I upgraded to El Capitan yesterday and everything was good until recently when I noticed I can't write anything (with sudo ofc) on /usr/bin as I tried to install phpbrew.
What could be causing this and how to troubleshoot it?
Since OSX 10.11, Apple reinforce the security system. Called System Integrity Protection, Apple locks down :
/System /sbin /usr (with the exception of /usr/local subdirectory)
To disable this security feature you have to reboot your computer and hold
CMD+R at start to boot into OS X Recovery Mode.
OS X Utilities > Terminal
Type the command
csrutil disable; reboot
Your computer will restart. You will see a confirmation message about the desactivation.
To verified the status of CRS type
As mentioned by Ragnar, the
/usr directory is locked down by the system, with the exception of
/usr/local. Then, if your scenario allows, I'd recommend adding the symbolic link to
/usr/local/bin. If you don't have a strict requirement on using
/usr/bin, that's one way to work around the "Operation not permitted" error.
One can verify if a particular file or directory is restricted by OSX's System Integrity Protection (SIP)/Rootless by listing the file flags using the
-O option to ls (e.g. to see which directories in / are restricted):
ls -Ol /
The directories or files that are controlled by SIP show as 'restricted'.
There's full details in the answers to this question about SIP/rootless.