Installing RStan on Windows 10 64bit...Error


Thanks. On the laptops where it failed, do you still have the error message or at least remember at what step the problem appeared?


I don’t have the exact error message, but the error occurred at the C++ compilation stage when running brms::brm() or rstan::stan()


OK. If you see another student with this issue, try to capture the error message before doing your workaround. Thanks!


I just learned that an alternative workaround for the one I posted here is to enable 8.3 names in the following way (replaces step 2 in that post - however, it requires you to have admin rights, which are not needed for the directory junction):

fsutil.exe 8dot3name set 0

This is explained here.



I can help you with instructions on how to install RTools, RStudio and R within RStudio. I went through this situation just last week. I ran into a host of problems because of lack of Admin privileges.
Do the following:

  1. Uninstall RTools from it’s current location or rename the directory so that RCpp will not look for that.
  2. Install Anaconda 3 in the following location:
    (AppData is a hidden folder, so first make sure WIndows Explorer will show you hidden folders
  3. After Anaconda3 is installed, launch Anaconda Navigator and find the RStudio link and install RStudio.
  4. RStudio installs Microsoft R3.5.1 - download all the necessary packages. Make sure you download devtools
  5. Then download the correct RTools (RTools3.5) and install it under
  6. Under the Lib section of Anaconda3, go to R installation folder, search for Makevars.conf file and change BINPREF to the new RTools3.5 mingw-64 chain location.
  7. devtools does not need RTools to be located in C:\RTools (thank the Almighty and the creator of devtools for that).
  8. RStudio and R3.5.1 combination has a problem where they do not recognize the RTools3.5 correctly (glitch in RStudio). There is a syntax file you need to run to correct this problem.
  9. In an hour or so I will post that syntax here for you.

the steps I outlines above will work only if RTools is not installed elsewhere. Make sure you take care of that.




Please see my note for a workaround to get RStudio, R, and RTools working together. And you are right about the problem being RStudio and RTools. My problems started with not having Admin rights.
Last week I finally figured out fully how to install using Anaconda3 and RStudio and RTools with that installation to get the ability to work with packages that need C++ compilation (rstan. brms, Bioconductor etc)



@jtp @hansvancelster

See the R commands you need to run in RStudio to ensure R.3.5.1, RTools 3.5. and RStudio play together nicely.
This is the last step in my notes above. I found the solution at the RStudio Forums<//a>

#Set path of Rtools
Sys.setenv(PATH = paste(Sys.getenv(“PATH”), “InstallDirectory/Rtools/bin/”, “InstallDirectory/Rtools/mingw_64/bin”, sep = “;”))

#for 64 bit version
Sys.setenv(BINPREF = “InstallDirectory/Rtools/mingw_64/bin”)


#Manually “force” version to be accepted
assignInNamespace(“version_info”, c(devtools:::version_info, list(“3.5” = list(version_min = “3.3.0”, version_max = “99.99.99”, path = “bin”))), “devtools”)

find_rtools() # is TRUE now # Now you can install transformr then gganimate devtools::ins…