The new drush make based upgrade process for Aegir is very difficult at the moment. There are 2 main cases we have here :

1) upgrades from aegir releases before 0.4 alpha 2
2) upgrades from aegir 0.4 alpha 2

The process should be :

a) upgrade drush to drush 2.1
b) upgrade provision to the new alpha
c) download the latest beta of drush make
d) run 'drush hostmaster make /path/to/new/platform'
e) cd /path/to/old/platform
f) run 'drush hostmaster migrate site.com /path/to/new/platform

So here are the following issues :

a) when drush is updated to 2.1, the queue stops working because of drupal.org/node/586466 and the fact that the drush_scan_directory parameters have changed
b) to get the newest release, with the additional dependencies it is recommended that you use drush make, which requires the new HEAD.
c) The jquery_ui and modalframe modules, and the jquery ui library needs to be present before you can run the update functions, or http://drupal.org/node/620686 happens.
d) 0.4 alpha 2 already has a hostmaster park command, which validates that the platform you are migrating to has already been added, but to get the new platform you need the new backend and if you have the new backend your task queue is broken.
e) because of the changes in drush, a new platform won't be able to get verified and added and for the settings to propogate to the target platform, it needs to be verified by the front end, otherwise the drushrc.php file is incorrect.
f) when you follow through with the process anyway you get the following AND the sites directory on the target platform is wiped out completely :

