Diffeqr does not work in a VSCode terminal

[danieleboaretti]

Describe the bug 🐞

It is not possible to define the ODEProblem in R with diffeqr as outlined in the examples of the package using the terminal on VSCode, while it works using the Git Bash standalone terminal and on RStudio.

Expected behavior

The ODEProblem in R with diffeqr can be defined as the examples of the package regardless of the terminal used.

Minimal Reproducible Example 👇

library(diffeqr)
de <- diffeqr::diffeq_setup()
f <- function(u,p,t) {
return(1.01*u)
}
u0 <- 0.5
tspan <- c(0., 1.)
prob = de$ODEProblem(f, u0, tspan)

Please note that the code errors when executing the last line of the code block above.

Error & Stacktrace ⚠️

Error happens in Julia.
MethodError: no method matching size(::ODEProblem{Float64, Tuple{Float64, Float64}, false, SciMLBase.NullParameters, ODEFunction{false, SciMLBase.AutoSpecialize, RCall.RFunction{RObject{ClosSxp}}, UniformScaling{Bool}, Nothing, Nothing, Nothing, 
Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}}, Base.Pairs{Symbol, Union{}, Tuple{}, @NamedTuple{}}, SciMLBase.StandardODEProblem})

Closest candidates are:
  size(!Matched::BitVector)
   @ Base bitarray.jl:104
  size(!Matched::BitVector, !Matched::Integer)
   @ Base bitarray.jl:107
  size(!Matched::Base.ExceptionStack)
   @ Base errorshow.jl:1018
  ...

Stacktrace:
 [1] dim(x::ODEProblem{Float64, Tuple{Float64, Float64}, false, SciMLBase.NullParameters, ODEFunction{false, SciMLBase.AutoSpecialize, RCall.RFunction{RObject{ClosSxp}}, UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, 
Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}}, @Kwargs{}, SciMLBase.StandardODEProblem})
   @ Main.JuliaCall C:\Users\boaretti\AppData\Local\Programs\R\R-4.3.2\library\JuliaCall\julia\dispatch.jl:78
 [2] simple_call(fname::String, args::ODEProblem{Float64, Tuple{Float64, Float64}, false, SciMLBase.NullParameters, ODEFunction{false, SciMLBase.AutoSpecialize, RCall.RFunction{RObject{ClosSxp}}, UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}}, @Kwargs{}, SciMLBase.StandardODEProblem}; kwargs::@Kwargs{})   
   @ Main.JuliaCall C:\Users\boaretti\AppData\Local\Programs\R\R-4.3.2\library\JuliaCall\julia\interface1.jl:11
 [3] simple_call(fname::String, args::ODEProblem{Float64, Tuple{Float64, Float64}, false, SciMLBase.NullParameters, ODEFunction{false, SciMLBase.AutoSpecialize, RCall.RFunction{RObject{ClosSxp}}, UniformScaling{Bool}, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, Nothing, typeof(SciMLBase.DEFAULT_OBSERVED), Nothing, SymbolicIndexingInterface.SymbolCache{Nothing, Nothing, Nothing}}, @Kwargs{}, SciMLBase.StandardODEProblem})
   @ Main.JuliaCall C:\Users\boaretti\AppData\Local\Programs\R\R-4.3.2\library\JuliaCall\julia\interface1.jl:1
 [4] julia_extptr_callback(p::Ptr{ListSxp})
>  @ RCall C:\Users\boaretti\.julia\packages\RCall\gOwEW\src\callback.jl:56

Environment (please complete the following information):

• Output of using Pkg; Pkg.status()

Status `C:\Users\boaretti\.julia\environments\v1.10\Project.toml`
  [0c46a032] DifferentialEquations v7.13.0
⌅ [961ee093] ModelingToolkit v8.76.0
  [429524aa] Optim v1.9.4
⌃ [1dea7af3] OrdinaryDiffEq v6.70.1
⌃ [91a5bcdd] Plots v1.40.4
⌃ [6f49c342] RCall v0.13.18
⌃ [0bca4576] SciMLBase v2.17.1
⌃ [220ca800] StructuralIdentifiability v0.5.1
  [fd094767] Suppressor v0.2.7

