Permissions problem
I installed a patch to the comment module. I got the following messages:
warning: include_once(./modules/comment/comment.module) [function.include-once]: failed to open stream: Permission denied in /var/www/html/mysite/includes/bootstrap.inc on line 512.
warning: include_once() [function.include]: Failed opening './modules/comment/comment.module' for inclusion (include_path='.:/usr/share/pear:/usr/share/php') in /var/www/html/mysite/includes/bootstrap.inc on line 512.
The file and diesctory permissions have not changed, nor has the ownership, and as far as I can see there is no process locking the file, so the 'permission denied' is a mystery to me.
I tried removing the patch, I tried re-writing the file from an earlier backup, but now I always get the 'permission denied'. If anyone can suggest anything else to try, I'll be most grateful!
If it matters, the patch was comment_notify_patch_to_comment.patch from the comment_notify module.

Make sure that you don't have
Make sure that you don't have a second copy of comment module somewhere accessible under Drupal, and check the "system" table in the database to see if the comment module is enabled (status=0) and has the correct path.
Thanks!
Thank you C.R. I got rid of the problem by replacing the entire directory, which is great because it worked, but annoying because I learned nothing from it. Next time I'll try it your way! Thanks again.
I should add an obvious
I should add an obvious correction here, "is enabled (status=1)" and not 0.