MacOS – MySQL fails to start after update

I am on Yosemite 10.10.5 and just now I updated my outdated MySQL to the latest version. I made a copy of my existing databases /usr/local/mysql/data/ somewhere safe.

I have tried to setup MySQL both via brew & via the package installer, but seems I managed to mess up with both ways.

There is a new icon in preferences panel that was created via the package installer but it doesn't seem to start MySQL.

I tried running mysql.server start on terminal but i received the following error:

Starting MySQL
. ERROR! The server quit without updating PID file (/usr/local/var/mysql/myname.local.pid).

I tried brew services start mysql and I get:

==> Successfully started `mysql` (label: homebrew.mxcl.mysql)

But I can't access to it via Sequel Pro or via Terminal. Since brew services starts mysql, I try mysql but I get:

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)

I have the following logs at /usr/local/var/mysql/myname.local.err

2016-03-30T21:58:53.6NZ mysqld_safe Starting mysqld daemon with databases from /usr/local/mysql/data
2016-03-30T21:58:53.791807Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-03-30T21:58:53.792478Z 0 [Warning] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.
2016-03-30T21:58:53.792493Z 0 [Warning] 'NO_AUTO_CREATE_USER' sql mode was not set.
2016-03-30T21:58:53.792573Z 0 [Warning] Insecure configuration for --secure-file-priv: Current value does not restrict location of generated files. Consider setting it to a valid, non-empty path.
2016-03-30T21:58:53.793639Z 0 [Note] /usr/local/mysql/bin/mysqld (mysqld 5.7.11) starting as process 5922 ...
2016-03-30T21:58:53.807159Z 0 [Warning] Setting lower_case_table_names=2 because file system for /usr/local/mysql/data/ is case insensitive
2016-03-30T21:58:53.829847Z 0 [ERROR] Plugin keyring_file reported: 'keyring_file initialization failure. Please check if the keyring_file_data points to readable keyring file or keyring file can be created in the specified location. The keyring_file will stay unusable until correct path to the keyring file gets provided'
2016-03-30T21:58:53.834848Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
...
2016-03-30T21:58:54.063594Z 0 [Note] InnoDB: Loading buffer pool(s) from /usr/local/mysql-5.7.11-osx10.9-x86_64/data/ib_buffer_pool
2016-03-30T21:58:54.065139Z 0 [Note] Plugin 'FEDERATED' is disabled.
2016-03-30T21:58:54.066443Z 0 [Note] InnoDB: Buffer pool(s) load completed at 160331  0:58:54
2016-03-30T21:58:54.073134Z 0 [Warning] System table 'plugin' is expected to be transactional.
2016-03-30T21:58:54.081061Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2016-03-30T21:58:54.083246Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2016-03-30T21:58:54.090221Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2016-03-30T21:58:54.090273Z 0 [Note] IPv6 is available.
2016-03-30T21:58:54.090299Z 0 [Note]   - '::' resolves to '::';
2016-03-30T21:58:54.090310Z 0 [Note] Server socket created on IP: '::'.
2016-03-30T21:58:54.091554Z 0 [Warning] Failed to open optimizer cost constant tables

2016-03-30T21:58:54.099383Z 0 [ERROR] Fatal error: mysql.user table is damaged. Please run mysql_upgrade.
2016-03-30T21:58:54.099725Z 0 [ERROR] Aborting

2016-03-30T21:58:54.099763Z 0 [Note] Binlog end
2016-03-30T21:58:54.100531Z 0 [Note] Shutting down plugin 'ngram'
...
2016-03-30T21:58:55.476257Z 0 [Note] Shutting down plugin 'binlog'
2016-03-30T21:58:55.476370Z 0 [Note] /usr/local/mysql/bin/mysqld: Shutdown complete

2016-03-30T21:58:55.6NZ mysqld_safe mysqld from pid file /usr/local/mysql/data/myuser.local.pid ended