aegir@ubuntu:~/drupal-6.13$ php /var/aegir/drush/drush.php hostmaster migrate aegir.vm /var/aegir/hm-0.4-alpha3 --debug
Drush bootstrap phase : _drush_bootstrap_drupal_root() [0.086 sec]   [bootstrap]
Loading drushrc "/var/aegir/drupal-6.13/drushrc.php" into "drupal"   [bootstrap]
scope. [0.087 sec]
Initialized Drupal 6.13 root directory at /var/aegir/drupal-6.13        [notice]
[0.104 sec]
Found command: hostmaster migrate [0.111 sec]                        [bootstrap]
Initializing drush commandfile: provision_apache [0.112 sec]         [bootstrap]
Initializing drush commandfile: provision_drupal [0.113 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [0.113 sec]          [bootstrap]
Including /var/aegir/.drush/provision/migrate.hostmaster.inc [0.114  [bootstrap]
sec]
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--master_url='http://aegir.vm'
--publish_path='/var/aegir/drupal-6.13' --web_host='aegir.vm'
--web_group='www-data' --script_user='aegir' --restart_cmd='sudo
/usr/sbin/apache2ctl graceful' --backup_path='/var/aegir/backups'
--config_path='/var/aegir/config'
--master_db='mysqli://aegir:pass@localhost' --debug
--root='/var/aegir/hm-0.4-alpha3' --r='/var/aegir/hm-0.4-alpha3' 
'provision' 'verify' --backend [0.117 sec]
Undefined variable: context [0.118 sec]                                 [notice]
Undefined variable: string [0.689 sec]                                  [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.69 sec]      [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.69 sec]      [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.691 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.691 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.692 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.692 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.693 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.715 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [0.715 sec]     [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [0.717 sec]         [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [0.717 sec]   [bootstrap]
Initialized Drupal 6.14 root directory at /var/aegir/hm-0.4-alpha3      [notice]
[0.718 sec]
Found command: provision verify [0.718 sec]                          [bootstrap]
Initializing drush commandfile: provision_apache [0.718 sec]         [bootstrap]
Undefined index:  base_url [0.718 sec]                                  [notice]
Initializing drush commandfile: provision_drupal [0.718 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [0.719 sec]          [bootstrap]
Undefined index:  db_url [0.719 sec]                                    [notice]
Including /var/aegir/.drush/provision/web_server/verify.provision.inc[bootstrap]
[0.719 sec]
Including /var/aegir/.drush/provision/platform/verify.provision.inc  [bootstrap]
[0.719 sec]
Including /var/aegir/.drush/provision/db_server/verify.provision.inc [bootstrap]
[0.719 sec]
Including /var/aegir/.drush/provision/ssl/verify.provision.inc [0.72 [bootstrap]
sec]
Virtual host configuration path exists. [0.72 sec]                     [message]
Virtual host configuration ownership of path has been changed to       [message]
aegir. [0.72 sec]
Virtual host configuration permissions of path have been changed to    [message]
0700. [0.721 sec]
Virtual host configuration path is writable. [0.721 sec]               [message]
Undefined index:  platform [0.721 sec]                                  [notice]
Generating apache host configuration file platform_.conf. [0.721 sec]   [notice]
Generating apache host configuration file aegir.vm.server. [0.721       [notice]
sec]
Executing: sudo /usr/sbin/apache2ctl graceful [0.721 sec]               [notice]
Apache has been restarted [0.722 sec]                                   [notice]
Provision configuration path exists. [0.722 sec]                       [message]
Provision configuration ownership of path has been changed to aegir.   [message]
[0.722 sec]
Provision configuration permissions of path have been changed to       [message]
0711. [0.722 sec]
Provision configuration path is writable. [0.722 sec]                  [message]
Provision PHP configuration path exists. [0.723 sec]                   [message]
Provision PHP configuration ownership of path has been changed to      [message]
aegir. [0.723 sec]
Provision PHP configuration permissions of path have been changed to   [message]
0711. [0.723 sec]
Provision PHP configuration path is writable. [0.723 sec]              [message]
Global configuration file exists [0.723 sec]                           [message]
Backup path exists. [0.724 sec]                                        [message]
Backup ownership of path has been changed to aegir. [0.724 sec]        [message]
Backup permissions of path have been changed to 0700. [0.724 sec]      [message]
Backup path is writable. [0.724 sec]                                   [message]
Drupal sites directory is writable by the provisioning script [0.724   [message]
sec]
Undefined variable: sites [0.726 sec]                                   [notice]
This platform is running drupal 6.14 [0.726 sec]                        [notice]
Including non-version specific file :                                   [notice]
/var/aegir/.drush/provision/platform/drupal/packages.inc [0.726 sec]
Found 33 modules in base [0.727 sec]                                    [notice]
Found 6 themes in base [0.727 sec]                                      [notice]
Found install profile hostmaster [0.728 sec]                            [notice]
Found install profile default [0.728 sec]                               [notice]
Found 19 modules in profiles/hostmaster [0.728 sec]                     [notice]
Found 1 themes in profiles/hostmaster [0.729 sec]                       [notice]
Mysql can create new databases. [0.729 sec]                            [message]
Generating drushrc.php file [0.73 sec]                                  [notice]
Drushrc file (/var/aegir/hm-0.4-alpha3/drushrc.php) was written         [notice]
successfully [0.73 sec]
Changed permissions of drushrc.php to 0400 [0.733 sec]                 [message]
Command dispatch complete [0.733 sec]                                   [notice]
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/MN3] does not exist
  Warning: DocumentRoot [/var/aegir/atrium-1-0-beta1] does not exist
  Warning: DocumentRoot [/var/aegir/wordpress] does not exist
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--root='/var/aegir/drupal-6.13'  'provision' 'verify' --backend
[0.735 sec]
Undefined variable: context [0.736 sec]                                 [notice]
