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How do I fix a “Problem with MergeList” error when trying to do an update?

I always have been a Windows guy but with my recent interesting and degree (Microbiology) of bioinformatics I am finding a need for the command line and higher computational power.

I am making the full conversion to Ubuntu 12.04 LTS and honestly just need help setting it up for my/it's first time. I lack the command line knowledge to navigate some problems.

First off I keep getting a handful of errors withing sudo apt-get update

Reading package lists... Error!
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: GPG error: htt://security.ubuntu.com precise-security Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: htt://extras.ubuntu.com precise Release: The following signatures were invalid: BADSIG 16126D3A3E5C1192 Ubuntu Extras Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: htt://us.archive.ubuntu.com precise-updates Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

W: GPG error: htt://us.archive.ubuntu.com precise-backports Release: The following signatures were invalid: BADSIG 40976EAF437D05B5 Ubuntu Archive Automatic Signing Key <ftpmaster@ubuntu.com>

E: Encountered a section with no Package: header
E: Problem with MergeList /var/lib/apt/lists/us.archive.ubuntu.com_ubuntu_dists_precise_restricted_binary-amd64_Packages
E: The package lists or status file could not be parsed or opened.

Secondly, I have various random problems with the new OS. I click on the "Ubuntu Software Center" and it opens then crashes without a error box :

"Ubuntu has encountered an internal error"

that can't show details

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marked as duplicate by January, hexafraction, Jorge Castro, Ringtail, devav2 Oct 10 '12 at 4:32

This question has been asked before and already has an answer. If those answers do not fully address your question, please ask a new question.

    
P.S. you can find my e-mail if you go through my profile carefuly. I'm a bioinformatician myself. Regarding your second problem: note that you should only post one question. Read the FAQ and use google. –  January Oct 9 '12 at 22:35

1 Answer 1

I would love to be your penpal - but the time diff would be quite a problem. Additionally I have not really a lot of free time. And others are much better than me ...

But now to get rid of some of your problems:

Your BADSIG Problem is an easy one. Your signatures are uncorrect.

Update them with:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 40976EAF437D05B5

Please do that with every wrong key by just changing the last key number and keeping the rest.

Rebuild your software cache:

cd /var/lib/apt
sudo mv lists lists.old
sudo mkdir -p lists/partial
sudo apt-get update

Maybe that will fix your Software Center Problem as well ...

Good Luck!

PS: But if you ask here - many nice people will surely help you here and you will learn a lot! But please keep on giving as much error output as possible.

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Q: How do I find these "keys" is there a command to look them up for the problem programs? –  jon_shep Oct 9 '12 at 22:49
    
If you mean how does the command find the keys it passes the number to keyserver.ubuntu.com and that keyserver returns the public key you need to securely verify the package information you are downloading from the archive. If you man how do you yourself find the number 40976EAF437D05B--it was mentioned in the error messages you posted (scrolling right). –  John S Gruber Oct 9 '12 at 23:43
    
That should have been 40976EAF437D05B5 in my last comment. Once you get this fixed I suggest that you reinstall the package ubuntu-keyring. That package should have installed that key when you installed your system. –  John S Gruber Oct 10 '12 at 0:20

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