

    EDIT: Use at your own risk. It worked for another user, but YMMV.
    Last edited by ThomasMcA; 8th February 2013 at 09:16 PM.

  4. #4
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    Re: F18 How to resolve yum file conflict.

    you really don't want to be specifying the --replacefiles option, especially when the conflict is a part of the system filesystem. You could totally hose your entire install that way.

    It needs to be fixed in the package, not forcing a workaround and risking your system. Packages like that have no business trying to claim ownership (or change permissions) of system directories.

    Edit:
    One way around it would be to rebuild the package yourself. Grab the source rpm and rebuild it.
    .

  5. #5
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    Re: F18 How to resolve yum file conflict.

    Quote Originally Posted by ThomasMcA
    Some posts suggest that the error is a bug in the package. Others suggest this fix:

    Add the --replacefiles option to rpm, e.g:

    sudo rpm -i --replacefiles downloaded_file_name.rpm
    Brilliant ! Yeah, you could do that. But then, sometime afterwards, you could also do:

    sudo rpm -e liboci8-zend

    only to find after that the entire /usr/lib64 directoy was now gone. Were that to be the case, you would no longer have a bootable Fedora system.

    Is the source code or the SRPM package available for this package? Are there other companion rpm packages that go with this libocii-zend package? With the SRPM (*.src.rpm), you could fix the specfile and generate a proper rpm package (if you have the skills). Or with just the source code, you could compile/install without fear of rpm packages that might eat your system.

    Another alternative is to just extract the rpm package contents using rpmdev-extract to some safe location in your home user directory then move the relevant bits to their intended location in the filesystem. Doing this, depending on what's contained in the package, you may also then need to run a command or two to make things work right (things that the scripts in the package would do.

    rpm -qp --scripts liboci8-zend-11.2.0.2-1.x86_64.rpm

    No way in hell would I install a "bad" rpm package to my system via rpm or yum. You're free to do as you wish with your system.

    ---------- Post added at 03:16 PM ---------- Previous post was at 02:57 PM ----------

    You might also post (or at least have a look for yourself) the output of:
    Code:
    rpm -qpl liboci8-zend-11.2.0.2-1.x86_64.rpm
    to see if the file placements are at least compatible with Fedora. If they are, then it would be OK to extract the rpm contents directly to the root partition "/".

  6. #6
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    Re: F18 How to resolve yum file conflict.

    Thanks to everyone for the replies.

    Now that I understand what's going on a little better, the --replacefiles path would be a little too haphazard for my taste. I need long term stability.

    I'm a user, web application engineer, and at best an average level sysadmin. I don't have the knowledge to rebuild the packages on my own.

    To answer a few questions to PabloTwo:

    I can't find an SRPM package for it.
    It is part of a larger compilation.
    As stated, I don't have these skills and your questions are honestly going over my head.

    I'm going to do some research and figure out the best course of action. I'll update my post once I collect more information.


    I've used zend-server-ce for some time now. We use a lot of zend technology at our workplace so for the past 5 years this has been our primary php server.

    To install zend-server-ce I usually simply follow the manual install instructions here: http://files.zend.com/help/previous-...stallation.htm

  7. #7
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    Re: F18 How to resolve yum file conflict.

    OK, from the link you posted I was able to have a browse of the repository files where you are installing from. I downloaded the liboci8-zend-11.2.0.2-1.x86_64.rpm package to have a look at it, and used rpm to query it's contents.
    Code:
    BASH:work/-> rpm -qpl liboci8-zend-11.2.0.2-1.x86_64.rpm 
    warning: liboci8-zend-11.2.0.2-1.x86_64.rpm: Header V3 DSA/SHA1 Signature, key ID f7d2c623: NOKEY
    /usr/lib64   <== Here is the "problem file". It shouldn't be here.
    /usr/lib64/libclntsh.so.11.1
    /usr/lib64/libnnz11.so
    /usr/lib64/libociicus.so
    Just 3 shared object files. I can see it is just part of many other rpm packages that would be installed. I also checked what this package requires, and it appears nothing more than what can be provided by the normal Fedora repos.

