Hi joblo,
thx for this. It seems there is a bug in the Code

Freshly downloaded the sources on another machine and gone through configure.ac
My version shows as follows, which explains the problem we got. (I manually edited and corrected it, and it works fine now)
Another thing is that I have to install libgmpv4-dev to meet another requirement, but after that cpuminer binary got compiled fine

if test "x$OS" = "xWindows_NT" ; then
   # MinGW
   AC_CHECK_LIB([pthread], [pthread_create], PTHREAD_LIBS="-lpthreadGC2",[])
else
   AC_CHECK_LIB([pthread], [pthread_create], PTHREAD_LIBS="-lpthreadGC2",[])
fi