Hi there Ewan Lamont,
It sounds from your post that you verified and repaired the permissions on your startup volume but received this error message that a SUID file would not be repaired. First that doesn't sound too worrying to me because it is likely something that can be safely ignored. You can verify that by checking to see if that error is listed in the following article:
Mac OS X: Disk Utility's Repair Disk Permissions messages that you can safely ignore
I would actually verify and repair the disk itself, rather than the permissions with this article as that will evaluate the system file structure for damage:
Disk Utility (Yosemite): Repair a disk
Then try again to see if the issue persists. It may be possible that you might need to perform a safe boot if the issue persists. This will clean some system level caches that may be interfering with the erasure of free space you are trying to do:
Try safe mode if your Mac doesn't finish starting up
Starting up in safe mode
Follow these steps to start up into safe mode.
- Start or restart your Mac.
- Immediately after you hear the startup sound, press and hold the Shift key.
- Release the Shift key when you see the Apple logo appear on the screen.
After the Apple logo appears, it might take longer than usual to reach the login screen or your desktop. This is because your Mac performs a directory check of your startup disk as part of safe mode.
To leave safe mode, restart your computer without pressing any keys during startup.
Once you boot into safe mode and log in, the caches have been cleared and there is nothing else to do so restart as normal and try again.
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