setupJulia() says 'RCall not properly installed'

[ellisztamas]

Dear RTIGER devs,

I am having an issue setting up rtiger on ubuntu 24 (x86_64-pc-linux-gnu) in R 4.3.3. I'm new to Julia.

Error message

Running this:

library(RTIGER)
setupJulia()

produces the following error message:

Julia version 1.0.5 at location /home/thomas.ellis/julia-1.0.5/bin will be used.
Loading setup script for JuliaCall...
WARNING: Method definition getproperty(Tuple, Int64) in module Tables at /home/thomas.ellis/.julia/packages/Tables/8p03y/src/Tables.jl:8 overwritten in module ChainRulesCore at /home/thomas.ellis/.julia/packages/ChainRulesCore/8NXnp/src/compat.jl:2.
WARNING: Method definition getproperty(Tuple, Int64) in module Tables at /home/thomas.ellis/.julia/packages/Tables/8p03y/src/Tables.jl:8 overwritten in module ChainRulesCore at /home/thomas.ellis/.julia/packages/ChainRulesCore/8NXnp/src/compat.jl:2.
ERROR: LoadError: RCall not properly installed. Please run Pkg.build("RCall")
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] top-level scope at /home/thomas.ellis/.julia/packages/RCall/gOwEW/src/RCall.jl:36
 [3] include at ./boot.jl:317 [inlined]
 [4] include_relative(::Module, ::String) at ./loading.jl:1044
 [5] include(::Module, ::String) at ./sysimg.jl:29
 [6] top-level scope at none:2
 [7] eval at ./boot.jl:319 [inlined]
 [8] eval(::Expr) at ./client.jl:393
 [9] top-level scope at ./none:3
in expression starting at /home/thomas.ellis/.julia/packages/RCall/gOwEW/src/RCall.jl:33
LoadError("/home/thomas.ellis/R/x86_64-pc-linux-gnu-library/4.3/JuliaCall/julia/setup.jl", 80, ErrorException("Failed to precompile RCall [6f49c342-dc21-5d91-9882-a32aef131414] to /home/thomas.ellis/.julia/compiled/v1.0/RCall/8GFyb.ji.")) 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,"/home/thomas.ellis/R/x86_64-pc-linux-gnu-library/4.3/JuliaCall/julia/setup.jl") in Julia.
                        To have more helpful error messages,
                        you could considering running the command in Julia directly

Attempts to fix

Following the suggestion from another issue I deleted

user/.julia/registries/General/

then ran

using Pkg; Pkg.add("Suppressor"); Pkg.add("RCall"); 
using Suppressor; using RCall;

The first runs without error, but the second command returns:

[ Info: Precompiling RCall [6f49c342-dc21-5d91-9882-a32aef131414]
WARNING: Method definition getproperty(Tuple, Int64) in module Tables at /home/thomas.ellis/.julia/packages/Tables/8p03y/src/Tables.jl:8 overwritten in module ChainRulesCore at /home/thomas.ellis/.julia/packages/ChainRulesCore/8NXnp/src/compat.jl:2.
ERROR: LoadError: RCall not properly installed. Please run Pkg.build("RCall")
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] top-level scope at /home/thomas.ellis/.julia/packages/RCall/gOwEW/src/RCall.jl:36
 [3] include at ./boot.jl:317 [inlined]
 [4] include_relative(::Module, ::String) at ./loading.jl:1044
 [5] include(::Module, ::String) at ./sysimg.jl:29
 [6] top-level scope at none:2
 [7] eval at ./boot.jl:319 [inlined]
 [8] eval(::Expr) at ./client.jl:393
 [9] top-level scope at ./none:3
in expression starting at /home/thomas.ellis/.julia/packages/RCall/gOwEW/src/RCall.jl:33
ERROR: Failed to precompile RCall [6f49c342-dc21-5d91-9882-a32aef131414] to /home/thomas.ellis/.julia/compiled/v1.0/RCall/8GFyb.ji.
Stacktrace:
 [1] error(::String) at ./error.jl:33
 [2] compilecache(::Base.PkgId, ::String) at ./loading.jl:1203
 [3] _require(::Base.PkgId) at ./loading.jl:960
 [4] require(::Base.PkgId) at ./loading.jl:858
 [5] require(::Module, ::Symbol) at ./loading.jl:853

Running Pkg.build("RCall") returns

  Building SpecialFunctions → `~/.julia/packages/SpecialFunctions/ne2iw/deps/build.log`
  Building Rmath ───────────→ `~/.julia/packages/Rmath/BoBag/deps/build.log`
  Building Conda ───────────→ `~/.julia/packages/Conda/sNGum/deps/build.log`
  Building RCall ───────────→ `~/.julia/packages/RCall/gOwEW/deps/build.log`
┌ Error: Error building `RCall`: 
│ ERROR: LoadError: Could not find library /usr/local/lib/R/lib/libR.so. Make sure that R shared library exists.
│ Stacktrace:
│  [1] error(::String) at ./error.jl:33
│  [2] validate_libR(::String) at /home/thomas.ellis/.julia/packages/RCall/gOwEW/deps/setup.jl:11
│  [3] locate_libR(::String) at /home/thomas.ellis/.julia/packages/RCall/gOwEW/deps/setup.jl:43
│  [4] top-level scope at /home/thomas.ellis/.julia/packages/RCall/gOwEW/deps/build.jl:58
│  [5] include at ./boot.jl:317 [inlined]
│  [6] include_relative(::Module, ::String) at ./loading.jl:1044
│  [7] include(::Module, ::String) at ./sysimg.jl:29
│  [8] include(::String) at ./client.jl:392
│  [9] top-level scope at none:0
│ in expression starting at /home/thomas.ellis/.julia/packages/RCall/gOwEW/deps/build.jl:11
└ @ Pkg.Operations /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.0/Pkg/src/Operations.jl:1096

I checked, and /usr/local/lib/R/lib/libR.so does exist.
I tried adding this to the path with the following, but this also didn't solve the problem.

echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib/R/lib' >> ~/.bashrc
source ~/.bashrc

At this point I am out of ideas.

Can you help?

Thanks!