Does set_target_properties in CMake override CMAKE_CXX_FLAGS?

^{The accepted answer is still working but outdated since 2013.
This answer is based and new functions from CMake v2.8.12, v3.3 and v3.13.}

Since CMake-2.8.12 (2013)

Two new commands to set CMAKE_CXX_FLAGS:

• target_compile_options() (for one single target)
• add_compile_options() (for all targets)

The documentation of last version has not changed a lot since cmake-2.8.12:

• target_compile_options()
• add_compile_options()

In you case you can use:

target_compile_options(${TARGET} PRIVATE ${BUILD_FLAGS})

Or simply if you have a single target:

add_compile_options(${BUILD_FLAGS})

More examples

target_compile_options(mylib PRIVATE   -O2) # only internal
target_compile_options(mylib INTERFACE -gl) # only external
target_compile_options(mylib PUBLIC    -g)  # same as PRIVATE + INTERFACE

# multiple targets and flags
target_compile_options(mylib1 mylib2 PRIVATE -Wall -Wextra)

target_compile_options(    mylib PUBLIC -DUSEXX)  # Bad
target_compile_definitions(mylib PUBLIC -DUSEXX)  # OK

add_compile_options(-Wall -Wextra) # for all targets in current directory
add_compile_options(-DUSEXX)       # Bad
add_definitions(-DUSEXX)           # OK

Deprecated COMPILE_FLAGS

cmake-3.0 documentation flags COMPILE_FLAGS as deprecated:

COMPILE_FLAGS

Additional flags to use when compiling this target’s sources.

The COMPILE_FLAGS property sets additional compiler flags used to build sources within the target. Use COMPILE_DEFINITIONS to pass additional preprocessor definitions.

This property is deprecated. Use the COMPILE_OPTIONS property or the target_compile_options command instead.

If you still want to use set_target_properties() you may use COMPILE_OPTIONS instead of COMPILE_FLAGS:

set_target_properties(${TARGET} PROPERTIES COMPILE_OPTIONS ${BUILD_FLAGS})

Since CMake-3.3 (2015)

Anton Petrov suggests to use generator expressions as presented in an answer of ar31.

The CMake generator expressions applies your ${BUILD_FLAGS} to:

• C++ language using $<COMPILE_LANGUAGE:CXX> (can also be C, CUDA...)
• Clang compiler using $<CXX_COMPILER_ID:Clang>
  (can also be GNU for gcc, or MSVCfor Visual C++... see full list)
  (use $<C_COMPILER_ID:Clang> instead if language is C)
• and more as supported C++ feature or compiler version... (see documentation)

In you case you can use:

target_compile_options(${TARGET} PRIVATE
          $<$<COMPILE_LANGUAGE:CXX>:${BUILD_FLAGS_FOR_CXX}>
          $<$<COMPILE_LANGUAGE:C>:${BUILD_FLAGS_FOR_C}>)

or about compilers:

target_compile_options(${TARGET} PRIVATE
          $<$<CXX_COMPILER_ID:Clang>:${BUILD_FLAGS_FOR_CLANG}>
          $<$<CXX_COMPILER_ID:GNU>:${BUILD_FLAGS_FOR_GCC}>
          $<$<CXX_COMPILER_ID:MSVC>:${BUILD_FLAGS_FOR_VISUAL}>)

Since CMake-3.13 (2018)

A new function target_link_options() allow to pass options to the linker, as mentioned by Craig Scott.

Different options for C and C++ files

The best way is to distinguish C files and C++ files using two different targets.

Use the first one:

set_target_properties(${TARGET} PROPERTIES COMPILE_FLAGS ${BUILD_FLAGS})

The flags stored in BUILD_FLAGS are appended after CMAKE_CXX_FLAGS when compiling the sources of TARGET. The documentation hints at this, but I've just tried it to make sure.

COMPILE_FLAGS

   Additional flags to use when compiling this target's sources. 
   
   The COMPILE_FLAGS property sets additional compiler flags used to
   build sources within the target.  Use COMPILE_DEFINITIONS to
   pass additional preprocessor definitions.

The full command line will be the equivalent of:

${CMAKE_CXX_COMPILER} ${CMAKE_CXX_FLAGS} ${COMPILE_FLAGS} -o foo.o -c foo.cc

And as Ramon said, you can always check with make VERBOSE=1.