Cocoa Pods not updating pods on El Capitan

This is caused by the new System integrity protection feature introduced in El Capitan. It restricts even administrators from writing to /usr/bin.

Your best option would be to install gems without needing sudo. There is a good guide on how to do that:

export GEM_HOME=$HOME/.gemexport PATH=$GEM_HOME/bin:$PATHgem install cocoapods

From CocoaPods issues 3736

1. Uninstall all instances of cocopods (just to be safe and keep things clean) see fully uninstall Cocoapods

   sudo gem uninstall cocoapods

   or even better fully uninstall all components (and select All versions for each)

   gem list --local | grep cocoapods | awk '{print $1}' | xargs sudo gem uninstall

2. Install again

   sudo gem install -n /usr/local/bin cocoapods

3. Change access permission

   sudo chmod +rx /usr/local/bin/

This should work for you

sudo gem install -n /usr/local/bin cocoapods

Operation not permitted - /usr/bin/xcodeproj #3692

For whatever reason, the rootless stuff seems less restrictive when one simply upgrades the system. I could sudo gem install cocoapods just fine on a machine upgraded from 10.10 - however, binstubs are no longer installed into /usr/bin:

$ sudo gem install cocoapods[...]1 gem installed$ export PATH=$PATH:/Library/Ruby/bin$ pod --version0.37.2

We have heard from some users that they receive this error when doing a system-wide installation:

ERROR: While executing gem ... (Errno::EPERM) Operation not permitted - /usr/bin/pod

We aren't sure why gem behaves differently on some systems, but this can be solved by passing -n /usr/local/bin to the install command, so that the pod executable gets installed there.