ERROR: invalid redefinition of constant with R library

[gaballench]

Hello!

I am trying to load the r package ape from within julia using RCall.

It fails when trying to load it with the @rlibrary macro:

julia> @rlibrary ape
ERROR: invalid redefinition of constant node_depth_edgelength
Stacktrace:
 [1] top-level scope
   @ none:1
 [2] eval
   @ ./boot.jl:360 [inlined]
 [3] rimport(pkg::String, s::Symbol; normalizenames::Bool)
   @ RCall ~/.julia/packages/RCall/3mHXJ/src/namespaces.jl:41
 [4] rimport
   @ ~/.julia/packages/RCall/3mHXJ/src/namespaces.jl:22 [inlined]
 [5] rimport (repeats 2 times)
   @ ~/.julia/packages/RCall/3mHXJ/src/namespaces.jl:46 [inlined]
 [6] top-level scope
   @ ~/.julia/packages/RCall/3mHXJ/src/namespaces.jl:95

however, it works when calling library inside an R string (i.e., using R""):

julia> R"library(ape)"
RObject{StrSxp}
[1] "ape"       "stats"     "graphics"  "grDevices" "utils"     "datasets" 
[7] "methods"   "base"     

My guess is that something happens when loading ape's namespace but I don't understand why the macro fails while the R string does not. I have been unable to find a similar case in earlier issues.

Thanks in advance,

Gustavo

[palday]

I'm able to replicate on recent Julia, R and RCall:

julia> versioninfo()
Julia Version 1.10.4
Commit 48d4fd48430 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: macOS (arm64-apple-darwin22.4.0)
  CPU: 8 × Apple M1
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, apple-m1)
Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)

julia> using Pkg; Pkg.status()
Status `/private/var/folders/yy/nyj87tsn7093bb7d84rl64rh0000gp/T/jl_LF3K4R/Project.toml`
  [6f49c342] RCall v0.14.1

julia> reval("version")
RObject{VecSxp}
               _                           
platform       aarch64-apple-darwin20.0.0  
arch           aarch64                     
os             darwin20.0.0                
system         aarch64, darwin20.0.0       
status                                     
major          4                           
minor          3.3                         
year           2024                        
month          02                          
day            29                          
svn rev        86002                       
language       R                           
version.string R version 4.3.3 (2024-02-29)
nickname       Angel Food Cake 

[palday]

@rlibrary actually calls rimport which does a little bit more than just reval("library(...)").

If we disable name normalization, then things seem to work:

julia> ape = rimport("ape"; normalizenames=false)
Main.__anonymous__

julia> using .ape

julia> node_depth_edgelength
RObject{VecSxp}
$name
[1] "node_depth_edgelength"

$address
<pointer: 0x6000010dbd60>
attr(,"class")
[1] "RegisteredNativeSymbol"

$dll
DLL name: ape
Filename:
        /Users/palday/.julia/conda/3/aarch64/lib/R/library/ape/libs/ape.dylib
Dynamic lookup: FALSE

$numParameters
[1] 5

attr(,"class")
[1] "CRoutine"         "NativeSymbolInfo"

But that actually hiding the real problem: ape defines both node_depth_edgelength and node.depth.edgelength. Normalization converts . in R names to _ in Julia, thus creating a name collision.

[ararslan]

I wonder if normalizenames should actually be false by default given that Julia identifiers can contain arbitrary characters if defined and referenced using var"".

[palday]

@ararslan That would be a breaking change (which I'm not adverse to), but I would like to gather a few more breaking changes first.