Bom dia! Instalei o mysql a partir do apt-get. Já tinha em minha máquina o servidor 5.5.41, deste modo instalei a versão 5.6.23, sobrescrevendo o antigo. Depois rodei o mysql_upgrade. Quando reinicio o MySQL aparece esta mensagem:

#etc/init.d/mysql reload
[info] Stopping MySQL Community Server 5.6.23.
....
[info] MySQL Community Server 5.6.23 is stopped.
[info] Re-starting MySQL Community Server 5.6.23.
Sem diretório, logando com HOME=/
......
[info] MySQL Community Server 5.6.23 is started.

Como resolver esta localização do diretório? Já olhei no my.cnf e me parece estar tudo ok:

[client]
port = 3306
socket = /var/run/mysqld/mysqld.sock

[mysqld_safe]
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
nice = 0

[mysqld]
user = mysql
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
port = 3306
basedir = /usr
datadir = /var/lib/mysql
tmpdir = /tmp
lc-messages-dir = /usr/share/mysql
explicit_defaults_for_timestamp

Instead of skip-networking the default is now to listen only on

localhost which is more compatible and is not less secure.

bind-address = 127.0.0.1

No log de erros:

150323 11:59:39 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
2015-03-23 11:59:39 22794 [Warning] Buffered warning: Changed limits: max_open_files: 1024 (requested 500$
2015-03-23 11:59:39 22794 [Warning] Buffered warning: Changed limits: table_cache: 431 (requested 2000)
2015-03-23 11:59:39 22794 [Note] Plugin 'FEDERATED' is disabled.
2015-03-23 11:59:39 22794 [Note] InnoDB: Using atomics to ref count buffer pool pages

2015-03-23 11:59:39 22794 [Note] InnoDB: The InnoDB memory heap is disabled
2015-03-23 11:59:39 22794 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-03-23 11:59:39 22794 [Note] InnoDB: Memory barrier is not used
2015-03-23 11:59:39 22794 [Note] InnoDB: Compressed tables use zlib 1.2.7
2015-03-23 11:59:39 22794 [Note] InnoDB: Using Linux native AIO
2015-03-23 11:59:39 22794 [Note] InnoDB: Not using CPU crc32 instructions
2015-03-23 11:59:39 22794 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2015-03-23 11:59:39 22794 [Note] InnoDB: Completed initialization of buffer pool
2015-03-23 11:59:39 22794 [Note] InnoDB: Highest supported file format is Barracuda.
2015-03-23 11:59:39 22794 [Note] InnoDB: 128 rollback segment(s) are active.
2015-03-23 11:59:39 22794 [Note] InnoDB: Waiting for purge to start
2015-03-23 11:59:39 22794 [Note] InnoDB: 5.6.23 started; log sequence number 1629946
2015-03-23 11:59:39 22794 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
2015-03-23 11:59:39 22794 [Note] - '127.0.0.1' resolves to '127.0.0.1';
2015-03-23 11:59:39 22794 [Note] Server socket created on IP: '127.0.0.1'.
2015-03-23 11:59:39 22794 [Note] Event Scheduler: Loaded 0 events
2015-03-23 11:59:39 22794 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.23' socket: '/var/run/mysqld/mysqld.sock' port: 3306 MySQL Community Server (GPL)