Unable to upgrade apps: org.freedesktop.DBus.Error.TimedOut [SOLVED]

My YunoHost server

Hardware: Old laptop or computer
YunoHost version: x.x.x
I have access to my server : Through SSH | through the webadmin | direct access via keyboard
Are you in a special context or did you perform some particular tweaking on your YunoHost instance ? : no
If yes, please explain:
yunohost:
repo: stable
version: 3.6.4.3
yunohost-admin:
repo: stable
version: 3.6.4
moulinette:
repo: stable
version: 3.6.4
ssowat:
repo: stable
version: 3.6.4

Description of my issue

Iā€™m trying to upgrade apps but it fails.

sudo yunohost tools upgrade --apps writefreely --debug
207  DEBUG loading actions map namespace 'yunohost'
244  DEBUG extra parameter classes loaded: ['comment', 'ask', 'password', 'required', 'pattern']
244  DEBUG initializing base actions map parser for cli
246  DEBUG registering new callback action 'yunohost.utils.packages.ynh_packages_version' to ['-v', '--version']
357  DEBUG lock has been acquired
443  DEBUG loading python module yunohost.tools took 0.085s
443  INFO processing action [2553.1]: yunohost.tools.upgrade with args={'apps': ['writefreely'], 'system': False}
1633 INFO Now upgrading app writefreelyā€¦
1680 DEBUG Downloadingā€¦
4323 DEBUG Extractingā€¦
4335 DEBUG Done
4341 DEBUG Checking required packages for writefreelyā€¦
4921 DEBUG Checking that required services are up and running...
12576 WARNING unable to upgrade apps: org.freedesktop.DBus.Error.TimedOut: Failed to activate service 'org.freedesktop.systemd1': timed out
12576 ERROR Unable to upgrade some applications

In web admin, I went to Tools > Diagnosis and I get the same type of error.

Action
GET /diagnosis
{"locale":"en"}

Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/moulinette/interfaces/api.py", line 439, in process
    ret = self.actionsmap.process(arguments, timeout=30, route=_route)
  File "/usr/lib/python2.7/dist-packages/moulinette/actionsmap.py", line 523, in process
    return func(**arguments)
  File "/usr/lib/moulinette/yunohost/tools.py", line 802, in tools_diagnosis
    services = service_status()
  File "/usr/lib/moulinette/yunohost/service.py", line 287, in service_status
    status = _get_service_information_from_systemd(name)
  File "/usr/lib/moulinette/yunohost/service.py", line 348, in _get_service_information_from_systemd
    systemd = d.get_object('org.freedesktop.systemd1', '/org/freedesktop/systemd1')
  File "/usr/lib/python2.7/dist-packages/dbus/bus.py", line 241, in get_object
    follow_name_owner_changes=follow_name_owner_changes)
  File "/usr/lib/python2.7/dist-packages/dbus/proxies.py", line 248, in __init__
    self._named_service = conn.activate_name_owner(bus_name)
  File "/usr/lib/python2.7/dist-packages/dbus/bus.py", line 180, in activate_name_owner
    self.start_service_by_name(bus_name)
  File "/usr/lib/python2.7/dist-packages/dbus/bus.py", line 278, in start_service_by_name
    'su', (bus_name, flags)))
  File "/usr/lib/python2.7/dist-packages/dbus/connection.py", line 651, in call_blocking
    message, timeout)
DBusException: org.freedesktop.DBus.Error.TimedOut: Failed to activate service 'org.freedesktop.systemd1': timed out

NOTE: Before having this problem I did install Mastodon app, found it didnā€™t work so uninstalled.

Then I also installed Pleroma, but also didnā€™t work.

I see that my WriteFreely instance is now showing 502 error (blog.arkadi.one). Iā€™m not sure if any of this is related.

Uuh okay, for example, are you able to run systemctl status dbus and is it running ?

this is what i got for that command.

admin@arkadi:~$ sudo systemctl status dbus
ā— dbus.service - D-Bus System Message Bus
   Loaded: loaded (/lib/systemd/system/dbus.service; static; vendor preset: enabled)
   Active: active (running) since Fri 2019-07-12 23:06:26 CST; 10h ago
     Docs: man:dbus-daemon(1)
 Main PID: 718 (dbus-daemon)
    Tasks: 1 (limit: 4915)
   Memory: 1.4M
      CPU: 2.856s
   CGroup: /system.slice/dbus.service
           ā””ā”€718 /usr/bin/dbus-daemon --system --address=systemd: --nofork --nopidfile --systemd-activation

Jul 13 09:07:09 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:07:34 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:07:59 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:08:24 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:08:49 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:09:14 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:09:24 arkadi.one dbus[718]: [system] Activating systemd to hand-off: service name='org.freedesktop.login1' unit=
Jul 13 09:09:39 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out
Jul 13 09:09:49 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.login1': timed out
Jul 13 09:10:04 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out

i also just tried these commands but no change.

