Thanks for your bugreport.
Can you please attach the output of:
$ ls -l /var/lib/apt/lists
and
$ /usr/lib/update-notifier/apt-check
to this bugreport?
** Changed in: update-notifier (Ubuntu)
Status: New => Incomplete
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Update Notifier does not work
https://bugs.launchpad.net/bugs/126775
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Bugs, which is the bug contact for Ubuntu.
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