How report similar to current bug? apt bug symbol _ZN9pkgSystem9LockInnerEvdpkg vs _ZlsRSoRKN3APT9

For diagnostic purposes please provide the output of the commands

uname -a
lsb_release -crid
apt-cache policy apt libapt-pkg5.0

From my broken VM, actual box taken down for security reasons, unable to patch.

# uname -a
Linux 1604VM 4.4.0-138-generic #164-Ubuntu SMP Tue Oct 2 17:16:02 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

# lsb_release -crid
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 LTS
Release: 16.04
Codename: xenial

# apt-cache policy apt libapt-pkg5.0
apt-cache: relocation error: /usr/lib/x86_64-linux-gnu/libapt-private.so.0.0: symbol _ZN9pkgSystem9LockInnerEv, version APTPKG_5.0 not defined in file libapt-pkg.so.5.0 with link time reference

https://forum.zentyal.org/index.php/topic,32403.new.html#new

Ok, the apt-cache command fails, maybe we receive the desired information in a different way:

What is the output of the commands

grep -A 15 'Package: apt$' /var/lib/dpkg/status
grep -A 15 'Package: libapt-pkg5.0$' /var/lib/dpkg/status
cat -n /etc/apt/sources.list

# grep -A 15 'Package: apt$' /var/lib/dpkg/status
Package: apt
Status: install ok installed
Priority: important
Section: admin
Installed-Size: 3350
Maintainer: Ubuntu Developers <email address hidden>
Architecture: amd64
Version: 1.2.29
Replaces: bash-completion (<< 1:2.1-4.2+fakesync1), manpages-it (<< 2.80-4~), ma npages-pl (<< 20060617-3~), openjdk-6-jdk (<< 6b24-1.11-0ubuntu1~), sun-java5-jd k (>> 0), sun-java6-jdk (>> 0)
Depends: libapt-pkg5.0 (>= 1.2.29), libc6 (>= 2.15), libgcc1 (>= 1:3.0), libstdc ++6 (>= 5.2), init-system-helpers (>= 1.18~), ubuntu-keyring, gpgv | gpgv2, gnup g | gnupg2, adduser
Suggests: aptitude | synaptic | wajig, dpkg-dev (>= 1.17.2), apt-doc, python-apt
Breaks: apt-utils (<< 1.1.3), manpages-it (<< 2.80-4~), manpages-pl (<< 20060617 -3~), openjdk-6-jdk (<< 6b24-1.11-0ubuntu1~), sun-java5-jdk (>> 0), sun-java6-jd k (>> 0)
Conffiles:
 /etc/apt/apt.conf.d/01-vendor-ubuntu 5232396660502461fc834c0a1229dbe4
 /etc/apt/apt.conf.d/01autoremove 735050108d38dbf99e933a9f647f6892
 /etc/cron.daily/apt-compat bc4a71cbcaeed4179f25d798257fa980

# grep -A 15 'Package: libapt-pkg5.0$' /var/lib/dpkg/status
Package: libapt-pkg5.0
Status: install ok installed
Priority: important
Section: libs
Installed-Size: 3001
Maintainer: Ubuntu Developers <email address hidden>
Architecture: amd64
Multi-Arch: same
Source: apt
Version: 1.5.1
Provides: libapt-pkg (= 1.5.1)
Depends: libbz2-1.0, libc6 (>= 2.15), libgcc1 (>= 1:3.0), liblz4-1 (>= 0.0~r127), liblzma5 (>= 5.1.1alpha+20120614), libstdc++6 (>= 5.2), libudev1 (>= 183), zlib1g (>= 1:1.2.2.3)
Recommends: apt (>= 1.5.1)
Breaks: appstream (<< 0.9.0-3~), apt (<< 1.1~exp14), libapt-inst1.5 (<< 0.9.9~)
Description: package management runtime library
 This library provides the common functionality for searching and

This last line ends like that.

