Dealing with Catalina III

Interfaces RStan
41

@lakemonster Sorry for the hassle but glad it’s working now!

42

Hi everyone!
I am new to RStan. I am trying to run a model with RStan but all in vain. It looks like RStan is not properly installed or I am missing any part of it. Could someone please guide me how to uninstall and reinstall RStan on my Mac?
I am using macOS Catalina version 10.15.7

Thank you!

43

What version of R?

44

Its 1.3.1093

45

I think that is your version of RStudio (which also could stand to be upgraded). What is the result when you execute

R.version

in R?

46

I am sorry, 1.3.1093 is the version of R studio. the R version is 4.0.3 as shown by the command R.version.

47

In the case of R 4.x, then you should be able to install XCode and then do

file.remove("~/.R/Makevars")
file.remove("~/.Renviron")
# restart RStudio
install.packages("rstan", dependencies = TRUE, type = "binary")

and it should be fine.

48

How to I install Xcode?
I think I installed it using the instruction above but not sure it it is properly installed. I ran the command install.packages(“rstan”, dependencies = TRUE, type = “binary”)

Rstan is installed but it still is not working. When I run the model it prompts me to install build toots and I click yes a couple of times but still doesn’t work.

49

Open a terminal and type:

xcode-select --install
50

I did and got the following:
error: command line tools are already installed, use “Software Update” to install updates

51

@bgoodri I seem to recall this from a while back, when OS X consistently said that the tools were not installed?

52

Possibly doing

library(rstan)
rstan_options(required = FALSE)

will allow it to go through but my guess is you would have to fix XCode so that R knows whether it is or is not installed.

53

How do I fix it? do you mean installing a newer version or changing its location?

54

Well, something is clearly wrong in that R doesn’t find your compiler it seems. So, I assume you have OS X 10.15.7,

  1. Remove XCode (and remove any other compiler you might have installed previously, e.g., using brew).
  2. Remove rstan, StanHeaders, and other Stan related packages.
  3. Close RStudio and remove ~/.R/Makevars, ~/.Rprofile, ~/.Renviron.
  4. Install XCode and then run xcode-select --install in the terminal.
  5. Restart your laptop (shouldn’t be needed but who knows…)
  6. Start RStudio.
  7. Try to install what you need, i.e., rstan first using
    install.packages("rstan", dependencies = TRUE, type = "binary")

Several of the steps above shouldn’t be needed, but let’s exclude things here…

1 Like
55

Something strange is going on. when I run the command: Xcode-select --install,
I receive the message: error: command line tools are already installed, use “Software Update” to install updates

but when I check in app and library , there is no Xcode
not sure how to deal with this.

56

Go to App Store and download Xcode. I hope you did all the step above?

R

57

I am following the steps, when I run the command Xcode-select --install, it prompt me to install the command line tools which I click yes to install. then an error comes that:
“Can’t install the software because it is not currently available from the software update server”.
Then a software update for command line comes up.
I think that the command line tools might not be the updated one with software update.

Shall I update the software update to install command line tools or is there any other way to install the most recent one.

I am using macOS Catalina version 10.15.7.

Thank you!

58

Hmm, so you can’t install the command line tools. I honestly have no idea what might be causing this…

59

I can through the software update! I am not sure if that would be sufficient. when I checked the apple developers website, I don’t find command line tools for 10.15.7 Mac OS version. therefore I am not sure which version to install.

60

Install Xcode through software update, then run xcode-select --install in the terminal.