PANDA 0.0.8 and RCall 0.14.7

[grcolli]

Cannot use PANDA 0.0.8 with RCall 0.14.7 (R 4.5.0 in Ubuntu 24.04 LTS and Julia 1.11.6):

julia> using RCall

julia> using PANDA

julia> my_tree = load_tree("/home/grcolli/Documents/GitHub/Halluametal2025/tree_pruned.nex") ┌ Warning: RCall.jl: Loading required package: ape └ @ RCall ~/.julia/packages/RCall/gOwEW/src/io.jl:172 ERROR: could not load symbol "SET_SYMVALUE": /usr/lib/R/lib/libR.so: undefined symbol: SET_SYMVALUE Stacktrace: [1] set_last_value(s::Ptr{VecSxp}) @ RCall ~/.julia/packages/RCall/gOwEW/src/methods.jl:588 [2] reval_p(expr::Ptr{RCall.ExprSxp}, env::Ptr{EnvSxp}) @ RCall ~/.julia/packages/RCall/gOwEW/src/eval.jl:126 [3] reval(str::String, env::RObject{EnvSxp}) @ RCall ~/.julia/packages/RCall/gOwEW/src/eval.jl:136 [4] reval(str::String) @ RCall ~/.julia/packages/RCall/gOwEW/src/eval.jl:136 [5] load_tree(file::String) @ PANDA.ClaDS ~/.julia/packages/PANDA/plKS9/src/clads/load_tree.jl:176 [6] top-level scope @ REPL[7]:1

julia>

Notice that RCall v0.14.7 is not compatible with PANDA 0.0.8. Therefore, one cannot solve the issue!

julia> Pkg.status() Status ~/.julia/environments/v1.11/Project.toml [57a71ab2] PANDA v0.0.8 ⌅ [6f49c342] RCall v0.13.18 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use status --outdated

julia> using Pkg

julia> Pkg.add(name="RCall", version="0.14.8") Resolving package versions... ERROR: Unsatisfiable requirements detected for package PANDA [57a71ab2]: PANDA [57a71ab2] log: ├─possible versions are: 0.0.1 - 0.0.8 or uninstalled ├─restricted to versions * by project [cf96c74d], leaving only versions: 0.0.1 - 0.0.8 │ └─project [cf96c74d] log: │ ├─possible versions are: 0.0.0 or uninstalled │ └─project [cf96c74d] is fixed to version 0.0.0 └─restricted by compatibility requirements with RCall [6f49c342] to versions: uninstalled — no versions left └─RCall [6f49c342] log: ├─possible versions are: 0.12.0 - 0.14.8 or uninstalled ├─restricted to versions * by project [cf96c74d], leaving only versions: 0.12.0 - 0.14.8 │ └─project [cf96c74d] log: see above └─restricted to versions 0.14.8 by an explicit requirement, leaving only versions: 0.14.8

Therefore, one cannot use PANDA in Julia, at least with the combination I'm using: R 4.5.0 in Ubuntu 24.04 LTS and Julia 1.11.6. Any hints?

Originally posted by @grcolli in #566

[palday]

You can use an older R version or you can ask the PANDA developers to update the compat bounds for RCall. The bump from 0.13 to 0.14 was technically breaking, but in most cases downstream package developers should be able to bump the compat bound and everything will 🤞 work.