Trying to build my game on Linux, I get the same error building on ubuntu 16 lts and manjaro:
Using clang version '5.0.1' (string), 5 (major), 0 (minor), 1 (patch)
@progress push 5%
@progress 'Generating code...' 0%
ERROR: All source files in module "InputCore" must include the same precompiled header first. Currently "/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Public/InputCore.h" is included by most of the source files. The following source files are not including "/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Public/InputCore.h" as their first include:
/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Private/InputCoreModule.cpp (including /home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Public/InputCoreModule.h)
/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Private/InputCoreTypes.cpp (including /home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Classes/InputCoreTypes.h)
/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Private/GenericPlatform/GenericPlatformInput.cpp (including /home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Public/GenericPlatform/GenericPlatformInput.h)
/home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Private/Linux/LinuxPlatformInput.cpp (including /home//Projects/DogFight/Build/UnrealEngine/Engine/Source/Runtime/InputCore/Public/Linux/LinuxPlatformInput.h)
To compile this module without implicit precompiled headers, add "PCHUsage = ModuleRules.PCHUsageMode.UseExplicitOrSharedPCHs;" to InputCore.build.cs.
LogModuleManager: Display: Found up-to-date module file ../../../Engine/Plugins/Developer/NullSourceCodeAccess/Binaries/Linux/libUE4Editor-NullSourceCodeAccess.so (API version 0).