By default settings unattended-upgrade does not automatically remove kernel packages that become unused in conjunction with updating by other software

Can you please talk us through exactly how to reproduce the issue?
I have used u-u with a wide variety of other apt frontends in 16.04 without seeing that problem yet.

Install each kernel update by update-manager and notice no kernels will be automatically removed by U-U.

It seems like the bug occured here:
http://askubuntu.com/q/827114/21005

Status changed to 'Confirmed' because the bug affects multiple users.

I find that on most times the bug occurs, but not always. Though it has caused me some problems before with /boot filling up and me being forced to manually remove the old kernels.

Nikita, what do you mean by that it does not occur always?

I run /etc/kernel/postinst.d/apt-auto-removal on each boot. That also makes the "Unattended-Upgrade::Remove-New-Unused-Dependencies" setting not work.
(See Bug #1615381.)

A fix could be adding line
Unattended-Upgrade::Remove-Unused-Dependencies "true";
in /etc/apt/apt.conf.d/50unattended-upgrades
But does it remove too many packages? Why was
Unattended-Upgrade::Remove-New-Unused-Dependencies "true";
setting ever added?

Besides:
If you do not want automatic updates, but just automatic removal of unnecessary software including kernels, you could have 'Download and install updates automatically' set, but edit /etc/apt/apt.conf.d/50unattended-upgrades to have only comments within Unattended-Upgrade::Allowed-Origins section.

@Jarno: IMO Unattended-Upgrade::Remove-Unused-Dependencies is already a risky option and I don't recommend enabling it because it may remove packages which are not used according the to package-dependency chain but which users rely on using software that is not packaged.
The only place I would use this option are dedicated server systems where everything is packaged and which run services only without allowing user shell/GUI logins.

This bug is about removing packages which became unused as a result of running other package management tools, not u-u.

I consider this out of scope for u-u because it can be solved easily by the used other package management tool and this feature will most likely unpleasantly surprise users by removing unexpected packages.

I suggest marking that bug as Won't Fix.

Added update-manager as affected package because update-manager is the tool leaving newly unused packages around.

rbalint, user could mark such packages as manually installed (by apt-mark), so autoremove will not remove them.

If you mark update-manager affected, you should mark other updaters, too. E.g. 'apt full-upgrade' or Synaptic will not remove newly unused packages, right?

I think less advanced users do not install software that is not packaged. Advanced users can configure system to work as they wish. IMO currently Unattended-Upgrade::Remove-New-Unused-Dependencies is more risky as default.

@Jarno I added update-manager based on my experience with (less experienced) users, who kept their system up-to-date by saying yes to everything regarding updates which popped up on their system.

They never touched apt or synaptic nor installed packages by themselves by other means.

I think removing newly unused packages would be a reasonable default for u-u and update-manager.

I agree that Remove-New-Unused-Dependencies=true is riskier than having it disabled but it still removes a subset of what Remove-Unused-Dependencies=true would thus Remove-Unused-Dependencies=true would be more risky.

Remove-New-Unused-Dependencies=true is needed to clean up old kernel packages filling up /boot (and the whole disk).
If update-manager defaults to that by default, too, the system won't break itself.

I think removing "newly unused" packages is an ugly hack. Deciding which packages are excessive or unneeded should not depend on how some packages were removed previously. If the reason for this automatic remove thing is to get rid of excessive kernels, a specific tool for that could be used. I have written such a tool. It is called linux-purge (https://launchpad.net/linux-purge)

I meant deciding which packages are excessive or unneeded should be possible also after upgrading, not only in conjunction with upgrading.

I still do not get it why advanced users could not make sure the packages needed by their not packaged software is not marked as manually installed.

Minus last "not"

Anyway, it would be good, if other software could optionally remove new unused packages.
I do not consider Unattended-Upgrade::Remove-New-Unused-Dependencies as an reasonable default option for unattended-upgrades before the feature has been released for at least apt, update-manager, gnome-software and possible other related software installed by default.

E.g. Apt could have --autoremove-new option which would work with apt and apt-get

I found the description somewhat confusing because 'Unattended-Upgrade::Remove-New-Unused-Dependencies "true"; doesn't actually exist in /etc/apt/apt.conf.d/50unattended-upgrades, rather that's the default setting in unattended-upgrades since 0.90. Regardless, I was able to recreate the issue on an Ubuntu 16.04 system via the following procedure.

