Test case

CMakeLists.txt:

project(add_custom_target_bug)
cmake_minimum_required(VERSION 3.10)
add_executable(target foo.cpp)
add_custom_target(run target DEPENDS target VERBATIM)

foo.cpp:

#include <iostream>

int main()
{
  std::cout << "Hello World.\n";
  return 0;
}

toolchain-arm-linux.cmake:

SET(CMAKE_SYSTEM_NAME Linux)
SET(CMAKE_SYSTEM_PROCESSOR arm)

This works

mkdir native
cd native
cmake ..
make VERBOSE=1 run

This fails

mkdir aarch64
cd aarch64
cmake -DCMAKE_TOOLCHAIN_FILE=toolchain-arm-linux.cmake ..
make VERBOSE=1 run

but this works (via binfmt calling qemu):

./target

Instead of calling ./target as the "native" version did, it calls target. Since the CWD isn't in the PATH, this can't work.

Discussion

It seems, cmake assumes cross compiled targets to not be executable on the host system. Due to binfmt support this assumption is incorrect. If necessary, the assumption should be trivially testable: Compile int main() {} and test whether it runs successfully.