Rudder

This looks like a timing issue between deletion of old config file and apache restart

On debian 7:

dpkg: warning: unable to delete old directory '/opt/rudder/etc/ssl': Directory not empty
dpkg: warning: unable to delete old directory '/var/rudder/inventories/accepted-nodes-updates': Directory not empty

But no apache error.

On Debian 8:

Reading state information... Done
The following extra packages will be installed:
  libxrender1 openjdk-8-jre-headless rudder-agent rudder-inventory-endpoint rudder-inventory-ldap rudder-jetty rudder-reports rudder-server-relay
  rudder-techniques rudder-webapp
Suggested packages:
  cfengine3 cfengine-community openjdk-8-jre-jamvm libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho ttf-wqy-microhei ttf-wqy-zenhei
  fonts-indic
The following NEW packages will be installed:
  libxrender1 openjdk-8-jre-headless rudder-server-relay
The following packages will be upgraded:
  ncf ncf-api-virtualenv rudder-agent rudder-inventory-endpoint rudder-inventory-ldap rudder-jetty rudder-reports rudder-server-root rudder-techniques
  rudder-webapp
10 upgraded, 3 newly installed, 0 to remove and 88 not upgraded.
Need to get 212 MB of archives.
After this operation, 141 MB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://ftp.debian.org/debian/ jessie/main libxrender1 amd64 1:0.9.8-1+b1 [31.4 kB]
Get:2 http://ci.normation.com/apt-repos/4.1/ jessie/main openjdk-8-jre-headless amd64 8u111-b14-2~bpo8+1 [26.9 MB]
Get:3 http://ci.normation.com/apt-repos/4.1/ jessie/main ncf all 1.1.0.201703211206-jessie1 [1,251 kB]
Get:4 http://ci.normation.com/apt-repos/4.1/ jessie/main ncf-api-virtualenv all 4.1.0~rc2~git201703211204-jessie1 [2,641 kB]
Get:5 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-inventory-ldap amd64 4.1.0~rc2~git201703211204-jessie0 [14.6 MB]
Get:6 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-webapp all 4.1.0~rc2~git201703211204-jessie0 [84.5 MB]                                        
Get:7 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-agent amd64 4.1.0~rc2~git201703211204-jessie0 [14.1 MB]                                       
Get:8 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-server-root all 4.1.0~rc2~git201703211204-jessie0 [3,172 B]                                   
Get:9 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-inventory-endpoint all 4.1.0~rc2~git201703211204-jessie0 [39.7 MB]                            
Get:10 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-jetty all 4.1.0~rc2~git201703211204-jessie0 [5,672 kB]                                       
Get:11 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-techniques all 4.1.0~rc2~git201703211204-jessie0 [17.9 MB]                                   
Get:12 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-server-relay amd64 4.1.0~rc2~git201703211204-jessie0 [4,588 kB]                              
Get:13 http://ci.normation.com/apt-repos/4.1/ jessie/main rudder-reports all 4.1.0~rc2~git201703211204-jessie0 [7,350 B]                                      
Fetched 212 MB in 2min 20s (1,508 kB/s)                                                                                                                       
Selecting previously unselected package libxrender1:amd64.
(Reading database ... 60999 files and directories currently installed.)
Preparing to unpack .../libxrender1_1%3a0.9.8-1+b1_amd64.deb ...
Unpacking libxrender1:amd64 (1:0.9.8-1+b1) ...
Selecting previously unselected package openjdk-8-jre-headless:amd64.
Preparing to unpack .../openjdk-8-jre-headless_8u111-b14-2~bpo8+1_amd64.deb ...
Unpacking openjdk-8-jre-headless:amd64 (8u111-b14-2~bpo8+1) ...
Preparing to unpack .../ncf_1.1.0.201703211206-jessie1_all.deb ...
Unpacking ncf (1.1.0.201703211206-jessie1) over (0.201703210718-jessie1) ...
Preparing to unpack .../ncf-api-virtualenv_4.1.0~rc2~git201703211204-jessie1_all.deb ...
Unpacking ncf-api-virtualenv (4.1.0~rc2~git201703211204-jessie1) over (3.1.19~rc1~git201703210718-jessie1) ...
Preparing to unpack .../rudder-inventory-ldap_4.1.0~rc2~git201703211204-jessie0_amd64.deb ...
Unpacking rudder-inventory-ldap (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Preparing to unpack .../rudder-webapp_4.1.0~rc2~git201703211204-jessie0_all.deb ...
********************************************************************************
INFO: dpkg may ask you if you want to replace rudder-web.properties or          
INFO: inventory-web.properties with the maintainer version if you modified it.  
INFO:                                                                           
INFO: If you accept, please keep in mind that you will lose any manual          
INFO: modification in this file, like the syslog port or the workflows and will 
INFO: certainly have to add them again.                                         
INFO:                                                                           
INFO: We recommend that you respond NO to this question                         
INFO: ('keep your currently-installed version'). Rudder's upgrade script will   
INFO: take care of this automatically.                                          
INFO:                                                                           
********************************************************************************
Unpacking rudder-webapp (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
dpkg: warning: unable to delete old directory '/opt/rudder/etc/ssl': Directory not empty
dpkg: warning: unable to delete old directory '/var/rudder/inventories/accepted-nodes-updates': Directory not empty
Preparing to unpack .../rudder-agent_4.1.0~rc2~git201703211204-jessie0_amd64.deb ...
INFO: A back up copy of the /opt/rudder/etc/uuid.hive has been created in /var/backups/rudder
INFO: A back up copy of the /var/rudder/cfengine-community/policy_server.dat has been created in /var/backups/rudder
INFO: A back up copy of the /var/cfengine/policy_server.dat has been created in /var/backups/rudder
INFO: A back up copy of the /var/rudder/cfengine-community/ppkeys has been created in /var/backups/rudder
Unpacking rudder-agent (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Preparing to unpack .../rudder-server-root_4.1.0~rc2~git201703211204-jessie0_all.deb ...
Unpacking rudder-server-root (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Preparing to unpack .../rudder-inventory-endpoint_4.1.0~rc2~git201703211204-jessie0_all.deb ...
Unpacking rudder-inventory-endpoint (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Preparing to unpack .../rudder-jetty_4.1.0~rc2~git201703211204-jessie0_all.deb ...
Unpacking rudder-jetty (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Preparing to unpack .../rudder-techniques_4.1.0~rc2~git201703211204-jessie0_all.deb ...
Unpacking rudder-techniques (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Selecting previously unselected package rudder-server-relay.
Preparing to unpack .../rudder-server-relay_4.1.0~rc2~git201703211204-jessie0_amd64.deb ...
Unpacking rudder-server-relay (4.1.0~rc2~git201703211204-jessie0) ...
Preparing to unpack .../rudder-reports_4.1.0~rc2~git201703211204-jessie0_all.deb ...
Unpacking rudder-reports (4.1.0~rc2~git201703211204-jessie0) over (3.1.19~rc1~git201703210718-jessie0) ...
Processing triggers for systemd (215-17+deb8u1) ...
Setting up libxrender1:amd64 (1:0.9.8-1+b1) ...
Setting up openjdk-8-jre-headless:amd64 (8u111-b14-2~bpo8+1) ...
update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode
Setting up ncf (1.1.0.201703211206-jessie1) ...
Setting up ncf-api-virtualenv (4.1.0~rc2~git201703211204-jessie1) ...
Conf ncf-api-virtualenv already enabled
INFO: Restarting Apache HTTPd...dpkg: error processing package ncf-api-virtualenv (--configure):
 subprocess installed post-installation script returned error exit status 1
Setting up rudder-inventory-ldap (4.1.0~rc2~git201703211204-jessie0) ...

