Override compile flags for single files

Your attempts above are adding further flags to your file/target rather than overwriting as you seem to expect. For example, from the docs for Properties on Source Files - COMPILE_FLAGS:

These flags will be added to the list of compile flags when this source file builds.

You should be able to countermand the -Weffc++ flag for foo.cpp by doing

set_source_files_properties(foo.cpp PROPERTIES COMPILE_FLAGS -Wno-effc++)

This should have the effect of adding -Wno-effc++ after -Weffc++ in the compiler command, and the latter setting wins. To see the full command and check that this is indeed the case, you can do

make VERBOSE=1

As an aside, one of the maintainers of the GNU C++ Standard Library presents a pretty negative opinion on -Weffc++ in this answer.

Another point is that you're misusing add_definitions in the sense that you're using this for compiler flags rather than the intended preprocessor definitions.

It would be preferable to use add_compile_options

add_compile_options(-Wall -Weffc++ -pedantic -std=c++0x)

or for CMake versions < 3.0 to do something more like:

set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Weffc++ -pedantic -std=c++0x")

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In response to further questions in the comments below, I believe it's impossible to reliably remove a flag on a single file. The reason is that for any given source file, it has the COMPILE_OPTIONS and COMPILE_FLAGS¹ of its target applied, but these don't show up in any of the properties for that source file.

You could look at stripping the problem flag from the target's COMPILE_OPTIONS, then applying it to each of the target's sources individually, omitting it from the specific source file as required.

However, while this could work in many scenarios, it has a couple of problems.

First - source files' properties don't include COMPILE_OPTIONS, only COMPILE_FLAGS. This is a problem because the COMPILE_OPTIONS of a target can include generator expressions, but COMPILE_FLAGS doesn't support them. So you'd have to accommodate generator expressions while searching for your flag, and indeed you'd maybe even have to "parse" generator expressions if your flag was contained in one or more to see whether it should be re-applied to the remaining source files.

Second - since CMake v3.0, targets can specify INTERFACE_COMPILE_OPTIONS. This means that a dependency of your target can add or override your target's COMPILE_OPTIONS via its INTERFACE_COMPILE_OPTIONS. So you'd further have to recursively iterate through all your target's dependencies (not a particularly easy task since the list of LINK_LIBRARIES for the target can also contain generator expressions) to find any which are applying the problem flag, and try and remove it from those targets' INTERFACE_COMPILE_OPTIONS too.

At this stage of complexity, I'd be looking to submit a patch to CMake to provide the functionality to remove a specific flag unconditionally from a source file.

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1: Note that unlike the COMPILE_FLAGS property on source files, the COMPILE_FLAGS property on targets is deprecated.

Just adding to @Fraser's correct answer.

In case if you want to add the special flag to specific folders you could do:

file(GLOB SPECIAL_SRC_FILES
        "path/one/src/*.cpp"
        "path/two/src/*.cpp")
set_property(SOURCE ${SPECIAL_SRC_FILES} PROPERTY COMPILE_FLAGS -Wno-effc++)

or

file(GLOB SPECIAL_SRC_FILES
        "path/one/src/*.cpp"
        "path/two/src/*.cpp")
set_source_files_properties(${SPECIAL_SRC_FILES} PROPERTIES COMPILE_FLAGS -Wno-effc++)

Note that its not recommended to use GLOB as discussed here