I ran into that problem too.  I opened up a terminal and ran the
following command:

     sudo nautilus /var/lib/apt/lists/

That will open up the folder containing all of the files that need to be
changed as root in nautilus.  As root you can double-click on a file to
edit it, or for some it may be necessary to right-click and select Open
With Other Application... and then choose the text editor you want to
use to delete the contents of all of the files--I used gedit b/c its
simple and it works.

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https://bugs.launchpad.net/bugs/988841

Title:
  cannot use update manager

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