sudo systemctl reload dbus
sudo systemctl restart dbus
Jul 13 09:13:49 arkadi.one systemd[1]: Reloading D-Bus System Message Bus.
Jul 13 09:13:50 arkadi.one dbus[718]: [system] Reloaded configuration
Jul 13 09:13:50 arkadi.one dbus-send[16136]: method return time=1562980430.014318 sender=org.freedesktop.DBus -> destinati
Jul 13 09:13:50 arkadi.one systemd[1]: Reloaded D-Bus System Message Bus.
Jul 13 09:13:50 arkadi.one dbus[718]: [system] Failed to activate service 'org.freedesktop.systemd1': timed out

while investigating my problem, i uninstalled docker-compose and got some weird error message.



apt remove docker-compose
...
Removing docker-compose (1.8.0-2) ...
Processing triggers for man-db (2.7.6.1-2) ...
fatal: confused by unstable object source data for 9fb941b0b0c163a3514bd16cd2817b8c7662d759
etckeeper warning: git add --all
On branch master
Changes not staged for commit:
modified: default/postsrsd
deleted: dnsmasq.d/fedi.arkadi.one
modified: group
modified: group-
modified: gshadow
modified: gshadow-
modified: hosts
deleted: logrotate.d/pleroma
deleted: metronome/conf.d/fedi.arkadi.one.cfg.lua
deleted: nginx/conf.d/fedi.arkadi.one.conf
deleted: nginx/conf.d/fedi.arkadi.one.d/pleroma.conf
deleted: nginx/conf.d/pleroma-cache.conf
modified: passwd
modified: passwd-
modified: pihole/pihole-FTL.db
modified: resolv.dnsmasq.conf
modified: shadow
modified: shadow-
modified: ssowat/conf.json
deleted: yunohost/apps/pleroma/conf/app.src
deleted: yunohost/apps/pleroma/conf/cache.conf
deleted: yunohost/apps/pleroma/conf/generated_config.exs
deleted: yunohost/apps/pleroma/conf/media.conf
deleted: yunohost/apps/pleroma/conf/nginx.conf
deleted: yunohost/apps/pleroma/conf/systemd.service
deleted: yunohost/apps/pleroma/manifest.json
deleted: yunohost/apps/pleroma/scripts/_common.sh
deleted: yunohost/apps/pleroma/scripts/backup
deleted: yunohost/apps/pleroma/scripts/change_url
deleted: yunohost/apps/pleroma/scripts/install
deleted: yunohost/apps/pleroma/scripts/remove
deleted: yunohost/apps/pleroma/scripts/restore
deleted: yunohost/apps/pleroma/scripts/upgrade
deleted: yunohost/apps/pleroma/scripts/ynh_add_secure_repos__3
deleted: yunohost/apps/pleroma/scripts/ynh_systemd_action
deleted: yunohost/apps/pleroma/settings.yml
deleted: yunohost/apps/pleroma/status.json
modified: yunohost/appslists.json
deleted: yunohost/certs/fedi.arkadi.one
modified: yunohost/regenconf.yml


no changes added to commit
warning: etckeeper failed to commit changes in /etc using git
Error: Timeout was reached

there were also some of these fatal: confused by unstable object source data warnings while installing mastodon and pleroma.

itā€™s scary to think that installing level 7 apps could screw up my system this badly.

at this point it feels like my system is completely ā€˜messed upā€™ so am starting to think about reinstalling whole server, unless anybody has some ideas how to fix this?

Well uh, do you know where that docker-compose comes from ? I canā€™t see any reference do docker in the 3 apps you mentionnedā€¦

yes youā€™re right. i installed docker and docker-compose to try using Own Photos (Google Photos replacement) but wasnā€™t happy with it.

So order of things installed:
Own Photos
Mastodon
Pleroma

I didnā€™t mention it because Iā€™ve installed docker and docker-compose on many systems and havenā€™t had any issues with it, so I donā€™t think this problem could be related.

so any ideas? iā€™m open to trying anything. if it canā€™t be fixed, iā€™ll just have to reinstall everything. i have backups so I can do it, but itā€™s just time consuming.

I guess the whole docker thing is unrelated, nor the scary messages about ā€œdeletedā€ files (thatā€™s just log from etckeeper trying to version config files, but not so important)

Well uh, did you already tried to reboot the machine ? Some thread on the internet suggest it might solve the issue ā€¦ But thatā€™s pretty weird :confused:

ok now iā€™m very confusedā€¦

i rebooted but nothing worked. then i restarted ā€˜nginxā€™ service using:
sudo yunohost service restart nginx

now suddenly everything works??!?!?!?

iā€™m so confused because i rebooted once before posting this problem here.

well anyways iā€™ll leave this thread here, if you have weird problems, reboot (a few times) and maybe itā€™ll work?!?

thanks for your help aleks. changed topic to [solved]

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