ERROR: Cannot set preferences of an unknown package that is not loaded!

[schlichtanders]

Trying to define the preferences for RCall, I am running into an error. How to actually do this?

julia> import Pkg; Pkg.add(["UUIDs", "Preferences", "CondaPkg"])

julia> using UUIDs, Preferences, CondaPkg

julia> envdir = CondaPkg.envdir()

julia> RCALL_UUID = UUID("6f49c342-dc21-5d91-9882-a32aef131414")
UUID("6f49c342-dc21-5d91-9882-a32aef131414")

julia> set_preferences!(RCALL_UUID, "Rhome" => "$envdir/lib/R", "libR" => "$envdir/lib/R/lib/libR.so")
ERROR: Cannot set preferences of an unknown package that is not loaded!
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] set_preferences!(::UUID, ::Pair{String, String}, ::Vararg{Pair{String, String}}; export_prefs::Bool, active_project_only::Bool, kwargs::@Kwargs{})
   @ Preferences ~/.julia/packages/Preferences/enLcN/src/Preferences.jl:281
 [3] set_preferences!(::UUID, ::Pair{String, String}, ::Pair{String, String})
   @ Preferences ~/.julia/packages/Preferences/enLcN/src/Preferences.jl:223
 [4] top-level scope
   @ REPL[8]:1

[schlichtanders]

It seems the only way to actually fix this is to first add the RCall package (which will trigger precompilation of RCall) and then add the preferences like above.

I tried writing the LocalPreferences.toml directly, but it won't actually work, has_preferences will simply show false as long as RCall is not a top-level dependency, even if the preferences are set inside LocalPreferences.toml

[palday]

I think this setup is also desirable behavior -- I think it makes sense to require direct dependency for something you care enough about the details of to set a preference on.

[schlichtanders]

The confusing part is on reading the preferences. Despite having LocalPreferences.toml filled with an entry for RCall, you will get the following divergent behaviour between UUID and package-name, if RCall is not added as a toplevel dependency.

julia> using Preferences, UUIDs

julia> RCALL_UUID = UUID("6f49c342-dc21-5d91-9882-a32aef131414")

julia> has_preference(RCALL_UUID, "Rhome")
false

julia> has_preference("RCall", "Rhome")
ERROR: ArgumentError: Cannot resolve package 'RCall' in load path; have you added the package as a top-level dependency?
Stacktrace:
 [1] package_lookup_error(name::String)
   @ Preferences ~/.julia/packages/Preferences/enLcN/src/utils.jl:88
 [2] has_preference(name::String, key::String)
   @ Preferences ~/.julia/packages/Preferences/enLcN/src/Preferences.jl:76
 [3] top-level scope
   @ REPL[8]:1

[frankier]

This might be relevant/helpful: https://github.com/JuliaPackaging/Preferences.jl/issues/53