Yet another "Failed to get D-Bus connection: Connection refused"

It’s a fresh Yunohost install on a LIME2.

After upgrading packages with apt-get update && apt-get upgrade something must have gone wrong as systemctl --user no longer works.

admin@Gildurklaus:~$ systemctl --user enable duniter
Failed to get D-Bus connection: Connection refused
admin@Gildurklaus:~$ sudo apt-get install libpam-systemd
Reading package lists... Done
Building dependency tree       
Reading state information... Done
libpam-systemd is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

[update 1]

Looks like XDG_RUNTIME_DIR is not set either.

admin@Gildurklaus:~$ systemd --test
Trying to run as user instance, but $XDG_RUNTIME_DIR is not set.

[update 2]

Even more importantly $XDG_SESSION_ID is missing.

admin@Gildurklaus:~$ echo $XDG_SESSION_ID

admin@Gildurklaus:~$ sudo systemctl status systemd-logind.service
● systemd-logind.service - Login Service
   Loaded: loaded (/lib/systemd/system/systemd-logind.service; static)
   Active: active (running) since Sun 2018-03-25 12:24:39 CEST; 3h 42min ago
     Docs: man:systemd-logind.service(8)
 Main PID: 568 (systemd-logind)
   Status: "Processing requests..."
   CGroup: /system.slice/systemd-logind.service
           └─568 /lib/systemd/systemd-logind

Mar 25 12:24:39 Gildurklaus systemd-logind[568]: New seat seat0.
Mar 25 12:24:39 Gildurklaus systemd[1]: Started Login Service.

Systemd-logind is supposed to start a login session for the admin user after the login service has started.