I'm loading my silverstripe site onto a host (I've changed from one already as too many issues setting up) however I came across an open_basedir restriction in ManifestBuilder.php line 50.
So on investigating I think the issue is due to the scandir returning . and .. directories with the .. directory not being allowed in the open_basedir restriction.
So I added the following in the foreach loop also required at line 64 and 84 but with the variable $filename instead of $file and my warning has gone.
if(substr($file,0,1) == '.') continue;
Maybe a core developer could review this and add if appropriate.