The complete warning is

[!] The `PTE-V1 [Debug]` target overrides the `ALWAYS_EMBED_SWIFT_STANDARD_LIBRARIES` build setting defined in `Pods/Target Support Files/Pods-PTE-V1/Pods-PTE-V1.debug.xcconfig'. This can lead to problems with the CocoaPods installation

Solution:

Firstly, open the .xcworkspace, choose Always Embed Swift Standard Libraries. If it is bold, it is overriden. Then you can delete it. It should become normal which is inherited.

Secondly, you need to delete the Pods folder.

Then, if you run pod install again, the warning should disappear.