Following a couple of pages from the Arch forums, I believe that I have solved this problem (or at least hidden it)
I corrected the initial mysql errors by editing the configuration file found in ~/.local/share/akonadi and commenting out the following lines:
# use InnoDB for transactions and better crash recovery
I then received new errors about being unable to lock specific tables.
, I tried the following and it solved all of the remaining mysql errors:
remove the db_data dir:
rm -r ~/.local/share/akonadi/db_data
recreate mysqldb with
worked for me.
After installing Nepomuk and setting it for desktop search and deleting the Akonadi error logs, I was left with one error: protocol version could not be verified.
I corrected/avoided this error by following the recommendations on this Arch page: https://bbs.archlinux.org/viewtopic.php?pid=772278
alternatively, go to system settings -> advanced -> kde resources, add an akonadi resource for contacts and one for the calendar and make them standard.
This will ensure that the agent starts and will also get rid of the "akonadi-is-starting" bar that appears the first time you open kmail per every session.
Afterward, you may want to remove any other pre-existing non-akonadi resource, but remember to export your data to the new akonadi resource if you don't want to lose it.
On my next reboot and opening of Kontact/Kmail, the Akonadi server bar did not show, nor did the error message. My last test ws to disable nepomuk, reboot, and load Kontact. This too successfully avoided the error screen, even though checking the logs I find that the Nepomuk DBus error is logged.
Kontact and all of the features (calendars, contacts, etc) seem to be working fine.