Configuration file '/opt/rudder/etc/openldap/slapd.conf'
 ==> Modified (by you or by a script) since installation.
 ==> Package distributor has shipped an updated version.
   What would you like to do about it ?  Your options are:
    Y or I  : install the package maintainer's version
    N or O  : keep your currently-installed version
      D     : show the differences between the versions
      Z     : start a shell to examine the situation
 The default action is to keep your current version.
*** slapd.conf (Y/I/N/O/D/Z) [default=N] ? 
Installing new version of config file /etc/default/rudder-slapd ...
Installing new version of config file /etc/init.d/rudder-slapd ...
INFO: Restarting syslogd... Done
INFO: Stopping rudder-slapd... Done
rudder-slapd[24113]: [INFO] Using /etc/default/rudder-slapd for configuration
_#################### 100.00% eta   none elapsed            none fast!         
Closing DB...
INFO: Starting rudder-slapd... Done
INFO: OpenLDAP database was successfully upgraded to new format
INFO: You can safely remove the backups in /var/rudder/ldap/openldap-data-backup-upgrade-on-20170321134319/
INFO: and /var/rudder/ldap/backup/openldap-data-pre-upgrade-20170321134319.ldif
INFO: Restarting rudder-slapd... Done
Setting up rudder-jetty (4.1.0~rc2~git201703211204-jessie0) ...
Installing new version of config file /opt/rudder/etc/rudder-jetty.conf ...
Setting up rudder-techniques (4.1.0~rc2~git201703211204-jessie0) ...
Setting up rudder-agent (4.1.0~rc2~git201703211204-jessie0) ...
Installing new version of config file /etc/cron.d/rudder-agent ...
Installing new version of config file /etc/default/rudder-agent ...
Installing new version of config file /etc/init.d/rudder ...
Installing new version of config file /etc/init.d/rudder-agent ...
ok: Rudder agent is now disabled.
ok: stop service rudder-agent succeeded
INFO: Ensuring correct permissions on the keys directory... Done.
ok: Rudder agent has been enabled but not started, wait for next cron run.
ok: start service rudder-agent succeeded
INFO: Scheduling an inventory during next run...
Setting up rudder-server-relay (4.1.0~rc2~git201703211204-jessie0) ...
INFO: Creating the rudder user... Done
INFO: Importing existing webapp certificates... Done
INFO: Restarting Apache HTTPd... Done

