Various Errors after upgrade 2.1 > 2.3

After upgrading omeka using the guide from our local ubuntu server (via command line) we've been encountering errors. When I created a post about Collection-Tree I assumed that was the only part that didn't work, but now I'm seeing this error on many items:

Notice: Undefined index: linkAttributes in /var/www/html/application/views/helpers/FileMarkup.php on line 390

Have I screwed up my database, or just the install itself? I know the site wasn't displaying properly until some permissions were changed. Is it safe to attempt a reinstall by following the instructions as if I was upgrading Omeka again, or what are the best options for troubleshooting?

I'd be happy to relay any information you'd need. I'll attempt a Omeka reinstall later today to see if that changes anything.

Usually messages at the Notice level aren't too much to worry about (though they might be a precursor to larger issues at the Warning or Error level).

For production servers, the error reporting is usually set to ignore Notices. So, if there are no bigger issues being reported, it might be safe just to turn off development mode in Omeka, or lower the error messages on the server to just warnings and errors.

That was it patrickmj, I had left the setting in .htaccess for errors to On while debugging the other SQL issue. That took care of it.