Undefined variable: string [1.17 sec]                                   [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.171 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.172 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.172 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.173 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.173 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.174 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.174 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.2 sec]       [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [1.2 sec]       [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [1.203 sec]         [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [1.203 sec]   [bootstrap]
Loading drushrc "/var/aegir/drupal-6.13/drushrc.php" into "drupal"   [bootstrap]
scope. [1.203 sec]
Initialized Drupal 6.13 root directory at /var/aegir/drupal-6.13        [notice]
[1.203 sec]
Found command: provision verify [1.203 sec]                          [bootstrap]
Initializing drush commandfile: provision_apache [1.204 sec]         [bootstrap]
Undefined index:  base_url [1.204 sec]                                  [notice]
Initializing drush commandfile: provision_drupal [1.204 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [1.204 sec]          [bootstrap]
Undefined index:  db_url [1.204 sec]                                    [notice]
Including /var/aegir/.drush/provision/web_server/verify.provision.inc[bootstrap]
[1.204 sec]
Including /var/aegir/.drush/provision/platform/verify.provision.inc  [bootstrap]
[1.205 sec]
Including /var/aegir/.drush/provision/db_server/verify.provision.inc [bootstrap]
[1.205 sec]
Including /var/aegir/.drush/provision/ssl/verify.provision.inc [1.205[bootstrap]
sec]
Virtual host configuration path exists. [1.205 sec]                    [message]
Virtual host configuration ownership of path has been changed to       [message]
aegir. [1.205 sec]
Virtual host configuration permissions of path have been changed to    [message]
0700. [1.206 sec]
Virtual host configuration path is writable. [1.206 sec]               [message]
Undefined index:  platform [1.206 sec]                                  [notice]
Generating apache host configuration file platform_.conf. [1.206 sec]   [notice]
Generating apache host configuration file aegir.vm.server. [1.207       [notice]
sec]
Apache has been restarted [1.207 sec]                                   [notice]
Provision configuration path exists. [1.208 sec]                       [message]
Provision configuration ownership of path has been changed to aegir.   [message]
[1.209 sec]
Provision configuration permissions of path have been changed to       [message]
0711. [1.209 sec]
Provision configuration path is writable. [1.21 sec]                   [message]
Provision PHP configuration path exists. [1.21 sec]                    [message]
Provision PHP configuration ownership of path has been changed to      [message]
aegir. [1.211 sec]
Provision PHP configuration permissions of path have been changed to   [message]
0711. [1.211 sec]
Provision PHP configuration path is writable. [1.211 sec]              [message]
Global configuration file exists [1.212 sec]                           [message]
Backup path exists. [1.212 sec]                                        [message]
Backup ownership of path has been changed to aegir. [1.212 sec]        [message]
Backup permissions of path have been changed to 0700. [1.213 sec]      [message]
Backup path is writable. [1.213 sec]                                   [message]
Drupal sites directory is writable by the provisioning script [1.213   [message]
sec]
This platform is running drupal 6.13 [1.213 sec]                        [notice]
Including non-version specific file :                                   [notice]
/var/aegir/.drush/provision/platform/drupal/packages.inc [1.213 sec]
Found 33 modules in base [1.213 sec]                                    [notice]
Found 6 themes in base [1.214 sec]                                      [notice]
Found install profile hostmaster [1.214 sec]                            [notice]
Found install profile default [1.214 sec]                               [notice]
Found 13 modules in profiles/hostmaster [1.214 sec]                     [notice]
Found 1 themes in profiles/hostmaster [1.214 sec]                       [notice]
Mysql can create new databases. [1.215 sec]                            [message]
Found existing drushrc.php file [1.215 sec]                             [notice]
Changed permissions of drushrc.php to 0600 [1.215 sec]                 [message]
Drushrc file (/var/aegir/drupal-6.13/drushrc.php) was written           [notice]
successfully [1.215 sec]
Changed permissions of drushrc.php to 0400 [1.215 sec]                 [message]
Command dispatch complete [1.216 sec]                                   [notice]
Undefined index:  root [1.216 sec]                                      [notice]
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--root='/var/aegir/drupal-6.13'  'provision' 'verify' 'aegir.vm'
--backend [1.217 sec]
Undefined variable: context [1.217 sec]                                 [notice]
Undefined variable: string [3.229 sec]                                  [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.23 sec]      [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.231 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.232 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.232 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.233 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.233 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.234 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.234 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.286 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [3.286 sec]     [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [3.289 sec]         [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [3.289 sec]   [bootstrap]
Loading drushrc "/var/aegir/drupal-6.13/drushrc.php" into "drupal"   [bootstrap]
scope. [3.289 sec]
Initialized Drupal 6.13 root directory at /var/aegir/drupal-6.13        [notice]
[3.289 sec]
Found command: provision verify [3.29 sec]                           [bootstrap]
Initializing drush commandfile: provision_apache [3.29 sec]          [bootstrap]
Undefined index:  base_url [3.29 sec]                                   [notice]
Initializing drush commandfile: provision_drupal [3.29 sec]          [bootstrap]
Initializing drush commandfile: provision_mysql [3.29 sec]           [bootstrap]
Undefined index:  db_url [3.29 sec]                                     [notice]
