OK, the reason this happens is that some of your key files are not
readable (I'm not sure, but it might be running as _apt). The commit
mentioned introduced a regresssion in that it does not ignore failures
from unreadable key files.

This was fixed in 1.3~rc3 in commit
105503b4b470c124bc0c271bd8a50e25ecbe9133. I cherry-picked that change in
my for-1.2/apt-key branch in https://github.com/julian-klode/apt.

You should be able to verify this by adding -o Dir::Bin::Apt-
Key="$PWD/build/bin/apt-key" to the apt-get invocation in the script and
then running it once with the normal 1.2.y branch and once with my
for-1.2/apt-key branch.

The test suite currently fails, as the new tests added depend on some
other changes, once I got those merged I can upload it as 1.2.17 (1.2.16
is already in the unapproved queue for -proposed, it fixes bugs with
localized strings in protocols).

** Also affects: apt (Ubuntu Xenial)
   Importance: Undecided
       Status: New

** Changed in: apt (Ubuntu Xenial)
       Status: New => Triaged

** Changed in: apt (Ubuntu)
       Status: New => Fix Released

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