[Bug 1435550] [NEW] Unable to upgrade from mysql 5.5 to 5.6

Mon Mar 23 20:58:40 UTC 2015

Public bug reported:

I upgraded to 15.04 from 14.10 two days ago and an update to MySQL landed today which doesn't upgrade MySQL correctly.
Additionally on another machine I did a dist-upgrade and that caused the mariadb-server package on a update-manager -d to completely bomb out due to a package conflict (will file another report). Upgrading from 5.5 to 5.6 causes the following to occcur on a dist-upgrade:

The following packages will be REMOVED:
  mysql-client-5.5 mysql-client-core-5.5 mysql-server-5.5 mysql-server-core-5.5
The following NEW packages will be installed:
  mysql-client-5.6 mysql-client-core-5.6 mysql-server-5.6 mysql-server-core-5.6
The following packages will be upgraded:
  mysql-common mysql-server
2 upgraded, 4 newly installed, 4 to remove and 0 not upgraded.
Need to get 18.8 MB of archives.
After this operation, 56.3 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-server all 5.6.23-1~exp1~ubuntu3 [8,868 B]
Get:2 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-client-core-5.6 amd64 5.6.23-1~exp1~ubuntu3 [3,861 kB]
Get:3 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-common all 5.6.23-1~exp1~ubuntu3 [16.3 kB]
Get:4 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-client-5.6 amd64 5.6.23-1~exp1~ubuntu3 [5,089 kB]
Get:5 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-server-core-5.6 amd64 5.6.23-1~exp1~ubuntu3 [4,193 kB]
Get:6 http://za.archive.ubuntu.com/ubuntu/ vivid/main mysql-server-5.6 amd64 5.6.23-1~exp1~ubuntu3 [5,606 kB]
Fetched 18.8 MB in 1s (11.5 MB/s)       
Preconfiguring packages ...
(Reading database ... 316308 files and directories currently installed.)
Preparing to unpack .../mysql-server_5.6.23-1~exp1~ubuntu3_all.deb ...
Unpacking mysql-server (5.6.23-1~exp1~ubuntu3) over (5.5.41-0ubuntu1) ...
(Reading database ... 316305 files and directories currently installed.)
Removing mysql-server-5.5 (5.5.41-0ubuntu1) ...
Removing mysql-client-5.5 (5.5.41-0ubuntu1) ...
Removing mysql-client-core-5.5 (5.5.41-0ubuntu1) ...
Processing triggers for man-db (2.7.0.2-5) ...
Selecting previously unselected package mysql-client-core-5.6.
(Reading database ... 316175 files and directories currently installed.)
Preparing to unpack .../mysql-client-core-5.6_5.6.23-1~exp1~ubuntu3_amd64.deb ...
Unpacking mysql-client-core-5.6 (5.6.23-1~exp1~ubuntu3) ...
Preparing to unpack .../mysql-common_5.6.23-1~exp1~ubuntu3_all.deb ...
Unpacking mysql-common (5.6.23-1~exp1~ubuntu3) over (5.5.41-0ubuntu1) ...
Selecting previously unselected package mysql-client-5.6.
Preparing to unpack .../mysql-client-5.6_5.6.23-1~exp1~ubuntu3_amd64.deb ...
Unpacking mysql-client-5.6 (5.6.23-1~exp1~ubuntu3) ...
Processing triggers for man-db (2.7.0.2-5) ...
(Reading database ... 316233 files and directories currently installed.)
Removing mysql-server-core-5.5 (5.5.41-0ubuntu1) ...
Processing triggers for man-db (2.7.0.2-5) ...
Selecting previously unselected package mysql-server-core-5.6.
(Reading database ... 316146 files and directories currently installed.)
Preparing to unpack .../mysql-server-core-5.6_5.6.23-1~exp1~ubuntu3_amd64.deb ...
Unpacking mysql-server-core-5.6 (5.6.23-1~exp1~ubuntu3) ...
Processing triggers for man-db (2.7.0.2-5) ...
Setting up mysql-common (5.6.23-1~exp1~ubuntu3) ...
update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Removing obsolete conffile /etc/mysql/conf.d/.keepme ...
Removing obsolete conffile /etc/mysql/my.cnf ...
Selecting previously unselected package mysql-server-5.6.
(Reading database ... 316242 files and directories currently installed.)
Preparing to unpack .../mysql-server-5.6_5.6.23-1~exp1~ubuntu3_amd64.deb ...
Unpacking mysql-server-5.6 (5.6.23-1~exp1~ubuntu3) ...
Processing triggers for ureadahead (0.100.0-19) ...
ureadahead will be reprofiled on next reboot
Processing triggers for man-db (2.7.0.2-5) ...
Setting up mysql-client-core-5.6 (5.6.23-1~exp1~ubuntu3) ...
Setting up mysql-client-5.6 (5.6.23-1~exp1~ubuntu3) ...
Setting up mysql-server-core-5.6 (5.6.23-1~exp1~ubuntu3) ...
Setting up mysql-server-5.6 (5.6.23-1~exp1~ubuntu3) ...
Installing new version of config file /etc/apparmor.d/usr.sbin.mysqld ...
Installing new version of config file /etc/init.d/mysql ...
Installing new version of config file /etc/init/mysql.conf ...
Installing new version of config file /etc/logrotate.d/mysql-server ...
Installing new version of config file /etc/mysql/debian-start ...
update-alternatives: using /etc/mysql/mysql.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
insserv: script docker: service docker already provided!
Job for mysql.service failed. See "systemctl status mysql.service" and "journalctl -xe" for details.
invoke-rc.d: initscript mysql, action "start" failed.
dpkg: error processing package mysql-server-5.6 (--configure):
 subprocess installed post-installation script returned error exit status 1
dpkg: dependency problems prevent configuration of mysql-server:
 mysql-server depends on mysql-server-5.6; however:
  Package mysql-server-5.6 is not configured yet.

