I just updated my Mac to OSX 10.11 El Capitan and some gems didn't remain.
The problem arose when I tried to run installations of different gems... e.g.:
> sudo gem install compass
Once I execute, I get the error:
> ERROR: While executing gem ... (Errno::EPERM) Operation not permitted
This happens with other gems, as well...
I've run Homebrew and tried to install Ruby again, but nothing is working.