Package manager bonked

[tdlam]

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.

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

[wildmanne39]

Thread moved to General Help.

[TheFu]

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.

[jrog]

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:

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):

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:

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.

[oldos2er]

http://www.ubuntugeek.com/how-to-fix...or-badsig.html

[wildmanne39]

Hi, please be careful using and posting commands like this.

rm -rf

they need to include a warning that if the path is not typed correctly you can break your system.
Thanks

[jrog]

Hi, please be careful using and posting commands like this.

rm -rf

they need to include a warning that if the path is not typed correctly you can break your system.
Thanks

Sorry. That^ is correct. Edited the earlier post.

[tdlam]

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

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?

[TheFu]

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.

[tdlam]

@ 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