Including /var/aegir/.drush/provision/web_server/verify.provision.inc[bootstrap]
[3.291 sec]
Including /var/aegir/.drush/provision/platform/verify.provision.inc  [bootstrap]
[3.291 sec]
Including /var/aegir/.drush/provision/db_server/verify.provision.inc [bootstrap]
[3.291 sec]
Including /var/aegir/.drush/provision/ssl/verify.provision.inc [3.291[bootstrap]
sec]
Drush bootstrap phase : _drush_bootstrap_drupal_site() [3.291 sec]   [bootstrap]
Initialized Drupal site aegir.vm at sites/aegir.vm [3.292 sec]          [notice]
Loading drushrc "/var/aegir/drupal-6.13/sites/aegir.vm/drushrc.php"  [bootstrap]
into "site" scope. [3.292 sec]
Generate settings.php file [3.292 sec]                                  [notice]
Changed permissions of settings.php to 0640 [3.292 sec]                [message]
Changed permissions of settings.php to 0440 [3.292 sec]                [message]
Change group ownership of settings.php to www-data [3.292 sec]         [message]
Drush bootstrap phase : _drush_bootstrap_drupal_configuration()      [bootstrap]
[3.293 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_database() [3.293    [bootstrap]
sec]
Successfully connected to the Drupal database. [3.293 sec]           [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_full() [3.293 sec]   [bootstrap]
Including non-version specific file :                                   [notice]
/var/aegir/drush/commands/core/drupal/environment.inc [3.293 sec]
Generating apache host configuration file <em>aegir.vm_80</em>.         [notice]
[3.294 sec]
Apache has been restarted [3.294 sec]                                   [notice]
Including non-version specific file :                                   [notice]
/var/aegir/.drush/provision/platform/drupal/packages.inc [3.294 sec]
Found install profile <em>hostmaster</em> [3.294 sec]                   [notice]
Found install profile <em>default</em> [3.294 sec]                      [notice]
Found 46 modules [3.294 sec]                                            [notice]
Found 7 themes [3.295 sec]                                              [notice]
Changed permissions of sites/aegir.vm to 0755 [3.295      [message]
sec]
Changed permissions of sites/aegir.vm/files to 2770       [message]
[3.295 sec]
Changed permissions of sites/aegir.vm/files/tmp to 2770   [message]
[3.295 sec]
Changed permissions of sites/aegir.vm/files/images to     [message]
2770 [3.295 sec]
Changed permissions of sites/aegir.vm/files/pictures to   [message]
2770 [3.296 sec]
Changed permissions of sites/aegir.vm/themes to 0755      [message]
[3.296 sec]
Changed permissions of sites/aegir.vm/modules to 0755     [message]
[3.297 sec]
Changed ownership of sites/aegir.vm/files [3.297 sec]     [message]
Changed group ownership of sites/aegir.vm/files [3.298    [message]
sec]
Changed ownership of sites/aegir.vm/files/tmp [3.298      [message]
sec]
Changed group ownership of sites/aegir.vm/files/tmp       [message]
[3.299 sec]
Changed ownership of sites/aegir.vm/files/images [3.299   [message]
sec]
Changed group ownership of sites/aegir.vm/files/images    [message]
[3.299 sec]
Changed ownership of sites/aegir.vm/files/pictures [3.3   [message]
sec]
Changed group ownership of sites/aegir.vm/files/pictures  [message]
[3.3 sec]
Generate settings.php file [3.301 sec]                                  [notice]
Changed permissions of settings.php to 0640 [3.301 sec]                [message]
Changed permissions of settings.php to 0440 [3.301 sec]                [message]
Change group ownership of settings.php to www-data [3.302 sec]         [message]
Including version specific file :                                       [notice]
/var/aegir/.drush/provision/platform/drupal/clear_6.inc [3.302 sec]
Cleared all caches [3.303 sec]                                          [notice]
Rebuild node type cache [3.303 sec]                                     [notice]
Rebuild module cache [3.304 sec]                                        [notice]
Rebuild theme cache [3.304 sec]                                         [notice]
Rebuild node access cache [3.304 sec]                                   [notice]
Rebuild menu cache [3.305 sec]                                          [notice]
Drushrc file (sites/aegir.vm/drushrc.php) was written successfully      [notice]
[3.305 sec]
Command dispatch complete [3.306 sec]                                   [notice]
Timer 'page' is  1.848 sec. [3.306 sec]                                  [timer]
This command will replace your crontab entry. continue? (y/n): y
no crontab for aegir
Undefined index:  root [7.403 sec]                                      [notice]
Running: /usr/bin/php /var/aegir/drush/drush.php  --uri='aegir.vm'     [command]
--root='/var/aegir/drupal-6.13'  'hostmaster' 'park' 'aegir.vm'
--backend [7.404 sec]
Undefined variable: context [7.404 sec]                                 [notice]
Undefined variable: string [7.85 sec]                                   [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.851 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.851 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.851 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.852 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.852 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.852 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.853 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.882 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [7.883 sec]     [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [7.886 sec]         [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [7.886 sec]   [bootstrap]
Loading drushrc "/var/aegir/drupal-6.13/drushrc.php" into "drupal"   [bootstrap]
scope. [7.886 sec]
Initialized Drupal 6.13 root directory at /var/aegir/drupal-6.13        [notice]
[7.886 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_site() [7.886 sec]   [bootstrap]
Initialized Drupal site aegir.vm at sites/aegir.vm [7.887 sec]          [notice]
Loading drushrc "/var/aegir/drupal-6.13/sites/aegir.vm/drushrc.php"  [bootstrap]
into "site" scope. [7.887 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_configuration()      [bootstrap]
[7.887 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_database() [7.887    [bootstrap]
sec]
Successfully connected to the Drupal database. [7.887 sec]           [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_full() [7.887 sec]   [bootstrap]
Including non-version specific file :                                   [notice]
/var/aegir/drush/commands/core/drupal/environment.inc [7.888 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_login() [7.888 sec]  [bootstrap]