1) Use apt-get install to install a new kernel (linux-image-generic)
2) Run unattended-upgrades (observe "no pending auto-removals")

However, running 'sudo apt autoremove' does want to remove an old kernel.

Brian, however, as you installed the kernel by apt-get install, the kernel becomes manually installed, and will not later be removed by 'sudo apt autoremove', unless you change it to be marked as automatically installed.

I question the use of 'sudo apt autoremove' in this case. If its action was the desired one, setting
Unattended-Upgrade::Remove-Unused-Dependencies "false";
would be the setting to use, instead of the current default
Unattended-Upgrade::Remove-New-Unused-Dependencies "true";
Balint Reczey tries to explain in #11 why that setting is not desired.

On Thu, Sep 21, 2017 at 02:03:41PM -0000, Jarno Suni wrote:
> Brian, however, as you installed the kernel by apt-get install, the
> kernel becomes manually installed, and will not later be removed by
> 'sudo apt autoremove', unless you change it to be marked as
> automatically installed.

No, this is not the behavior I observed. After installing a new kernel
version via update-manager or 'sudo apt-get install' on Ubuntu 16.04, 'sudo
apt autoremove' does the right thing and wants to remove my third newest
kernel.

--
Brian Murray

It will remove the third newest kernel, but later, when the one you installed by "apt install" will become third newest, it will not be removed automatically. That is by design.

Anyway, in my view
Unattended-Upgrade::Remove-Unused-Dependencies "true";
would be the default setting to have now, and advanced users should mark the dependencies of their unpackaged software as "manual".

The get_auto_removable function in unattended-ugprades just checks to see if the package has the "is_auto_removable" flag set. So setting "Unattended-Upgrade::Remove-Unused-Dependencies" to "true" will produce the same outcome as using "sudo apt autoremove" e.g.:

bdmurray@clean-xenial-amd64:~$ sudo apt autoremove
[sudo] password for bdmurray:
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  libllvm3.8 libmircommon5 libsnapd-glib1 linux-headers-4.4.0-31 linux-headers-4.4.0-31-generic linux-image-4.4.0-31-generic
  linux-image-extra-4.4.0-31-generic snap-confine snapd-login-service ubuntu-core-launcher

bdmurray@clean-xenial-amd64:~$ sudo unattended-upgrade --dry-run
/usr/bin/dpkg --status-fd 9 --force-depends --remove libllvm3.8:amd64 libmircommon5:amd64 snapd-login-service:amd64 libsnapd-glib1:amd64 linux-headers-4.4.0-31-generic:amd64 linux-headers-4.4.0-31:all linux-image-extra-4.4.0-31-generic:amd64 linux-image-4.4.0-31-generic:amd64 snap-confine:amd64 ubuntu-core-launcher:amd64
/usr/bin/dpkg --status-fd 11 --configure --pending

So I think the question here is whether or not we think it is safe to run autoremovals without user interaction.

@Balint re "@Jarno: IMO Unattended-Upgrade::Remove-Unused-Dependencies is already a risky option and I don't recommend enabling it because it may remove packages which are not used according the to package-dependency chain but which users rely on using software that is not packaged."

Could you give me an example of how people would install dependencies for software that is not package that would also set the "is_auto_removable" flag in the apt cache to True? I can't think of a situation like this.

On Wed, Sep 27, 2017 at 1:49 PM, Brian Murray <email address hidden> wrote:
> @Balint re "@Jarno: IMO Unattended-Upgrade::Remove-Unused-Dependencies
> is already a risky option and I don't recommend enabling it because it
> may remove packages which are not used according the to package-
> dependency chain but which users rely on using software that is not
> packaged."
>
> Could you give me an example of how people would install dependencies
> for software that is not package that would also set the
> "is_auto_removable" flag in the apt cache to True? I can't think of a
> situation like this.

I had the opposite situation in my mind. People would remove packages
which are not auto removable, like ubuntu-desktop (for example because
something ubuntu-desktop depends on is acting badly) and then many
package in ubuntu-desktop's dependency change become auto removable:

$ sudo apt-get remove ubuntu-desktop
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  a11y-profile-manager-indicator activity-log-manager adium-theme-ubuntu
  aisleriot app-install-data-partner apturl apturl-common baobab bluez-cups
...
  xorg
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  ubuntu-desktop
0 upgraded, 0 newly installed, 1 to remove and 7 not upgraded.
After this operation, 46,1 kB disk space will be freed.
Do you want to continue? [Y/n]

It is a simpler problematic situation than the one I originally mentioned, u-u
would remove software which is probably in use, no additional software is
broken.

