unfortunatly it is not possible to know what is the reason and exactly what to do. I started here in this topic with this problem in my MacMini 2011, which runs only exclusively Apple software. I use this computer as a server machine and I have absolutly no other softwares installed and I had this problem, only at the 3rd try out was solved, without knowing what was the reason for the failure!
the other 2 computers, 2x MacBook Pro also 2011, my inclusive has a lot of try outs softwares and ******** installed I had no problems at all, at the first try out updated as a clean blue sky 🙂
what I still advice is to keep your system backup, if you have this hanging problem, don't loose more time - restore your system back, build a USB drive with the El Captain.dmg (Apple teach it, or googling) and install it from a clean formated hard drive. then you can restore back the Applications or user preferences as you like it from your backup.
<Edited by Host>