Hi,

A new strange thing, I don't know if you encountered that, today at 6h32
packagekit run, tried to restart gitlab, and failed:

Nov 27 06:32:18 weboob dbus-daemon[464]: [system] Activating via systemd: 
service name='org.freedesktop.PackageKit' unit='packagekit.service' requested 
by ':1.10456' (uid=0 pid=28562 comm="/usr/bin/gdbus call --system --dest 
org.freedeskto")
Nov 27 06:32:18 weboob systemd[1]: Starting PackageKit Daemon...
Nov 27 06:32:18 weboob PackageKit: daemon start
Nov 27 06:32:18 weboob dbus-daemon[464]: [system] Successfully activated 
service 'org.freedesktop.PackageKit'
Nov 27 06:32:18 weboob systemd[1]: Started PackageKit Daemon.
Nov 27 06:32:18 weboob gitlab-workhorse[20628]: git.weboob.org 46.229.168.139 - 
- [2019/11/27:06:32:18 +0100] "GET 
/P4ncake/devel/tree/6f5f41fe574ad35b11e024b7c10bb2950d0689b2 HTTP/1.1" 200 
40794 "" "Mozilla/5.0 (compatible; SemrushBot/6~bl; 
+http://www.semrush.com/bot.html)" %!f(int64=108)
Nov 27 06:32:19 weboob systemd[1]: Reloading.
Nov 27 06:32:19 weboob systemd[1]: /lib/systemd/system/dbus.socket:5: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/dbus/system_bus_socket → /run/dbus/system_bus_socket; please update 
the unit file accordingly.
Nov 27 06:32:19 weboob systemd[1]: Configuration file 
/etc/systemd/system/postfix.service.d/override.conf is marked 
world-inaccessible. This has no effect as configuration data is accessible via 
APIs without restrictions. Proceeding anyway.
Nov 27 06:32:19 weboob systemd[1]: 
/lib/systemd/system/gitlab-sidekiq.service:18: Ignoring unknown escape 
sequences: "for i in 4 4 4 4 4 4 4 4; do sleep $i; (ps -h -o command -p 
$MAINPID | grep -q -P "sidekiq \d\.\d\.\d") && exit 0; done"
Nov 27 06:32:19 weboob systemd[1]: /lib/systemd/system/docker.socket:6: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/docker.sock → /run/docker.sock; please update the unit file 
accordingly.
Nov 27 06:32:20 weboob systemd[1]: Reloading.
Nov 27 06:32:20 weboob systemd[1]: /lib/systemd/system/dbus.socket:5: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/dbus/system_bus_socket → /run/dbus/system_bus_socket; please update 
the unit file accordingly.
Nov 27 06:32:20 weboob systemd[1]: Configuration file 
/etc/systemd/system/postfix.service.d/override.conf is marked 
world-inaccessible. This has no effect as configuration data is accessible via 
APIs without restrictions. Proceeding anyway.
Nov 27 06:32:20 weboob systemd[1]: 
/lib/systemd/system/gitlab-sidekiq.service:18: Ignoring unknown escape 
sequences: "for i in 4 4 4 4 4 4 4 4; do sleep $i; (ps -h -o command -p 
$MAINPID | grep -q -P "sidekiq \d\.\d\.\d") && exit 0; done"
Nov 27 06:32:20 weboob systemd[1]: /lib/systemd/system/docker.socket:6: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/docker.sock → /run/docker.sock; please update the unit file 
accordingly.
Nov 27 06:32:20 weboob systemd[1]: Reloading.
Nov 27 06:32:20 weboob systemd[1]: /lib/systemd/system/dbus.socket:5: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/dbus/system_bus_socket → /run/dbus/system_bus_socket; please update 
the unit file accordingly.
Nov 27 06:32:20 weboob systemd[1]: Configuration file 
/etc/systemd/system/postfix.service.d/override.conf is marked 
world-inaccessible. This has no effect as configuration data is accessible via 
APIs without restrictions. Proceeding anyway.
Nov 27 06:32:20 weboob systemd[1]: 
/lib/systemd/system/gitlab-sidekiq.service:18: Ignoring unknown escape 
sequences: "for i in 4 4 4 4 4 4 4 4; do sleep $i; (ps -h -o command -p 
$MAINPID | grep -q -P "sidekiq \d\.\d\.\d") && exit 0; done"
Nov 27 06:32:20 weboob systemd[1]: /lib/systemd/system/docker.socket:6: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/docker.sock → /run/docker.sock; please update the unit file 
accordingly.
Nov 27 06:32:20 weboob gitaly[20604]: time="2019-11-27T06:32:20+01:00" 