Hmm, I thought we would not do that anymore, and packages get marked as manual when removing a meta package, but I might be missing something.

On Wed, Sep 27, 2017 at 2:42 PM, Julian Andres Klode
<email address hidden> wrote:
> Hmm, I thought we would not do that anymore, and packages get marked as
> manual when removing a meta package, but I might be missing something.

I ran this on zesty, but if meta packages are handled differently then
I could imagine a similar
case when meta packages are not involved.

On Wed, Sep 27, 2017 at 08:36:13PM -0000, Balint Reczey wrote:
> On Wed, Sep 27, 2017 at 2:42 PM, Julian Andres Klode
> <email address hidden> wrote:
> > Hmm, I thought we would not do that anymore, and packages get marked as
> > manual when removing a meta package, but I might be missing something.
>
> I ran this on zesty, but if meta packages are handled differently then
> I could imagine a similar
> case when meta packages are not involved.

I ran the same metapackage removal test on Xenial, so if Julian is right
and this is a regression its a rather old one. Do you have any more
details about your thoughts Julian?

--
Brian Murray

There were like 3 versions of metapackage auto removal, I don't remember exactly.

I think in the beginning, we just autoremovef everything.

Then we did not mark packages as automatically installed if installed by a meta package.

Then we moved to moving the auto bit on uninstall, but maybe only if the meta is removed due to a conflict, and not when manually.

I only followed this on the sidelines.

Well this does work in Trusty, Ubuntu 14.04, perhaps this is a regression in support "Never-MarkAuto-Sections"?

One thing to note is that using 'apt-mark' I saw that vino was marked as manual on Ubuntu 14.04, but automatic on Ubuntu 16.04.

I reported bug 1721364 regarding the Never-MarkAuto-Sections issue.

Changed to title to reflect that the issue is not about something not implemented, but something not set as default.

s/to title/the title/

Status changed to 'Confirmed' because the bug affects multiple users.

Observe #1267059 about 'Unattended-Upgrade::Remove-Unused-Dependencies' not working as expected for old versions of unattended-upgrades, also resulting e.g. in obsolete kernel packages not getting removed.

I'm working on removing old kernels in u-u and also make the similar changes to update-manager: https://github.com/mvo5/unattended-upgrades/pull/97

This bug was fixed in the package unattended-upgrades - 1.0ubuntu1

---------------
unattended-upgrades (1.0ubuntu1) bionic; urgency=medium

  * Merge from Debian unstable
    - Remaining changes:
      - unattended-upgrades: Do not automatically upgrade the development
        release of Ubuntu unless Unattended-Upgrade::DevRelease is true.
    - Dropped changes, included in Debian:
      - Run upgrade-between-snapshots only on amd64.
        The test exercises only unattented-upgrade's Python code and uses
        dependencies from the frozen Debian snapshot archive thus running
        it on all architectures would provide little benefit.

unattended-upgrades (1.0) unstable; urgency=medium

  [ Simon Arlott ]
  * Revert sending mails on WARNINGS when in MailOnlyOnError mode"
  * Consider conffile prompts to be errors (Closes: #852465)
    Flag packages that have to be upgraded manually because of a conffile
    prompt and consider this to be an error when sending email or exiting.

  [ Simon McVittie ]
  * Add python, python3, setuptools, DistutilsExtra to Build-Depends.
    They are needed for `clean`, so Build-Depends-Indep is not enough.
  * Add .gitignore and debian/.gitignore
  * Remove bzr configuration.
    This is unnecessary now that u-u is in git.

