Wolverton: Mac bug can thwart El Capitan upgrade

I like the latest version of Apple’s OS X and had no problem installing it on my MacBook Air.

But my iMac was a completely different story.

I’ve upgraded the operating system on my Macs numerous times over the years without a hitch. So I didn’t spend a whole lot of time mulling whether to install the latest update, dubbed El Capitan, on my primary home computer as part of my review of the new software.

After bricking that computer four times, restoring it from backups twice and finally having to resort to typing commands into a command-line interface with the assistance of technical support folks from Apple to fix the problem, I wish I’d given it a bit more thought. My iMac is mostly up and running with El Capitan now, but it was not a fun process getting it there.

The funny thing is that the installation seemed to be going fine at first. My iMac downloaded the software, rebooted and started installing it, showing me a black Apple logo and progress bar on a gray screen. The progress bar got to about 80 or 90 percent complete before it stalled out. Eventually, my computer rebooted and showed a message — again on a gray background — that it had run into a problem with the installation and would reboot again.

I didn’t worry too much about the problem right then. I have a backup drive attached to my computer, so I figured I could revert to one of my backups and then try again. I found a help page on the Web that told me how to do it — you turn off the computer, then hold down command-R when you press then power button again to get to a menu of options that includes restoring from backups.

I went through that process and then let the computer restore itself overnight — it took about 12 hours or so. When it was fully restored, I made sure everything was working, made sure to back it up again and then tried again to install El Capitan.

When the same thing happened — a stalled install, followed by a warning message repeated over and over as the computer rebooted numerous times — I started to get a bit more concerned. Instead of simply restoring the machine, I tried some of the other options in the repair menu.

I first used the Disk Utility app to check my disk, but it didn’t find any problems. I then tried to reinstall the update directly from the repair menu, without restoring my system first. But I ran into the same problem with the failed install. So, I went back to square one and again restored my computer from a backup.

In the meantime, I’d been searching the Web and found reports of other people experiencing similar problems. Unfortunately, the few solutions users posted in forums didn’t help my situation. So I turned to Apple’s technical support folks.

After going back and forth with them over the course of two days, they finally were able to diagnose and resolve the problem. They figured out that even though the computer was saying that it hadn’t completed the installation of El Capitan, it actually had. But that there was a conflict that was preventing from actually loading the new operating system.

In OS X, some of the programs you use or accessories you attach to your Mac will modify some of the core code in the operating system with little bits of software called kernel extensions. Those bits of software can make it so that your computer will automatically recognize and be able to work with the accessories you attach when you connect them or with the programs you use when you load them.

As helpful as these kernel extensions can be, they can also be dangerous, because they are placed so close to the heart of the operating system. If they have a bit of bad code, they can prevent the computer from starting up. That’s what was happening with my machine.

The technical support folks had me stop the repeated rebooting process, shut down my computer and restart it in “safe” mode. When I was able to do that, it showed the computer actually had installed El Capitan. They then had been look up and send them a list of my kernel extensions. It turns out — unbeknownst to me — I had a lot of them, likely because I test a lot of different equipment on my iMac for my column.

After examining those extensions, the Apple folks found a couple they thought might be causing the conflict. Both were related to a program used to interact with a LiveScribe pen I once tested. Under the direction of Apple’s representatives, I moved the LiveScribe extensions out of the hidden directory in which they were stored, typing commands into the Terminal program.

Moving those extensions solved the problem. After that, I was able to reboot the computer and it started up running El Capitan without having to go into safe mode.

It’s unclear why El Capitan didn’t recognize and move the problematic kernel extensions on its own — or prompt me to do so before I installed it. But Apple’s technical support folks said they would take note of the problematic kernel extensions, presumably so future versions of the operating system would know how to handle them.

It doesn’t look like the problem is widespread. Aside from a few forum posts and an one reader email, I hadn’t seen many reports of similar issues.

And it’s not like Mac OS is unique for having an installation problem. As I reported in August, a problem with Microsoft’s Windows 10 made some consumers’ machines unusable when they tried to upgrade to the new software.

Still, the incident is a good illustration that even Macs can have critical problems. It’s also a good reminder of the importance of backups. As frustrating as this process was, at least I didn’t have to worry that it was going to result in a loss of years of photographs or documents.

Photo: Apple’s latest iMac computers (courtesy of Apple).


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  • leafmen

    In my case, I had a problem even before it got to the installation. I had a “disk verify” problem early in the install and could not get back to my old OS (Yosemite). Got stuck in a loop where I could not return to my old OS. Tried various things from recovery mode, checking the date on the system etc. Fortunately, my data was not corrupted and I managed to transfer all my data files to another Mac using target mode and then do a wipe disk on my Mac. Then reinstalled from scratch El Capitan. I had never thought twice about upgrading the OS in a Mac but from now on I will be wary.

  • BurningThumb

    I reported this bug to Apple a long time ago. In the end I finally put my files on an external HD, wiped the internal HD, did a clean install from a downloaded image on a USB stick, and manually copied my files back. All the while Apple know they are bricking machines – sad to see the company become everything that it once stood in opposition too.

    • Dan Andersen

      Why would you expect Apple to fix a bug in another company’s software?

      • BurningThumb

        Because its not a bug in another company’s software.

        It is a bug in the OS X Installer that leaves the computer in an unusable state.

        Looking at the installer log you will see the Installer is crashing because its trying to index into an array with an invalid index – an obvious, and easy to fix bug.

        The scenario is (1) run installer, (2) install fails and gives you a dialog saying the install failed and the option to try again, (3) try again and the install fails – rinse and repeat.

        Nicely bricked computer.

        • Dan Andersen

          Even if your interpretation of the log is correct, you don’t know the source of the error. Since you indicated you were able to clean install successfully, it’s obviously not the installer itself.

          Check the low-level software on your system.

          • BurningThumb

            The crash log was sent to Apple and they acknowledge its a bug in the installer. Maybe you want to take it up with them 😉

  • Randy Singer

    The root of the problem is that Apple no longer offers the “Archive and Install” feature when upgrading the OS. So potentially conflicting software from previous versions of the OS sometimes gets left behind. (The install runs a check for conflicting software, but it is far from perfect.) The easy solution is to do a clean install of the OS when doing a major upgrade. I make it easy by cloning my internal drive to an external drive, having the installer wipe clean my internal drive and install a clean version of OS X, then I use the installer’s built-in version of the Migration Assistant to move all of my software from the external clone to the internal drive.

  • Makikiguy

    I installed el Capitan and had no problem, except one Nikon program does not work with it. AND Nikon does not seem too concerned.

    • eljobsodiablo

      Nikon has terrible support for Mac and PC software.

    • Makikiguy

      You and me both. I only used NIkon to transfer pics from the camera. I can work around it with just a few extra steps.

  • Dana Marks

    Thanks for taking one for your readers, Troy! We appreciate what you do, and I will wait for the all clear signal before I update.