Package evaluation to test PlantSimEngine on Julia 1.14.0-DEV.2207 (8c4818189c*) started at 2026-05-17T23:31:17.260 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.83s ################################################################################ # Installation # Installing PlantSimEngine... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [9a576370] + PlantSimEngine v0.14.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.44 [dce04be8] + ArgCheck v2.5.0 [ec485272] + ArnoldiMethod v0.4.0 [198e06fe] + BangBang v0.4.9 [9718e550] + Baselet v0.1.1 [d1d4a3ce] + BitFlags v0.1.9 [336ed68f] + CSV v0.10.16 [da1fd8a2] + CodeTracking v3.0.2 [6309b1aa] + CodecInflate64 v0.1.3 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.1 [187b0558] + ConstructionBase v1.6.0 [6add18c4] + ContextVariablesX v0.1.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.4 [e2d170a0] + DataValueInterfaces v1.0.0 [244e2a9f] + DefineSingletons v0.1.2 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [48062228] + FilePathsBase v0.9.24 [53c48c17] + FixedPointNumbers v0.8.5 [86223c79] + Graphs v1.14.0 [cd3eb016] + HTTP v1.11.0 ⌅ [eafb193a] + Highlights v0.5.3 [d25df0c9] + Inflate v0.1.5 [22cec73e] + InitialValues v0.3.1 [842dd82b] + InlineStrings v1.4.5 [0c81fc1b] + InputBuffers v1.1.1 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.6.0 [b14d175d] + JuliaVariables v0.2.4 [b964fa9f] + LaTeXStrings v1.4.0 [e6f89c97] + LoggingExtras v1.2.0 [d8e11817] + MLStyle v0.4.17 [1914dd2f] + MacroTools v0.5.16 [739be429] + MbedTLS v1.1.10 [fa8bd995] + MetaGraphsNext v0.8.0 [128add7d] + MicroCollections v0.2.0 [e1d29d7a] + Missings v1.2.0 [dd4a991b] + MultiScaleTreeGraph v0.15.4 [af6c499f] + MutableNamedTuples v0.1.3 [1c23619d] + MyterialColors v0.3.0 [71a1bf82] + NameResolution v0.1.5 [4d8831e6] + OpenSSL v1.6.1 [bac558e1] + OrderedCollections v1.8.1 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.4 [4630fe09] + PlantMeteo v0.8.3 [9a576370] + PlantSimEngine v0.14.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [8162dcfd] + PrettyPrint v0.2.0 [08abe8d2] + PrettyTables v3.3.2 [33c8b6b6] + ProgressLogging v0.1.6 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [171d559e] + SplittablesBase v0.1.15 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [69024149] + StringEncodings v0.3.7 [892a3eda] + StringManipulation v0.4.4 [ec057cc2] + StructUtils v2.8.2 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [22787eb5] + Term v2.0.8 [3bb67fe8] + TranscodingStreams v0.11.3 [28d57a85] + Transducers v0.4.85 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [fdbf4ff8] + XLSX v0.11.8 [72c71f33] + XML v0.3.8 [ddb6d928] + YAML v0.4.16 [49080126] + ZipArchives v2.6.0 [94ce4f54] + Libiconv_jll v1.18.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.1+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.88s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 56.4 s ✓ PlantSimEngine 30.4 s ✓ PlantSimEngine → PlantSimEngineGraphEditorExt 2 dependencies successfully precompiled in 94 seconds. 170 already precompiled. Precompilation completed after 116.4s ################################################################################ # Testing # Testing PlantSimEngine Status `/tmp/jl_Rc0qal/Project.toml` [4c88cf16] Aqua v0.8.14 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [e30172f5] Documenter v1.17.0 [cd3eb016] HTTP v1.11.0 [dd4a991b] MultiScaleTreeGraph v0.15.4 [4630fe09] PlantMeteo v0.8.3 [9a576370] PlantSimEngine v0.14.1 [10745b16] Statistics v1.11.1 [bd369af6] Tables v1.12.1 [ade2ca70] Dates v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Rc0qal/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.44 [4c88cf16] Aqua v0.8.14 [dce04be8] ArgCheck v2.5.0 [ec485272] ArnoldiMethod v0.4.0 [198e06fe] BangBang v0.4.9 [9718e550] Baselet v0.1.1 [6e4b80f9] BenchmarkTools v1.8.0 [d1d4a3ce] BitFlags v0.1.9 [336ed68f] CSV v0.10.16 [da1fd8a2] CodeTracking v3.0.2 [6309b1aa] CodecInflate64 v0.1.3 [944b1d66] 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InvertedIndices v1.3.1 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.6.0 [b14d175d] JuliaVariables v0.2.4 [b964fa9f] LaTeXStrings v1.4.0 [0e77f7df] LazilyInitializedFields v1.3.0 [e6f89c97] LoggingExtras v1.2.0 [d8e11817] MLStyle v0.4.17 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.3 [739be429] MbedTLS v1.1.10 [fa8bd995] MetaGraphsNext v0.8.0 [128add7d] MicroCollections v0.2.0 [e1d29d7a] Missings v1.2.0 [dd4a991b] MultiScaleTreeGraph v0.15.4 [af6c499f] MutableNamedTuples v0.1.3 [1c23619d] MyterialColors v0.3.0 [71a1bf82] NameResolution v0.1.5 [4d8831e6] OpenSSL v1.6.1 [bac558e1] OrderedCollections v1.8.1 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.4 [4630fe09] PlantMeteo v0.8.3 [9a576370] PlantSimEngine v0.14.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [8162dcfd] PrettyPrint v0.2.0 [08abe8d2] PrettyTables v3.3.2 [33c8b6b6] ProgressLogging v0.1.6 [189a3867] 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[e66e0078] CompilerSupportLibraries_jll v1.5.1+0 [deac9b47] LibCURL_jll v8.20.0+1 [e37daf67] LibGit2_jll v1.9.3+0 [29816b5a] LibSSH2_jll v1.11.101+0 [14a3606d] MozillaCACerts_jll v2026.5.14 [4536629a] OpenBLAS_jll v0.3.33+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: Ignoring incompatible compat entry `SHA = "0.7.0"` in "/home/pkgeval/.julia/packages/PlantSimEngine/YgR8Q/Project.toml". │ SHA is a non-upgradable standard library with version 1.13.0 in the current Julia version. │ Fix by setting compat to "0.7.0, 1" to mark support of the current version 1.13.0. └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:520 [ Info: Some variables must be initialized before simulation: (process1 = (:var1, :var2), process2 = (:var1,)) (see `to_initialize()`) [ Info: Some variables must be initialized before simulation: (process1 = (:var1, :var2), process2 = (:var1,)) (see `to_initialize()`) [ Info: Model Process3Model from process process3 needs a model that is a subtype of Process2Model in process process2, but the process is not parameterized in the ModelList. ┌ Warning: `merge(combine::Callable, d::AbstractDict, others::AbstractDict...)` is deprecated, use `mergewith(combine, d, others...)` instead. │ caller = mapped_variables(mapping::Dict{Symbol, Tuple}, dependency_graph::PlantSimEngine.DependencyGraph{Dict{Symbol, Any}, Any}; verbose::Bool) at compute_mapping.jl:28 └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/compute_mapping.jl:28 ┌ Warning: `merge(combine::Callable, d::AbstractDict, others::AbstractDict...)` is deprecated, use `mergewith(combine, d, others...)` instead. │ caller = mapped_variables(mapping::ModelMapping{PlantSimEngine.MultiScale, Dict{Symbol, Tuple}}, dependency_graph::PlantSimEngine.DependencyGraph{Dict{Symbol, Any}, Any}; verbose::Bool) at compute_mapping.jl:28 └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/compute_mapping.jl:28 ┌ Warning: No model runs at the meteo base timestep (3600.0 s). Resolved model timesteps: Leaf/mrmeteodailyconsumer=7200.0s (ModelSpec). └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/time/runtime/clocks.jl:387 ┌ Warning: `run!(mtg, mapping::AbstractDict, ...)` is deprecated. Use `run!(mtg, ModelMapping(mapping), ...)` or construct `ModelMapping(...)