  [ Michael Vogt ]
  * unattended-upgrades: tweak mail-on-warnings PR
  * unattended-upgrade: extract is_autoremove_valid helper

  [ Balint Reczey ]
  * Run upgrade-between-snapshots only on amd64.
    The test exercises only unattented-upgrade's Python code and uses
    dependencies from the frozen Debian snapshot archive thus running
    it on all architectures would provide little benefit.
  * Clean up processes started for getting md5 sums
  * Don't keep /var/lib/dpkg/status open multiple times
  * Adjust candidates in UnattendedUpgradesCache.open()
  * Perform autoremovals in minimal steps, too.
    Also add check to remove only the set of packages selected for autoremoval.
    Without that check unattended-upgrades when (by default) configured to
    remove newly unused packages could also remove auto removable packages
    which were unused before starting starting the upgrade step.
  * Remove unused automatically installed kernel packages
    (LP: #1357093, #1624644, #1675079, #1698159)
  * Stop including Python syntax in the report (Closes: #876796)
  * Do not auto remove packages related to the running kernel (LP: #1615381)
  * Check packages to be autoremoved against blacklists, whitelists.
    Also check if the packages are held.
  * Report package removals in the summary email (Closes: #876797)
  * Run upgrade-between-snapshots test with debugging enabled
  * Don't create new UnattendedUpgradesCache for checking for autoremovals
    .open() refreshes the state in each cache_commit(), this is enough
  * Update .pot and .po files
  * Update .travis.yml to actually build and test u-u from the repo
  * Run only a simple installation test on Travis, the system upgrade
    test was always failing

 -- Balint Reczey <email address hidden> Thu, 01 Mar 2018 17:29:33 +0700

This bug was fixed in the package update-manager - 1:18.04.9

---------------
update-manager (1:18.04.9) bionic; urgency=medium

  * Keep PEP 8 checks happy

 -- Balint Reczey <email address hidden> Wed, 21 Mar 2018 17:53:59 +0000

Please fill in the Impact, Test Case and Regression Potential fields of the SRU recommended bug description [1]. Thank you!

[1] https://wiki.ubuntu.com/StableReleaseUpdates#SRU_Bug_Template

Hello Jarno, or anyone else affected,

Accepted update-manager into artful-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/update-manager/1:17.10.14 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed.Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested and change the tag from verification-needed-artful to verification-done-artful. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-artful. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance!

Hello Jarno, or anyone else affected,

Accepted update-manager into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/update-manager/1:16.04.13 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed.Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested and change the tag from verification-needed-xenial to verification-done-xenial. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-xenial. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance!

Testing is painfully slow because connection to e.g. archive.canonical.com is very slow.

Downgrading in step 2 does not work without --allow-downgrades

Brian, I tested the update-manager version you told. It is true that update-manager removes the unused packages, but step 3. (unattended-upgrades) does not remove the unused kernels.

I add failed tag as this bug is originally about unattended-upgrades.

On Fri, Mar 30, 2018 at 3:12 PM, Jarno Suni <email address hidden> wrote:
> Brian, I tested the update-manager version you told. It is true that
> update-manager removes the unused packages, but step 3. (unattended-
> upgrades) does not remove the unused kernels.
>
> I add failed tag as this bug is originally about unattended-upgrades.

Thanks for testing the fix and also thank you for preparing the
linux-purge script. I read it but integrating it to to current tools
would have been problematic and I hope you agree that the solution
finally used is minimally intrusive and achieves removing unused
kernels in a safe way.

The fix for unattended-upgrades is not uploaded yet but is available
Bionic and in the ppa:rbalint/scratch PPA if you would like to give it
a try.

Yes, it is good that update-manager can do removing, as that is what most people use anyway. linux-purge might still have some use e.g. if for some reason /boot becomes full, or there are non-autoremovable kernel packages (which may happen in 14.04 even with kernels installed using update-manager Bug #1439769).

@jarnos Verification is needed only for update-manager for now, thus I think you verified that the fix worked for Xenial. Could you please change the tag to reflect that or you would like to wait for the u-u fix, - which may come later?

Can anyone potentially perform verification of the artful packages? We usually prefer releasing packages for newer series first, although it's not really a big deal right now because xenial -> artful is not an official upgrade path anymore.

Verified update-manager for artful.

This bug was fixed in the package update-manager - 1:16.04.13

---------------
update-manager (1:16.04.13) xenial; urgency=medium

  * Offer removal of unused autoremovable kernel packages
    (LP: #1624644, #1675079)
  * Support package removals in install backends and really remove packages
    (LP: #1624644, #1675079)
  * Keep PEP 8 checks happy
  * Place .keep files in empty directories to keep them when converting the
    repo to git (LP: #1758963)

 -- Balint Reczey <email address hidden> Sun, 25 Mar 2018 20:10:49 +0100

The verification of the Stable Release Update for update-manager has completed successfully and the package has now been released to -updates. Subsequently, the Ubuntu Stable Release Updates Team is being unsubscribed and will not receive messages about this bug report. In the event that you encounter a regression using the package from -updates please report a new bug using ubuntu-bug and tag the bug report regression-update so we can easily find any regressions.

