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lisavader / plasmidEC

An ensemble of plasmid classification tools
MIT License
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Missing R packages #11

Open JesseKerkvliet opened 2 years ago

JesseKerkvliet commented 2 years ago

Hi! I'm running plasmidEC to work with gplas, and it seems that two R packages are not (correctly) installed in the plasmidEC_R conda environment:

Installing them fixes the issue, but it would be nice if plasmidEC did this while making the environment

Update: It might be due to an earlier error with R where some C libraries couldn't be found. This was fixed by removing the conda env and recreating the env. Might be a problem on our HPC.

lisavader commented 2 years ago

Hi Jesse, Yes I remember there were some earlier issues with the conda environment for R. If problems like this persist, maybe it would be better to use base R for the gplas script (the only place where plyr/dplyr are used)? Or even rewrite the r scripts in python.