MySQL error 2006 MySQL server has gone away after upgrade to 5.6.10 using homebrew on Max OS X 10.8.3

Question

I upgraded my installation of MySQL on my Mac OS X 10.8.3 using homebrew

brew install mysql

Everything seemed to go smoothly, but...not really, as it turns out.

I cannot add a new user (neither through the command line nor through phpmyadmin. I always get the error

Error in processing request: #2006 MySQL server has gone away

I can create new databases without a problem, and I can install, for example Joomla 3.1.1 with no problems.

However, when I try to install a new extension into my Joomla installation, I get errors. For example, I get the following error when I try to install a component from NoNumber:

1062 Duplicate entry '1' for key 'PRIMARY' SQL=INSERT INTO `u5z87_extensions` (`name`,`type`,`element`,`folder`,`client_id`,`enabled`,`access`) VALUES ('plg_system_nnframework','plugin','nnframework','system','0','1','1')

Same thing for many other extensions.

I tried to start mysql with

mysql.server start --log-warnings=2

and it started with no problem

Starting MySQL
 SUCCESS!

I looked up issues where error #2006 were being reported and how to solve them, and they referred to modifying /etc/my.cnf but there is no /etc/my.cnf configuration file on my system, and there wasn't one in the previous installation of MySQL 5.5.29 (also installed with homebrew) and I had no problems.

I ran brew doctor and the output is below

$ brew doctor
Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:

    /usr/local/opt/php54/bin/php-config

The output from brew --config is also below:

$ brew --config
HOMEBREW_VERSION: 0.9.4
ORIGIN: https://github.com/mxcl/homebrew
HEAD: 86ce842c700a47abdc354e80cc3b0b3938ab2132
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: 8-core 64-bit nehalem
OS X: 10.8.3-x86_64
Xcode: 4.6.2
CLT: 4.6.0.0.1.1365549073
LLVM-GCC: build 2336
Clang: 4.2 build 425
X11: 2.7.4 => /opt/X11
System Ruby: 1.8.7-358
Perl: /usr/bin/perl
Python: /usr/bin/python
Ruby: /Users/alisamii/.rvm/rubies/ruby-1.9.3-p374/bin/ruby

Exploring a little further, I tried to revert to my previous install of MySQL using

brew switch mysql 5.5.29

This resulted in the following output:

$ brew switch mysql 5.5.29
Cleaning /usr/local/Cellar/mysql/5.5.29
Cleaning /usr/local/Cellar/mysql/5.6.10
135 links created for /usr/local/Cellar/mysql/5.5.29

I then accessed mysql from the command line and ran status:

mysql> status
--------------
mysql  Ver 14.14 Distrib 5.5.29, for osx10.8 (i386) using readline 5.1

Connection id:      13
Current database:
Current user:       alisamii@localhost
SSL:            Not in use
Current pager:      stdout
Using outfile:      ''
Using delimiter:        ;
Server version:     5.6.10 Source distribution
Protocol version:       10
Connection:         Localhost via UNIX socket
Server characterset:    utf8
Db     characterset:    utf8
Client characterset:    utf8
Conn.  characterset:    utf8
UNIX socket:        /tmp/mysql.sock
Uptime:         1 hour 56 min 24 sec

As you can see above, it reports mysql Ver 14.14 Distrib 5.5.29, for osx10.8 (i386) using readline 5.1

But, it also says Server version: 5.6.10 Source distribution

So something isn't syncing up.

Furthermore, when I show databases, I get the following output:

mysql> show databases
    -> ;
+--------------------+
| Database           |
+--------------------+
| information_schema |
+--------------------+
1 row in set (0.00 sec)

But I know I have more than just an information_schema database.

So, somehow, it seems to me that mysql is not connecting to the right server, as phpmyadmin reports the same server information that mysql's status command reports: Software version: 5.6.10 - Source distribution.

At this point, I am completely lost, and would really need some help.

Answer 1

OK, so partially resolved the issue.

At the recommendation of https://stackoverflow.com/users/201789/tehshrike I read the pages related to mysql_update and followed the recommendations there.

Upgrading MySQL does not upgrade the information_schema, and so some things don't work. This command helps fix some of those issues.

Now, I can add new users and the #2006 - MySQL server has gone away error is no longer an issue.

However, I am still getting the #1062 errors when trying to install extensions in Joomla, for example. Still exploring solutions to that. Will update this answer with details when solved.