I can reproduce this in Debian 7.2, like this:
[1] $ sudo apt-get update
[ lots of output ]
[2] $ /usr/lib/update-notifier/apt-check;echo
0;0
[3] $ sudo touch /etc/apt/sources.list.d/foo.list
[4] $ sudo chmod 600 /etc/apt/sources.list.d/foo.list
[5] $ /usr/lib/update-notifier/apt-check;echo
E: Error: Opening the cache (E:Opening
/etc/apt/sources.list.d/foo.list - ifstream::ifstream (13: Permission
denied), E:The list of sources could not be read., E:The package lists
or status file could not be parsed or opened.
[6] $ sudo apt-get update
[ lots of output ]
[7] $ /usr/lib/update-notifier/apt-check;echo
Segmentation fault (core dumped)
[8] $ sudo chmod 644 /etc/apt/sources.list.d/foo.list
[9] $ /usr/lib/update-notifier/apt-check;echo
0;0
[10] $ sudo rm /etc/apt/sources.list.d/foo.list
[11] $ /usr/lib/update-notifier/apt-check;echo
0;0
In step 2 I have a system where the apt-check command works.
Steps 3 and 4 creates a file that is unreadable by the current user.
Step 5 shows apt-check printing an error message. (This isn't pretty, as
it contains no newlines, but it works.)
In step 6, I run apt-get update. Afterwards, in step 7, the apt-check
command no longer gives an error message. Instead, it crashes.
Step 8 and 9 shows that setting the permissions so that the file
is readable is enough to make apt-check work.
Step 10 and 11 shows that removing the unreadable file also
makes apt-cehck work. (This actually works even if you skip
step 8 and 9 as well.)
Yours,
/ceder
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