Fixed with this command :

sudo mkdir /var/lib/mysql-files

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https://bugs.launchpad.net/bugs/1633855

Title:
  akonadi fails to start after upgrade to yakkety

Status in akonadi package in Ubuntu:
  Confirmed

Bug description:
  After yesterday 15 sept. upgrade to Kubuntu 16.10 Yakkety Yak, kmail
  fails to start, because akonadi backend fails.

  Starting akonadi from command line, 
      $ akonadictl start
  the output contains:
     stderr: "mysqld: Error on realpath() on '/var/lib/mysql-files' (Error 2 - 
No such file or directory)\n2016-10-16T11:54:23.365277Z 0 [Warning] The syntax 
'--log_warnings/-W' is deprecated and will be removed in a future release. 
Please use '--log_error_verbosity' instead.\n2016-10-16T11:54:23.365377Z 0 
[Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use 
--explicit_defaults_for_timestamp server option (see documentation for more 
details).\n2016-10-16T11:54:23.365479Z 0 [ERROR] Failed to access directory for 
--secure-file-priv. Please make sure that directory exists and is accessible by 
MySQL Server. Supplied value : 
/var/lib/mysql-files\n2016-10-16T11:54:23.365488Z 0 [ERROR] 
Aborting\n\n2016-10-16T11:54:23.365508Z 0 [Note] Binlog end\n"

  The cause is a regression in the file 
      /etc/xdg/akonadi/mysql-global.conf
  provided by the package
      akonadi-backend-mysql

  Diff of the content of mysql-global.conf from Yakkety vs Xenial:
  <code>

  diff -u "akonadi-backend-mysql_16.04.3-0ubuntu2_all.deb - mysql-global.conf" 
"akonadi-backend-mysql_15.12.3-0ubuntu6_all.deb - mysql-global.conf" 
  --- "akonadi-backend-mysql_16.04.3-0ubuntu2_all.deb - mysql-global.conf"      
  2016-06-24 15:51:12.000000000 +0200
  +++ "akonadi-backend-mysql_15.12.3-0ubuntu6_all.deb - mysql-global.conf"      
  2016-04-20 10:42:09.000000000 +0200
  @@ -100,5 +100,14 @@
   # We use InnoDB, so don't let MyISAM eat up memory
   key_buffer_size=16K
   
  +# KUBUNTU:
  +# Unset the export dir check as only the full mysql-server package creates it
  +secure_file_priv=
  +
  +# KUBUNTU:
  +# workaround for 5.7 being more strict with column types
  +# (reverts to 5.6 behavior)
  +sql_mode=NO_ENGINE_SUBSTITUTION
  +
   [client]
   default-character-set=utf8

  </code>

  Applying this patch fixes the bug.

  The "secure_file_priv" setting went missing is referenced in the package 
changelog:
     akonadi (4:15.12.3-0ubuntu5) xenial; urgency=medium

       * kubuntu_disable_secure_file_priv_check.diff:
      - Set secure_file_priv to empty as that directory is not set in a default
        kubuntu install

      -- Philip Muškovac <yo...@kubuntu.org>  Mon, 18 Apr 2016 15:24:43
  +0200

  Marco Gamberoni

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