Public bug reported:

I may have messed up the setuid bits in /usr.
I wasn't paying attention when I did a chmod -R as root. I thought I fixed them 
all because "Software Center" and "MySQL" were working fine again, after I 
compared all files with "rws" with my Ubuntu 16.04 system and updated the 16.10 
system with that permission. Now that, "Software Center" doesn't install with 
Polkit and I got this error, I assume it's related to file ownership or setuid.

Maybe this isn't a bug per se, but it would be nice to get some pointer
from the error message for users who tend to be oblivious like me when
doing "User" stuff v. "Developer" stuff (well - I'm oblivious then too,
at times. :->)

ProblemType: Package
DistroRelease: Ubuntu 16.10
Package: mysql-common 5.7.16-0ubuntu0.16.10.1
ProcVersionSignature: Ubuntu 4.8.0-26.28-generic 4.8.0
Uname: Linux 4.8.0-26-generic x86_64
ApportVersion: 2.20.3-0ubuntu8
Architecture: amd64
Date: Wed Oct 26 21:14:07 2016
Dependencies:
 
DuplicateSignature:
 package:mysql-common:5.7.16-0ubuntu0.16.10.1
 Setting up mysql-common (5.7.16-0ubuntu0.16.10.1) ...
 update-alternatives: error: unable to read link '/etc/alternatives/my.cnf': 
Invalid argument
 dpkg: error processing package mysql-common (--configure):
  subprocess installed post-installation script returned error exit status 2
ErrorMessage: subprocess installed post-installation script returned error exit 
status 2
InstallationDate: Installed on 2016-10-25 (4 days ago)
InstallationMedia: Ubuntu 16.10 "Yakkety Yak" - Release amd64 (20161012.2)
Logs.var.log.daemon.log:
 
Logs.var.log.mysql.error.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: ['ibdata1', 'mysql', 'performance_schema', 'auto.cnf', 
'ib_buffer_pool', 'sys', 'ib_logfile0', 'gc2014', 'ib_logfile1', 'ibtmp1']
PackageArchitecture: all
ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-4.8.0-26-generic.efi.signed 
root=UUID=62b3af60-dc9d-4a03-9c45-7dae0e1c162f ro quiet splash vt.handoff=7
RelatedPackageVersions:
 dpkg 1.18.10ubuntu1
 apt  1.3.1
SourcePackage: mysql-5.7
Title: package mysql-common 5.7.16-0ubuntu0.16.10.1 failed to install/upgrade: 
subprocess installed post-installation script returned error exit status 2
UpgradeStatus: No upgrade log present (probably fresh install)

** Affects: mysql-5.7 (Ubuntu)
     Importance: Undecided
         Status: New


** Tags: amd64 apport-package need-duplicate-check yakkety

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https://bugs.launchpad.net/bugs/1637770

Title:
  package mysql-common 5.7.16-0ubuntu0.16.10.1 failed to
  install/upgrade: subprocess installed post-installation script
  returned error exit status 2

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