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Thread: Package manager bonked

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  1. #1
    Join Date
    Apr 2012
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    66

    Package manager bonked

    Hi all...
    Just starting recieving this error message this morning. It came out of nowhere. Installation was fine yesterday before I ran normal suggested updates that popped up last night, so something has bonked.
    Code:
    Reading package lists... Error!
    W: GPG error: http://dl.google.com stable Release: The following signatures were invalid: BADSIG A040830F7FAC5991 Google, Inc. Linux Package Signing Key <linux-packages-keymaster@google.com>
    W: GPG error: http://download.bitdefender.com bitdefender Release: The following signatures were invalid: BADSIG A373FB480EC4FE05 BitDefender Packages <packages@bitdefender.com>
    W: GPG error: http://us.archive.ubuntu.com precise Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    W: A error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://us.archive.ubuntu.com precise-updates Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    
    W: A error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://extras.ubuntu.com precise Release: The following signatures were invalid: BADSIG 16126D3A3E5C1192 Ubuntu Extras Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    
    W: GPG error: http://us.archive.ubuntu.com precise-backports Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    W: GPG error: http://ppa.launchpad.net precise Release: The following signatures were invalid: BADSIG FC6FA5EB4357B38A Launchpad PPA for Arx Libertatis
    W: A error occurred during the signature verification. The repository is not updated and the previous index files will be used. GPG error: http://us.archive.ubuntu.com precise-security Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    
    W: GPG error: http://archive.canonical.com precise Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    W: GPG error: http://ppa.launchpad.net precise Release: The following signatures were invalid: BADSIG 3BDAAC08614C4B38 Launchpad otto06217
    W: GPG error: http://ppa.launchpad.net precise Release: The following signatures were invalid: BADSIG 0D91713165530E6C Launchpad PPA for Screenlets Dev Team
    W: GPG error: http://archive.canonical.com precise Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>
    W: GPG error: http://ppa.launchpad.net precise Release: The following signatures were invalid: BADSIG 94E58C34A8670E8C Launchpad PPA for Screenlets
    W: GPG error: http://ppa.launchpad.net precise Release: The following signatures were invalid: BADSIG EB563F93142986CE Launchpad PPA for Xubuntu Developers
    W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/precise-updates/Release  
    
    W: Failed to fetch http://us.archive.ubuntu.com/ubuntu/dists/precise-security/Release  
    
    W: Failed to fetch http://extras.ubuntu.com/ubuntu/dists/precise/Release  
    
    W: Some index files failed to download. They have been ignored, or old ones used instead.
    E: Encountered a section with no Package: header
    E: Problem with MergeList /var/lib/apt/lists/us.archive.ubuntu.com_ubuntu_dists_precise-security_main_binary-i386_Packages
    E: The package lists or status file could not be parsed or opened.
    as I said all was fine yesterday before running updates that popped up in the normal notifier.

    Any help would be appreciated!
    Thanks in advance

  2. #2
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  3. #3
    Join Date
    Sep 2012
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    Virginia, USA
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    209
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    Ubuntu Development Release

    Re: Package manager bonked

    OP, the last few sentences of your output suggest that there is a problem with your files in /var/lib/apt/lists ("E: Problem with MergeList /var/lib/apt/lists/us.archive.ubuntu.com_ubuntu_dists_precise-security_main_binary-i386_Packages E: The package lists or status file could not be parsed or opened."). The following commands should (hopefully!) take care of that. At a terminal (CTRL + ALT + T), type:

    Code:
    sudo apt-get clean
    sudo mv /var/lib/apt/lists /var/lib/apt/lists.old
    sudo mkdir -p /var/lib/apt/lists/partial
    sudo apt-get clean
    sudo apt-get update
    If that works (I'm guessing it will), you can delete the backup directory with the old lists (be careful to type this command exactly, as mistakes with 'rm -rf' can result in serious data loss):

    Code:
    sudo rm -rf /var/lib/apt/lists.old
    If it didn't work, you can try manually adding the keys. Look at the BADSIG errors, note the key hash for each one (e.g., BADSIG 40976EAF437D05B5), and then type:

    Code:
    sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 40976EAF437D05B5
    Do that for each. But again, given the last few sentences of your output, I'm suspecting that re-creating the lists (in the first step) will clear things up.
    Last edited by jrog; October 11th, 2012 at 04:28 PM.
    Asus K55A (Core i5-3210M @ 2.5GHz/8GB RAM/120GB SSD/Intel HD 4000) with Ubuntu 12.10 Beta 2
    Compaq Presario C700 (Pentium Dual-Core @ 1.6GHz/2.5GB RAM/500GB HDD/Intel GM965) with Arch Linux and Linux Mint Debian Edition

  4. #4
    Join Date
    Apr 2012
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    66

    Re: Package manager bonked

    Var has so many files in it that I wouldn't even know where to begin to look

    sudo mv /var/lib/apt/lists /var/lib/apt/lists.old
    When I type the above command it tells me it can't be moved because the directory is not empty
    Code:
    mv: cannot move `/var/lib/apt/lists' to `/var/lib/apt/lists.old/lists': Directory not empty
    one thing I did notice is that on boot up Xubuntu did a "routine disk check" and its not the first time it has done this...could I be having a hard drive failure?

