1
$\begingroup$

I recently tried to load library(Seurat) after installing Seurat package. It caused my R studio to have a fatal error and abort my session. I have successfully downloaded it before. I have uninstalled R and R studio and reinstalled, restarted my computer. I am new to R too, so I'm not sure what I'm doing.

I am following the directions provided on the satijalab.org website on how to install Seurat.

Here's a screenshot of the error message. enter image description here

I ran install.packages("Seurat") in R. R is also crashing as soon as I run library(Seurat). Here's a screenshot right before I hit run, and when it crashes, R application just closes.

enter image description here

$\endgroup$
14
  • 1
    $\begingroup$ hi @DianaatDuke, looking at the screen shot, seems like it downloaded the package.. i am surprised it doesn't try to install other dependencies, since you installed a new R or Rstudio? can you load other libraries, save library(uwot) , since this is needed for Seurat too $\endgroup$
    – StupidWolf
    Apr 21 '20 at 19:08
  • $\begingroup$ Yes, no error message when i run the code library(uwot). $\endgroup$ Apr 21 '20 at 20:06
  • 1
    $\begingroup$ Okay it might be Seurat is not checking for the installation of core dependencies $\endgroup$
    – M__
    Apr 21 '20 at 20:06
  • 1
    $\begingroup$ i would go crazy if that's the case lol... can you try opening R , preferably use a terminal , powershell whichever you are on, and try to load Seurat.. just check it's not Rstudio $\endgroup$
    – StupidWolf
    Apr 21 '20 at 20:10
  • 1
    $\begingroup$ Let us continue this discussion in chat. $\endgroup$
    – StupidWolf
    Apr 21 '20 at 20:31
1
$\begingroup$

If you haven't already done so I would make a complete installation of Anaconda, particularly good with bash. The I would either install using Anaconda Navigator, or ...

# Create an R environment and activate it
conda create -n r_env r-essentials r-base python=3.7
conda activate r_env

# install Reurat
conda install -c bioconda r-seurat

# installing standard packages
conda install -c r r-randomforest --yes

If you have a Mac the instructions are here. In some systems you need to just activate r_env .

Please note if you've installed e.g. python3 with pip a conflict occurs with the Anaconda package.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.