` directly. │ caller = kwcall(::@NamedTuple{executor::SequentialEx{@NamedTuple{}}, tracked_outputs::Vector{OutputRequest{Nothing, HoldLast, Nothing}}, return_requested_outputs::Bool}, ::typeof(run!), object::Node{NodeMTG, MultiScaleTreeGraph.ColumnarAttrs}, mapping::Dict{Symbol, Tuple{ModelSpec{MRExportSourceModel, Nothing, Float64, @NamedTuple{}, @NamedTuple{}, Nothing, @NamedTuple{}, Symbol}}}, meteo::TimeStepTable{Atmosphere{(:date, :duration, :T, :Wind, :P, :Rh, :Precipitations, :Cₐ, :e, :eₛ, :VPD, :ρ, :λ, :γ, :ε, :Δ, :clearness, :Ri_SW_f, :Ri_PAR_f, :Ri_NIR_f, :Ri_TIR_f, :Ri_custom_f), Tuple{DateTime, Second, Vararg{Float64, 20}}}}) at run.jl:608 └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:608 [ Info: Model Process3Model from process process3 needs a model that is a subtype of Process2Model in process process2, but the process is not parameterized in the ModelList. ┌ Warning: String scale names are deprecated and will be removed in a future release. Use Symbol scales, e.g. `:Leaf` instead of `"Leaf"`. │ caller = top-level scope at test-simulation.jl:27 └ @ Core ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-simulation.jl:27 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = run!(object::Vector{ModelMapping{PlantSimEngine.SingleScale, ModelList{@NamedTuple{process1::Process1Model, process2::Process2Model, process3::Process3Model}, Status{(:var5, :var4, :var6, :var1, :var3, :var2), NTuple{6, Base.RefValue{Float64}}}}}}, meteo::Atmosphere{(:date, :duration, :T, :Wind, :P, :Rh, :Precipitations, :Cₐ, :e, :eₛ, :VPD, :ρ, :λ, :γ, :ε, :Δ, :clearness, :Ri_SW_f, :Ri_PAR_f, :Ri_NIR_f, :Ri_TIR_f, :Ri_custom_f), Tuple{DateTime, Second, Vararg{Float64, 20}}}, constants::Constants{Float64}, extra::Nothing; tracked_outputs::Nothing, check::Bool, executor::ThreadedEx{@NamedTuple{}}, return_requested_outputs::Bool, requested_outputs_sink::Type{DataFrame}) at run.jl:193 [inlined] └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:193 ┌ Warning: Parallelisation over objects was removed, (but may be reintroduced in the future). Parallelisation will only occur over timesteps. └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:461 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = run!(object::Dict{String, ModelMapping{PlantSimEngine.SingleScale, ModelList{@NamedTuple{process1::Process1Model, process2::Process2Model, process3::Process3Model}, Status{(:var5, :var4, :var6, :var1, :var3, :var2), NTuple{6, Base.RefValue{Float64}}}}}}, meteo::Atmosphere{(:date, :duration, :T, :Wind, :P, :Rh, :Precipitations, :Cₐ, :e, :eₛ, :VPD, :ρ, :λ, :γ, :ε, :Δ, :clearness, :Ri_SW_f, :Ri_PAR_f, :Ri_NIR_f, :Ri_TIR_f, :Ri_custom_f), Tuple{DateTime, Second, Vararg{Float64, 20}}}, constants::Constants{Float64}, extra::Nothing; tracked_outputs::Nothing, check::Bool, executor::ThreadedEx{@NamedTuple{}}, return_requested_outputs::Bool, requested_outputs_sink::Type{DataFrame}) at run.jl:193 [inlined] └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:193 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = #run!#319 at run.jl:193 [inlined] └ @ Core ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:193 ┌ Warning: Parallelisation over objects was removed, (but may be reintroduced in the future). Parallelisation will only occur over timesteps. └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:262 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = #run!#319 at run.jl:193 [inlined] └ @ Core ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:193 Issue in function #233 for node #3. ┌ Warning: A parallel executor was provided (`executor=ThreadedEx()`) but some models cannot be run in parallel: ToyRUEGrowthModel{Float64}(0.3). The simulation will be run sequentially. Use `executor=SequentialEx()` to remove this warning. └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/run.jl:376 Dependency graph view: Error During Test at /home/pkgeval/.julia/packages/PlantSimEngine/YgR8Q/test/test-dependency-graph-view.jl:80 Got exception outside of a @test Scale `Plant` defines duplicate process(es): graph_view_plant_age. Keep only one model per process at a given scale (or use hard dependencies). Stacktrace: [1] error(::String, ::String) @ Base ./error.jl:56 [2] _check_scale_process_uniqueness!