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Ran El Cap Update, but still running Yosemite after restart!

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Nov 21, 2014
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Motherboard
Asus Z97 Pro
CPU
i7-4790
Graphics
GTX 970
So I ran the El Cap update (I'm updating from 10.10.1 to 10.11.5), and when it prompts me to restart, I restart. Then I halt at the clover screen so I can add the nv_disable=1 boot arg (Maxwell GPU, GTX 970), then boot from my system drive "Yosemite". Boot goes fast, and I'm right back in 10.10.1. I feel like it should be running the actual install at this point, but it just goes straight to the desktop.

On the clover screen I'm given these options: Boot from USB, Boot OSX installer on USB, Boot from "Yosemite", and Boot OSX installer on Yosemite.

On my first attempt I booted from USB after the restart, and after that I was unable to boot at all from Yosemite. So I restored my backup and tried again.

Second attempt, which I've done a few times, i booted from Yosemite after the restart, but it went straight to desktop as described above.

In my most recent attempt, I chose Boot OSX Installer on Yosemite. Currently it's stuck on the loading bar with the apple logo screen, loading bar crept along a tiny bit but seems to be hanging. It hasn't moved the whole time I've been typing this.

Can anyone offer some suggestions?
 
Just wanted to bump this after the weekend. I feel like I'm missing something very simple here.

Thanks!
 
This procedure requires you to prepare a Unibeast installer with El Capitan as if you were going to do a fresh install, but instead you're going to install El Capitan over the top of you Yosemite install.
 
Thanks! I was following the wrong guide the whole time. However, I still can't get el cap installed. I followed the guide up to step 7, but get a white crossed-out circle on black screen, immediately after the white apple logo, and it just hangs there. This would be right after I hit "Boot OS X Install".

Any ideas what might be causing this?
 
Thanks, that big list eventually helped me get everything back up and running.

I have a general question about clover and EFI partitions. How does clover know which EFI partition to use if I have one on a USB stick and one on my system drive? When I was establishing clover last year, I was booting from the USB and never moved things over to the system drive until now (which was part of my problem). Now I can boot without the USB stick just fine, but would I run into trouble if I had the USB stick mounted during a restart?
 
Now I can boot without the USB stick just fine, but would I run into trouble if I had the USB stick mounted during a restart?

That would depend on what the difference is between them - No difference = No problem.
Why not make them both the same ?
 
Good point, I'll just have to make sure they're identical if I make any changes in the future.

Further question: I'm able to boot from the backup drive, but its EFI partition is completely empty. Does Clover just go with the first available properly configured EFI starting with the system drive?
 
Good point, I'll just have to make sure they're identical if I make any changes in the future.

Further question: I'm able to boot from the backup drive, but its EFI partition is completely empty. Does Clover just go with the first available properly configured EFI starting with the system drive?

If you are booting from a drive with an empty EFI partition I'm guessing you probably installed Clover in Legacy Mode.
 
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