I have not yet been able to reproduce this, but the stack trace is
suggestive of either memory corruption or a pointer walking beyond the
end of a list.

Consider a few choice entries from the 'stat' buffer shown in
debPackagesIndex::FindInCache in the stacktrace:

st_nlink = 0 (impossible)
st_blksize = 0 (impossible)
tv_sec = 140058388787402 (eermmm)
st_uid = 32609 (expected st_uid=0)
st_gid = 1 (expected st_gid=0)

These values are either impossible or highly unlikely.

Is this repeatable if a non-privileged user runs the check that is failing?:
 
    /usr/bin/python /usr/lib/update-notifier/apt-check

It would also be useful to see the output of:

    apt-config dump

I do wonder if this issue was caused due to 'srcpkgcache.bin' being
updated at the time /usr/lib/update-notifier/apt-check ran.

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https://bugs.launchpad.net/bugs/1016040

Title:
  apt_check.py crashed with SIGSEGV in FileName()

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