This bug was fixed in the package update-manager - 1:17.10.14

---------------
update-manager (1:17.10.14) artful; urgency=medium

  * Offer removal of unused autoremovable kernel packages
    (LP: #1624644, #1675079)
  * Support package removals in install backends and really remove packages
    (LP: #1624644, #1675079)
  * Keep PEP 8 checks happy
  * Place .keep files in empty directories to keep them when converting the
    repo to git (LP: #1758963)

 -- Balint Reczey <email address hidden> Sun, 25 Mar 2018 19:57:57 +0100

Hello Jarno, or anyone else affected,

Accepted unattended-upgrades into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/unattended-upgrades/1.1ubuntu1.18.04.7~16.04.0 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested and change the tag from verification-needed-xenial to verification-done-xenial. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-xenial. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Hello Jarno, or anyone else affected,

Accepted unattended-upgrades into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/unattended-upgrades/1.1ubuntu1.18.04.7~16.04.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested and change the tag from verification-needed-xenial to verification-done-xenial. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-xenial. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Hello Jarno, or anyone else affected,

Accepted unattended-upgrades into xenial-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/unattended-upgrades/1.1ubuntu1.18.04.7~16.04.2 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested and change the tag from verification-needed-xenial to verification-done-xenial. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-xenial. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

Tested with 1.1ubuntu1.18.04.7~16.04.2 on Xenial:

root@x-uu-lp-1260041:~# apt-mark auto linux-image-extra-4.8.0-56-generic linux-image-extra-4.8.0-58-generic linux-image-extra-4.8.0-54-generic linux-image-extra-4.8.0-53-generic
linux-image-extra-4.8.0-56-generic set to automatically installed.
linux-image-extra-4.8.0-58-generic set to automatically installed.
linux-image-extra-4.8.0-54-generic set to automatically installed.
linux-image-extra-4.8.0-53-generic set to automatically installed.
root@x-uu-lp-1260041:~# unattended-upgrade --verbose
Initial blacklisted packages:
Initial whitelisted packages:
Starting unattended upgrades script
Allowed origins are: o=Ubuntu,a=xenial, o=Ubuntu,a=xenial-security, o=UbuntuESM,a=xenial, o=Ubuntu,a=xenial-updates
Removing unused kernel packages: linux-image-extra-4.8.0-54-generic linux-image-4.8.0-54-generic
Keeping auto-removable linux-image-extra-4.8.0-54-generic package(s) because it would also remove the following packages which should be kept in this step: libpam-systemd libsystemd0 libudev1 systemd systemd-sysv udev
(Reading database ... 53554 files and directories currently installed.)
Removing linux-image-extra-4.8.0-54-generic (4.8.0-54.57~16.04.1) ...
run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
run-parts: executing /etc/kernel/postinst.d/initramfs-tools 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
update-initramfs: Generating /boot/initrd.img-4.8.0-54-generic
W: mdadm: /etc/mdadm/mdadm.conf defines no arrays.
run-parts: executing /etc/kernel/postinst.d/unattended-upgrades 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
run-parts: executing /etc/kernel/postinst.d/update-notifier 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
run-parts: executing /etc/kernel/postinst.d/zz-update-grub 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
Removing linux-image-4.8.0-54-generic (4.8.0-54.57~16.04.1) ...
Examining /etc/kernel/postrm.d .
run-parts: executing /etc/kernel/postrm.d/initramfs-tools 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
update-initramfs: Deleting /boot/initrd.img-4.8.0-54-generic
run-parts: executing /etc/kernel/postrm.d/zz-update-grub 4.8.0-54-generic /boot/vmlinuz-4.8.0-54-generic
Packages that were successfully auto-removed: linux-image-4.8.0-54-generic linux-image-extra-4.8.0-54-generic
Packages that are kept back: linux-image-extra-4.8.0-54-generic
Packages that will be upgraded: libpam-systemd libsystemd0 libudev1 systemd systemd-sysv udev
Writing dpkg log to /var/log/unattended-upgrades/unattended-upgrades-dpkg.log
(Reading database ... 47681 files and directories currently installed.)
Preparing to unpack .../systemd-sysv_229-4ubuntu21.17_amd64.deb ...
Unpacking systemd-sysv (229-4ubuntu21.17) over (229-4ubuntu21.16) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up systemd-sysv (229-4ubuntu21.17) ...
Log ended: 2019-03-13 17:17:36

