Much like Yosemite last year, it looks like Apple’s latest OS doesn’t like doing an upgrade (in place) install on a system drive that is in software raid (in my case a 2010 Mac Pro with 2x SSD drives).
Just a word of warning for anyone who’s about to attempt it.
I’ll try creating a netboot image on my OSX server and see if that method will be more successful.
The other option may be (as it was last year) to create a USB install. Last year I used DiskMakerX, but it would seem the just released version at the time of writing doesn’t work on either my Mac Pro or a Macbook Pro to create the install. Troubleshooting steps on the author’s Facebook page haven’t helped.
Instead, there is a command that can be run in terminal that will perform the same essential function. The command to be run is: sudo /Applications/Install\ OS\ X\ El\ Capitan.app/Contents/Resources/createinstallmedia –volume /Volumes/Untitled –applicationpath /Applications/Install\ OS\ X\ El\ Capitan.app –nointeraction
Thanks to Arstechnica for that one. It even gives you a fun little warning when running the command obviously from a staff member or two from Apple with a sense of humour. (See below.)
It looks like as I was writing this, DiskMakerX was updated (to version 5.0.1) which fixes the bug I (and a few others) were experiencing. Now to create a new USB stick and test if it will work.
It appears all went smoothly after booting from a USB stick. El Capitan installed without much user interaction and all. So it looks like if you have a RAID volume, do the same as with Yosemite. Boot from an external drive and upgrade that way rather than attempting to do it all through the App Store.