package mysql-server-5.7 5.7.13-0ubuntu0.16.04.2 failed to install/upgrade: subprocess installed post-installation script returned error exit status 1

[Shevek]

shevek@raven:~$ sudo apt-get dist-upgrade
Reading package lists... Done
Building dependency tree
Reading state information... Done
Calculating upgrade... Done
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
2 not fully installed or removed.
After this operation, 0 B of additional disk space will be used.
Do you want to continue? [Y/n]
Setting up mysql-server-5.7 (5.7.13-0ubuntu0.16.04.2) ...
Renaming removed key_buffer and myisam-recover options (if present)
insserv: warning: current start runlevel(s) (empty) of script `mysql' overrides LSB defaults (2 3 4 5).
insserv: warning: current stop runlevel(s) (0 1 2 3 4 5 6) of script `mysql' overrides LSB defaults (0 1 6).
mysql_upgrade: Got error: 2002: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2) while connecting to the MySQL server
Upgrade process encountered error and will not continue.
mysql_upgrade failed with exit status 11
dpkg: error processing package mysql-server-5.7 (--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-5.7; however:
  Package mysql-server-5.7 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.
                          Errors were encountered while processing:
 mysql-server-5.7
 mysql-server
E: Sub-process /usr/bin/dpkg returned an error code (1)

ProblemType: Package
DistroRelease: Ubuntu 16.04
Package: mysql-server-5.7 5.7.13-0ubuntu0.16.04.2
ProcVersionSignature: Ubuntu 4.4.0-31.50-generic 4.4.13
Uname: Linux 4.4.0-31-generic x86_64
ApportVersion: 2.20.1-0ubuntu2.1
Architecture: amd64
Date: Fri Jul 22 09:36:06 2016
ErrorMessage: subprocess installed post-installation script returned error exit status 1
InstallationDate: Installed on 2015-05-18 (430 days ago)
InstallationMedia: Xubuntu 15.04 "Vivid Vervet" - Release amd64 (20150422.1)
Logs.var.log.daemon.log:

MySQLConf.etc.mysql.conf.d.mysql.cnf: [mysql]
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: ['debian-5.7.flag', 'mysql', 'ib_logfile1', 'ib_buffer_pool', 'ib_logfile0', 'mysql_upgrade_info', 'sys', 'debian-5.6.flag', 'ibdata1', 'hive', 'auto.cnf', 'performance_schema']
ProcCmdline: BOOT_IMAGE=/vmlinuz-4.4.0-31-generic.efi.signed root=/dev/mapper/xubuntu--vg-root ro noprompt persistent quiet splash vt.handoff=7
RelatedPackageVersions:
 dpkg 1.18.4ubuntu1.1
 apt 1.2.12~ubuntu16.04.1
SourcePackage: mysql-5.7
Title: package mysql-server-5.7 5.7.13-0ubuntu0.16.04.2 failed to install/upgrade: subprocess installed post-installation script returned error exit status 1
UpgradeStatus: Upgraded to xenial on 2016-06-23 (29 days ago)
upstart.mysql.override: manual

[Launchpad Janitor (janitor)]

Status changed to 'Confirmed' because the bug affects multiple users.

[Ivan (hyllo.ivan)]

Have a look at the following: https://github.com/ankane/groupdate#for-mysql

Could this bug be related to the script that's linked where it says:

   "or copy and paste these statements into a SQL console." ?

Might be unrelated, but if someone's trying to solve this, take a peak...I'm just guessing.

[Shevek (r-launchpad-anarres-org)]