Log started: 2019-03-13 17:17:36
(Reading database ... 47681 files and directories currently installed.)
Preparing to unpack .../udev_229-4ubuntu21.17_amd64.deb ...
Unpacking udev (229-4ubuntu21.17) over (229-4ubuntu21.16) ...
Preparing to unpack .../libudev1_229-4ubunt...

rbalint, in the output there is some oddity:
"Keeping auto-removable linux-image-extra-4.8.0-54-generic package(s) because it would also remove the following packages which should be kept in this step: libpam-systemd libsystemd0 libudev1 systemd systemd-sysv udev
(Reading database ... 53554 files and directories currently installed.)
Removing linux-image-extra-4.8.0-54-generic (4.8.0-54.57~16.04.1) ..."

So it says it is keeping linux-image-extra-4.8.0-54-generic and right thereafter it is removing the same package.

@rbalint about your test case: I wonder why linux-image-4.8.0-53-generic was not removed by u-u? Was it the booted kernel? You also did not run 'sudo /etc/kernel/postinst.d/apt-auto-removal' before running u-u. Your test case does not show how the kernels were installed.

In the following, I show the extraction of terminal output of a more complete test case for u-u. It installs linux-image-extra-4.4.0-141-generic by apt. Output of 'apt autoremove --simulate' shows it would remove the kernel, and one unneeded package that is not a kernel related. Whereas u-u just removes the kernel (which may be the expected behavior).

$ set -x; sudo apt install -y unattended-upgrades/xenial-proposed linux-image-extra-4.4.0-141-generic; sudo apt-mark auto linux-image-extra-4.4.0-141-generic; sudo /etc/kernel/postinst.d/apt-auto-removal; apt autoremove --simulate; sudo unattended-upgrade -v; set +x
+ sudo apt install -y unattended-upgrades/xenial-proposed linux-image-extra-4.4.0-141-generic
Reading package lists... Done
Building dependency tree
Reading state information... Done
unattended-upgrades is already the newest version (1.1ubuntu1.18.04.7~16.04.2).
Selected version '1.1ubuntu1.18.04.7~16.04.2' (Ubuntu:16.04/xenial-proposed [all]) for 'unattended-upgrades'
The following package was automatically installed and is no longer required:
  xscreensaver-data
Use 'sudo apt autoremove' to remove it.
Suggested packages:
  fdutils linux-doc-4.4.0 | linux-source-4.4.0 linux-tools linux-headers-4.4.0-141-generic
The following NEW packages will be installed:
  linux-image-4.4.0-141-generic linux-image-extra-4.4.0-141-generic
0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded.
Need to get 58,7 MB of archives.
After this operation, 224 MB of additional disk space will be used.
Get:1 http://ubuntu.mirror.true.nl/ubuntu xenial-updates/main amd64 linux-image-4.4.0-141-generic amd64 4.4.0-141.167 [22,2 MB]
Get:2 http://ubuntu.mirror.true.nl/ubuntu xenial-updates/main amd64 linux-image-extra-4.4.0-141-generic amd64 4.4.0-141.167 [36,5 MB]
Fetched 58,7 MB in 26s (2 233 kB/s)
Selecting previously unselected package linux-image-4.4.0-141-generic.
(Reading database ... 332942 files and directories currently installed.)
Preparing to unpack .../linux-image-4.4.0-141-generic_4.4.0-141.167_amd64.deb ...
Examining /etc/kernel/preinst.d/
run-parts: executing /etc/kernel/preinst.d/intel-microcode 4.4.0-141-generic /boot/vmlinuz-4.4.0-141-generic
Done.
Unpacking linux-image-4.4.0-141-generic (4.4.0-141.167) ...
Selecting previously unselected package linux-image-extra-4.4.0-141-generic.
Preparing to unpack .../linux-image-extra-4.4.0-141-generic_4.4.0-141.167_amd64.deb ...
Unpacking linux-image-extra-4.4.0-141-generic (4.4.0-141.167) ...
Setting up linux-image-4.4.0-141-generic (4.4.0-141.167) ...
Running depmod.
update-initramfs: deferring update (hook will be called later)
Examining /etc/kernel/postinst.d.
run-parts: executing /etc/kernel/postinst.d/apt-auto-removal 4.4.0-141-generic /boot/vmlinuz-4.4.0-141-generic
run-parts: executing /etc/kernel/postinst.d/dkms 4.4.0-14...

