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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

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    $\begingroup$ 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
    Commented Apr 21, 2020 at 19:08
  • $\begingroup$ Yes, no error message when i run the code library(uwot). $\endgroup$
    – Diana at Duke
    Commented Apr 21, 2020 at 20:06
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    $\begingroup$ Okay it might be Seurat is not checking for the installation of core dependencies $\endgroup$
    – M__ ♦
    Commented Apr 21, 2020 at 20:06
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    $\begingroup$ 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
    Commented Apr 21, 2020 at 20:10
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    $\begingroup$ Let us continue this discussion in chat. $\endgroup$
    – StupidWolf
    Commented Apr 21, 2020 at 20:31

2 Answers 2

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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.

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I just saw this question. The solution to your problem is here

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    Commented Aug 10, 2022 at 20:01

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