    The problem lies in that's this package is just one package in a group of packages that your install is trying to do, and there is at least one of those packages that almost certainly has a "dependency" on this liboci8-zend package. That means yum will fail to install the other package(s) that has a dependency on liboci8-zend due to the failure of of the liboci8-zend package to install via yum, due to the mis-configuration in it's spec file. A real "catch 22".

    It is super simple to just download that package as I have done and then extract it's contents into the filesystem (rather than yum or rpm install), but that does nothing to let rpm/yum know those files are installed. Rpm and yum don't look at files at all, but go by the metadata contained within the rpm package. That metadata references "resources", not files. Rpm can read the metadata from an rpm package and see that this package requires this, this and this resource, but it can't figure out what other package(s) provides those resources that aren't already installed. Yum can, that's its job.

    I couldn't find any SRPM files (*.src.rpm) packages for packages on that repository, so no luck at just grabbing the source rpm, fixing the spec file in it and rebuilding the rpm package so yum won't complain.

    It might help some if you would post the command you are using to install, and then list all the packages that yum has tagged to be installed. I think you're options right now are to follow the first suggestion, and be extremely careful not to erase the "bad" package, or send an email to the providers and let them know of the problem and hope they fix it in a timely manner and then do the install from their repo. The edit to the spec file to fix that issue is minuscule...would take seconds, then just a few more minutes to rebuild the package.

    ---------- Post added at 07:48 PM ---------- Previous post was at 05:18 PM ----------

    Fortunately, the email addy to contact at Zend is right there in the package INFO:
    Code:
    BASH:work/-> rpm -qpi liboci8-zend-11.2.0.2-1.x86_64.rpm 
    warning: liboci8-zend-11.2.0.2-1.x86_64.rpm: Header V3 DSA/SHA1 Signature, key ID f7d2c623: NOKEY
    Name        : liboci8-zend
    Version     : 11.2.0.2
    Release     : 1
    Architecture: x86_64
    Install Date: (not installed)
    Group       : Zend/Server
    Size        : 67992800
    License     : Oracle
    Signature   : DSA/SHA1, Wed 15 Dec 2010 09:08:56 AM EST, Key ID 2eae1437f7d2c623
    Source RPM  : liboci8-zend-11.2.0.2-1.src.rpm
    Build Date  : Wed 15 Dec 2010 09:08:34 AM EST
    Build Host  : il-build-centos5-64-01.zend.net
    Relocations : (not relocatable)
    Packager    : Zend <packaging-feedbacks@zend.com>
    Vendor      : Zend
    URL         : http://www.php.net
    Summary     : OCI8 libraries.
    Description :
    OCI8 libraries needed for the PHP OCI extensions


    ---------- Post added at 10:13 PM ---------- Previous post was at 07:48 PM ----------

    If you're still having trouble with this, I offer another way to resolve it. I extracted the downloaded rpm file and just copied the 3 binary files into a directory I made for it, tarred and bzip2'd it up into a SOURCE package to use and created my own spec file to create an rpm file. Same name as the original, same contents, but sans the problematic /usr/lib64.
    Code:
    BASH:x86_64/-> rpm -qpl liboci8-zend-11.2.0.2-1.x86_64.rpm 
    /usr/lib64/libclntsh.so.11.1
    /usr/lib64/libnnz11.so
    /usr/lib64/libociicus.so
    You can download this rpm file from here. Once you have it, you can install it like so:
    Code:
    # yum --nogpgcheck install liboci8-zend-11.2.0.2-1.x86_64.rpm
    I did a test install and all dependencies of this package can be met from the normal Fedora repos. Once this is installed, you should be able to install the rest of the packages (provided none of those have issues) from the Zend repos that you're after.
    Last edited by PabloTwo; 8th February 2013 at 11:27 PM.

