I am having issues cloning sites. I have narrowed it down to 2 senarios:
Works:
Create site from platfrom (i.e. Drupal 6.15)
Do nothing to it (virgin site)
Run Clone: it works
Doesn't Work:
Create site from platform
Do normal dev, install modules, themes etc...
- Modules are installed via Drush DL or FTP via SSH as root.
- Things like CKEditor need FTP uploads and can not be done solely by Drush
- This caused some ownership issues so ran verifiy, noted permission issues and made corrections via command-line
- Verify, backup and restore all work fine after resetting permissions
Run Clone: it fails with the error below (bolded)
It looks like the "Undefined index: driver" or "Undefined index: site_port" errors may be the culprit but I can't figure how to troubleshoot them (no google answers)
Here are the errors I'm getting:
...
Loading drushrc "/var/aegir/platforms/drupal-6.15/sites/www.brennercg.com/drushrc.php" into "site" scope.
Found command: updatedb
Initializing drush commandfile: drush_make
Initializing drush commandfile: drush_make_d_o
Initializing drush commandfile: provision_apache
Initializing drush commandfile: provision_drupal
Initializing drush commandfile: provision_mysql
Including version specific file : /var/aegir/drush/commands/core/drupal/update_6.inc
Drush bootstrap phase : _drush_bootstrap_drupal_configuration()
Drush bootstrap phase : _drush_bootstrap_drupal_database()
Successfully connected to the Drupal database.
Drush bootstrap phase : _drush_bootstrap_drupal_full()
Drush command could not be completed.
Output from failed command :
Undefined index: driver
Undefined index: driver
PDO support available, but the driver has not been installed. Assuming success.
An error occurred at function : drush_provision_drupal_post_provision_deploy
Undefined index: site_port
Removed apache virtual host configuration
Apache has been restarted
Changes for drush_provision_apache_post_provision_deploy module have been rolled back.
Dropping database site_402
Revoking privileges of site_402@localhost from site_402
Changes for drush_provision_mysql_provision_deploy module have been rolled back.
...

Comments
I even tried setting chmod
I even tried setting chmod 777 -R on the /sites/"example.com" directory to no avail. It appears to not be a permissions issue.
I also noticed further up the
I also noticed further up the output these errors (bold):
Created site_402 database
Found database dump at /var/aegir/platforms/drupal-6.15/sites/brennercg.com/database.sql.
Database dump at /var/aegir/platforms/drupal-6.15/sites/brennercg.com/database.sql is readable
Importing database using command: mysql --defaults-file=/dev/fd/3 site_402
Undefined index: site_port
Generating apache host configuration file brennercg.com_80.
Apache has been restarted
Generate settings.php file
Changed permissions of settings.php to 0640
Changed permissions of settings.php to 0440
Change group ownership of settings.php to www-data
Drushrc file (sites/brennercg.com/drushrc.php) was written successfully
Undefined index: root
Running: /var/aegir/drush/drush.php --uri='http://brennercg.com' --root='/var/aegir/platforms/drupal-6.15' updatedb --backend
The external command could not be executed due to an application error.
In any case, don't run drush
In any case, don't run drush as root.
Before trying to clone, make sure (twice) you have correct permissions in your Aegir dir-tree.
Next, re-verify the site and the platform you will use for cloning the site.
Also, check if there is directory or symlink left in sites/* after any broken attempt to install/verify/delete the site.
In short: you can expect many strange errors when you have invalid permissions in the Aegir system.
It is always better to fix simple things first, before looking for other reasons of errors.