• Output of using Pkg; Pkg.status(; mode = PKGMODE_MANIFEST)

Status `C:\Users\boaretti\.julia\environments\v1.10\Manifest.toml`
⌅ [47edcb42] ADTypes v0.2.6
⌅ [c3fe647b] AbstractAlgebra v0.33.0
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⌅ [79e6a3ab] Adapt v3.7.2
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⌃ [4fba245c] ArrayInterface v7.7.0
⌃ [4c555306] ArrayLayouts v1.5.1
⌃ [aae01518] BandedMatrices v1.4.0
⌃ [6e4b80f9] BenchmarkTools v1.4.0
⌃ [e2ed5e7c] Bijections v0.1.6
⌃ [d1d4a3ce] BitFlags v0.1.8
⌃ [62783981] BitTwiddlingConvenienceFunctions v0.1.5
⌃ [764a87c0] BoundaryValueDiffEq v5.6.3
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⌃ [2a0fbf3d] CPUSummary v0.2.4
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⌃ [8f4d0f93] Conda v1.10.0
⌃ [187b0558] ConstructionBase v1.5.4
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⌃ [102ac46a] MultivariatePolynomials v0.5.4
⌃ [d8a4904e] MutableArithmetics v1.4.0
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⌃ [1dea7af3] OrdinaryDiffEq v6.70.1
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⌅ [3e851597] ParamPunPam v0.2.3
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⌃ [7e49a35a] RuntimeGeneratedFunctions v0.5.12
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⌃ [47a9eef4] SparseDiffTools v2.15.0
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⌃ [276daf66] SpecialFunctions v2.3.1
⌅ [aedffcd0] Static v0.8.8
⌃ [0d7ed370] StaticArrayInterface v1.5.0
⌃ [90137ffa] StaticArrays v1.9.0
⌃ [1e83bf80] StaticArraysCore v1.4.2
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⌃ [2913bbd2] StatsBase v0.34.2
⌃ [4c63d2b9] StatsFuns v1.3.0
⌃ [3eaba693] StatsModels v0.7.3
⌃ [9672c7b4] SteadyStateDiffEq v2.0.1
⌃ [789caeaf] StochasticDiffEq v6.65.1
⌃ [7792a7ef] StrideArraysCore v0.5.2
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⌃ [220ca800] StructuralIdentifiability v0.5.1
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⌃ [2efcf032] SymbolicIndexingInterface v0.3.3
⌅ [d1185830] SymbolicUtils v1.5.0
⌅ [0c5d862f] Symbolics v5.16.0
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  [1270edf5] x264_jll v2021.5.5+0
  [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.10.0
  [de0858da] Printf
  [9abbd945] Profile
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [781609d7] GMP_jll v6.2.1+6
  [deac9b47] LibCURL_jll v8.4.0+0
  [e37daf67] LibGit2_jll v1.6.4+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [3a97d323] MPFR_jll v4.2.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.8.0+1
  [8e850ede] nghttp2_jll v1.52.0+1
  [3f19e933] p7zip_jll v17.4.0+2

• Output of versioninfo()

Julia Version 1.10.4
Commit 48d4fd4843 (2024-06-04 10:41 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Windows (x86_64-w64-mingw32)
  CPU: 12 × 13th Gen Intel(R) Core(TM) i7-1355U
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-15.0.7 (ORCJIT, goldmont)
Threads: 1 default, 0 interactive, 1 GC (on 12 virtual cores)

Additional context

Output of sessionInfo() in R:

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United Kingdom.utf8
[2] LC_CTYPE=English_United Kingdom.utf8
[3] LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8    

time zone: Europe/Rome
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] diffeqr_2.0.1

loaded via a namespace (and not attached):
[1] compiler_4.3.2 cli_3.6.2      jsonlite_1.8.8 rlang_1.1.3 

[ChrisRackauckas]

Why is it trying to use the size to display in the VS Code output anyways? That looks like it's a bug in the display system for the R VS Code plugin.