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Here is the code from allseen/core/alljoyn/common/os/posix/ that you are referring to:

Thread* thread(reinterpret_cast<Thread*>(arg));
sigset_t newmask;

sigaddset(&newmask, SIGUSR1);

QCC_ASSERT(thread != NULL);

As can be seen from above, sigemptyset takes a pointer to sigset_t. Hence, your explanation of the bigger sizeof(sigset_t) doesn't seem to be likely. May be the issue is coming from some other place?

One way to debug this would be to run the unit test binary, cmtest on your target platfrom and see if ThreadTest is passing. To build cmtest binary for your platform, pass the variable GTEST_DIR to SCons, where GTEST_DIR points to unpacked googletest sources from this zip archive.