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When ubuntu boots, I get this error:

The NTFS partition was not cleanly unmounted. This probably indicates that the system was not shut down properly. Please run chkdsk /r from Windows; once that is fixed you should be able to resume the installation. Press OK to reboot.

I tried that and nothing special happened (except that error again).

What should I do?

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Assuming that you were booting Windows from that partition, I believe you should be getting a message asking if you want to schedule the chkdsk, and after saying yes you have to reboot Windows again and wait quite a while for it to run before bringing all of Windows up. Is that what happened? –  John S Gruber Aug 1 '12 at 18:46
    
Yes. That happened. –  Matej Kranjec Aug 1 '12 at 19:53
    
Can you describe in more detail what you are doing when this happens and when you get the message? This is happening sometime during installation? –  John S Gruber Aug 1 '12 at 20:57
    
@johnsgruber I installed ubuntu using wubi a long time ago. Then it booted and I got a small window titled installation. First it told me to delete root.disk and I deleted it. Then I got "The NTFS partition was not cleanly unmounted. This probably indicates that the system was not shut down properly. Please run "chkdsk /r" from Windows; once that is fixed you should be able to resume the installation. Press OK to reboot." –  Matej Kranjec Aug 1 '12 at 20:59
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