Environment:
I have the same issue since I installed Xcode 8.1 beta and created a new Swift project. Currently I "fixed" the issue by unchecking the "Run script only when installing" the first time (causing a longer build time), for every following build I am able to build and run the app with the checkbox "Run script only when installing" checked. This works until I do a "pod install" or "pod update". I am eagerly waiting for an official update to Xcode 8.1, but perhaps it has something to do with cocoapods itself?
If you use the new beta of Cocoapods - 1.2.1.beta.1
at the time of writing, which you can install sudo pod install --pre
then you have access to the super cool COCOAPODS_PARALLEL_CODE_SIGN
option.
This has sped up the Embed Pods Frameworks
build stage for me by 75% on device.
Instructions in below image.