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PANDA 0.0.8 and RCall 0.14.7 #573

@grcolli

Description

@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 To see why use status --outdated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

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