CI problem - can't import dependency

[adamhaber]

Hi,

First of all - thanks for sharing this! I'm just starting to use nbdev but it looks like an amazing platform for library development.

I'm having trouble setting up CI with nbdev. This is possibly not nbdev-related - in which case, I'd appreciate any pointers you might have regarding where to ask this.

One of the dependencies of my library is rpy2. At first I was thinking that Github's CI would "catch" the dependencies and install them (similarly to find_packages()) but the first build failed because rpy2 wasn't installed. I then manually added pip install rpy2 to main.yaml and got:

Collecting rpy2
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  Downloading https://files.pythonhosted.org/packages/d9/51/d5c41ac70e0aa3272f24cf836bd35d6246c95b98d8d811f338cec5a8098e/rpy2-3.2.2.tar.gz (162kB)
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    ERROR: Command errored out with exit status 1:
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     command: /opt/hostedtoolcache/Python/3.6.9/x64/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-alanql6m/rpy2/setup.py'"'"'; __file__='"'"'/tmp/pip-install-alanql6m/rpy2/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-alanql6m/rpy2/pip-egg-info
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         cwd: /tmp/pip-install-alanql6m/rpy2/
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    Complete output (1 lines):
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    There is no R_HOME and the R executable cannot be found.

I wasn't able to solve this, so I tried replacing pip install rpy2 with conda install -c r rpy2 in main.yaml. In this case installation was successful, but in the "Run tests" stage I got ModuleNotFoundError: No module named 'rpy2'. The entire trace is available here.

Any help would be much appreciated, and thanks again!

[sgugger]

I don't think this is related to nbdev. You need to have R installed according to the docs of rpy2 so you need to add lines to your main.yaml file to do that (I have no knowledge of R so can't help you there).