apt-get autoremove not removing old kernels when package virtualbox-5.1 is installed

[thermoman]

'apt-get autoremove` does not remove old 'linux-image-*` packages as long as virtualbox-5.1 package is installed on system.

% cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04.1 LTS"

% lsb_release -rd
Description: Ubuntu 16.04.1 LTS
Release: 16.04

% apt-cache policy apt
apt:
  Installed: 1.2.12~ubuntu16.04.1
  Candidate: 1.2.12~ubuntu16.04.1

There are 7 different kernel versions installed
===============================================

% dpkg -l | grep linux-im | cut -c 1-80
ii linux-image-4.4.0-31-generic 4.4.0-31.50
ii linux-image-4.4.0-34-generic 4.4.0-34.53
ii linux-image-4.4.0-36-generic 4.4.0-36.55
ii linux-image-4.4.0-38-generic 4.4.0-38.57
ii linux-image-4.4.0-42-generic 4.4.0-42.62
ii linux-image-4.4.0-43-generic 4.4.0-43.63
ii linux-image-4.4.0-45-generic 4.4.0-45.66
ii linux-image-extra-4.4.0-43-generic 4.4.0-43.63
ii linux-image-extra-4.4.0-45-generic 4.4.0-45.66
ii linux-image-generic 4.4.0.45.48

% ls -1 /boot/vmlinuz-*
/boot/vmlinuz-4.4.0-31-generic
/boot/vmlinuz-4.4.0-34-generic
/boot/vmlinuz-4.4.0-36-generic
/boot/vmlinuz-4.4.0-38-generic
/boot/vmlinuz-4.4.0-42-generic
/boot/vmlinuz-4.4.0-43-generic
/boot/vmlinuz-4.4.0-45-generic

Running kernel
==============

% uname -r
4.4.0-43-generic

Only 4.4.0-43 and 4.4.0-45 protected from autoremove
====================================================

% cat /etc/apt/apt.conf.d/01autoremove-kernels
// DO NOT EDIT! File autogenerated by /etc/kernel/postinst.d/apt-auto-removal
APT::NeverAutoRemove
{
   "^linux-image-4\.4\.0-43-generic$";
   "^linux-image-4\.4\.0-45-generic$";
   "^linux-headers-4\.4\.0-43-generic$";
   "^linux-headers-4\.4\.0-45-generic$";
   "^linux-image-extra-4\.4\.0-43-generic$";
   "^linux-image-extra-4\.4\.0-45-generic$";
   "^linux-signed-image-4\.4\.0-43-generic$";
   "^linux-signed-image-4\.4\.0-45-generic$";
   "^kfreebsd-image-4\.4\.0-43-generic$";
   "^kfreebsd-image-4\.4\.0-45-generic$";
   "^kfreebsd-headers-4\.4\.0-43-generic$";
   "^kfreebsd-headers-4\.4\.0-45-generic$";
   "^gnumach-image-4\.4\.0-43-generic$";
   "^gnumach-image-4\.4\.0-45-generic$";
   "^.*-modules-4\.4\.0-43-generic$";
   "^.*-modules-4\.4\.0-45-generic$";
   "^.*-kernel-4\.4\.0-43-generic$";
   "^.*-kernel-4\.4\.0-45-generic$";
   "^linux-backports-modules-.*-4\.4\.0-43-generic$";
   "^linux-backports-modules-.*-4\.4\.0-45-generic$";
   "^linux-tools-4\.4\.0-43-generic$";
   "^linux-tools-4\.4\.0-45-generic$";
};
/* Debug information:
# dpkg list:
ii linux-image-4.4.0-31-generic 4.4.0-31.50 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-34-generic 4.4.0-34.53 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-36-generic 4.4.0-36.55 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-38-generic 4.4.0-38.57 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-42-generic 4.4.0-42.62 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-43-generic 4.4.0-43.63 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-4.4.0-45-generic 4.4.0-45.66 amd64 Linux kernel image for version 4.4.0 on 64 bit x86 SMP
ii linux-image-extra-4.4.0-43-generic 4.4.0-43.63 amd64 Linux kernel extra modules for version 4.4.0 on 64 bit x86 SMP
iF linux-image-extra-4.4.0-45-generic 4.4.0-45.66 amd64 Linux kernel extra modules for version 4.4.0 on 64 bit x86 SMP
iU linux-image-generic 4.4.0.45.48 amd64 Generic Linux kernel image
# list of installed kernel packages:
4.4.0-31-generic 4.4.0-31.50
4.4.0-34-generic 4.4.0-34.53
4.4.0-36-generic 4.4.0-36.55
4.4.0-38-generic 4.4.0-38.57
4.4.0-42-generic 4.4.0-42.62
4.4.0-43-generic 4.4.0-43.63
4.4.0-45-generic 4.4.0-45.66
# list of different kernel versions:
4.4.0-45.66
4.4.0-43.63
4.4.0-42.62
4.4.0-38.57
4.4.0-36.55
4.4.0-34.53
4.4.0-31.50
# Installing kernel: 4.4.0-45.66 (4.4.0-45-generic)
# Running kernel: 4.4.0-43.63 (4.4.0-43-generic)
# Last kernel: 4.4.0-45.66
# Previous kernel: 4.4.0-43.63
# Kernel versions list to keep:
4.4.0-43.63
4.4.0-45.66
# Kernel packages (version part) to protect:
4\.4\.0-43-generic
4\.4\.0-45-generic
*/

