"Database integrity check" performance

“database integrity checking” scheduled with the cleanup step is very long compared to a pragma integrity_check of the same db :

Output from server’s log

10/06/16 12:37  	INFO  	Checking database integrity of main database...
10/06/16 12:49  	INFO  	Looking for old Sessions... 1 sessions
10/06/16 13:12  	INFO  	Checking integrity of backup_server_files.db
10/06/16 13:19  	INFO  	Looking for old Sessions... 1 sessions
10/06/16 13:33  	DEBUG  	Sending file "/usr/share/urbackup/www/js/urbackup_functions.js"
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/js/urbackup_functions.js
10/06/16 13:33  	DEBUG  	Sending file "/usr/share/urbackup/www/images/indicator.gif"
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/js/urbackup_functions.js done
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/js/dust-full.min.js done
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/images/indicator.gif
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/images/indicator.gif done
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/js/jquery.js done
10/06/16 13:33  	INFO  	Sending file: /usr/share/urbackup/www/js/templates.js done
10/06/16 13:49  	INFO  	Looking for old Sessions... 1 sessions
10/06/16 13:59  	INFO  	Checking integrity of backup_server_links.db
10/06/16 13:59  	INFO  	Checking integrity of backup_server_link_journal.db
10/06/16 13:59  	INFO  	Starting database backup of main db...
10/06/16 13:59  	INFO  	Database backup done.
10/06/16 13:59  	INFO  	Starting database backup of backup_server_files.db...
10/06/16 13:59  	INFO  	Stop checkpointing of backup_server_files.db...
10/06/16 13:59  	INFO  	Stop writes to backup_server_files.db...
10/06/16 14:00  	INFO  	Backup of backup_server_files.db done.
10/06/16 14:00  	INFO  	Starting database backup of backup_server_links.db...
10/06/16 14:00  	INFO  	Stop checkpointing of backup_server_links.db...
10/06/16 14:00  	INFO  	Stop writes to backup_server_links.db...
10/06/16 14:00  	INFO  	Backup of backup_server_links.db done.
10/06/16 14:00  	INFO  	Starting database backup of backup_server_link_journal.db...
10/06/16 14:00  	INFO  	Stop checkpointing of backup_server_link_journal.db...
10/06/16 14:00  	INFO  	Stop writes to backup_server_link_journal.db...
10/06/16 14:00  	INFO  	Backup of backup_server_link_journal.db done.

Integrity check of backup_server_files.db takes about 47 minutes, okay.

Now if i run a pragma check_integrity from the cli :

root@urbackup1:/var/urbackup# sqlite3 backup_server_files.db
SQLite version 3.8.7.1 2014-10-29 13:59:56
Enter ".help" for usage hints.
sqlite> .timer on
sqlite> pragma integrity_check;
ok
Run Time: real 13.960 user 9.892000 sys 3.484000
sqlite>

What should explain this difference ?
Or maybe i miss something …

UrBackup does PRAGMA quick_check. Could be a SQLite performance regression (or it is checking more) – try a recent version from https://sqlite.org/download.html.

Also drop caches before testing etc. (the usual performance testing things you have to take into account).