The usual procedure to compile the InChI code is to type "make" in INCHI_API/gcc_so_makefile. Instead, comment out line 2 of the Makefile and then do the following to run make:
LINKER=/home/user/Tools/emscripten-git/tools/emmaken.py SHARED_LINK=/home/user/Tools/emscripten-git/tools/emmaken.py C_COMPILER=/home/user/Tools/emscripten-git/tools/emmaken.py make
llvm-dis -show-annotations libinchi.so.1.03.00
$EMSCRIPTEN/emscripten.py libinchi.so.1.03.00.ll $V8/d8 > inchi.js
The next step is to write some code that does something useful with the library. That's all covered in Part III of course.