# cat -n /etc/apt/sources.list
     1 # deb http://gb.archive.ubuntu.com/ubuntu/ xenial main restricted
     2
     3 # deb http://gb.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
     4 # deb http://security.ubuntu.com/ubuntu xenial-security main restricted
     5
     6 # See http://help.ubuntu.com/community/UpgradeNotes for how to upgrade to
     7 # newer versions of the distribution.
     8 deb http://gb.archive.ubuntu.com/ubuntu/ xenial main restricted
     9 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial main restricted
    10
    11 ## Major bug fix updates produced after the final release of the
    12 ## distribution.
    13 deb http://gb.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
    14 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial-updates main restricted
    15
    16 ## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
    17 ## team. Also, please note that software in universe WILL NOT receive any
    18 ## review or updates from the Ubuntu security team.
    19 deb http://gb.archive.ubuntu.com/ubuntu/ xenial universe
    20 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial universe
    21 deb http://gb.archive.ubuntu.com/ubuntu/ xenial-updates universe
    22 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial-updates universe
    23
    24 ## N.B. software from this repository is ENTIRELY UNSUPPORTED by the Ubuntu
    25 ## team, and may not be under a free licence. Please satisfy yourself as to
    26 ## your rights to use the software. Also, please note that software in
    27 ## multiverse WILL NOT receive any review or updates from the Ubuntu
    28 ## security team.
    29 deb http://gb.archive.ubuntu.com/ubuntu/ xenial multiverse
    30 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial multiverse
    31 deb http://gb.archive.ubuntu.com/ubuntu/ xenial-updates multiverse
    32 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial-updates multiverse
    33
    34 ## N.B. software from this repository may not have been tested as
    35 ## extensively as that contained in the main release, although it includes
    36 ## newer versions of some applications which may provide useful features.
    37 ## Also, please note that software in backports WILL NOT receive any review
    38 ## or updates from the Ubuntu security team.
    39 deb http://gb.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multi verse
    40 # deb-src http://gb.archive.ubuntu.com/ubuntu/ xenial-backports main restricted universe multiverse
    41
    42 ## Uncomment the following two lines to add software from Canonical's
    43 ## 'partner' repository.
    44 ## This software is not part of Ubuntu, but is offered by Canonical and the
    45 ## respective vendors as a service to Ubuntu users.
    46 # deb http://archive.canonical.com/ubuntu xenial partner
    47 # deb-src http://archive.canonical.com/ubuntu xenial partner
    48
    49 deb http://security.ubuntu.com/ubuntu xenial-security main restricted
    50 # deb-src http://security.ubuntu.com/ubuntu xenial-security main restricted
    51 deb http://security.ubuntu.com/ubuntu xenial-security universe
    52 # deb-src http://security.ubuntu.com/ubuntu xenial-security universe
    53 deb http://security.ubuntu.com/ubuntu xenial-security multiverse
    54 # deb-src http://security.ubuntu.com/ubuntu xenial-security multiverse
    55
    56 #zentyal
    57 deb http://archive.zentyal.org/zentyal 5.1 main
    58

This seems not to be an Ubuntu problem, but most probably is caused by zentyal.

In Ubuntu xenial the packages apt and libapt-pkg5.0 are built from the same source (apt version 1.2.29).

The zentyal repository provides libapt-pkg5.0 version 1.5.1 which apparently conflicts with apt 1.2.29

My suggestion:
Manually download and install the original version of libapt-pkg5.0 from the Ubuntu repositories.

wget https://launchpad.net/ubuntu/+archive/primary/+files/libapt-pkg5.0_1.2.29_amd64.deb
sudo dpkg --install --force-downgrade libapt-pkg5.0_1.2.29_amd64.deb

Remark: If that works, you have to prevent that the libapt-pkg5.0 package gets updated to the version form zentyal again (e.g. by apt-pinning).

Addition:
Maybe the same is valid for libapt-inst2.0, and the following commands might be required as well:

wget https://launchpad.net/ubuntu/+archive/primary/+files/libapt-inst2.0_1.2.29_amd64.deb
sudo dpkg --install --force-downgrade libapt-inst2.0_1.2.29_amd64.deb

Just ran apt update and apt upgrade with the commands of your first message with success,
wget https://launchpad.net/ubuntu/+archive/primary/+files/libapt-pkg5.0_1.2.29_amd64.deb
sudo dpkg --install --force-downgrade libapt-pkg5.0_1.2.29_amd64.deb

My VM appears to be up to date.

Do I need to run the second set of commands or should I leave it as is?

Just rebooted, apt update, apt upgrade, libapt-pkg5.0 held back, I think this has fixed the issue for now, thank you Manfred :-)

Seems to be all working as expected. https://i.imgur.com/Fb8cxI3.png

Can be closed -> answers in bug #1644643

Same cause, Zentyal upgraded to newer APT package, solution described resolves the issue.
Thanks!