  8. #8
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    Re: F18 How to resolve yum file conflict.

    Wow PabloTwo,

    Thank you very much for your time and attention to this. You've been more than helpful.

    I sent an email to the packager. Of course that email got returned with a permanent failure. We'll see what the standard support channels do with it.

    I used the RPM that you created for me.

    I can't thank you enough. It worked like a charm.

  9. #9
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    Exclamation Re: F18 How to resolve yum file conflict.

    Quote Originally Posted by PabloTwo
    sudo rpm -e liboci8-zend

    only to find after that the entire /usr/lib64 directoy was now gone. Were that to be the case, you would no longer have a bootable Fedora system.
    That is misinformation. RPM does not erase a directory (or its contents) as long as any other installed package still owns the directory (or files in it). Only an empty directory gets removed, if the last package that contains the directory gets removed.

  10. #10
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    Re: F18 How to resolve yum file conflict.

    Well, I certainly don't want to be the propagator of misinformation, so thank you for the correction.

    @joshuailivesay- It took very little and effort and time on my part to provide a problem free rpm package. I'm pleased my small contribution eased your zend server installation.

  11. #11
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    Re: F18 How to resolve yum file conflict.

    Quote Originally Posted by joshualivesay
    This is really holding me up. I need to install zend-server-ce, however i'm having an issue that I cannot seem to get around.

    To narrow it down a little. Here's the specific issue.

    Code:
    Downloading Packages:
    Running Transaction Check
    Running Transaction Test
    
    
    Transaction Check Error:
      file /usr/lib64 from install of liboci8-zend-11.2.0.2-1.x86_64 conflicts with file from package filesystem-3.1-2.fc18.x86_64
    
    Error Summary
    -------------
    The "Error Summary" contains nothing. Is there a way I can resolve this and get zend-ce installed? Where can I go from here? I've never dealt with a conflict like this.

    Thank you in advance for your time.
    Hey there,

    I also had this problem and just rpm -Uvh --force and have had 0 problems with the install or my machine.

    Thanks,

    Skip

  12. #12
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    Re: F18 How to resolve yum file conflict.

    Thanks Pablo!

    your solution worked for me.

  13. #13
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    Arrow SOLUTION: Re: F18 How to resolve yum file conflict.

    I ran into this same issue again, on a new system, after 6 months. It took some googling but I found this thread again! I'm simply adding some search terms here to make it easier for others and outlining the solution again. Also i'm verifying that this problem still exists and this IS the best solution i've found.

    file /usr/lib64 from install of liboci8-zend-11.2.0.2-1.x86_64 conflicts with file from package filesystem-3.2-13.fc19.x86_64
    file /usr/lib64 from install of liboci8-zend-11.2.0.2-1.x86_64 conflicts with file from package filesystem

    SOLUTION

    Download the repackaged rpm

    Code:
    yum --nogpgcheck install liboci8-zend-11.2.0.2-1.x86_64.rpm
    Then simply yum install zend-server-ce-php-5.3 again.

    Look at the above comments to see why this issue exists and what this solution actually does. I hope more people with this issue can find this thread.

  14. #14
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    Re: F18 How to resolve yum file conflict.

    try to remove one of the package using --force and then use yum reinstall that package. These errors are common in fedora though by mistake. Its all about number.. sometime they too slip from developer hand.

  15. #15
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    Re: F18 How to resolve yum file conflict.

    Hi,
    I installed some packages using the rpm --force trick, but now I can't update my system, because with 'yum update' I get:
    Code:
    file /usr/bin from install of filesystem-3.2-13.fc19.x86_64 conflicts with file from package spotify-client-0.9.1.55.gbdd3b79.203-2.x86_64
    and more like that for other packages.
    Is there a commandline flag for yum to just ignore that and install the update packages anyway, or do I really have to remove the conflicting packages before I can update??
    Thanks

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