From my experience, I have to say that lot errors may occur at the parameter 'atlas' in make_brainGraphList.
I defined my self atlas, and I run it successfully in the Linux system. However, when I run the same code in Windows, I get error in make_brainGraphList saying "cannot find objective 'shaefer' " (I have named my atlas as shaefer). I am sure that I have load my atlas and I can see the atlas when I type it in the terminal. Also, my atlas meets your standards.
I have to say that the parameter 'atlas' really brings some difficulties to users. I suggest that in the future, maybe you can make 'atlas' as an optional parameter, so that it can be suitable for more types of data, rather than fMRI dataset. : )