MySQL Error, I've tried everything I could

Question

My MySQl server was working fine yesterday, but then all the sudden this morning I've been getting this error:

[Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
[Warning] Can't create test file /usr/local/mysql-5.6.15-osx10.6-x86/data/Xero.lower-test
[Warning] Can't create test file /usr/local/mysql-5.6.15-osx10.6-x86/data/Xero.lower-test
[Note] Plugin 'FEDERATED' is disabled.
mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
[ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
[Note] InnoDB: The InnoDB memory heap is disabled
[Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
[Note] InnoDB: Compressed tables use zlib 1.2.3
[Note] InnoDB: Not using CPU crc32 instructions
[Note] InnoDB: Initializing buffer pool, size = 128.0M
[Note] InnoDB: Completed initialization of buffer pool
[ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
[ERROR] InnoDB: The system tablespace must be writable!
[ERROR] Plugin 'InnoDB' init function returned error.
[ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
[ERROR] Unknown/unsupported storage engine: InnoDB
[ERROR] Aborting

when I try mysqld

I've tried:

Reinstalling

can't start MySql in Mac OS 10.6 Snow Leopard

(since I noticed [ERROR] Unknown/unsupported storage engine: InnoDB )

http://www.debian-tutorials.com/how-to-fix-error-unknownunsupported-storage-engine-innodb

Solution

[ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
[ERROR] InnoDB: The system tablespace must be writable!

It sounds like this file (among others) is not writable by the user that mysqld is running as. Check your file permissions.

It's also possible that the file has been deleted.