Troubleshooting R - NUPulmonary/utils GitHub Wiki

Here I am including some helpful fixes when setting up Seurat in an R environment that may be difficult to find on the internet. Ideally, Seurat will install with simple install and library commands.

  1. It is common to receive an error along the lines of "could not install package hdf5". The following is courtesy of Nik.
  • ssh into quest and type: module load R/4.1.1
  • module load hdf5/1.8.19-serial
  • R
  • install.packages("hdf5r") To make sure it loads in your RStudio, add the line below to your .Rprofile file (which may be hidden, thus you need the . and will not see it in your terminal). This file is in your project folder, or the current working directory in your RStudio terminal
  • dyn.load("/software/hdf5/1.8.19-serial/lib/libhdf5_hl.so.10")
  1. Another problem I just encountered that Rogan solved had to do with R failing to install the rgeos package. Granted, I was using an older version of R at first, but even with version 4.1.1 I had to load R and manually install the rgeos package with the following code.
  • ssh into quest and run: module load R
  • module avail geos
  • module load geos (here specifically install the version or latest version listed)
  • renv::load(<path to your r environment folder, likely just called renv in your project folder>) Now you should be able to install Seurat, which can be down from terminal or in RStudio (make sure to refresh RStudio and ensure rgeos is an available package).
  1. Not sure if others have gotten the following error, but upon loading my RStudio session, when I try to load packages I get: Error in renv_snapshot_auto_update(project = project) : could not find function "renv_snapshot_auto_update". The solution for this was to restore the project from the lockfile, which I did via the command line. Cd into the folder of the r environment you're using, then do module load R/4.1.1 (or whichever version you're using), then type R. With R pulled up on the command line, do renv::init(). You should be prompted with 4 options because the project already has a lockfile, select 1 (restore the project from the lockfile). Now, when you refresh RStudio the packages and environment should load correctly. You can quit R in the terminal with quit(), and no need to save the workspace image there.