Re: Phenograph
Yeah, installing XCode is a critical step to use the Github version. You will also need XQuartz installed from here. But I don't think either of these will fix the error you're seeing.
It looks like you're running into a compilation error because there was a change in the headers in High Sierra. Others have described the same type of error in other software (example). To get past this error, the authors of cytofkit will need to updaet their code to properly handle High Sierra. If you don't mind, could you please file a bug report on the cytofkit Github page here?
In the meantime, you can try installing from BioConductor. The "random clustering" bug has been squashed in the version of cytofkit currently on BioConductor (1.10.0). Hopefully this will work since it involves pre-compiled binaries for Mac. Install from BioConductor with this code in R:
Let me know if that works!
ES