package mysql-server-5.7 5.7.12-0ubuntu1 failed to install/upgrade: subprocess installed post-installation script returned error exit status 1

[Prafulkr]

upgrading from 15.10 to 16.04.

ProblemType: Package
DistroRelease: Ubuntu 16.04
Package: mysql-server-5.7 5.7.12-0ubuntu1
ProcVersionSignature: Ubuntu 4.2.0-35.40-generic 4.2.8-ckt5
Uname: Linux 4.2.0-35-generic x86_64
ApportVersion: 2.20.1-0ubuntu2
Architecture: amd64
Date: Tue Apr 26 15:24:43 2016
ErrorMessage: subprocess installed post-installation script returned error exit status 1
InstallationDate: Installed on 2015-08-17 (253 days ago)
InstallationMedia: Ubuntu 14.04.1 LTS "Trusty Tahr" - Release amd64 (20140722.2)
Logs.var.log.daemon.log:

MySQLConf.etc.mysql.conf.d.mysql.cnf: [mysql]
MySQLConf.etc.mysql.conf.d.mysqld_safe_syslog.cnf:
 [mysqld_safe]
 syslog
MySQLConf.etc.mysql.conf.d.mysqldump.cnf:
 [mysqldump]
 quick
 quote-names
 max_allowed_packet = 16M
MySQLConf.etc.mysql.mysql.conf.d.mysqld_safe_syslog.cnf:
 [mysqld_safe]
 syslog
MySQLVarLibDirListing: ['task_board_tut', 'mozaic_devsite', 'browniee', 'debian-5.7.flag', 'sqaskmecpanelBKP', 'abcdef', 'bugtracker', 'chikaraks', 'sqaskmecpanel', 'jiskotwitter', 'brownie', 'rydercycles', 'test', 'ifund', 'auto.cnf', 'trackerror', 'apiEcommDB', 'mysql_upgrade_info', 'debian-5.6.flag', 'pk_cscart', 'saashi', 'ux', 'tweetDB', 'debian-5.5.flag', 'wordpress', 'pk_oscomm', 'pk_magentoo', 'bowty', 'pk_mybrokers', 'skypeDB', 'testing', 'onida', 'mysql', 'socialnets', 'whm2', 'houseofnirvana', 'performance_schema', 'phonebook', 'pk_wp@002decomm', 'flyspray', 'volarbus', 'mem_test', 'localfacebook', 'prafulkr@002dtest', 'oppcart', 'sq_androidDB', 'socialEngine', 'opencartThemesTesting', 'ibtmp1', 'ibdata1', 'study@002dlocal', 'ib_logfile1', 'newopct', 'uexchange', 'chikaraksworld', 'olliphans', 'ifundDB', 'magentoDB', 'sys', 'oppcarts', 'guestbook', 'pk_englishWd', 'ib_logfile0', 'sq_offersTesting', 'sqaskmecpanell', 'magentodatabse', 'sq_offers']
ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-4.2.0-35-generic.efi.signed root=UUID=8e69da17-cf5e-4670-9c1c-c61d1a5cae11 ro quiet splash vt.handoff=7
RelatedPackageVersions:
 dpkg 1.18.4ubuntu1
 apt 1.2.10ubuntu1
SourcePackage: mysql-5.7
Title: package mysql-server-5.7 5.7.12-0ubuntu1 failed to install/upgrade: subprocess installed post-installation script returned error exit status 1
UpgradeStatus: Upgraded to xenial on 2016-04-26 (0 days ago)

[Robie Basak (racb)]

From log:

Setting up mysql-server-5.7 (5.7.12-0ubuntu1) ...
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/mysql/mysql.conf.d/mysqld.cnf ...
invoke-rc.d: Unit mysql.service is masked
update-alternatives: using /etc/mysql/mysql.cnf to provide /etc/mysql/my.cnf (my.cnf) in auto mode
Checking if update is needed.
Checking server version.
Running queries to upgrade MySQL server.
mysql_upgrade: [ERROR] 1813: Tablespace '`mysql`.`innodb_table_stats`' exists.
mysql_upgrade failed with exit status 5
dpkg: error processing package mysql-server-5.7 (--configure):
 subprocess installed post-installation script returned error exit status 1

error.log has various errors of the form:

2016-04-26T09:54:39.310881Z 0 [ERROR] /usr/sbin/mysqld: Can't find file: './performance_schema/cond_instances.frm' (errno: 13 - Permission denied)

[Robie Basak (racb)]

Thank you for taking the time to report this bug and helping to make Ubuntu better.

It's not clear to me if this is a duplicate of bug 1571764 or if there is a separate problem here. For now, I'll mark the dupe. Then the performance_schema related issues can all be addressed together more easily.