It is possible that something in that dependency change is referencing the standard SQLite pod which is interfering with linking. Please consult this document:
Note: Updated to clarify that this guidance applies to all projects built with Xcode 8, including for non-iOS targets).
Apple has recently released XCode 8, along with new SDKs (e.g. iOS 10, watchOS 3, mac OS, tvOS), with many new features and enhancements. The majority of projects that include SQLCipher should have no problems after upgrading. However, there are some important changes and edge cases, so we have prepared the following important recommendations for all SQLCipher developers upgra…