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Old 09-14-2016, 12:11 PM   #1
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Calibre unable to back up the database.
On my Kobo Glo FW ver. 3.19.5761, when I connect the device to Calibre (ver. 2.67 64bit Win10) I am getting the message : "Failed: Backing up Kobo device database".

Is it a sign of database getting corrupted? Should I backup all my notes and highlights and books immediately to avoid any upcoming disasters? Kindly advise.
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Old 09-14-2016, 08:26 PM   #2
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A failed backup usually means the database is corrupt. The process is to copy the database file and then run a check on it. If there are errors doing the check, then the file is renamed with the word "CORRUPT" in it.

I occasionally see other problems. They usually look like locked file issues, but by the time I can investigate, the problem has gone away. I don't know if it is the database that was locked or something else.

After error doing the backup, I recommend running a check on the database. This is part of the utilities plugin. If there are errors, some can be fixed by doing a compress. But, generally, I recommend restoring the last good backup. How well that works depends on how recent that last good backup is.
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Old 09-15-2016, 08:46 AM   #3
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Quote:
Originally Posted by davidfor View Post
After error doing the backup, I recommend running a check on the database. This is part of the utilities plugin. If there are errors, some can be fixed by doing a compress. But, generally, I recommend restoring the last good backup. How well that works depends on how recent that last good backup is.
Thanks davidfor, when I run the check on the database, I get following error log :

Spoiler:
Result of running 'PRAGMA integrity_check' on database on the Kobo device:


*** in database main ***
On tree page 2665 cell 120: 2nd reference to page 10029
On tree page 2665 cell 120: Child page depth differs
On tree page 2665 cell 121: 2nd reference to page 10015
On tree page 2665 cell 122: 2nd reference to page 24669
On tree page 12046 cell 1: Rowid 57423 out of order (max larger than parent max of 688)
On tree page 2665 cell 123: Child page depth differs
On tree page 16377 cell 75: Child page depth differs
On tree page 16377 cell 76: Child page depth differs
On tree page 19596 cell 1: invalid page number 218103808
On tree page 24577 cell 3: Rowid 32555 out of order (min less than parent min of 55925)
On tree page 16378 cell 70: 2nd reference to page 13440
On tree page 16378 cell 70: Child page depth differs
On tree page 16378 cell 71: Child page depth differs
On tree page 16378 cell 98: 2nd reference to page 7031
On tree page 16378 cell 98: Child page depth differs
On tree page 16378 cell 99: Child page depth differs
On page 21360 at right child: 2nd reference to page 12046
On tree page 4314 cell 4: 2nd reference to page 12443
On tree page 4314 cell 4: Child page depth differs
On tree page 4314 cell 5: Child page depth differs
On tree page 8414 cell 1: 2nd reference to page 13431
On tree page 8414 cell 1: Child page depth differs
On tree page 8414 cell 2: Child page depth differs
On tree page 1796 cell 2: 2nd reference to page 4717
On tree page 1796 cell 2: Child page depth differs
On tree page 1796 cell 3: 2nd reference to page 5090
On tree page 1796 cell 4: Child page depth differs
On page 4032 at right child: 2nd reference to page 22164
On page 162 at right child: 2nd reference to page 5127
On tree page 582 cell 44: 2nd reference to page 8180
On tree page 582 cell 44: Child page depth differs
On tree page 582 cell 45: 2nd reference to page 7909
On tree page 582 cell 46: Child page depth differs
On tree page 582 cell 100: 2nd reference to page 24577
On tree page 582 cell 100: Child page depth differs
On tree page 582 cell 101: Child page depth differs
On tree page 3315 cell 1: 2nd reference to page 8087
On tree page 3315 cell 1: Child page depth differs
On tree page 3315 cell 2: 2nd reference to page 5356
On tree page 3315 cell 3: 2nd reference to page 23653
On tree page 3315 cell 4: 2nd reference to page 12275
On tree page 3315 cell 5: 2nd reference to page 11455
On tree page 3315 cell 6: 2nd reference to page 4314
On tree page 3315 cell 7: 2nd reference to page 24552
On tree page 3315 cell 8: Child page depth differs
On tree page 3315 cell 10: 2nd reference to page 11567
On tree page 3315 cell 10: Child page depth differs
On tree page 3315 cell 11: Child page depth differs
On tree page 3315 cell 14: 2nd reference to page 6433
On tree page 3315 cell 14: Child page depth differs
On tree page 3315 cell 15: Child page depth differs
On tree page 3315 cell 25: 2nd reference to page 12425
On tree page 3315 cell 25: Child page depth differs
On tree page 3315 cell 26: Child page depth differs
On tree page 1820 cell 6: 2nd reference to page 863
On tree page 1820 cell 6: Child page depth differs
On tree page 1820 cell 7: Child page depth differs
On page 1573 at right child: 2nd reference to page 13383
On page 1960 at right child: 2nd reference to page 8185
On tree page 2296 cell 6: 2nd reference to page 19916
On tree page 2296 cell 6: Child page depth differs
On tree page 2296 cell 7: Child page depth differs
On tree page 2258 cell 7: 2nd reference to page 2959
On tree page 2258 cell 7: Child page depth differs
On page 2258 at right child: 2nd reference to page 4022
On tree page 61 cell 1: Child page depth differs
On tree page 61 cell 2: Child page depth differs
On tree page 2400 cell 0: 2nd reference to page 21660
On tree page 2400 cell 1: 2nd reference to page 21279
On tree page 2400 cell 2: 2nd reference to page 21337
On tree page 2400 cell 3: 2nd reference to page 21631
On tree page 2400 cell 4: 2nd reference to page 21633
On page 2400 at right child: 2nd reference to page 21717
On tree page 3288 cell 1: Child page depth differs
On tree page 2402 cell 2: 2nd reference to page 22327
On tree page 2402 cell 2: Child page depth differs
On tree page 98 cell 4: Child page depth differs
On tree page 149 cell 0: 2nd reference to page 481
On tree page 3620 cell 2: 2nd reference to page 8400
On tree page 3620 cell 2: Child page depth differs
On tree page 3620 cell 3: Child page depth differs
On tree page 880 cell 4: 2nd reference to page 1850
On tree page 880 cell 4: Child page depth differs
On tree page 149 cell 1: Child page depth differs
On tree page 1702 cell 0: 2nd reference to page 3472
On tree page 1702 cell 1: Child page depth differs
On tree page 149 cell 2: Child page depth differs
On tree page 11 cell 1: Child page depth differs
On tree page 20616 cell 95: 2nd reference to page 10286
On tree page 20616 cell 95: Child page depth differs
On tree page 20616 cell 96: 2nd reference to page 19875
On tree page 20616 cell 97: Rowid 20108 out of order (previous was 20117)
On tree page 20616 cell 97: Child page depth differs
On tree page 20616 cell 98: Rowid 6 out of order (previous was 20108)
On tree page 13426 cell 0: 2nd reference to page 13724
On tree page 13426 cell 1: Rowid 6 out of order (previous was 20109)
On tree page 13426 cell 2: Rowid 6 out of order (previous was 6)
On tree page 13426 cell 3: Rowid 6 out of order (previous was 6)
Corruption detected in cell 3 on page 13426
Multiple uses for byte 642 of page 13426


