Georgetown-IR-Lab / QuickUMLS

System for Medical Concept Extraction and Linking
MIT License
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Problem installing quickumls on Windows #71

Closed RonWilkinson closed 3 years ago

RonWilkinson commented 3 years ago

In attempting to install quickumls on Windows10 and Python 3.8.5 in an Anaconda environment, I get the following log:

(base) PS C:\Users\Ron> pip install quickumls Collecting quickumls Downloading quickumls-1.4.0.post1.tar.gz (22 kB) Requirement already satisfied: leveldb>=0.193 in c:\users\ron\anaconda3\lib\site-packages (from quickumls) (0.201) Requirement already satisfied: numpy>=1.8.2 in c:\users\ron\anaconda3\lib\site-packages (from quickumls) (1.19.2) Requirement already satisfied: spacy>=1.6.0 in c:\users\ron\anaconda3\lib\site-packages (from quickumls) (2.3.2) Requirement already satisfied: unidecode>=0.4.19 in c:\users\ron\anaconda3\lib\site-packages (from quickumls) (1.2.0) Requirement already satisfied: nltk>=3.3 in c:\users\ron\anaconda3\lib\site-packages (from quickumls) (3.5) Collecting quickumls_simstring>=1.1.5r1 Downloading quickumls_simstring-1.1.5r1.tar.gz (68 kB) |████████████████████████████████| 68 kB 1.2 MB/s ERROR: Command errored out with exit status 1: command: 'C:\Users\Ron\anaconda3\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\Ron\AppData\Local\Temp\pip-install-kzzwupen\quickumls-simstring\setup.py'"'"'; file='"'"'C:\Users\Ron\AppData\Local\Temp\pip-install-kzzwupen\quickumls-simstring\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egginfo --egg-base 'C:\Users\Ron\AppData\Local\Temp\pip-pip-egg-info-ia24qkh' cwd: C:\Users\Ron\AppData\Local\Temp\pip-install-kzzwupen\quickumls-simstring\ Complete output (7 lines): Traceback (most recent call last): File "", line 1, in File "C:\Users\Ron\AppData\Local\Temp\pip-install-kzzwupen\quickumls-simstring\setup.py", line 93, in readme = reader.read() File "C:\Users\Ron\anaconda3\lib\encodings\cp1252.py", line 23, in decode return codecs.charmap_decode(input,self.errors,decoding_table)[0] UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position 471: character maps to

ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

RonWilkinson commented 3 years ago

I found instructions for successfully installing quickUMLS on Windows at the medspacy site. I'm all set.

burgersmoke commented 3 years ago

I'm glad that our other documentation helped out. If you have other issues, let me know since I've spent a lot of hours making sure that QuickUMLS can build in various environments. Windows takes by far the most effort and care.