How to make RCall.jl use a CondaPkg.jl environment? about condapkg.jl HOT 8 CLOSED

Unfortunately, I'm afraid I haven't looked at RCall.jl for some time, and my bandwidth is rather limited at the moment.

from condapkg.jl.

Perhaps you need to activate the Conda environment in your Julia session first like PythonCall does here: https://github.com/JuliaPy/PythonCall.jl/blob/0056de8711e274b3d8084d19a23fe54adf5d0640/src/cpython/context.jl#L68

from condapkg.jl.

Short remark: When simple using R, it is probably sufficient to just set

ENV["R_HOME"] = CondaPkg.envdir() * "/lib/R"

and rebuild RCall (Probably a similar approach also works for PyCall)

from condapkg.jl.

I tried running the following

julia> using CondaPkg

julia> ENV["R_HOME"] = CondaPkg.envdir() * "/lib/R"

julia> import Pkg

julia> Pkg.build("RCall")

julia> import RCall
┌ Warning: RCall.jl: During startup - Warning messages:
│ 1: package ‘utils’ in options("defaultPackages") was not found 
│ 2: package ‘stats’ in options("defaultPackages") was not found 
└ @ RCall ~/.julia/packages/RCall/gOwEW/src/io.jl:172

The CondaPkg environment does not have a proper R setup... I am confused. Any help is highly appreciated

Edit: CondaPkg.status() looks good

julia> CondaPkg.status()
CondaPkg Status /home/ssahm/Tmp/tmp-julia/condapkg/CondaPkg.toml
Environment
  /home/ssahm/Tmp/tmp-julia/condapkg/.CondaPkg/env
Packages
  r-base v4.3.1
  r-codedepends v0.6.5
  r-globals v0.16.2
Channels
  bioconda
  conda-forge

from condapkg.jl.

@simonbyrne maybe you can help?

EDIT: This last error rather looks like this issue could be migrated to RCall.jl actually

from condapkg.jl.

Thank you for your comments. It turned out it was a linux distribution specific problem which is already reported at anaconda. Concretely you need to have /usr/bin/which available on your system for R...

It works now that I've symlinked /usr/bin/which

from condapkg.jl.

related issue: JuliaInterop/RCall.jl#480 (tries to improve RCall.jl for better integration with CondaPkg.jl without the need of Pkg.build("RCall"))

from condapkg.jl.

Short remark: When simple using R, it is probably sufficient to just set

ENV["R_HOME"] = CondaPkg.envdir() * "/lib/R"

and rebuild RCall (Probably a similar approach also works for PyCall)

this is the final way I am using

import CondaPkg
ENV["R_HOME"] = CondaPkg.envdir() * "/lib/R"
import Pkg
Pkg.build("RCall")
using RCall

from condapkg.jl.