When I try to compress the database with Kobo utilities, I get this error message :

Spoiler:
CorruptError: CorruptError: database disk image is malformed


calibre 2.67 [64bit] embedded-python: True is64bit: True
Windows-8-6.2.9200 Windows ('64bit', 'WindowsPE')
('Windows', '8', '6.2.9200')
Python 2.7.9
Windows: ('8', '6.2.9200', '', 'Multiprocessor Free')
Successfully initialized third party plugins: DeDRM (6, 4, 3) && Count Pages (1, 6, 9) && Modify ePub (1, 3, 13) && KoboTouchExtended (2, 8, 0) && Kobo Utilities (2, 4, 1)
Traceback (most recent call last):
File "calibre_plugins.koboutilities.action", line 1594, in vacuum_device_database
File "calibre_plugins.koboutilities.action", line 3296, in _vacuum_device_database
File "c:\cygwin64\home\kovid\sw\build\apsw-3.8.2-r1\src\cursor.c", line 231, in resetcursor
CorruptError: CorruptError: database disk image is malformed


I feel my database has gone wild now, and perhaps building a new database would be better, but I don't know how I can log out from my account on the device and again log in. Could you please help me?

Edit : Restoring an old backup of database is also not helping. When I connect to Calibre after restoring old backup, I get the same error message.
Last edited by drjd; 09-15-2016 at 08:51 AM.
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Old 09-15-2016, 09:12 AM   #4
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Quote:
Originally Posted by drjd View Post
Thanks davidfor, when I run the check on the database, I get following error log :

Spoiler:
Result of running 'PRAGMA integrity_check' on database on the Kobo device:


