The following module is missing from the file system: (Theme name) In D7, I'm getting many of these warnings:

User warning: The following module is missing from the file system: bootstrap_barrio. 
For information about how to fix this, see the documentation page. 
   in _drupal_trigger_error_with_delayed_logging() 
      (line 1143 of /home/xxxxx/www/www/includes/bootstrap.inc).

User warning: The following module is missing from the file system: XXXXX. 
For information about how to fix this, see the documentation page. 
   in _drupal_trigger_error_with_delayed_logging() 
      (line 1143 of /home/xxxxx/www/www/includes/bootstrap.inc).


The problem is that those 'modules': 


Are actually themes in the site.
They are being used and the files are there (under /sites/all/themes/)


I've installed the Missing Module module and it didn't detect those themes as missing.

Why is Drupal confusing modules with themes and how can I remove those messages?
This is probably due to the modules changing locations since they where installed.  One way to fix this is to just edit the system table.  You can do this via Drush like this:

drush sql-cli

&gt; select * from system where name = 'bootstrap_barrio';

Verify that the path column is not correct.

&gt; update system set path='correct path here' where name = 'bootstrap_barrio';


If the path is correct, then it might be a directory rights issue.  E.g. either the module or a parent can't be read by the webserver.