Found command: hostmaster park [7.888 sec]                           [bootstrap]
Initializing drush commandfile: provision_apache [7.888 sec]         [bootstrap]
Initializing drush commandfile: provision_drupal [7.888 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [7.889 sec]          [bootstrap]
Command dispatch complete [7.889 sec]                                   [notice]
Timer 'page' is  0.292 sec. [7.889 sec]                                  [timer]
Undefined index:  root [7.89 sec]                                       [notice]
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--root='/var/aegir/drupal-6.13'  'provision' 'clone' 'aegir.vm'
'aegir.vm' '/var/aegir/hm-0.4-alpha3' --backend [7.89 sec]
Undefined variable: context [7.891 sec]                                 [notice]
Undefined variable: string [8.61 sec]                                   [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.61 sec]      [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.611 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.611 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.612 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.612 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.613 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.613 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.614 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.614 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.637 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [8.637 sec]     [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [8.64 sec]          [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [8.64 sec]    [bootstrap]
Loading drushrc "/var/aegir/drupal-6.13/drushrc.php" into "drupal"   [bootstrap]
scope. [8.64 sec]
Initialized Drupal 6.13 root directory at /var/aegir/drupal-6.13        [notice]
[8.641 sec]
Found command: provision clone [8.641 sec]                           [bootstrap]
Initializing drush commandfile: provision_apache [8.641 sec]         [bootstrap]
Undefined index:  base_url [8.641 sec]                                  [notice]
Initializing drush commandfile: provision_drupal [8.641 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [8.642 sec]          [bootstrap]
Undefined index:  db_url [8.642 sec]                                    [notice]
Including /var/aegir/.drush/provision/platform/clone.provision.inc   [bootstrap]
[8.642 sec]
Including /var/aegir/.drush/provision/db_server/clone.provision.inc  [bootstrap]
[8.642 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_site() [8.642 sec]   [bootstrap]
Initialized Drupal site aegir.vm at sites/aegir.vm [8.643 sec]          [notice]
Loading drushrc "/var/aegir/drupal-6.13/sites/aegir.vm/drushrc.php"  [bootstrap]
into "site" scope. [8.643 sec]
Including /var/aegir/.drush/provision/platform/backup.provision.inc  [bootstrap]
[8.643 sec]
Including /var/aegir/.drush/provision/db_server/backup.provision.inc [bootstrap]
[8.643 sec]
Generating mysql dump for aegir.vm. [8.643 sec]                         [backup]
mysqldump --defaults-file=/dev/fd/3 -rsites/aegir.vm/database.sql       [notice]
hostmaster [8.644 sec]
Adding sites directory to                                               [backup]
/var/aegir/backups/aegir.vm-20091111.073514.tar.gz [8.644 sec]
tar -C /var/aegir/drupal-6.13/sites/aegir.vm -p -c -z -f                [notice]
/var/aegir/backups/aegir.vm-20091111.073514.tar.gz . [8.644 sec]
Deleted mysql dump from sites directory [8.644 sec]                    [message]
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--root='/var/aegir/hm-0.4-alpha3' --web_host='aegir.vm'
--db_host='localhost' --uri='http://aegir.vm'  'provision' 'deploy'
'aegir.vm' '/var/aegir/backups/aegir.vm-20091111.073514.tar.gz'
--backend [8.644 sec]
Undefined variable: context [8.645 sec]                                 [notice]
Undefined variable: string [8.645 sec]                                  [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [8.645 sec]         [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [8.645 sec]   [bootstrap]
Loading drushrc "/var/aegir/hm-0.4-alpha3/drushrc.php" into "drupal" [bootstrap]
scope. [8.645 sec]
Initialized Drupal 6.14 root directory at /var/aegir/hm-0.4-alpha3      [notice]
[8.645 sec]
Found command: provision deploy [8.646 sec]                          [bootstrap]
Initializing drush commandfile: provision_apache [8.646 sec]         [bootstrap]
Undefined index:  base_url [8.646 sec]                                  [notice]
Initializing drush commandfile: provision_drupal [8.646 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [8.646 sec]          [bootstrap]
Undefined index:  db_url [8.647 sec]                                    [notice]
Including /var/aegir/.drush/provision/web_server/deploy.provision.inc[bootstrap]
[8.648 sec]
Including /var/aegir/.drush/provision/platform/deploy.provision.inc  [bootstrap]
[8.648 sec]
Including /var/aegir/.drush/provision/db_server/deploy.provision.inc [bootstrap]
[8.649 sec]
Deploying site from                                                    [message]
/var/aegir/backups/aegir.vm-20091111.073514.tar.gz [8.649 sec]
Running: tar -zpxf /var/aegir/backups/aegir.vm-20091111.073514.tar.gz   [notice]
-C /var/aegir/hm-0.4-alpha3/sites/aegir.vm [8.649 sec]
tar -zpxf /var/aegir/backups/aegir.vm-20091111.073514.tar.gz -C         [notice]
/var/aegir/hm-0.4-alpha3/sites/aegir.vm [8.65 sec]
Successfully extracted the contents of                                 [message]
/var/aegir/backups/aegir.vm-20091111.073514.tar.gz [8.65 sec]
Drush bootstrap phase : _drush_bootstrap_drupal_site() [8.651 sec]   [bootstrap]
Initialized Drupal site aegir.vm at sites/aegir.vm [8.652 sec]          [notice]
Loading drushrc "/var/aegir/hm-0.4-alpha3/sites/aegir.vm/drushrc.php"[bootstrap]
into "site" scope. [8.652 sec]
Found a valid version of the block module with schema version 0         [notice]
[8.653 sec]
Found a valid version of the color module with schema version 0         [notice]
[8.653 sec]
Found a valid version of the filter module with schema version 0        [notice]
[8.654 sec]
Found a valid version of the help module with schema version 0 [8.654   [notice]
sec]
Found a valid version of the menu module with schema version 0 [8.654   [notice]
sec]
Found a valid version of the node module with schema version 0 [8.655   [notice]
sec]
Found a valid version of the system module with schema version 6053     [notice]
[8.655 sec]
Found a valid version of the update module with schema version 6000     [notice]
[8.656 sec]
Found a valid version of the user module with schema version 0 [8.656   [notice]