*** in database main ***
On tree page 2665 cell 120: 2nd reference to page 10029
On tree page 2665 cell 120: Child page depth differs
On tree page 2665 cell 121: 2nd reference to page 10015
On tree page 2665 cell 122: 2nd reference to page 24669
On tree page 12046 cell 1: Rowid 57423 out of order (max larger than parent max of 688)
On tree page 2665 cell 123: Child page depth differs
On tree page 16377 cell 75: Child page depth differs
On tree page 16377 cell 76: Child page depth differs
On tree page 19596 cell 1: invalid page number 218103808
On tree page 24577 cell 3: Rowid 32555 out of order (min less than parent min of 55925)
On tree page 16378 cell 70: 2nd reference to page 13440
On tree page 16378 cell 70: Child page depth differs
On tree page 16378 cell 71: Child page depth differs
On tree page 16378 cell 98: 2nd reference to page 7031
On tree page 16378 cell 98: Child page depth differs
On tree page 16378 cell 99: Child page depth differs
On page 21360 at right child: 2nd reference to page 12046
On tree page 4314 cell 4: 2nd reference to page 12443
On tree page 4314 cell 4: Child page depth differs
On tree page 4314 cell 5: Child page depth differs
On tree page 8414 cell 1: 2nd reference to page 13431
On tree page 8414 cell 1: Child page depth differs
On tree page 8414 cell 2: Child page depth differs
On tree page 1796 cell 2: 2nd reference to page 4717
On tree page 1796 cell 2: Child page depth differs
On tree page 1796 cell 3: 2nd reference to page 5090
On tree page 1796 cell 4: Child page depth differs
On page 4032 at right child: 2nd reference to page 22164
On page 162 at right child: 2nd reference to page 5127
On tree page 582 cell 44: 2nd reference to page 8180
On tree page 582 cell 44: Child page depth differs
On tree page 582 cell 45: 2nd reference to page 7909
On tree page 582 cell 46: Child page depth differs
On tree page 582 cell 100: 2nd reference to page 24577
On tree page 582 cell 100: Child page depth differs
On tree page 582 cell 101: Child page depth differs
On tree page 3315 cell 1: 2nd reference to page 8087
On tree page 3315 cell 1: Child page depth differs
On tree page 3315 cell 2: 2nd reference to page 5356
On tree page 3315 cell 3: 2nd reference to page 23653
On tree page 3315 cell 4: 2nd reference to page 12275
On tree page 3315 cell 5: 2nd reference to page 11455
On tree page 3315 cell 6: 2nd reference to page 4314
On tree page 3315 cell 7: 2nd reference to page 24552
On tree page 3315 cell 8: Child page depth differs
On tree page 3315 cell 10: 2nd reference to page 11567
On tree page 3315 cell 10: Child page depth differs
On tree page 3315 cell 11: Child page depth differs
On tree page 3315 cell 14: 2nd reference to page 6433
On tree page 3315 cell 14: Child page depth differs
On tree page 3315 cell 15: Child page depth differs
On tree page 3315 cell 25: 2nd reference to page 12425
On tree page 3315 cell 25: Child page depth differs
On tree page 3315 cell 26: Child page depth differs
On tree page 1820 cell 6: 2nd reference to page 863
On tree page 1820 cell 6: Child page depth differs
On tree page 1820 cell 7: Child page depth differs
On page 1573 at right child: 2nd reference to page 13383
On page 1960 at right child: 2nd reference to page 8185
On tree page 2296 cell 6: 2nd reference to page 19916
On tree page 2296 cell 6: Child page depth differs
On tree page 2296 cell 7: Child page depth differs
On tree page 2258 cell 7: 2nd reference to page 2959
On tree page 2258 cell 7: Child page depth differs
On page 2258 at right child: 2nd reference to page 4022
On tree page 61 cell 1: Child page depth differs
On tree page 61 cell 2: Child page depth differs
On tree page 2400 cell 0: 2nd reference to page 21660
On tree page 2400 cell 1: 2nd reference to page 21279
On tree page 2400 cell 2: 2nd reference to page 21337
On tree page 2400 cell 3: 2nd reference to page 21631
On tree page 2400 cell 4: 2nd reference to page 21633
On page 2400 at right child: 2nd reference to page 21717
On tree page 3288 cell 1: Child page depth differs
On tree page 2402 cell 2: 2nd reference to page 22327
On tree page 2402 cell 2: Child page depth differs
On tree page 98 cell 4: Child page depth differs
On tree page 149 cell 0: 2nd reference to page 481
On tree page 3620 cell 2: 2nd reference to page 8400
On tree page 3620 cell 2: Child page depth differs
On tree page 3620 cell 3: Child page depth differs
On tree page 880 cell 4: 2nd reference to page 1850
On tree page 880 cell 4: Child page depth differs
On tree page 149 cell 1: Child page depth differs
On tree page 1702 cell 0: 2nd reference to page 3472
On tree page 1702 cell 1: Child page depth differs
On tree page 149 cell 2: Child page depth differs
On tree page 11 cell 1: Child page depth differs
On tree page 20616 cell 95: 2nd reference to page 10286
On tree page 20616 cell 95: Child page depth differs
On tree page 20616 cell 96: 2nd reference to page 19875
On tree page 20616 cell 97: Rowid 20108 out of order (previous was 20117)
On tree page 20616 cell 97: Child page depth differs
On tree page 20616 cell 98: Rowid 6 out of order (previous was 20108)
On tree page 13426 cell 0: 2nd reference to page 13724
On tree page 13426 cell 1: Rowid 6 out of order (previous was 20109)
On tree page 13426 cell 2: Rowid 6 out of order (previous was 6)
On tree page 13426 cell 3: Rowid 6 out of order (previous was 6)
Corruption detected in cell 3 on page 13426
Multiple uses for byte 642 of page 13426


