FAQ



Below you can find some common error and problems you might face either during installations or during execution of softwares.

Command line developer tools not found (OSX)

If you don’t yet have Mac OSX command line developer tools, please install it using:

  xcode-select --install
Error - umap-learn not found

If your R does not find the correct python version, it will complain that umap-learn is not installed and ask you to install it. Here are some tips on how to find the correct python version that was installed in the conda environment.


Try selecting the correct conda env in R

In this example the conda environment is named scRNAseq2021.

  library(reticulate)
  reticulate::use_conda("scRNAseq2021")

Then check what python you have in R:

  reticulate::py_config()
  # should read at top:
  python:         /Users/asbj/miniconda3/envs/scRNAseq2021/bin/python

If that still is not right, you may have an r-reticulate python installation as well and need to perform the steps below.


Restart R and select python version

OBS! Before doing anything else you need to select python version.

First, find out what path you have to your conda python (in TERMINAL):

  which python
  /Users/asbj/miniconda3/envs/scRNAseq2021/bin/python

Then in R (after restarting):

  reticulate::use_python("/Users/asbj/miniconda3/envs/scRNAseq2021/bin/python", required=T)

Then check again with py_config if correct version of python is used:

  reticulate::py_config()

If you have the correct version now, you should be able to run UMAP without issues.

Unable to load stringi.so (UNIX/Windows)

You can install stringi in R using:

  install.packages('stringi')
ERROR: Failed building wheel for gevent / MacOSX10.9.sdk missing (MacOSX)

This is a problem with the MacOSX compiler, in which conda is unable to find it.

  #Download MacOSX10.9.sdk from Github
  curl -o MacOSX10.9.sdk.tar.gz "https://github-production-release-asset-2e65be.s3.amazonaws.com/13597203/f0123b00-34ab-11ea-84b1-27ccc324f983?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210122%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210122T065821Z&X-Amz-Expires=300&X-Amz-Signature=e11864967b0c9a1e1ba1121dbadd35bb3129ae1cd87bdf07b1a9965c731ae129&X-Amz-SignedHeaders=host&actor_id=22674952&key_id=0&repo_id=13597203&response-content-disposition=attachment%3B%20filename%3DMacOSX10.9.sdk.tar.xz&response-content-type=application%2Foctet-stream"

  #extract
  sudo tar -xzf MacOSX10.9.sdk.tar.xz

  #copy
  sudo cp -r MacOSX10.9.sdk /opt/

  #give executable permissions
  sudo chmod -R a+rX /opt

  #Link the path where conda looks to where the file is
  ln -s /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk /opt/MacOSX10.9.sdk
ERROR: option error has NULL value

This error happens when running code inline.

One possible solution is to restart Rstudio and type.

  if(interactive()) { options(error = utils::recover)}

Please try other solutions listed here: https://github.com/rstudio/rstudio/issues/4723

If none of those work, you can click on the wheel engine symbol and check Chunk output in console