You might have some other directories left over from an old version of
virtualbox under /var/lib/dkms/ . For example, I had some directories
left over from 3.2.6, and the fix for me was:

sudo rm -r /var/lib/dkms/vboxnetadp /var/lib/dkms/vboxdrv
/var/lib/dkms/vboxnetflt

Basically you should check the timestamps of any directories under
/var/lib/dkms that start with either 'vbox' or 'virtual'. If they're
fairly old (e.g. > 1 year) then there's a reasonable chance that they
might be cruft left over from an old version of VirtualBox. Deciding
whether to delete them or not is at your discretion.

And really, there are 2 entirely separate software problems here:
1) VirtualBox should clean up after itself by removing these old directories 
when being uninstalled or upgraded.
2) dkms should be explicit and unambiguous about which directory it has a 
problem with. For example there would be a LOT less confusion all round if it 
said "Error in directory /var/lib/dkms/vboxdrv , belonging to package 
'virtualbox' - Could not locate dkms.conf file."  instead of the completely 
non-specific: "Error! Could not locate dkms.conf file."

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https://bugs.launchpad.net/bugs/830915

Title:
  [Oneiric] Error during kernel upgrade: Could not locate dkms.conf file

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