When I try to compress the database with Kobo utilities, I get this error message :

Spoiler:
CorruptError: CorruptError: database disk image is malformed


calibre 2.67 [64bit] embedded-python: True is64bit: True
Windows-8-6.2.9200 Windows ('64bit', 'WindowsPE')
('Windows', '8', '6.2.9200')
Python 2.7.9
Windows: ('8', '6.2.9200', '', 'Multiprocessor Free')
Successfully initialized third party plugins: DeDRM (6, 4, 3) && Count Pages (1, 6, 9) && Modify ePub (1, 3, 13) && KoboTouchExtended (2, 8, 0) && Kobo Utilities (2, 4, 1)
Traceback (most recent call last):
File "calibre_plugins.koboutilities.action", line 1594, in vacuum_device_database
File "calibre_plugins.koboutilities.action", line 3296, in _vacuum_device_database
File "c:\cygwin64\home\kovid\sw\build\apsw-3.8.2-r1\src\cursor.c", line 231, in resetcursor
CorruptError: CorruptError: database disk image is malformed


I feel my database has gone wild now,
Yes, that is corrupt an won't be recoverable
Quote:
and perhaps building a new database would be better, but I don't know how I can log out from my account on the device and again log in. Could you please help me?
Go into the settings and then Accounts. Tap "Sign out" next to your account name.
Quote:
Edit : Restoring an old backup of database is also not helping. When I connect to Calibre after restoring old backup, I get the same error message.
Assuming the backup was OK, it should work. But, try powering off and on after ejecting the device.
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Old 09-16-2016, 01:04 AM   #5
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Originally Posted by davidfor View Post
Go into the settings and then Accounts. Tap "Sign out" next to your account name.
That worked. Thanks for the tip, davidfor. Although I lost my fancy reading stats of 150+ books read and 950+ hours read , I am still happy that the device is working properly.

Quote:
Originally Posted by davidfor View Post
Assuming the backup was OK, it should work. But, try powering off and on after ejecting the device.
Now since my device is working, can I take a second chance of replacing the database with an earlier back up prepared by Kobo utilities to see if can recover my reading stats?
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Old 09-16-2016, 01:11 AM   #6
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That worked. Thanks for the tip, davidfor. Although I lost my fancy reading stats of 150+ books read and 950+ hours read , I am still happy that the device is working properly.
Unfortunately, you lose the stats for sideloaded books.
Quote:
Now since my device is working, can I take a second chance of replacing the database with an earlier back up prepared by Kobo utilities to see if can recover my reading stats?
There should be no harm in trying. At the worst you will be back to the same point you were before and needing to do the sign-out again.
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Old 09-16-2016, 02:51 AM   #7
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There should be no harm in trying. At the worst you will be back to the same point you were before and needing to do the sign-out again.
Great, I will try it out today and will inform the outcome.
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Old 09-16-2016, 12:48 PM   #8
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After a few trials, I succeeded in replacing a two months old backup of database on the device, and got my reading stats (partially) back. Thank you again, davidfor, for the help!
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Old 09-16-2016, 09:04 PM   #9
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Good to hear.

I'll have to look at the stats again. It's possible that simply extracting certain entries and restoring them later is enough to save the finished book count. I haven't been able to create the entries, but an extract and reload of the database rows might work.
Last edited by davidfor; 09-16-2016 at 10:17 PM. Reason: I rarely claim to be able to spell.
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Old 09-17-2016, 08:58 AM   #10
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Quote:
Originally Posted by davidfor View Post
I'll have to look at the stats again. It's possible that simply extracting certain entries and restoring them later is enough to save the finished book count. I haven't been able to create the entries, but an extract and reload of the database rows might work.
That will be an exciting and helpful improvement, I think.
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Old 02-23-2017, 06:09 PM   #11
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i have the same error -CorruptError: database disk image is malformed.
i have logged out of Kobo and back. that didn't work.
i have added the kobo utilities- how do i run a database check ?
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