sec]
The version of the admin_menu module found on this platform has a    [error]
lower Schema version than the one the site has installed [8.657 sec]
Found a valid version of the hosting_client module with schema          [notice]
version 7 [8.657 sec]
Found a valid version of the hosting_db_server module with schema       [notice]
version 0 [8.658 sec]
Found a valid version of the hosting_migrate module with schema         [notice]
version 0 [8.658 sec]
Found a valid version of the hosting_package module with schema         [notice]
version 6001 [8.658 sec]
Found a valid version of the hosting_platform module with schema        [notice]
version 6000 [8.659 sec]
Found a valid version of the hosting_site module with schema version    [notice]
6004 [8.659 sec]
Found a valid version of the hosting_task module with schema version    [notice]
6003 [8.66 sec]
Found a valid version of the hosting_web_server module with schema      [notice]
version 2 [8.66 sec]
Found a valid version of the hosting module with schema version 6002    [notice]
[8.661 sec]
An error occurred at function :                                      [error]
drush_provision_drupal_pre_provision_deploy [8.661 sec]
Deleting sites/aegir.vm/themes directory successful. [8.661 sec]       [message]
Deleting sites/aegir.vm/modules directory successful. [8.662 sec]      [message]
Deleting sites/aegir.vm/files/pictures directory successful. [8.662    [message]
sec]
Deleting sites/aegir.vm/files/images directory successful. [8.663      [message]
sec]
Deleting sites/aegir.vm/files/tmp directory successful. [8.663 sec]    [message]
Deleting sites/aegir.vm/files directory successful. [8.664 sec]        [message]
Deleting sites/aegir.vm directory successful. [8.664 sec]              [message]
Changes for drush_provision_drupal_pre_provision_deploy module have   [rollback]
been rolled back. [8.664 sec]
Command dispatch complete [8.665 sec]                                   [notice]
An error occurred at function :                                      [error]
drush_provision_drupal_provision_clone [8.665 sec]
Removed unused clone site package [8.666 sec]                          [message]
Changes for drush_provision_drupal_pre_provision_clone module have    [rollback]
been rolled back. [8.666 sec]
Command dispatch complete [8.666 sec]                                   [notice]
An error occurred at function : drush_provision_hostmaster_migrate   [error]
[8.667 sec]
Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--root='/var/aegir/hm-0.4-alpha3'  'provision' 'delete' '' 'aegir.vm'
--backend [8.668 sec]
Undefined variable: context [8.669 sec]                                 [notice]
Undefined variable: string [9.023 sec]                                  [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.024 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.024 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.024 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.025 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.025 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.025 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.025 sec]     [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.06 sec]      [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [9.06 sec]      [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [9.063 sec]         [bootstrap]
Uninitialized string offset:  0 [9.063 sec]                             [notice]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [9.063 sec]   [bootstrap]
Loading drushrc "/var/aegir/hm-0.4-alpha3/drushrc.php" into "drupal" [bootstrap]
scope. [9.063 sec]
Initialized Drupal 6.14 root directory at /var/aegir/hm-0.4-alpha3      [notice]
[9.063 sec]
Found command: provision delete [9.064 sec]                          [bootstrap]
Initializing drush commandfile: provision_apache [9.064 sec]         [bootstrap]
Undefined index:  base_url [9.064 sec]                                  [notice]
Initializing drush commandfile: provision_drupal [9.064 sec]         [bootstrap]
Initializing drush commandfile: provision_mysql [9.064 sec]          [bootstrap]
Undefined index:  db_url [9.064 sec]                                    [notice]
Including /var/aegir/.drush/provision/web_server/delete.provision.inc[bootstrap]
[9.065 sec]
Including /var/aegir/.drush/provision/platform/delete.provision.inc  [bootstrap]
[9.065 sec]
Including /var/aegir/.drush/provision/db_server/delete.provision.inc [bootstrap]
[9.065 sec]
Including /var/aegir/.drush/provision/platform/backup.provision.inc  [bootstrap]
[9.065 sec]
Including /var/aegir/.drush/provision/db_server/backup.provision.inc [bootstrap]
[9.065 sec]
Could not find a Drupal settings.php file at                         [error]
./sites/default/settings.php. [9.066 sec]
clearing error [9.066 sec]                                              [notice]
Backing site up to aegir.vm. [9.066 sec]                               [message]
Generating mysql dump for . [9.066 sec]                                 [backup]
mysqldump --defaults-file=/dev/fd/3 -rsites//database.sql  [9.067       [notice]
sec]
Adding sites directory to aegir.vm [9.068 sec]                          [backup]
tar -C /var/aegir/hm-0.4-alpha3/sites/ -p -c -f aegir.vm . [9.068       [notice]
sec]
Deleted mysql dump from sites directory [9.068 sec]                    [message]
unlink(/var/aegir/config/vhost.d/): Is a directory [9.069 sec]       [warning]
Undefined variable: options [9.069 sec]                                 [notice]
Apache has been restarted [9.07 sec]                                    [notice]
Deleting /var/aegir/hm-0.4-alpha3/sites//all directory successful.     [message]
[9.07 sec]
Deleting /var/aegir/hm-0.4-alpha3/sites//default directory             [message]
successful. [9.071 sec]
Deleting /var/aegir/hm-0.4-alpha3/sites/ directory successful. [9.071  [message]
sec]
Dropping database  [9.071 sec]                                          [notice]
Incorrect database name ''                                           [error]
query: DROP DATABASE `` [9.072 sec]
Failed to drop database  [9.072 sec]                                 [warning]
Unable to drop database. [9.073 sec]                                 [error]
An error occurred at function :                                      [error]
drush_provision_mysql_provision_delete [9.073 sec]
Command dispatch complete [9.073 sec]                                   [notice]
Changes for drush_provision_hostmaster_migrate module have been       [rollback]
rolled back. [9.074 sec]
Command dispatch complete [9.075 sec]                                   [notice]

