In both error logs, I see this sequence (with varying timestamps and seq
numbers, of course):

2015-03-29 15:03:37 2265 [Note] InnoDB: The log sequence numbers 10740390801 
and 10740390801 in ibdata files do not match the log sequence number 
11404279789 in the ib_logfiles!
2015-03-29 15:03:37 2265 [Note] InnoDB: Database was not shutdown normally!
2015-03-29 15:03:37 2265 [Note] InnoDB: Starting crash recovery.

I think that's the core of the problem. 5.5 was not shut down properly
before upgrading, so it's left to 5.6 to try to recover. For some reason
it can't, and it crashes.

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https://bugs.launchpad.net/bugs/1437846

Title:
  akonadi mysql 5.6 crash with signal 11

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