If your on MySQL 8.0 or higher you can use Window functions:
Query:
SELECT DISTINCT
FIRST_VALUE(ID) OVER (PARTITION BY lms_attendance.USER ORDER BY lms_attendance.TIME DESC) AS ID,
FIRST_VALUE(USER) OVER (PARTITION BY lms_attendance.USER ORDER BY lms_attendance.TIME DESC) AS USER,
FIRST_VALUE(TIME) OVER (PARTITION BY lms_attendance.USER ORDER BY lms_attendance.TIME DESC) AS TIME,
FIRST_VALUE(IO) OVER (PARTITION BY lms_attendance.USER ORDER BY lms_attendance.TIME DESC) AS IO
FROM lms_attendance;
Result:
| ID | USER | TIME | IO |
--------------------------------
| 2 | 9 | 1370931664 | out |
| 3 | 6 | 1370932128 | out |
| 5 | 12 | 1370933037 | in |
The advantage I see over using the solution proposed by Justin is that it enables you to select the row with the most recent data per user (or per id, or per whatever) even from subqueries without the need for an intermediate view or table.
And in case your running a HANA it is also ~7 times faster :D