Problems Upgrading from OS X Yosemite to Sierra

Our main machine for managing photos is a Late 2012 Mac Mini running OS X Yosemite. Some of the software we use on it had problems when Yosemite first came out, so we didn’t upgrade at the time, but those problems have been resolved, so it was time to upgrade to Sierra. I cloned the disk with Clonezilla, and tried the upgrade. It did not go well. OS X started the upgrade, but failed with a message to restart and try again. And again.

On the failure screen, you can load Disk Utilities; I tried that and it discovered unrepairable problems. Next, I opened a command window and ran fsck_HFS on the drive. This time, it reported problems with the index but failed on the rebuilding the B-Tree due to lack of continguous space.

The disk would no longer boot.

Copy and Fix

Prior to attempting the upgrade, I made a copy using Clonezilla; at this point, I replaced the existing drive with a new 1T SanDisk SSD, and restored the Clonezilla copy from before the upgrade attempt. The drive replacement instructions are daunting, but it was not as bad as the instructions made it look. The instructions call for an Apple Logic Board Removal Tool–which Apple does not sell–but I was able to replace the drive without it. The new drive booted (fast), so I deleted some directories to make space for the B-tree rebuild. Next, I booted into the OS X Recovery image and ran DiskUtil to see if it could repair the drive. It tried and failed, leaving a drive that would not boot.

DiskWarrior to the Rescue

I restored from the pre-upgrade clone again, and again deleted unnecessary files. This time, I purchased a copy of DiskWarrior. You cannot read the documentation without a working OS X machine–a real problem for disk recovery software. I ended up having to install DiskWarrior on the still-working but broken OS X image, and then was able to make a bootable repair USB flash drive.

After booting from the DiskWarrior flash drive, I selected the Directory Repair option. While running “Rebuild Directory”, it hung up during test 9–Compare Directories–so I skipped that step. I wouldn’t boot. I still didn’t boot after running file check and repair.

Next, I booted to the standard OS X Recovery image, and selected Disk Utilties, where I ran a permissions check which indicated numerous problems, so I ran a permissions repair. I ran the disk verify option which showed as completely clean. It still would not boot.

Reinstall OS X

Since I could always go back to the Clonezilla image, I next tried the “Reinstall OS X” option. This reinstalled the OS and managed to keep all of the programs and user settings. I next ran an update to pick up application updates to about a half-dozen applications, followed by the upgrade to Sierra, which ran for about an hour on the SSD. Once Sierra installed, there were about seven applications that asked for updates.


I have had few problems with OS upgrades, but when I have had problems, I have been thankful for Clonezilla backups. This would probably have been very, very ugly without it.