  5. #5
    Join Date
    Mar 2010
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    Lubuntu 14.04 Trusty Tahr

    Re: Package manager bonked

    Quote Originally Posted by tdlam View Post
    Var has so many files in it that I wouldn't even know where to begin to look
    That's what grep is for.

    $ sudo grep -i error /var/log/*log

    The disk check happens from time to time based on file system settings or if the machine was shutdown without giving the file system time to cleaning unmount it.

    I'm inclined to think the other answers are more helpful for this issue, but a HDD failure could come at any time and they are seldom convenient. Every HDD will fail. Every one of them. The trick is to have already replace the HDD before that happens. Having a great backup solution can be the best solution.

    Again, the other answers are probably better.

  6. #6
    Join Date
    Apr 2012
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    66

    Re: Package manager bonked

    @ oldos2er:
    that link doesn't work for me. The first method I get the error saying I can't move again because the directory is not empty
    second method doesnt work because the word aptitude is not recognised

  7. #7
    Join Date
    Jul 2007
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    Magic City of the Plains
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    Hidden!
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    Xubuntu 17.04 Zesty Zapus

    Re: Package manager bonked

    Quote Originally Posted by tdlam View Post
    @ oldos2er:
    that link doesn't work for me. The first method I get the error saying I can't move again because the directory is not empty
    second method doesnt work because the word aptitude is not recognised
    Here are the commands:

    sudo -i

    apt-get clean

    cd /var/lib/apt

    mv lists lists.old

    mkdir -p lists/partial

    apt-get clean

    apt-get update

  8. #8
    Join Date
    Apr 2012
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    66

    Re: Package manager bonked

    wow this is getting complicated I tried running
    Code:
    sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com 40976EAF437D05B5
    inserting one of the keys and I get this error:
    Code:
     sudo apt-key adv --recv-keys --keyserver keyserver.ubuntu.com A040830F7FAC5991
    Executing: gpg --ignore-time-conflict --no-options --no-default-keyring --secret-keyring /tmp/tmp.Vi2IVQEfMX --trustdb-name /etc/apt/trustdb.gpg --keyring /etc/apt/trusted.gpg --primary-keyring /etc/apt/trusted.gpg --recv-keys --keyserver keyserver.ubuntu.com A040830F7FAC5991
    gpg: requesting key 7FAC5991 from hkp server keyserver.ubuntu.com
    ?: keyserver.ubuntu.com: Connection refused
    gpgkeys: HTTP fetch error 7: couldn't connect: Connection refused
    gpg: no valid OpenPGP data found.
    gpg: Total number processed: 0
    Edit: yes I see the commands are essentially the same thanks...just that the mv command in both instances doesnt work
    Last edited by tdlam; October 11th, 2012 at 05:01 PM.

  9. #9
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    Ubuntu Development Release

    Re: Package manager bonked

    Quote Originally Posted by tdlam View Post
    Var has so many files in it that I wouldn't even know where to begin to look

    sudo mv /var/lib/apt/lists /var/lib/apt/lists.old
    When I type the above command it tells me it can't be moved because the directory is not empty
    Code:
    mv: cannot move `/var/lib/apt/lists' to `/var/lib/apt/lists.old/lists': Directory not empty
    Okay, then instead of the original commands I gave you, edit them slightly to do this:

    Code:
    sudo apt-get clean
    mkdir ~/backup
    sudo mv /var/lib/apt/lists ~/backup/ 
    sudo mkdir -p /var/lib/apt/lists/partial
    sudo apt-get clean
    sudo apt-get update
    Quote Originally Posted by tdlam View Post
    one thing I did notice is that on boot up Xubuntu did a "routine disk check" and its not the first time it has done this...could I be having a hard drive failure?
    That's very unlikely right now. Routine disk checks are typically just routine disk checks.

    EDIT: The commands that oldos2er is giving you do essentially the same thing as the ones I'm giving you, BTW.
    Asus K55A (Core i5-3210M @ 2.5GHz/8GB RAM/120GB SSD/Intel HD 4000) with Ubuntu 12.10 Beta 2
    Compaq Presario C700 (Pentium Dual-Core @ 1.6GHz/2.5GB RAM/500GB HDD/Intel GM965) with Arch Linux and Linux Mint Debian Edition

  10. #10
    Join Date
    Mar 2010
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    11,152
    Distro
    Lubuntu 14.04 Trusty Tahr

    Re: Package manager bonked

    Could be anything from a back network connection to a failing HDD. What do the system log files say?

    /var/log/
    and dmesg would help.

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