...
Installing collected packages: monty, regex, urllib3, requests, unidecode, ruamel.yaml, pydispatcher, tabulate, spglib, palettable, pymatgen, pycryptodome, pdfminer.six, python-crfsuite, cssselect, appdirs, DAWG, chemdataextractor, jmespath, botocore, s3transfer, boto3, smart-open, gensim, tqdm
Found existing installation: urllib3 1.12
ERROR: Cannot remove entries from nonexistent file /xxx/.conda/envs/tshitoyan/lib/python3.6/site-packages/easy-install.pth
Beyond that, everything installed and ran as expected.
Hope this saves some headaches for others.