All marked auto
===============

% apt-mark showauto | grep linux
linux-firmware
linux-headers-4.4.0-31
linux-headers-4.4.0-31-generic
linux-headers-4.4.0-34
linux-headers-4.4.0-34-generic
linux-headers-4.4.0-36
linux-headers-4.4.0-36-generic
linux-headers-4.4.0-38
linux-headers-4.4.0-38-generic
linux-headers-4.4.0-42
linux-headers-4.4.0-42-generic
linux-headers-4.4.0-43
linux-headers-4.4.0-43-generic
linux-headers-4.4.0-45
linux-headers-4.4.0-45-generic
linux-headers-generic
linux-image-4.4.0-31-generic
linux-image-4.4.0-34-generic
linux-image-4.4.0-36-generic
linux-image-4.4.0-38-generic
linux-image-4.4.0-42-generic
linux-image-4.4.0-43-generic
linux-image-4.4.0-45-generic
linux-image-extra-4.4.0-43-generic
linux-image-extra-4.4.0-45-generic
linux-image-generic
linux-libc-dev
linux-sound-base
pptp-linux
syslinux
syslinux-common
syslinux-legacy

% apt-mark showmanual | grep linux
console-setup-linux
libselinux1
linux-base
linux-generic
util-linux

Virtualbox is installed
=======================

% dpkg -l virtualbox-5.1
ii virtualbox-5.1 5.1.8-111374~Ubuntu~xe

Command executed
================

% apt-get autoremove

Expected behaviour
==================

Remove all 'linux-image-X-generic` packages
where X not in (4.4.0-43, 4.4.0-45).

What happens instead
====================

% apt-get autoremove
Reading package lists... Done
Building dependency tree
Reading state information... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

Debugging Info

% apt-get -o Debug::pkgAutoRemove=true autoremove > autoremove_debug.txt 2>&1
(see attachments below this post)

How to fix this? Remove virtualbox-5.1 package
==============================================

% apt-get remove virtualbox-5.1
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
  libqt5x11extras5 linux-headers-4.4.0-31 linux-headers-4.4.0-31-generic linux-headers-4.4.0-34 linux-headers-4.4.0-34-generic linux-headers-4.4.0-36
  linux-headers-4.4.0-36-generic linux-headers-4.4.0-38 linux-headers-4.4.0-38-generic linux-headers-4.4.0-42 linux-headers-4.4.0-42-generic
  linux-image-4.4.0-31-generic linux-image-4.4.0-34-generic linux-image-4.4.0-36-generic linux-image-4.4.0-38-generic linux-image-4.4.0-42-generic
Use 'apt autoremove' to remove them.
The following packages will be REMOVED:
  virtualbox-5.1
0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded.
After this operation, 158 MB disk space will be freed.
Do you want to continue? [Y/n]

How come apt-get will not autoremove old kernel packages as long as virtualbox is installed?

