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For most users, we recommend installing the official Seurat release from CRAN, using the instructions here

Alternative : Install development version from source

Install the development version of Seurat - directly from Github.

# Enter commands in R (or R studio, if installed)

# Install the devtools package from Hadley Wickham
install.packages("devtools")

devtools::install_github("satijalab/seurat", ref = "develop")
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.

Install from GitHub 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", ref = "develop")
    library(Seurat)