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I've just been looking at the CMake code and I guess finding CppUnit needs to be improved. The lookup is also not completely unreasonable, though. So I am wondering whether the build system even used pkg-config at all in your case? If Cppunit not detected via pkg-config so the version couldn't be checked. shows up in the configuration logs then that's not the case and it had to resort to find_library. You can set CPP_UNIT_LIB and CPP_UNIT_INCLUDE_DIR to workaround this for now.
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It looks like pkg-config's output is ignored:
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