@jarnos #61
this is a separate issue fixed later, calculating upgradable packages leaves the upgradable packages in the cache, and u-u counts them as the reverse dependencies of the first kernel to be removed.
This keeps the first kernel on the system, but when there are no upgradable packages in a later run this kernel can be removed, too.

See:
https://github.com/mvo5/unattended-upgrades/commit/93d43fbcd53c5df5ce69a16b26a981bf06ce3085
https://github.com/mvo5/unattended-upgrades/commit/654898b05c933047ca8c97df655743aab0898db1
https://github.com/mvo5/unattended-upgrades/commit/1a39eb257ad786902de11add212879241919be44

In this particular case -extra was detected not autoremovable because of the dirty cache, but it was successfully removed when trying to remove linux-image-4.8.0-54-generic.
The printout is confusing indeed, but no harm was done, since only valid autoremovals were performed.

This bug was fixed in the package unattended-upgrades - 1.1ubuntu1.18.04.7~16.04.2

---------------
unattended-upgrades (1.1ubuntu1.18.04.7~16.04.2) xenial; urgency=medium

  * Don't check blacklist too early and report updates from not allowed origins
    as kept back. (LP: #1781176)
  * test/test_blacklisted_wrong_origin.py: Fix and enable test
  * Filter out progress indicator from dpkg log (LP: #1599646)
  * Clear cache when autoremoval fails (LP: #1779157)
  * Find autoremovable kernel packages using the patterns in APT's way
    (LP: #1815494)

unattended-upgrades (1.1ubuntu1.18.04.7~16.04.1) xenial; urgency=medium

  * Start service after systemd-logind.service to be able to take inhibition
    lock (LP: #1806487)
  * Handle gracefully when logind is down (LP: #1806487)

unattended-upgrades (1.1ubuntu1.18.04.7~16.04.0) xenial; urgency=medium

  * Backport to Xenial (LP: #1702793)
  * Revert to build-depending on debhelper (>= 9~) and dh-systemd
  * Revert configuration example changes to avoid triggering a debconf question
  * debian/postinst: Update recovery to be triggered on Xenial's package versions

unattended-upgrades (1.1ubuntu1.18.04.7) bionic; urgency=medium

  * Trigger unattended-upgrade-shutdown actions with PrepareForShutdown()
    Performing upgrades in service's ExecStop did not work when the upgrades
    involved restarting services because systemd blocked other stop/start
    actions making maintainer scripts time out and be killed leaving a broken
    system behind.
    Running unattended-upgrades.service before shutdown.target as a oneshot
    service made it run after unmounting filesystems and scheduling services
    properly on shutdown is a complex problem and adding more services to the
    mix make it even more fragile.
    The solution of monitoring PrepareForShutdown() signal from DBus
    allows Unattended Upgrade to run _before_ the jobs related to shutdown are
    queued thus package upgrades can safely restart services without
    risking causing deadlocks or breaking part of the shutdown actions.
    Also ask running unattended-upgrades to stop when shutdown starts even in
    InstallOnShutdown mode and refactor most of unattended-upgrade-shutdown to
    UnattendedUpgradesShutdown class. (LP: #1778219)
  * Increase logind's InhibitDelayMaxSec to 30s. (LP: #1778219)
    This allows more time for unattended-upgrades to shut down gracefully
    or even install a few packages in InstallOnShutdown mode, but is still a
    big step back from the 30 minutes allowed for InstallOnShutdown previously.
    Users enabling InstallOnShutdown node are advised to increase
    InhibitDelayMaxSec even further possibly to 30 minutes.
    - Add NEWS entry about increasing InhibitDelayMaxSec and InstallOnShutdown
      changes
  * Ignore "W503 line break before binary operator"
    because it will become the best practice and breaks the build
  * Stop using ActionGroups, they interfere with apt.Cache.clear()
    causing all autoremovable packages to be handled as newly autoremovable
    ones and be removed by default. Dropping ActionGroup usage does not slow
    down the most frequent case of not having anything to upgrade a...