Downloaded phpMyAdmin-2.9.2-all-languages-utf-8-only.tar.bz2 today and got error about missing file when running setup.php in the script dir.
Warning: main(./libraries/Theme.class.php): failed to open stream: No such file or directory in /var/www/phpMyAdmin/libraries/common.lib.php on line 593
Fatal error: main(): Failed opening required './libraries/Theme.class.php' (include_path='.:/usr/share/php:/usr/share/pear') in /var/www/phpMyAdmin/libraries/common.lib.php on line 593
Opened common.lib.php and line 593 is an include line for Theme.class.php.
File was not included in download.
Fixed by downloading phpMyAdmin-2.9.2-english.tar.bz2 and coping over the Theme.class.php from the libary folder.