(mapping::Dict{Symbol, Tuple}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:561 [3] _check_multiscale_mapping! @ ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:538 [inlined] [4] all(f::PlantSimEngine.var"#_all_scale_pairs##0#_all_scale_pairs##1", itr::Tuple{Pair{Symbol, Tuple{GraphViewPlantAgeModel, GraphViewPhytomerEmissionModel, Status{(:day,), Tuple{Base.RefValue{Float64}}}}}, Vararg{Any}}) @ Base ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:334 [inlined] [5] _all_scale_pairs(args::Tuple{Pair{Symbol, Tuple{GraphViewPlantAgeModel, GraphViewPhytomerEmissionModel, Status{(:day,), Tuple{Base.RefValue{Float64}}}}}, Vararg{Any}}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:332 [inlined] [6] ModelMapping(::Pair{Symbol, Tuple{GraphViewPlantAgeModel, GraphViewPhytomerEmissionModel, Status{(:day,), Tuple{Base.RefValue{Float64}}}}}, ::Vararg{Any}; scale::Symbol, status::Nothing, type_promotion::Nothing, check::Bool, processes::@Kwargs{}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:400 [7] ModelMapping(::Pair{Symbol, Tuple{GraphViewPlantAgeModel, GraphViewPhytomerEmissionModel, Status{(:day,), Tuple{Base.RefValue{Float64}}}}}, ::Vararg{Any}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:369 [8] top-level scope @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-dependency-graph-view.jl:81 [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [10] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-dependency-graph-view.jl:158 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [12] top-level scope @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:18 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [14] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:74 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [16] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:74 [inlined] [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [18] top-level scope @ none:6 [19] eval(m::Module, e::Any) @ Core ./boot.jl:517 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [21] _start() @ Base ./client.jl:596 ┌ Warning: `merge(combine::Callable, d::AbstractDict, others::AbstractDict...)` is deprecated, use `mergewith(combine, d, others...)` instead. │ caller = mapped_variables(mapping::Dict{Symbol, Tuple}, dependency_graph::PlantSimEngine.DependencyGraph{Dict{Symbol, Any}, DataType}; verbose::Bool) at compute_mapping.jl:28 └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/compute_mapping.jl:28 [ Info: Listening on: 127.0.0.1:39385, thread id: 1 Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. [ Info: Server on 127.0.0.1:39385 closing [ Info: Listening on: 127.0.0.1:35831, thread id: 1 Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. [ Info: Server on 127.0.0.1:35831 closing [ Info: Listening on: 127.0.0.1:32817, thread id: 1 Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. [ Info: Server on 127.0.0.1:32817 closing Issue in function #233 for node #4. ┌ Warning: Promoting `carbon_biomass` value taken from MTG node 4 (Internode) from Float64 to Float32: 1.0 (Float32) └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/initialisation.jl:130 ┌ Warning: Promoting `carbon_biomass` value taken from MTG node 5 (Leaf) from Float64 to Float32: 1.0 (Float32) └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/initialisation.jl:130 ┌ Warning: Promoting `carbon_biomass` value taken from MTG node 6 (Internode) from Float64 to Float32: 1.0 (Float32) └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/initialisation.jl:130 ┌ Warning: Promoting `carbon_biomass` value taken from MTG node 7 (Leaf) from Float64 to Float32: 1.0 (Float32) └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/initialisation.jl:130 ┌ Warning: Promoting `carbon_biomass` value taken from MTG node 4 (Internode) from Float64 to Float32: 1.0 (Float32) └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/initialisation.jl:130 Issue in function #233 for node #3. Issue in function #233 for node #5. Cyclic dependency -> error: Test Failed at /home/pkgeval/.julia/packages/PlantSimEngine/YgR8Q/test/test-mtg-multiscale-cyclic-dep.jl:59 Expression: cycle_vec == [ToyPlantRmModel() => :Plant, ToyMaintenanceRespirationModel{Float64}(2.1, 0.06, 25.0, 1.0, 0.025) => :Leaf, ToyCBiomassModel{Float64}(1.2) => :Leaf, ToyCAllocationModel() => :Plant, ToyPlantRmModel() => :Plant] Evaluated: Pair{AbstractModel, Symbol}[ToyCAllocationModel() => :Plant, ToyPlantRmModel() => :Plant, ToyMaintenanceRespirationModel{Float64}(2.1, 0.06, 25.0, 1.0, 0.025) => :Leaf, ToyCBiomassModel{Float64}(1.2) => :Leaf, ToyCAllocationModel() => :Plant] == Pair{AbstractModel, Symbol}[ToyPlantRmModel() => :Plant, ToyMaintenanceRespirationModel{Float64}(2.1, 0.06, 25.0, 1.0, 0.025) => :Leaf, ToyCBiomassModel{Float64}(1.2) => :Leaf, ToyCAllocationModel() => :Plant, ToyPlantRmModel() => :Plant] Stacktrace: [1] top-level scope @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-mtg-multiscale-cyclic-dep.jl:18 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [3] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-mtg-multiscale-cyclic-dep.jl:59 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] Soft dependency whose parent is a hard dependency of a parent at a different scale: Error During Test at /home/pkgeval/.julia/packages/PlantSimEngine/YgR8Q/test/test-corner-cases.jl:336 Got exception outside of a @test Scale `E3` defines duplicate process(es): hard_dep_same_scale_echelle3. Keep only one model per process at a given scale (or use hard dependencies). Stacktrace: [1] error(::String, ::String) @ Base ./error.jl:56 [2] _check_scale_process_uniqueness!(mapping::Dict{Symbol, Tuple}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:561 [3] _check_multiscale_mapping! @ ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:538 [inlined] [4] all(f::PlantSimEngine.var"#_all_scale_pairs##0#_all_scale_pairs##1", itr::Tuple{Pair{Symbol, Tuple{HardDepSameScaleEchelle1Model, MultiScaleModel{HardDepSameScaleEchelle1bisModel, Vector{Pair{Union{Symbol, PreviousTimeStep}, Union{Pair{Symbol, Symbol}, Vector{Pair{Symbol, Symbol}}}}}}, Status{(:a,), Tuple{Base.RefValue{Float64}}}}}, Vararg{Any}}) @ Base ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:334 [inlined] [5] _all_scale_pairs(args::Tuple{Pair{Symbol, Tuple{HardDepSameScaleEchelle1Model, MultiScaleModel{HardDepSameScaleEchelle1bisModel, Vector{Pair{Union{Symbol, PreviousTimeStep}, Union{Pair{Symbol, Symbol}, Vector{Pair{Symbol, Symbol}}}}}}, Status{(:a,), Tuple{Base.RefValue{Float64}}}}}, Vararg{Any}}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:332 [inlined] [6] ModelMapping(::Pair{Symbol, Tuple{HardDepSameScaleEchelle1Model, MultiScaleModel{HardDepSameScaleEchelle1bisModel, Vector{Pair{Union{Symbol, PreviousTimeStep}, Union{Pair{Symbol, Symbol}, Vector{Pair{Symbol, Symbol}}}}}}, Status{(:a,), Tuple{Base.RefValue{Float64}}}}}, ::Vararg{Any}; scale::Symbol, status::Nothing, type_promotion::Nothing, check::Bool, processes::@Kwargs{}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:400 [7] ModelMapping(::Pair{Symbol, Tuple{HardDepSameScaleEchelle1Model, MultiScaleModel{HardDepSameScaleEchelle1bisModel, Vector{Pair{Union{Symbol, PreviousTimeStep}, Union{Pair{Symbol, Symbol}, Vector{Pair{Symbol, Symbol}}}}}}, Status{(:a,), Tuple{Base.RefValue{Float64}}}}}, ::Vararg{Any}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/YgR8Q/src/mtg/mapping/mapping.jl:369 [8] top-level scope @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-corner-cases.jl:337 [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [10] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/test-corner-cases.jl:337 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [12] top-level scope @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:18 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [14] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:88 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [16] macro expansion @ ~/.julia/packages/PlantSimEngine/YgR8Q/test/runtests.jl:88 [inlined] [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:327 [18] top-level scope @ none:6 [19] eval(m::Module, e::Any) @ Core ./boot.jl:517 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [21] _start() @ Base ./client.jl:596 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 19 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:44 wait_forever at ./task.jl:1168:5 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 jl_apply at /source/src/julia.h:2328:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007dffed39ab30 Total snapshots: 556. Utilization: 0% ╎556 @Base/task.jl:1168 wait_forever() 555╎ 556 @Base/task.jl:1246 wait() Task 0x00007e000f5fc010 Total snapshots: 1. Utilization: 100% ╎1 @Base/client.jl:596 _start() ╎ 1 @Base/client.jl:321 exec_options(opts::Base.JLOptions) ╎ 1 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ 1 @Base/Base.jl:328 (::Base.IncludeInto)(fname::String) ╎ 1 @Base/Base.jl:327 include(mapexpr::Function, mod::Module, _path::Strin… ╎ 1 @Base/loading.jl:3173 _include(mapexpr::Function, mod::Module, _path:… ╎ ╎ 1 @Base/loading.jl:3113 include_string(mapexpr::typeof(identity), mod:… ╎ ╎ 1 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ 1 @Base/Base.jl:328 (::Base.IncludeInto)(fname::String) ╎ ╎ 1 @Base/Base.jl:327 include(mapexpr::Function, mod::Module, _path::… ╎ ╎ 1 @Base/loading.jl:3173 _include(mapexpr::Function, mod::Module, _… ╎ ╎ ╎ 1 @Base/loading.jl:3113 include_string(mapexpr::typeof(identity),… ╎ ╎ ╎ 1 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ ╎ 1 @BenchmarkTools/….jl:330 tune!(b::BenchmarkTools.Benchmark) ╎ ╎ ╎ 1 @BenchmarkTools/…jl:330 tune!(b::BenchmarkTools.Benchmark, p… ╎ ╎ ╎ 1 @BenchmarkTools/…jl:341 tune!(b::BenchmarkTools.Benchmark, … ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…jl:52 lineartrial ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…l:53 #lineartrial#32 ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…l:216 _lineartrial(b::BenchmarkTools.Be… ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…:230 _lineartrial(b::BenchmarkTools.Be… ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…:661 var"##sample#154"(::Tuple{}, __p… ╎ ╎ ╎ ╎ ╎ 1 @BenchmarkTools/…:647 var"##core#153"() ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:139 kwcall(::@NamedTuple{executor:… ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:139 run! ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:152 #run!#317 ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:338 _run_modellist_singleton ╎ ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:353 _run_modellist_singleton(o… ╎ ╎ ╎ ╎ ╎ ╎ 1 @PlantSimEngine/…:98 adjust_weather_timesteps_t… ╎ ╎ ╎ ╎ ╎ ╎ 1 @PlantMeteo/…l:56 getindex(rows::PlantMeteo.Ti… ╎ ╎ ