Ok, once I ran the mysql_install_db command as a normal user I got this:

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Installing MySQL system tables...
091223 14:40:32 [Warning] Can't create test file /var/lib/mysql/ederico-laptop.lower-test
091223 14:40:32 [Warning] Can't create test file /var/lib/mysql/ederico-laptop.lower-test
091223 14:40:32 [ERROR] /usr/sbin/mysqld: Can't find file: './mysql/db.frm' (errno: 13)
ERROR: 1017  Can't find file: './mysql/db.frm' (errno: 13)
091223 14:40:32 [ERROR] Aborting

091223 14:40:32 [Warning] Forcing shutdown of 2 plugins
091223 14:40:32 [Note] /usr/sbin/mysqld: Shutdown complete


Installation of system tables failed!  Examine the logs in
/var/lib/mysql for more information.

You can try to start the mysqld daemon with:

    shell> /usr/sbin/mysqld --skip-grant &

and use the command line tool /usr/bin/mysql
to connect to the mysql database and look at the grant tables:

    shell> /usr/bin/mysql -u root mysql
    mysql> show tables

Try 'mysqld --help' if you have problems with paths.  Using --log
gives you a log in /var/lib/mysql that may be helpful.

The latest information about MySQL is available on the web at
http://www.mysql.com/.  Please consult the MySQL manual section
'Problems running mysql_install_db', and the manual section that
describes problems on your OS.  Another information source are the
MySQL email archives available at http://lists.mysql.com/.

Please check all of the above before mailing us!  And remember, if
you do mail us, you MUST use the /usr/scripts/mysqlbug script!

The command to stop apparmor should have have worked, as I got an OK.

Did you have the correct argument passed to it?

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mysql_install_db --datadir=$HOME/.local/share/akonadi/db_data/

No, I just typed mysql_install_db. Yet, reunning the last command you posted gave me the same results.

Were they exactly the same? If so, the passing of arguments may not have happened correctly.

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091223 14:40:32 [Warning] Can't create test file /var/lib/mysql/ederico-laptop.lower-test
091223 14:40:32 [Warning] Can't create test file /var/lib/mysql/ederico-laptop.lower-test
091223 14:40:32 [ERROR] /usr/sbin/mysqld: Can't find file: './mysql/db.frm' (errno: 13)
ERROR: 1017  Can't find file: './mysql/db.frm' (errno: 13)

I did it again, and this is what I got. Unless my sight betrayed me, they seemed the same when I did it before:

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Installing MySQL system tables...
091225 19:28:21 [Warning] Can't create test file /home/ederico/.local/share/akonadi/db_data/ederico-laptop.lower-test
091225 19:28:21 [Warning] Can't create test file /home/ederico/.local/share/akonadi/db_data/ederico-laptop.lower-test
ERROR: 1005  Can't create table 'db' (errno: 13)
091225 19:28:21 [ERROR] Aborting

091225 19:28:21 [Warning] Forcing shutdown of 2 plugins
091225 19:28:21 [Note] /usr/sbin/mysqld: Shutdown complete


Installation of system tables failed!  Examine the logs in
/home/ederico/.local/share/akonadi/db_data/ for more information.

You can try to start the mysqld daemon with:

    shell> /usr/sbin/mysqld --skip-grant &

and use the command line tool /usr/bin/mysql
to connect to the mysql database and look at the grant tables:

    shell> /usr/bin/mysql -u root mysql
    mysql> show tables

Try 'mysqld --help' if you have problems with paths.  Using --log
gives you a log in /home/ederico/.local/share/akonadi/db_data/ that may be helpful.

The latest information about MySQL is available on the web at
http://www.mysql.com/.  Please consult the MySQL manual section
'Problems running mysql_install_db', and the manual section that
describes problems on your OS.  Another information source are the
MySQL email archives available at http://lists.mysql.com/.

Please check all of the above before mailing us!  And remember, if
you do mail us, you MUST use the /usr/scripts/mysqlbug script!


Unfortunately I have no idea why this is occuring then, however it is likely something related to your distributions configuration which is denying mysql_install_db write access to Akonadi's db. Please contact your distribution to determine why this occurs.

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sudo /etc/init.d/apparmor stop
sudo chown $(id -un):$(id -gn) $HOME/.local/share/akonadi/db_data/
chmod 744 -R $HOME/.local/share/akonadi/db_data
mysql_install_db --datadir=$HOME/.local/share/akonadi/db_data/