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I'm trying to run the Seurat pipeline in RStudio (Windows 10 , which requires having the python library 'umap-learn' installed (Seurat walkthrough: https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html).

To install said library, I'm using the reticulate library in R in the following manner:

library(reticulate)
py_install(packages = 'umap-learn')

I'm getting the following error:

Error in conda_python(envname = envname, conda = conda) : 
  conda environment r-reticulate not found

I've tried just about everything I can think of:

  • Providing py_install with a path to python directly
  • Uninstall / Reinstall of RStudio
  • Uninstall / Reinstall of Anaconda
  • Tried adding Anaconda to system path
  • Using devtools version of Reticulate
  • Using the use_python function: use_python("C://Users/lvlah/Anaconda3/python.exe")

At my wit's end with this - none of my colleagues have had this issue. Any help would be appreciated.

zx8754
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Lukas Vlahos
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2 Answers2

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I had the same problem and what seems to be an issue is that you need to first manually create the r-reticulate environment. I did it manually in Anaconda Navigator, but you can also do conda_create("r-reticulate") within R, as detailed in this tutorial.

Grzegorz Maciag
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I had exactly the same issue and after finding this helpful post I've solved it by installing OpenSSL. Hope it works for you!

Veronika Niederlova
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