*****************************************************************************************
INFO: rudder-server-relay setup complete.                                                
INFO:                                                                                    
INFO: * If you are installing a root server, configuration is automatically done         
INFO: * If you are installing a simple relay, run:                                       
INFO:   '/opt/rudder/bin/rudder-node-to-relay root'          
INFO:   on your root server to complete this node transition to a relay server.          
INFO:   Please look at the documentation for details (Section 'Relay servers')           
*****************************************************************************************
dpkg: dependency problems prevent configuration of rudder-webapp:
 rudder-webapp depends on ncf-api-virtualenv; however:
  Package ncf-api-virtualenv is not configured yet.

dpkg: error processing package rudder-webapp (--configure):
 dependency problems - leaving unconfigured
Setting up rudder-inventory-endpoint (4.1.0~rc2~git201703211204-jessie0) ...
INFO: Launching script to check if a migration is needed
INFO: End of migration script
Setting up rudder-reports (4.1.0~rc2~git201703211204-jessie0) ...
INFO: Waiting for PostgreSQL to be up... Done
dpkg: dependency problems prevent configuration of rudder-server-root:
 rudder-server-root depends on rudder-webapp (= 4.1.0~rc2~git201703211204-jessie0); however:
  Package rudder-webapp is not configured yet.

dpkg: error processing package rudder-server-root (--configure):
 dependency problems - leaving unconfigured
Processing triggers for libc-bin (2.19-18) ...
Processing triggers for systemd (215-17+deb8u1) ...
Errors were encountered while processing:
 ncf-api-virtualenv
 rudder-webapp
 rudder-server-root
E: Sub-process /usr/bin/dpkg returned an error code (1)

Happens also with upgrade on a relay of rudder-server-relay:

Preparing to unpack .../rudder-server-relay_4.1.0~rc2~git201703241433-jessie0_amd64.deb ...
Unpacking rudder-server-relay (4.1.0~rc2~git201703241433-jessie0) over (3.1.19~rc1~git201703240718-jessie0) ...
Processing triggers for man-db (2.7.0.2-5) ...
Processing triggers for mime-support (3.58) ...
Setting up libpython2.7-minimal:amd64 (2.7.9-2+deb8u1) ...
Setting up python2.7-minimal (2.7.9-2+deb8u1) ...
Setting up libpython2.7-stdlib:amd64 (2.7.9-2+deb8u1) ...
Setting up python2.7 (2.7.9-2+deb8u1) ...
Setting up libpython2.7:amd64 (2.7.9-2+deb8u1) ...
Setting up libapache2-mod-wsgi (4.3.0-1) ...
apache2_invoke: Enable module wsgi
apache2_reload: Your configuration is broken. Not restarting Apache 2
apache2_reload: apache2: Syntax error on line 219 of /etc/apache2/apache2.conf: Could not open configuration file /etc/apache2/sites-enabled/rudder-relay-vhost-ssl.conf: No such file or directory
Setting up rudder-server-relay (4.1.0~rc2~git201703241433-jessie0) ...
INFO: Creating group rudder... Done
INFO: Creating the rudder user... Done
INFO: Importing existing relay certificates... Done
INFO: Restarting Apache HTTPd... Done
Processing triggers for libc-bin (2.19-18) ...

When I restart manually apache2, it does work

I didn't had that one in an update from Rudder 4.0 to 4.1 (but I hit #10505 :/)