I got the following error when upgrading Moodle reader on http://hub.moodlejapan.org

Fatal error: Call to undefined method admin_setting_configduration::set_advanced_flag_options() in /home/majhub/moodle/mod/reader/settings.php on line 50

It looks like Reader expects set_advanced_flag_options to be available in post moodle 2.4 versions, but it is not present in 2.5.8 ( class admin_setting in file /lib/adminlib.php )

I just tweaked the setting.php code so on our site that Reader reverted to pre moodle 2.4 code for that bit, and we got past the error.