dpkg: error processing package mysql-server (--configure):
 dependency problems - leaving unconfigured
No apport report written because the error message indicates its a followup error from a previous failure.
                                                                                                          Processing triggers for ureadahead (0.100.0-19) ...
Errors were encountered while processing:
 mysql-server-5.6
 mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)

Meanwhile in the background in /var/log/mysql/error.log:
150323 17:20:22 [Note] /usr/sbin/mysqld: Normal shutdown

150323 17:20:22 [Note] Event Scheduler: Purging the queue. 0 events
150323 17:20:22  InnoDB: Starting shutdown...
150323 17:20:24  InnoDB: Shutdown completed; log sequence number 1492609726
150323 17:20:24 [Note] /usr/sbin/mysqld: Shutdown complete

150323 17:20:24 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 17:20:52 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 17:20:53 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 17:30:53 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 17:30:53 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 17:40:53 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 17:40:53 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 17:50:54 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 17:50:54 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:00:54 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:00:54 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:10:55 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:10:55 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:20:55 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:20:55 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:30:56 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:30:56 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:40:56 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:40:56 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 18:50:57 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 18:50:57 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:00:57 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:00:57 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:10:58 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:10:58 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:20:58 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:20:58 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:30:59 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:30:59 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:40:59 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:40:59 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 19:51:00 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 19:51:00 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:01:00 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:01:00 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:11:01 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:11:01 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:21:01 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:21:01 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:31:02 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:31:02 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:41:02 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:41:02 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 20:51:03 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 20:51:03 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:01:03 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:01:03 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:11:04 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:11:04 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:21:04 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:21:04 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:31:05 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:31:05 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:41:05 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:41:05 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 21:51:06 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 21:51:06 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:01:06 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:01:06 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:11:07 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:11:07 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:21:07 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:21:07 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:31:08 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:31:08 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:41:08 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:41:08 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended
150323 22:51:09 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
/usr/sbin/mysqld: Can't read dir of '/etc/mysql/mysql.conf.d/' (Errcode: 13 - Permission denied)
Fatal error in defaults handling. Program aborted
150323 22:51:09 mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended

As you can see above, it took over 5 hours for the install to eventually
fail with the dpkg: error processing package.

The libmysqlclient18:amd64 (5.6.23-1~exp1~ubuntu3) package was update
with a regular apt-get upgrade.

Let me know if you need more info.

ProblemType: Bug
DistroRelease: Ubuntu 15.04
Package: mysql-server-5.6 5.6.23-1~exp1~ubuntu3
ProcVersionSignature: Ubuntu 3.19.0-9.9-generic 3.19.1
Uname: Linux 3.19.0-9-generic x86_64
NonfreeKernelModules: fglrx
ApportVersion: 2.16.2-0ubuntu4
Architecture: amd64
CurrentDesktop: GNOME
Date: Mon Mar 23 22:46:43 2015
InstallationDate: Installed on 2014-03-10 (377 days ago)
InstallationMedia: Ubuntu-GNOME 13.10 "Saucy Salamander" - Release amd64 (20131017)
SourcePackage: mysql-5.6
UpgradeStatus: Upgraded to vivid on 2015-03-21 (2 days ago)

** Affects: mysql-5.6 (Ubuntu)
     Importance: Undecided
         Status: New

** Tags: amd64 apport-bug vivid

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https://bugs.launchpad.net/bugs/1435550

Title:
  Unable to upgrade from mysql 5.5 to 5.6

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