I have a site recently moved from D6 to D7. The search in D7 was not finding nodes containing the search terms, so I began a re-index in the search settings. This has stalled at 11% of site (with 3570 items left to index), and running cron does nothing to advance the re-index.
The log messages show that when cron runs, it encounters this error:
EntityMalformedException: Missing bundle property on entity of type comment. in entity_extract_ids() (line 7766 of /var/www/html/[domain]/includes/common.inc).
And this notice:
Notice: Undefined variable: key in comment_prepare_thread() (line 901 of /var/www/html/[domain]/modules/comment/comment.module).
Also, there are many instances of this notice, which is associated with use of the site, not cron:
Undefined index: weblinks in custom_search_form_alter() (line 232 of /var/www/html/[domain]/sites/all/modules/custom_search/custom_search.module).
None of these seem to affect the function of the site, and it's not clear to me that they are actually related to the stalled re-indexing. But it's all I've got to go on at this point.
If anyone could give me some ideas for how to troubleshoot this, I'd very much appreciate it.