As root, place a shell script into the /etc/cron.daily/ or /etc/cron.weekly/ directory—or schedule one using the crontab -e command—that contains the touch /forcequotacheck command. This creates an empty forcequotacheck file in the root directory, which the system init script looks for at boot time. If it is found, the init script runs quotacheck. Afterward, the init script removes the /forcequotacheck file; thus, scheduling this file to be created periodically with cron ensures that quotacheck is run during the next reboot.

For more information about cron, refer to man cron.

An alternative way to safely run quotacheck is to (re-)boot the system into single-user mode to prevent the possibility of data corruption in quota files and run the following commands:

If necessary, it is possible to run quotacheck on a machine during a time when no users are logged in, and thus have no open files on the file system being checked. Run the command quotacheck -vaug file_system ; this command will fail if quotacheck cannot remount the given file_system as read-only. Note that, following the check, the file system will be remounted read-write.