JuliaCall setup script not working (Ubuntu)

Rohit
Wed, 15 May 2024 22:30:54 +0000
General Usage

Hi,

I installed the latest version of Julia 1.10.3 in my AWS Ubuntu and I’m now trying to set it up in R. I tried using JuliaCall’s setup function but it shows me the following error:

> library(JuliaCall)
> julia <- julia_setup(JULIA_HOME = "/home/ubuntu/julia-1.10.3/bin")
Julia version 1.10.3 at location /home/ubuntu/julia-1.10.3/bin will be used.
Loading setup script for JuliaCall...
LoadError("/usr/local/lib/R/site-library/JuliaCall/julia/setup.jl", 16, ArgumentError("Package Suppressor not found in current path.\n- Run `import Pkg; Pkg.add(\"Suppressor\")` to install the Suppressor package.")) Error in .julia$cmd(paste0(Rhomeset, "Base.include(Main,\"", system.file("julia/setup.jl",  :
  Error happens when you try to execute command ENV["R_HOME"] = "/usr/lib/R";Base.include(Main,"/usr/local/lib/R/site-library/JuliaCall/julia/setup.jl") in Julia.
                        To have more helpful error messages,
                        you could considering running the command in Julia directly
In addition: Warning message:
In system2(file.path(.julia$bin_dir, "julia"), shQuote(command),  :
  running command ''/home/ubuntu/julia-1.10.3/bin/julia' '--startup-file=no' '/usr/local/lib/R/site-library/JuliaCall/julia/install_dependency.jl' '/usr/lib/R' 2>&1' had status 139

Then I looked online and some other people had this issue so I checked in Julia if the packages are installed or not but it does show both the packages:

julia> using Pkg

julia> Pkg.status()
Status `~/.julia/environments/v1.10/Project.toml`
  [6f49c342] RCall v0.14.1
  [fd094767] Suppressor v0.2.7

I also saw someone mentioning an issue with the General folder in the Registries directory but I checked and I do not have any folder:

~/.julia/registries$ cd ~/.julia/registries/General
ls
-bash: cd: /home/ubuntu/.julia/registries/General: No such file or directory

I also tried running this setup with a different package diffeqr but got the same error:

> de <- diffeqr::diffeq_setup(JULIA_HOME = "/home/ubuntu/julia-1.10.3/bin")
Julia version 1.10.3 at location /home/ubuntu/julia-1.10.3/bin will be used.
Loading setup script for JuliaCall...
WARNING: replacing module JuliaCall.
LoadError("/usr/local/lib/R/site-library/JuliaCall/julia/setup.jl", 16, ArgumentError("Package Suppressor not found in current path.\n- Run `import Pkg; Pkg.add(\"Suppressor\")` to install the Suppressor package.")) Error in .julia$cmd(paste0(Rhomeset, "Base.include(Main,\"", system.file("julia/setup.jl",  :
  Error happens when you try to execute command ENV["R_HOME"] = "/usr/lib/R";Base.include(Main,"/usr/local/lib/R/site-library/JuliaCall/julia/setup.jl") in Julia.
                        To have more helpful error messages,
                        you could considering running the command in Julia directly
In addition: Warning message:
In system2(file.path(.julia$bin_dir, "julia"), shQuote(command),  :
  running command ''/home/ubuntu/julia-1.10.3/bin/julia' '--startup-file=no' '/usr/local/lib/R/site-library/JuliaCall/julia/install_dependency.jl' '/usr/lib/R' 2>&1' had status 139

My main goal is to try to run the diffeqr package in R but the setup is not working.

Question: What is going on? How can I set my Julia up so R can call it and not face issues? Thanks!

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