macOS MySQL server issues after Yosemite upgrade

[Abhinav1993]

Hi!

I am a student learning database systems and have been working with mysql for about 3 months now. I upgraded to Yosemite last night and ever since MySQL has failed to start. I tried starting it from Workbench and gives me the following error:

Could not open error log file: [Errno 13] Permission denied: '/usr/local/mysql/data/Abhinavs-MacBook-Pro.local.err'
2014-10-18 12:22:01 - Command to start the server is not configured. Please set the command that must be used to start the server in the remote management section of this connections settings.

So I tried to start from the terminal and got this error:

$ ./mysqld
2014-10-18 12:22:37 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2014-10-18 12:22:37 24230 [Warning] Can't create test file /usr/local/mysql-5.6.19-osx10.7-x86_64/data/Abhinavs-MacBook-Pro.lower-test
2014-10-18 12:22:37 24230 [Warning] Can't create test file /usr/local/mysql-5.6.19-osx10.7-x86_64/data/Abhinavs-MacBook-Pro.lower-test
2014-10-18 12:22:37 24230 [Note] Plugin 'FEDERATED' is disabled.
./mysqld: Can't find file: './mysql/plugin.frm' (errno: 13 - Permission denied)
2014-10-18 12:22:37 24230 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2014-10-18 12:22:37 24230 [Note] InnoDB: Using atomics to ref count buffer pool pages
2014-10-18 12:22:37 24230 [Note] InnoDB: The InnoDB memory heap is disabled
2014-10-18 12:22:37 24230 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2014-10-18 12:22:37 24230 [Note] InnoDB: Compressed tables use zlib 1.2.3
2014-10-18 12:22:37 24230 [Note] InnoDB: Using CPU crc32 instructions
2014-10-18 12:22:37 24230 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2014-10-18 12:22:37 24230 [Note] InnoDB: Completed initialization of buffer pool
2014-10-18 12:22:37 24230 [ERROR] InnoDB: ./ibdata1 can't be opened in read-write mode
2014-10-18 12:22:37 24230 [ERROR] InnoDB: The system tablespace must be writable!
2014-10-18 12:22:37 24230 [ERROR] Plugin 'InnoDB' init function returned error.
2014-10-18 12:22:37 24230 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2014-10-18 12:22:37 24230 [ERROR] Unknown/unsupported storage engine: InnoDB
2014-10-18 12:22:37 24230 [ERROR] Aborting

2014-10-18 12:22:37 24230 [Note] Binlog end
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'partition'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_METRICS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMPMEM'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_CMP'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_LOCKS'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'INNODB_TRX'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'BLACKHOLE'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'ARCHIVE'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'MRG_MYISAM'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'MyISAM'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'MEMORY'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'CSV'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'sha256_password'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'mysql_old_password'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'mysql_native_password'
2014-10-18 12:22:37 24230 [Note] Shutting down plugin 'binlog'
2014-10-18 12:22:37 24230 [Note] ./mysqld: Shutdown complete

I tried to fix the table using mysql_upgrade but with no success

$ ./mysql_upgrade -u root -p
Enter password: 
Looking for 'mysql' as: ./mysql
Looking for 'mysqlcheck' as: ./mysqlcheck
FATAL ERROR: Upgrade failed

So I tried to read the errors thoroughly and I think it is a file permission issue but I have no idea how to fix that. Can someone help me?

 

[JustMartin]

It certainly looks like a permissions error. I would do a Get Info from Finder on those directories and see what the permissions are set to. You should be able to change them from that screen as well.