shevek@raven:~$ sudo dpkg --debug=3 --configure mysql-server-5.7
D000001: ensure_diversions: new, (re)loading
D000001: process queue pkg mysql-server-5.7:amd64 queue.len 0 progress 1, try 1
Setting up mysql-server-5.7 (5.7.13-0ubuntu0.16.04.2) ...
D000002: fork/exec /var/lib/dpkg/info/mysql-server-5.7.postinst ( configure 5.7.12-0ubuntu1.1 )
+ . /usr/share/debconf/confmodule
++ '[' '!' '' ']'
++ PERL_DL_NONLAZY=1
++ export PERL_DL_NONLAZY
++ '[' '' ']'
++ exec /usr/share/debconf/frontend /var/lib/dpkg/info/mysql-server-5.7.postinst configure 5.7.12-0ubuntu1.1
+ . /usr/share/debconf/confmodule
++ '[' '!' 1 ']'
++ '[' -z '' ']'
++ exec
++ '[' '' ']'
++ exec
++ DEBCONF_REDIR=1
++ export DEBCONF_REDIR
+ '[' -n '' ']'
+ export PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin:/usr/sbin:/bin:/usr/bin
+ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin:/usr/sbin:/bin:/usr/bin
+ ERR_LOGGER='logger -p daemon.err -t mysqld_safe -i'
+ set +e
+ invoke stop
+ pathfind invoke-rc.d
+ OLDIFS='
'
+ IFS=:
+ for p in '$PATH'
+ '[' -x /usr/local/sbin/invoke-rc.d ']'
+ for p in '$PATH'
+ '[' -x /usr/local/bin/invoke-rc.d ']'
+ for p in '$PATH'
+ '[' -x /usr/sbin/invoke-rc.d ']'
+ IFS='
'
+ return 0
+ invoke-rc.d mysql stop
+ set -e
+ case "$1" in
+ mysql_datadir=/usr/share/mysql
+ mysql_statedir=/var/lib/mysql
+ mysql_rundir=/var/run/mysqld
+ mysql_logdir=/var/log/mysql
+ mysql_cfgdir=/etc/mysql
+ mysql_upgradedir=/var/lib/mysql-upgrade
+ mysql_filesdir=/var/lib/mysql-files
+ mysql_keyringdir=/var/lib/mysql-keyring
+ aa-status --enabled
+ apparmor_parser -r -T -W /etc/apparmor.d/usr.sbin.mysqld
+ /usr/share/mysql-common/configure-symlinks install mysql /etc/mysql/mysql.cnf
+ for d in '$mysql_statedir' '$mysql_filesdir' '$mysql_keyringdir' '$mysql_logdir'
+ '[' '!' -d /var/lib/mysql -a '!' -L /var/lib/mysql ']'
+ chown -R mysql:mysql /var/lib/mysql
+ chmod 0700 /var/lib/mysql
+ for d in '$mysql_statedir' '$mysql_filesdir' '$mysql_keyringdir' '$mysql_logdir'
+ '[' '!' -d /var/lib/mysql-files -a '!' -L /var/lib/mysql-files ']'
+ chown -R mysql:mysql /var/lib/mysql-files
+ chmod 0700 /var/lib/mysql-files
+ for d in '$mysql_statedir' '$mysql_filesdir' '$mysql_keyringdir' '$mysql_logdir'
+ '[' '!' -d /var/lib/mysql-keyring -a '!' -L /var/lib/mysql-keyring ']'
+ chown -R mysql:mysql /var/lib/mysql-keyring
+ chmod 0700 /var/lib/mysql-keyring
+ for d in '$mysql_statedir' '$mysql_filesdir' '$mysql_keyringdir' '$mysql_logdir'
+ '[' '!' -d /var/log/mysql -a '!' -L /var/log/mysql ']'
+ chown -R mysql:mysql /var/log/mysql
+ chmod 0700 /var/log/mysql
+ set +e
+ chown -R 0:0 /usr/share/mysql
+ touch /var/log/mysql/error.log
+ chown -R mysql:adm /var/log/mysql
+ chmod 0750 /var/log/mysql
+ chmod 0640 /var/log/mysql/error.log
+ set -e
+ db_set mysql-server/postrm_remove_database false
+ _db_cmd 'SET mysql-server/postrm_remove_database' false
+ _db_internal_IFS='
'
+ IFS=' '
+ printf '%s\n' 'SET mysql-server/postrm_remove_database false'
+ IFS='
'
+ IFS='
'
+ read -r _db_internal_line
+ RET='10 mysql-server/postrm_remove_database doesn'\''t exist'
+ case ${_db_internal_line%%[ ]*} in
+ return 10
+ true
+ dpkg --compare-versions 5.7....

[Shevek (r-launchpad-anarres-org)]

The problem is that invoke-rc.d is not invoking mysql's start-stop script properly. Swapping 'invoke-rc.d' for 'service' in invoke() makes the script succeed. My system is now correctly configured.

[Shevek (r-launchpad-anarres-org)]

When I say "invoke-rc.d is not working", I mean that a service status on the service suggests that invoke-rc.d did nothing whatsoever. No errors, nothing. The mysql service didn't even notice that invoke-rc.d had been run.

[Chris Siebenmann (cks)]

When this happened to us during a mysql-server upgrade, the root
cause is that we had mysql (the server) disabled, ie 'systemctl disable
mysql'. When you do this, 'invoke-rc.d mysql start' winds up doing nothing
and not starting the server, which causes mysql_upgrade to fail because
it requires a running server.

Explicitly starting mysql before you do the upgrade doesn't help,
because the mysql-server-5.7 postinst script starts out by shutting it
down. What does work around the issue is re-enabling mysql beforehand:
'systemctl enable mysql', do the upgrade, then 'systemctl disable mysql;
systemctl stop mysql'.

(Invoke-rc.d does not directly ask systemd for the status of mysql.
Instead it looks at /etc/rc5.d/ S* and K* symlinks, which systemctl
manipulates for systemd services that also have an /etc/init.d
script, which mysql does. Finding this takes tracing through a lot
of layers.)

A correct bugfix for our issue would be for the mysql-server postinst
script to unconditionally start mysql using eg 'service mysql start',
instead of relying on invoke-rc.d. The ideal sequence would be to
explicitly start mysql, run mysql_upgrade, shut mysql down, and then run
'invoke-rc.d mysql start' to restart it only if it's been enabled.

[Shevek (r-launchpad-anarres-org)]

@cks You are correct, I also have the mysql service disabled, which explains the behaviour of rc.d. Editing the postinst script to use service instead of invoke-rc.d did fix it, though.