level=error msg="lstat /var/lib/gitlab/repositories/+gitaly/cache: no such file 
or directory" storage=default
Nov 27 06:32:20 weboob systemd[1]: Reloading.
Nov 27 06:32:21 weboob systemd[1]: /lib/systemd/system/dbus.socket:5: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/dbus/system_bus_socket → /run/dbus/system_bus_socket; please update 
the unit file accordingly.
Nov 27 06:32:21 weboob systemd[1]: Configuration file 
/etc/systemd/system/postfix.service.d/override.conf is marked 
world-inaccessible. This has no effect as configuration data is accessible via 
APIs without restrictions. Proceeding anyway.
Nov 27 06:32:21 weboob systemd[1]: 
/lib/systemd/system/gitlab-sidekiq.service:18: Ignoring unknown escape 
sequences: "for i in 4 4 4 4 4 4 4 4; do sleep $i; (ps -h -o command -p 
$MAINPID | grep -q -P "sidekiq \d\.\d\.\d") && exit 0; done"
Nov 27 06:32:21 weboob systemd[1]: /lib/systemd/system/docker.socket:6: 
ListenStream= references a path below legacy directory /var/run/, updating 
/var/run/docker.sock → /run/docker.sock; please update the unit file 
accordingly.
Nov 27 06:32:21 weboob systemd[1]: Stopped target GitLab Service.
Nov 27 06:32:21 weboob systemd[1]: Stopping GitLab Service.
Nov 27 06:32:21 weboob systemd[1]: gitlab.service: Succeeded.
Nov 27 06:32:21 weboob systemd[1]: Stopped GitLab Services.
Nov 27 06:32:21 weboob systemd[1]: Stopping GitLab Services...
Nov 27 06:32:21 weboob systemd[1]: Stopping Gitlab mailroom Worker...
Nov 27 06:32:21 weboob systemd[1]: Stopping GitLab Sidekiq Worker...
Nov 27 06:32:21 weboob systemd[1]: Stopping Gitlab Workhorse handles slow HTTP 
requests for Gitlab....
Nov 27 06:32:21 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:21.133Z 20644 
TID-goijjrii4 INFO: Shutting down
Nov 27 06:32:21 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:21.133Z 20644 
TID-goin08v3c INFO: Scheduler exiting...
Nov 27 06:32:21 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:21.133Z 20644 
TID-goijjrii4 INFO: Terminating quiet workers
Nov 27 06:32:21 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:21.135Z 20644 
TID-goin0a0a0 INFO: Scheduler exiting...
Nov 27 06:32:21 weboob systemd[1]: gitlab-workhorse.service: Succeeded.
Nov 27 06:32:21 weboob systemd[1]: Stopped Gitlab Workhorse handles slow HTTP 
requests for Gitlab..
Nov 27 06:32:21 weboob systemd[1]: gitlab-mailroom.service: Succeeded.
Nov 27 06:32:21 weboob systemd[1]: Stopped Gitlab mailroom Worker.
Nov 27 06:32:21 weboob systemd[1]: Stopping GitLab Unicorn Server...
Nov 27 06:32:21 weboob systemd[1]: gitlab-unicorn.service: Succeeded.
Nov 27 06:32:21 weboob systemd[1]: Stopped GitLab Unicorn Server.
Nov 27 06:32:21 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:21.635Z 20644 
TID-goijjrii4 INFO: Pausing to allow workers to finish...
Nov 27 06:32:23 weboob gitlab-sidekiq[20644]: 2019-11-27T05:32:23.639Z 20644 
TID-goijjrii4 INFO: Bye!
Nov 27 06:32:23 weboob systemd[1]: gitlab-sidekiq.service: Succeeded.
Nov 27 06:32:23 weboob systemd[1]: Stopped GitLab Sidekiq Worker.
Nov 27 06:32:23 weboob systemd[1]: Stopping Advanced key-value store...
Nov 27 06:32:24 weboob systemd[1]: redis-server.service: Succeeded.
Nov 27 06:32:24 weboob systemd[1]: Stopped Advanced key-value store.
Nov 27 06:32:24 weboob systemd[1]: Starting Advanced key-value store...
Nov 27 06:32:24 weboob systemd[1]: redis-server.service: Can't open PID file 
/run/redis/redis-server.pid (yet?) after start: No such file or directory
Nov 27 06:32:24 weboob systemd[1]: Started Advanced key-value store.
Nov 27 06:32:24 weboob systemd[1]: Starting GitLab Sidekiq Worker...
Nov 27 06:32:24 weboob systemd[1]: gitlab-unicorn.service: Ignoring invalid 
environment assignment 'for i in $(grep -v '#' /etc/gitlab/gitlab-debian.conf | 
cut -d=-f 1)': /etc/default/gitlab                                              
   
