Are you using SDL2 and SDL_ttf 2.0.*? If so, I just ran in to this problem today and was able to resolve it. You'll need to compile the library to LLVM bytecode and then link it in at the last step when linking your project. Here are the steps:
2. Enter the freetype directiory, then run:
EMSCRIPTEN_JS=1 emconfigure ./configure
emmake make
3. After this step is done, in the objs directory you should see a number of .o files. Open up one of these and verify that it starts with "BC" - that is, it's bytecode.
5. Enter the SDL_ttf directory, then run the same commands as above to compile the project.
6. Look in the .libs folder. You should see some static and dynamic libraries, including a .o and a .a file. Verify that the last two files are bytecode files.
7. Copy all .o files from freetype and the .o and .a file from SDL_ttf into a folder within your project.
8. Edit your makefile so that when linking your project, all these bytecode files are linked as well.
That should do it! Let me know how it goes for you.