It's strange to file this here, but I think this module (or maybe backup_migrate) is interacting with a bug in taxonomy_manager to cause my sites directory to be deleted when I try to upgrade taxonomy_manager. Here's the transcript of the drush update. I'd appreciate any suggestions:

healingthresholds:/var/www/backup.healingthresholds.com$ drush up taxonomy_manager
Refreshing update status information ...
Done.
Update information last refreshed: Sat, 2010-02-20 16:22

Update status information on all installed and enabled Drupal modules:
 Name                         Installed        Proposed        Status           
                              version          version                          
 Advertisement                6.x-2.2          6.x-2.2         Up to date       
 Ad GeoIP                     6.x-2.0-rc1      6.x-2.0-rc1     Up to date       
 Administration menu          6.x-1.5          6.x-1.5         Up to date       
 lm_paypal                    6.x-1.0          6.x-1.0         Up to date       
 Backup and Migrate           6.x-2.2          6.x-2.2         Up to date       
 Backup and Migrate Files     6.x-1.x-dev      6.x-1.x-dev     Up to date       
 Bibliography Module          6.x-1.10         6.x-1.10        Up to date       
 Drupal                       6.15             6.15            Up to date       
 Boost                        6.x-1.17         6.x-1.18        Update available 
 Content Construction Kit     6.x-2.6          6.x-2.6         Up to date       
 (CCK)                                                                          
 Chaos tool suite             6.x-1.2          6.x-1.3         Update available 
 Email Field                  6.x-1.2          6.x-1.2         Up to date       
 Environment Indicator        6.x-1.0          6.x-1.0         Up to date       
 External Links               6.x-1.9          6.x-1.9         Up to date       
 FileField                    6.x-3.2          6.x-3.2         Up to date       
 GeoIP API                    6.x-1.x-dev      6.x-1.x-dev     Up to date       
 Global Redirect              6.x-1.2          6.x-1.2         Up to date       
 Glossary                     6.x-1.6          6.x-1.6         Up to date       
 GMap Module                  6.x-1.0          6.x-1.0         Up to date       
 Google Custom Search Engine  6.x-1.2          6.x-1.2         Up to date       
 Google Ad Manager            6.x-1.0          6.x-1.0         Up to date       
 Google Analytics             6.x-2.2          6.x-2.2         Up to date       
 ImageAPI                     6.x-1.6          6.x-1.6         Up to date       
 ImageCache                   6.x-2.0-beta10   6.x-2.0-beta10  Up to date       
 ImageField                   6.x-3.2          6.x-3.2         Up to date       
 Imagefield Crop              6.x-1.0-rc1      6.x-1.0-rc1     Up to date       
 IMCE                         6.x-1.3          6.x-1.3         Up to date       
 IMCE Wysiwyg bridge          6.x-1.0          6.x-1.0         Up to date       
 jQuery plugins               6.x-1.10         6.x-1.10        Up to date       
 jQuery UI                    6.x-1.3          6.x-1.3         Up to date       
 Keys                         6.x-2.0          6.x-2.0         Up to date       
 Link                         6.x-2.8          6.x-2.8         Up to date       
 Location                     6.x-3.0          6.x-3.0         Up to date       
 LoginToboggan                6.x-1.6          6.x-1.6         Up to date       
 Term lower name              6.x-1.1          6.x-1.1         Up to date       
 Mollom                       6.x-1.10         6.x-1.12        Update available 
 Nice Menus                   6.x-1.3          6.x-1.3         Up to date       
 Nodewords                    6.x-1.11         6.x-1.11        Up to date       
 Page Title                   6.x-2.3          6.x-2.3         Up to date       
 Panels                       6.x-3.2          6.x-3.3         Update available 
 Path redirect                6.x-1.0-beta6    6.x-1.0-beta6   Up to date       
 Pathauto                     6.x-1.2          6.x-1.2         Up to date       
 Prepopulate                  6.x-1.1          6.x-1.1         Up to date       
 Quick Tabs                   6.x-2.0-rc4      6.x-2.0-rc4     Up to date       
 Rotor Banner                 6.x-2.4          6.x-2.4         Up to date       
 Rules                        6.x-1.1          6.x-1.1         Up to date       
 Scheduler                    6.x-1.6          6.x-1.6         Up to date       
 Search 404                   6.x-1.8          6.x-1.8         Up to date       
 Special menu items module    6.x-1.4          6.x-1.4         Up to date       
 Taxonomy Manager             6.x-2.1          6.x-2.2         Update available 
 Term Node Count              6.x-1.3          6.x-1.3         Up to date       
 Token                        6.x-1.12         6.x-1.12        Up to date       
 Top Searches                 6.x-1.1          6.x-1.1         Up to date       
 Upload element               6.x-1.2          6.x-1.2         Up to date       
 Views                        6.x-2.8          6.x-2.8         Up to date       
 Views Type Block             6.x-1.0          6.x-1.0         Up to date       
 Views Bulk Operations (VBO)  6.x-1.8          6.x-1.9         Update available 
 Webform                      6.x-2.9          6.x-2.9         Up to date       
 Wysiwyg                      6.x-2.0          6.x-2.0         Up to date       
 XML sitemap                  6.x-2.0-unstabl  6.x-2.0-alpha2  Update available 
                              e6                                                

Code updates will be made to the following projects:
Taxonomy Manager [taxonomy_manager-6.x-2.2]

Note: Updated modules can potentially break your site. It's not recommended to update production sites without prior testing.
Note: A backup of your package will be stored to backups directory if it is not managed by a supported version control system.
Note: If you have made any modifications to any file that belongs to one of these projects, you will have to migrate those modifications after updating.
Do you really want to continue? (y/n): y
Project taxonomy_manager was updated successfully. Installed version is now 6.x-2.2.
Backups were saved into the directory                                [ok]
/var/www/backup.healingthresholds.com/backup/modules/20100220212228.

Fatal error: require_once(): Failed opening required './sites/all/modules/backup_migrate/includes/crud.inc' (include_path='.:/usr/share/php:/usr/share/pear') in /var/www/backup.healingthresholds.com/sites/all/modules/backup_migrate/backup_migrate.module on line 208
Drush command could not be completed.                                [error]

Comments

dankohn’s picture

Status: Active » Closed (fixed)

Actually, I don't think this is a backup_migrate issue. See #720784: drush update taxonomy_manager deletes sites directory. Thanks.