"ModuleNotFoundError: No module named 'rdkit'" when running "_Plumber set up" in compliance.R

[robertyoung3]

I am using RStudio 2023.12.1 Build 402 with R version 4.3.3 on an Ubuntu 22.04 laptop. I also installed conda 24.1.2 with auto_activate_base set to false.

While performing the quick install with compliance.R, which I was running line-by-line in RStudio to follow its progress, I ran into the following error while running the code for "_Plumber set up": ModuleNotFoundError: No module named 'rdkit'. "inst/plumber/env_plumb.R" contains a section called "Enable RDKit", so I ran the code for "_RDKit set up" before "_Plumber set up" (reversing their order in compliance.R), and the installation was successful. This suggests that their order should be switched in compliance.R.

Caveat: I do have to activate conda in the terminal before the code in "_RDKit set up" will run using conda environments, and did not try this until after the ModuleNotFoundError, so it is possible that activating conda in advance would also have prevented the error.

[jmr-nist-gov]

Great report. We didn't run into that issue with our testing on Ubuntu, but it makes sense and shouldn't impact the rest of the setup routine. Look for that switch (provided it passes testing) in the next release.