% apt-cache show virtualbox-5.1
Package: virtualbox-5.1
Version: 5.1.8-111374~Ubuntu~xenial
Architecture: amd64
Maintainer: Oracle Corporation <email address hidden>
Installed-Size: 154040
Pre-Depends: debconf (>= 1.1) | debconf-2.0
Depends: libc6 (>= 2.15), libcurl3 (>= 7.16.2), libdevmapper1.02.1 (>= 2:1.02.97), libgcc1 (>= 1:3.0), libgl1-mesa-glx | libgl1, libpng12-0 (>= 1.2.13-4), libpython2.7 (>= 2.7), libqt5core5a (>= 5.5.0), libqt5gui5 (>= 5.3.0) | libqt5gui5-gles (>= 5.3.0), libqt5opengl5 (>= 5.0.2) | libqt5opengl5-gles (>= 5.0.2), libqt5printsupport5 (>= 5.0.2), libqt5widgets5 (>= 5.2.0), libqt5x11extras5 (>= 5.1.0), libsdl1.2debian (>= 1.2.11), libssl1.0.0 (>= 1.0.0), libstdc++6 (>= 5.2), libvpx3 (>= 1.5.0), libx11-6, libxcb1, libxcursor1 (>> 1.1.2), libxext6, libxinerama1, libxml2 (>= 2.7.4), libxmu6, libxt6, zlib1g (>= 1:1.1.4), psmisc, adduser
Recommends: libasound2, libpulse0, libsdl-ttf2.0-0, kmod | kldutils | module-init-tools, linux-headers-generic | linux-headers-generic-pae | linux-headers-686-pae | linux-headers-amd64 | linux-headers-2.6-686 | linux-headers-2.6-amd64 | linux-headers, linux-image, gcc, make | build-essential | dpkg-dev, binutils, pdf-viewer, libgl1
Conflicts: virtualbox, virtualbox-guest-additions-iso, virtualbox-ose
Replaces: virtualbox
Provides: virtualbox
Priority: optional
Section: contrib/misc
Filename: pool/contrib/v/virtualbox-5.1/virtualbox-5.1_5.1.8-111374~Ubuntu~xenial_amd64.deb
Size: 65225770
SHA256: 66d8900d5428aad7e7c955971153d45a2ddb65c113002c33dfa31f80b7f92ec0
SHA1: 78648eb646b0488c01f69f52be89e04e80541db2
MD5sum: ad328e1a7fb5f1e087b145dbcaff7f4e
Description: Oracle VM VirtualBox
 VirtualBox is a powerful PC virtualization solution allowing you to run a
 wide range of PC operating systems on your Linux system. This includes
 Windows, Linux, FreeBSD, DOS, OpenBSD and others. VirtualBox comes with a broad
 feature set and excellent performance, making it the premier virtualization
 software solution on the market.
Description-md5: 914c1338bb9a4b67fae39e48412d76f8
Python-Version: 2.7

[thermoman (thermoman)]

There are no dependencies that would prevent removing these old kernel versions when trying to remove them manually:

% apt-get remove linux-headers-4.4.0-31 linux-headers-4.4.0-31-generic linux-image-4.4.0-31-generic
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages will be REMOVED:
  linux-headers-4.4.0-31 linux-headers-4.4.0-31-generic linux-image-4.4.0-31-generic
0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded.
After this operation, 133 MB disk space will be freed.
Do you want to continue? [Y/n] n
Abort.

This issue is a real pain in the a** because we just rolled out new desktop images to all the people in the company with 300 MB of disk space allocated to /boot and with this many old kernel versions around /boot fills up easily.

[thermoman (thermoman)]

#1605160 might be related

[dino99 (9d9)]

Note:

I suspect that issue is related to the fact that some 'package(s)' (virtualbox in your case) are simply 'removed' (letting their settings still active).

Myself always 'purge' the package when removing them. Virtualbox is also install on a few machines here; and never had apt refusing the autoremoval. That it.

Also seen many users reporting against 'dpkg' (apport choice) most of the time, with a title such "package xxxx failed to install, package is already installed and configured" . I also never had such an issue; so also suspecting old settings left behind, disturbing the autoremoval process.

That said, "apt-get autoremove" should really 'purge' not only 'remove' to avoid a durty system.

[thermoman (thermoman)]

I might have found the cause: bug #1472351

This seems to be the case for my issue with virtualbox and might be the case for bug #1605160 (he has ZFS installed which might have a Recommends tag on linux-headers or linux-image, too).