Comments

adrian’s picture

The new drush make based upgrade process for Aegir is very difficult at the moment. There are 2 main cases we have here :

1) upgrades from aegir releases before 0.4 alpha 2
2) upgrades from aegir 0.4 alpha 2

The process should be :

a) upgrade drush to drush 2.1
b) upgrade provision to the new alpha
c) download the latest beta of drush make
d) run 'drush hostmaster make /path/to/new/platform'
e) cd /path/to/old/platform
f) run 'drush hostmaster migrate site.com /path/to/new/platform

So here are the following issues :

a) when drush is updated to 2.1, the queue stops working because of drupal.org/node/586466 and the fact that the drush_scan_directory parameters have changed
b) to get the newest release, with the additional dependencies it is recommended that you use drush make, which requires the new HEAD.
c) The jquery_ui and modalframe modules, and the jquery ui library needs to be present before you can run the update functions, or http://drupal.org/node/620686 happens.
d) 0.4 alpha 2 already has a hostmaster park command, which validates that the platform you are migrating to has already been added, but to get the new platform you need the new backend and if you have the new backend your task queue is broken.
e) because of the changes in drush, a new platform won't be able to get verified and added and for the settings to propogate to the target platform, it needs to be verified by the front end, otherwise the drushrc.php file is incorrect.
f) when you follow through with the process anyway you get the following AND the sites directory on the target platform is wiped out completely :

adrian’s picture

adrian’s picture

Status: Active » Fixed

well. after a lot of back and forth I finally have the upgrade process automated.

after upgrading provision, drush and installing the latest beta of drush make you upgrade the front end by simply running :

'php ~/drush/drush.php --root='/path/to/current/platform' hostmaster migrate aegir.mydomain.com /var/aegir/aegir-0.4-alpha3'

This command will automatically download and register the new platform for you, but it may take a while.
it also wipes out your current crontab and replaces it with one that _will_ work, due to the drush 2.1 issues we have been facing

adrian’s picture

updated the docs too.

Anonymous’s picture

Status: Fixed » Needs work

The migrate seemed to work well on my initial test. There was only one error that occurred. During the migrate, a 'platform_.conf' was created, which contains settings specific to the *old* platform that is being migrated away from.

All other new configs and ones rewritten, look normal, so this is just the one anomaly.

Snippet from logs

Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--master_url='http://aegir1.mig5-forge.net'
--publish_path='/var/aegir/hostmaster-0.4alpha3'
--web_host='aegir1.mig5-forge.net' --web_ip='127.0.1.1'
--web_group='www-data' --script_user='aegir' --restart_cmd='sudo
/usr/sbin/apache2ctl graceful' --backup_path='/var/aegir/backups'
--config_path='/var/aegir/config'
--master_db='mysqli://aegir_root:xxxxx@localhost' --debug
--root='/var/aegir/hostmaster-0.4alpha3'
--r='/var/aegir/hostmaster-0.4alpha3'  'provision' 'verify' --backend
[46.443 sec]
Undefined variable: context [46.443 sec]                                [notice]
Undefined variable: string [47.395 sec]                                 [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
ob_flush(): failed to flush buffer. No buffer to flush. [47.396 sec]    [notice]
Drush bootstrap phase : _drush_bootstrap_drush() [47.425 sec]        [bootstrap]
Drush bootstrap phase : _drush_bootstrap_drupal_root() [47.425 sec]  [bootstrap]
Initialized Drupal 6.14 root directory at                               [notice]
/var/aegir/hostmaster-0.4alpha3 [47.425 sec]
Found command: provision verify [47.425 sec]                         [bootstrap]
Initializing drush commandfile: provision_apache [47.425 sec]        [bootstrap]
Undefined index:  base_url [47.425 sec]                                 [notice]
Initializing drush commandfile: provision_drupal [47.425 sec]        [bootstrap]
Initializing drush commandfile: provision_mysql [47.425 sec]         [bootstrap]
Undefined index:  db_url [47.425 sec]                                   [notice]
Including /var/aegir/.drush/provision/web_server/verify.provision.inc[bootstrap]
[47.426 sec]
Including /var/aegir/.drush/provision/platform/verify.provision.inc  [bootstrap]
[47.426 sec]
Including /var/aegir/.drush/provision/db_server/verify.provision.inc [bootstrap]
[47.426 sec]
Including /var/aegir/.drush/provision/ssl/verify.provision.inc       [bootstrap]
[47.426 sec]
Virtual host configuration path exists. [47.426 sec]                   [message]
Virtual host configuration ownership of path has been changed to       [message]
aegir. [47.426 sec] 
Virtual host configuration permissions of path have been changed to    [message]
0700. [47.426 sec]   
Virtual host configuration path is writable. [47.426 sec]              [message]
Undefined index:  platform [47.426 sec]                                 [notice]
Generating apache host configuration file platform_.conf. [47.427       [notice]
sec]
Generating apache host configuration file                               [notice]
aegir1.mig5-forge.net.server. [47.427 sec]
Executing: sudo /usr/sbin/apache2ctl graceful [47.427 sec]              [notice]
Apache has been restarted [47.427 sec]    
 