Nov 27 06:32:24 weboob systemd[1]: gitlab-unicorn.service: Ignoring invalid 
environment assignment 'export app_user=${gitlab_user}': /etc/default/gitlab    
                                                                                
   
Nov 27 06:32:24 weboob systemd[1]: Started GitLab Unicorn Server.
Nov 27 06:32:24 weboob systemd[1]: Started Gitlab mailroom Worker.
Nov 27 06:32:24 weboob systemd[1]: Started Gitlab Workhorse handles slow HTTP 
requests for Gitlab..
Nov 27 06:32:24 weboob gitlab-workhorse[28833]: 
time="2019-11-27T06:32:24+01:00" level=info msg=Starting 
version="gitlab-workhorse (unknown version)"                                    
                                                      
Nov 27 06:32:24 weboob gitlab-unicorn[28831]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-unicorn[28831]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-unicorn[28831]: bundler: failed to load command: 
unicorn_rails (/usr/local/bin/unicorn_rails)                                    
                                                                                
Nov 27 06:32:24 weboob gitlab-unicorn[28831]: Bundler::GemNotFound: Could not 
find gem 'rubyzip (>= 1.2.2, ~> 1.2)' in any of the gem sources listed in your 
Gemfile.                                                                        
  
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:287:in
 `block in verify_gemfile_dependencies_are_found!'                              
                         
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:255:in
 `each'                                                                         
                         
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:255:in
 `verify_gemfile_dependencies_are_found!'                                       
                         
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:49:in
 `start'                                                                        
                          
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:22:in
 `resolve'                                                                      
                          
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:258:in
 `resolve'                                                                      
                       
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:170:in
 `specs'                                                                        
                       
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:237:in
 `specs_for'                                                                    
                       
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:226:in
 `requested_specs'                                                              
                       
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/runtime.rb:108:in
 `block in definition_method'                                                   
                          
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/runtime.rb:20:in
 `setup'                                                                        
                           
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler.rb:107:in 
`setup'                                                                         
                                 
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/setup.rb:20:in
 `<top (required)>'                                                             
                             
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
Nov 27 06:32:24 weboob gitlab-unicorn[28831]:   
/usr/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
Nov 27 06:32:24 weboob systemd[1]: gitlab-unicorn.service: Main process exited, 
code=exited, status=1/FAILURE
Nov 27 06:32:24 weboob systemd[1]: gitlab-unicorn.service: Failed with result 
'exit-code'.
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-sidekiq[28829]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-sidekiq[28829]: fatal: not a git repository (or 
any of the parent directories): .git
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:287:in
 `block in verify_gemfile_dependencies_are_found!': Could not find gem 'rubyzip 
(>= 1.2.2, ~> 1.2)' in any
of the gem sources listed in your Gemfile. (Bundler::GemNotFound)
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:255:in
 `each'                                                                         
                 
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:255:in
 `verify_gemfile_dependencies_are_found!'                                       
                 
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:49:in
 `start'                                                                        
                  
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/resolver.rb:22:in
 `resolve'                                                                      
                  
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:258:in
 `resolve'                                                                      
               
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:170:in
 `specs'                                                                        
               
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:237:in
 `specs_for'                                                                    
               
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/definition.rb:226:in
 `requested_specs'                                                              
               
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/runtime.rb:108:in
 `block in definition_method'                                                   
                  
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/runtime.rb:20:in
 `setup'                                                                        
                   
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler.rb:107:in 
`setup'                                                                         
                         
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/share/rubygems-integration/all/gems/bundler-1.17.3/lib/bundler/setup.rb:20:in
 `<top (required)>'                                                             
                     
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'         
                                                                                
                       
Nov 27 06:32:24 weboob gitlab-mailroom[28832]: #011from 
/usr/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'         
                                                                                
                       
Nov 27 06:32:24 weboob systemd[1]: gitlab-mailroom.service: Main process 
exited, code=exited, status=1/FAILURE
Nov 27 06:32:24 weboob systemd[1]: gitlab-mailroom.service: Failed with result 
'exit-code'.

I had to install manually rubyzip with gem at the right version to fix gitlab.

To understand, packagekit has updated something?

Romain

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