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Installation Instructions for Seurat

NOTE: If you installed the pre-release of v2.0, please update to the official v2.0 release.

If you have installed a previous version of Seurat, it is recommended that you restart your R session before loading the new version. First install R and the devtools package.

  1. Install R (v >= 3.3). We recommend using R 3.4.1
  2. Recommended : Install R Studio
  3. Install the “devtools” package from Hadley Wickham

    # Enter commands in R (or R studio, if installed)
    install.packages("devtools")
    library(devtools)
    

Instructions for Mac and Linux

Option 1: Install From Release Binaries (Mac only)

Install Seurat - directly from Github.

If you are running an R version >= 3.4, use the following command to install Seurat:

install_url("https://github.com/satijalab/seurat/releases/download/v2.0.0/Seurat_2.0.0_R3.4.tgz", binary = TRUE)
library(Seurat)

For older R versions, please use the command below:

install_url("https://github.com/satijalab/seurat/releases/download/v2.0.0/Seurat_2.0.0_R3.3.tgz", binary = TRUE)
library(Seurat)

Option 2: Install From Source (Required on Linux)

Install Seurat - directly from Github.

install_github("satijalab/seurat")
library(Seurat)

Troubleshooting

If you see the following message: Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11). Please reinstall dplyr to avoid random crashes or undefined behavior. Reinstall dplyr from source with the following command:

install.packages("dplyr", type = "source")
library(dplyr)

If you are trying to compile under R >= 3.4 on a Mac, the latest versions of R use Clang 4.0.0 and GNU Fortran 6.1 which you will need to successfully compile and install Seurat. Here’s a link to the official R page that provides some guidance on those.

For older R versions, installing from source causes errors on some standard Mac installs due to R being compiled using gfortran-4.8. They will look something like

-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2'
ld: library not found for -lgfortran

To fix this, refer to the following blog post. NOTE: you will need sudo permissions.

Another potential solution to this issue that doesn’t require sudo permission (credit to Michael Steinbaugh) can be found here.

Installation on Windows

  1. Install R (v >= 3.2)
  2. Recommended : Install R Studio
  3. Install the “devtools” package from Hadley Wickham

    # Enter commands in R (or R studio, if installed)
    install.packages("devtools")
    library(devtools)
    
  4. Install Rtools

  5. Ensure that Java is installed.
    • Open CommandPrompt and type java -version
    • If this doesn’t return a version of java >= 1.6, download the latest Java SDK from Oracle and run the installer.
    • Restart the R session
  6. Install Seurat - directly from Github.

    install_github("satijalab/seurat")
    library(Seurat)