Can't rmdir './mydatabase', Errno: 39

Issue

Mysql drop table command returns:

ERROR 1010 (HY000): Error dropping database (can't rmdir './mydatabase', errno: 39)

Likely Cause

There is a file in the database folder which isn't being managed by Mysql. This file could be hidden detritus or, more likely, an orphaned .ibd file.

# cd /var/log/mysql/mydatabase
# ls -la
total 72
drwx------ 2 mysql mysql  4096 Jun 23 19:57 ./
drwx------ 7 mysql mysql  4096 Jun 23 21:08 ../
-rw-rw---- 1 mysql mysql 65536 Jun 23 19:56 actions.ibd

Something Like a Solution

I just delete the problem file and run the database drop command again.

# rm -f actions.idd

mysql> drop database mydatabase;
Query OK, 0 rows affected (0.00 sec)

References

• MySQL: Error dropping database (errno 13; errno 17; errno 39)
• Connecting orphaned .ibd files