Usually this error, "PackageNotInstalledError: Package is not installed in prefix." is because your custom environment doesn’t have the conda infrastructure. Instead, it is in your base only. To update the base environment:
conda update --name base conda
To see what version you have installed:
conda list --name base conda
example output of list;
# packages in environment at /Users/me/miniconda2:
#
# Name Version Build Channel
conda 4.6.14 py27_0
conda-env 2.6.0 h36134e3_0