We bought a new MacBook Pro late last year and I had not run into any issues until yesterday, when I tried to install the LAME MP3 Encoder for use with Audacity. I was in a pinch, needing to convert a *.wav file to *.mp3 for the Dots, Lines, and Destinations podcast. When trying to install the encoder it appeared to work, but on closer inspection, the files were never written to the correct folder. After doing a little research, I noticed that the /usr/lib/local directory was not writable and threw an error when accessed. So, to Google I went. Turns out this is a “feature” and part of Apple’s System Integrity Protection. Basically, it keeps certain directories inaccessible to even root level access to try and prevent malicious applications from modifying things they shouldn’t be touching. The side effect is that when you legitimately need to modify those directories you can’t. I did not have the luxury of time when going through all this and opted to just use an older Mac that did not have El Capitan installed to convert the audio files I needed.
Glenn Fleishman provides a better description of System Integrity Protection, including how to disable it, in his article on Macworld.
Early reports of problems with rootless mode seemed to indicate that a wider set of software might be unable to work with the restriction enabled, such as SuperDuper! from Shirt Pocket Software. However, Apple made changes during beta testing that resolved concerns with that app and others. (Shirt Pocket had to update SuperDuper! to deal with the omission of an open-source program, which breaks scheduled updates; those have to be re-created in the El Capitan-compatible release.)