The status of sen2cor installation is really frustrating.
On windows, following the quick installation instructions of the sen2cor release notes, a (somehow) working installation resulted. Then trying to address the environment variable issues of the SNAP tool manager, I decided to de-install and re-install sen2cor again. This time I did as the sen2cor user manual instructed and updated anaconda after installing it, but before installing sen2cor. As others have mentioned on this forum, no way. So back to de-installing sen2cor and anaconda and installing everything exactly in line with the quick installation instructions of the sen2cor release notes (which seems to work, at least this week in March 2017).
After processing one tile, I started to wonder why this level 2A product has sub directories (R10m, R20m, and R60m) between the granule directory and the actual .jp2 files. The documentation said that level 2A should be like level 1C, which does not have resolution-wise sub directories. I then decided to compare this output to the output produced on Linux/Ubuntu 16.04.
On Linux, first installation following the “official” instructions. No success even in installation of sen2cor after the anaconda installation. After some surfing here on this forum (which looks like an integral part of sen2cor and SNAP documentation) I found that anaconda must be down-graded form the current release 4.3.0 to 4.2.0. After this and also downgrading numpy (as instructed in some thread on this forum), I finally arrived at a point where I can run L2A_Process without error messages on Linux. The outcome, however is just an output directory containing an empty AUX_DAT directory.
I think, I will wait some time before I next try sen2cor. It is just a prototype, after all (as defined in the user manual).