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The auto generated intermediate compilation Makefile targets .s and .i are only present the target sources are added in the top level CMakeLists.txt.

Example:

CMAKE_MINIMUM_REQUIRED(VERSION 3.0)
PROJECT(TEST C CXX)

FILE(WRITE ${CMAKE_BINARY_DIR}/main.c "int main(void){return 0;}\n")
ADD_EXECUTABLE(main ${CMAKE_BINARY_DIR}/main.c)
FILE(WRITE ${CMAKE_BINARY_DIR}/mainxx.cxx "int main(void){return 0;}\n")
ADD_EXECUTABLE(mainxx ${CMAKE_BINARY_DIR}/mainxx.cxx)

Results in:

make help
(...)
... main
... mainxx
... main.o
... main.i
... main.s
... mainxx.o
... mainxx.i
... mainxx.s

However doing the FILE / ADD_EXECUTABLE bits in a subdir's CMakeLists.txt

# Top level CMakeLists.txt
CMAKE_MINIMUM_REQUIRED(VERSION 3.0)
PROJECT(TEST C CXX)

ADD_SUBDIRECTORY(sub)

# sub/CMakeLists.txt
FILE(WRITE ${CMAKE_BINARY_DIR}/main.c "int main(void){return 0;}\n")
ADD_EXECUTABLE(main ${CMAKE_BINARY_DIR}/main.c)
FILE(WRITE ${CMAKE_BINARY_DIR}/mainxx.cxx "int main(void){return 0;}\n")
ADD_EXECUTABLE(mainxx ${CMAKE_BINARY_DIR}/mainxx.cxx)

results in :

make help
(...)
... main
... mainxx