In 3 places in Makefile.in and in the configured Makefile , libstdbuf.so$(EXEEXT) is specified. When EXEEXT is not empty, make cannot find the rule to make libstdbuf.so and aborts. I am fairly sure it is not Makefile.in that needs to be modified but a patch to Makefile.in is attached showing the location of the erroneous items. FWIW - I am using Cygwin (coreutils-8.26) with EXEEXT=.exe .