I'll continue to do more tests (this was a migrate from a slightly-old-head to HEAD. Will test older versions too)

Anonymous’s picture

For the benefit of testing, a migrate from 0.3 to HEAD was also successful. Same issue again with a platform_.conf that was created with the contents of the old platform. But otherwise working well.

Anonymous’s picture

Where is the logic for 'hostmaster pause' ? I found resume.hostmaster.inc but I can't find pause anywhere. Surprisingly despite this, the command is run and doesn't throw any drush errors so I assume it's somewhere and I can't find it.

We seem to want to verify both old and new platforms in drush_provision_hostmaster_migrate_validate()

 drush_backend_invoke('provision verify', array('root' => drush_get_option(array('r', 'root'), drush_locate_root())));

Both items r and root in this array are the target platform, as seen in;

Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--master_url='http://aegir2.mig5-forge.net'
--publish_path='/var/aegir/hostmaster-test'
--web_host='aegir2.mig5-forge.net' --web_ip='127.0.1.1'
--web_group='www-data' --script_user='aegir' --restart_cmd='sudo
/usr/sbin/apache2ctl graceful' --backup_path='/var/aegir/backups'
--config_path='/var/aegir/config'
--master_db='mysqli://aegir_root:xxxxxxx@localhost' --debug
--root='/var/aegir/hostmaster-test' --r='/var/aegir/hostmaster-test'
'provision' 'verify' --backend [56.278 sec]

because

 $data['root'] = $platform;
 $data['r'] = $platform; 

is this right?

two verifies are run: the first gets the platform_.conf and contains info on the *old* platform, which is baffling to me, as I expected platform_.conf to occur because no nid exists yet for the target platform, and yet it is using the old platform's data (context issue?)

Anonymous’s picture

Removing $data['root'] = $platform fixes the verify issue and actually runs the verify on the old and target platforms respectively, because $data['root'] is picked straight out of the drush_get_merged_options() (as it should, or from the current pwd per the fallback there)

Running: /usr/bin/php /var/aegir/drush/drush.php                       [command]
--master_url='http://aegir2.mig5-forge.net'
--publish_path='/var/aegir/hostmaster-test2'
--web_host='aegir2.mig5-forge.net' --web_ip='127.0.1.1'
--web_group='www-data' --script_user='aegir' --restart_cmd='sudo
/usr/sbin/apache2ctl graceful' --backup_path='/var/aegir/backups'
--config_path='/var/aegir/config'
--master_db='mysqli://aegir_root:xxxxx@localhost' --debug
--r='/var/aegir/hostmaster-test2' --root='/var/aegir/hostmaster-test'
 'provision' 'verify' --backend [57.533 sec]

However *both* of them generate the platform_.conf . And I suspect that is why it ends up with the old platform's contents: the old platform gets verified *after* the target platform, and so it overwrites the file. Either way it's a moot point since it should be doing this properly (I still don't see why the old platform is unable to find a platform nid)

Anonymous’s picture

anarcat points out we need to write the platform nid to drushrc.php to avoid that old issue.

We need to persist the platform nid for the old platform, but we are doing a verify of the *new* platform before it exists as a node in the aegir db yet. We add that platform via node_save etc much later, *after* we migrate to it, in 'hostmaster resume'. So even if we fix that old bug of persisting the platform nid in a verify task, we don't actually *have* one yet for the new platform. Perhaps we need to take that logic from resume.hostmaster.inc and do that first in the validation, and then do the verify? This then follows the typical procedure of adding a platform that one does through the frontend (node_save, then verify)

adrian’s picture

the platform will get re-verified after creation anyway, and we can't create it on pause, because it won't be available yet on 0.3 sites.

i am going to suggest we

1. provide a sensible fallback for the platform_X file, like we do for site_id
2. just not write the platform file if the X file is missing, it will get created later anyway
3. never use the platform id in the file creation to begin with

a lot of this stuff becomes irrelevant in alpha 4 anyway because we will be producing a server level verify task.

adrian’s picture

Status: Needs work » Fixed

no longer creates the files when no platform id is specified.

Anonymous’s picture

While not a major issue, is this not still a problem?

$data['root'] = $platform;
$data['r'] = $platform;

Am I right in thinking the first one should be removed, and just inherited from the merged options? Otherwise we are verifying the same platform twice.

adrian’s picture

they are both specified because we don't want a case where -r and --root are different values, because then we depend on drush to know what the precedence is

Status: Fixed » Closed (fixed)

Automatically closed -- issue fixed for 2 weeks with no activity.