The following changes got me part of the way to a working setup. It would have been nice if this anaconda stuff was not mandatory. A list of required versions and compilers (VC9 for compatibility with binary components on windows im guessing) would suffice (and cause less headaches).
setup.py of sen2cor
os.system(‘conda install --no-update-dependencies --yes --channel https://conda.binstar.org/s2tbx proj4’)
os.system(‘conda install --no-update-dependencies --yes --channel https://conda.binstar.org/s2tbx contextlib2’)
os.system(‘conda install --no-update-dependencies --yes --channel https://conda.binstar.org/s2tbx glymur’)
os.system(‘conda update --no-update-dependencies --yes --channel https://conda.binstar.org/s2tbx pytables’)