I'm on Debian 9.3 32 bit stable. Today I started encountering the following issue.

I updated and fully upgraded the system (ffmpeg + some attendant libraries; about 10 packages). All went smoothly, but now

apt upgrade
apt full-upgrade
apt-get upgrade
apt-get dist-upgrade
apt autoremove

all show

0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded

Aptitude shows no packages marked for upgrading, 'dpkg --audit' returns with exit code 0, 'apt update' says everything's up to date, 'dpkg -l' returns only packages marked 'ii' (I've grepped for anything *not* starting with 'ii' with no results).

Is there any way to figure out which package dpkg is dropping the ball on?

Edit: I forgot to mention, 'apt-mark showhold' returns nothing (i.e. no held packages).

What's the output of

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Ah, that's yet more info I forgot to add: I'd tried that with no hits. So that command returns nothing. Well, to be precise, it returns

Listing... Done

and nothing else.

Interesting.
Did you check apt-get logs? Usually located at /var/log/apt/term.log

Sure did, but I'm giving that file another go as we speak.

Nothing looks suspicious though. I can see all of the activity for the day, some packages installed, some removed / purged, etc. I recognize what's logged and I don't see any warnings, errors, and so on. Nor did I get any throughout the day while undergoing all of this; I just happened to notice the stray '1' by accident under 'not upgraded' when running autoremove.

If I could somehow increase the verbosity of the commands I listed (which return the errant '1') perhaps that would help, but the closest I can get to 'verbose' looking through the apt / apt-get man pages is the -V flag for apt-get, and running either

apt-get -V autoremove
or
apt-get -V dist-upgrade

makes no difference (same '1 not upgraded' message).

Strange. Well that's about as far as I can take you. I've never experienced that problem before. Hopefully someone else may have another suggestion of where to look.

You don't mention any loss of functionality, so hopefully you will be good until it gets resolved. Good luck!

No worries at all, it's much appreciated regardless!

Oh, yes, as far as I can tell it's all in good order, just somewhat strange. It'd be interesting to get to the bottom of it, but it doesn't seem to have affected functionality thus far.

All right, tracked down the issue:

A few days back I installed a package from source with checkinstall because the newer upstream version fixed a bug in Debian's version. I then pinned that package to pin priority -1 in /etc/apt/preferences.d/preferences so Debian wouldn't downgrade it to its own version.

I then apparently promptly forgot about it.. I also seem to have never run 'apt autoremove' after those changes, so was not familiar with the apt behavior under the circumstances.

I tested that this was the problem by removing the package; sure enough, the '1 not upgraded' went away. I've since re-installed it, now that I know this is normal behavior.

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