When Yosemite went wonky: Fixing an OS X systems failure

Shortly after upgrading to Mac OS X Yosemite, David Gewirtz' maxed-out iMac became unusable. This article details the not-so-uncommon problem he encountered and the steps taken to restore his machine.
Written by David Gewirtz, Senior Contributing Editor

Back in October, I wrote, "So far, Yosemite has been out about a week and we're not hearing posts about systems failing terribly." And, other than Wi-Fi problems, we haven't heard all that much about Yosemite being a nightmare.

That is, until last night, when my machine crashed right after I upgraded to Yosemite.

I've told you a lot about the heavily configured non-Retina iMac that I bought just about 13 months ago. Until this hard crash, I've been surprisingly satisfied with the machine. I started it on Mountain Lion, waited until Mavericks seemed to have most of the kinks worked out of it, and then moved to Mavericks.

Then, a day or so ago, I moved to Yosemite. I upgraded to Yosemite for a few reasons. The biggest is that a number of the Mac applications I use every day have started to nag me with upgrade notices, even while running on Mavericks.

It's incredibly annoying to get an upgrade notice from Parallels, for example, every time you need to launch a Windows VM. These naggings were interrupting my flow and my thinking was that since I hadn't heard many complaints about upgrading to Yosemite, I might as well just do the deed.

Second is my gig. I write about new technology and if I don't eat my own dog food, I won't be able to tell you about my experiences. So, this last 24 hours of pain-in-the-butt has been all for you! You're welcome.

Finally, I'm about to get started on a big project that will require loading a pile of new software. I considered that I might as well upgrade and make sure everything was configured right, before adding those products into the mix.

All are good and fair reasons. Unfortunately, shortly after upgrading, my machine became unusable.

Here's what happened. All of a sudden, I couldn't see any applications in my Applications folder. If I tried to run an application by using an existing Dock item or shortcut, it would run. But if I tried to move an application into the Applications folder or look at the contents, nothing.

I launched Terminal and was able to do an "ls" and see all the applications. But Finder couldn't see them. I was also experiencing other application-related failures (like some maintenance tasks weren't running).

The very first thing I did was launch Disk Utility and run some disk checks and repair sweeps. Disk Utility found some permissions incorrect, and fixed them. But as it turns out, those permission fixes didn't stick, because subsequent Disk Utility runs found those same permission errors and fixed them again.

The problem didn't go away, so I went online.

I did a Google search on "yosemite applications folder empty" and turned up a relatively active list of results. In particular, I found an Apple support forum filled with discussion on this exact issue, along with discussions about how to fix it.

I dutifully followed the various recommendations without success. I was also running iStatMenus and Creative Cloud (two applications many of the troubled users found to be using in common), so I made sure to turn them off. I was not, however, experiencing this problem on a Retina machine (which many of the forum posters thought was a common symptom), so that wasn't a match.

In any case, none of the recommended fixes fixed the problem. It was time to go old-school on the problem.

First, I rebooted, holding down Command and the "R" key to go into the Recovery Console. I tried to do an OS restore without zeroing my flash storage. The restore completed successfully, keeping all my settings and applications in place. Unfortunately, the Applications folder and system problems also remained. It was a no-go.

Next, I took a deep breath, rebooted into the Recovery Console, and launched Disk Utility. I selected my internal flash storage and hit Erase. I did a fresh install of Yosemite (because the Recovery Console, apparently, won't recover earlier OS versions) and rebooted.

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This was interesting. I had what was essentially a fresh machine. The Applications folder opened just fine. That was a good sign. I was starting to worry that my internal flash memory had failed. I'm still not ruling out an error or glitch, but there doesn't appear to be a problem with the hardware.

I keep backups using a number of techniques. I have a local Time Machine backup, along with copies of critical files sent to my local file server and up to CrashPlan. I didn't want to do a CrashPlan recovery because that would take a hellava long time to complete. So I decided to try recovering using Time Machine.

I launched Migration Assistant and selected the Time Machine volume. Somewhat to my dismay, the only Time Machine backup archive that Migration Assistant was willing to restore from was the most recent backup — which occurred after I installed Yosemite. I'm thinking Apple is doing its normal dastardly deed of forcing us to its latest OS. Feh. In any case, I selected it and told Migration Assistant to restore everything, including Applications.

Two hours later, the machine was telling me that it was restoring my applications and that there were only seven minutes left. I was told there were only seven minutes left for well over an hour. I let it run another hour, and still no movement.

I hard powered off and booted into the Recovery Console again, launched Disk Utility again, erased my flash memory again, and installed Yosemite from the Recovery volume again. When all that was done, I rebooted, and when I checked, was able to access my Applications folder again. Then, I ran Migration Assistant again.

This time, while selecting the only backup archive Migration Assistant would allow, I unchecked the Applications option. This effectively told Migration Assistant to restore all my data and settings, but not to restore my applications.

I once again let the iMac do its thing, and this time the Migration Assistant completed. I rebooted my Mac and had my data and settings, but none of my specially installed apps. Fortunately, I installed two of the most important ones for projects I am working on, and both accessed the recovered data correctly. Whew!

So that's where I am now. I can open the Applications folder and it looks like most of my applications, once reinstalled, should be able to find their data. I'm hoping I don't encounter another glitch of this magnitude, so cross your fingers.

To be fair, I can't completely blame Yosemite. I have had a few systems crashes while testing software where I had to power cycle the iMac. While there were no apparent problems from those hard reboots, it's possible that something got corrupted and when I upgraded to Yosemite, that corruption became somewhat magnified, causing my system to error out.

On the other hand, it's hard to ignore pages of forum complaints from users with exactly the same problems.

How has your Yosemite experience been so far? Have you had any crippling problems or has it been smooth sailing? Let me know in the TalkBacks below.

By the way, I'm doing more updates on Twitter and Facebook than ever before. Be sure to follow me on Twitter at @DavidGewirtz and on Facebook at Facebook.com/DavidGewirtz.

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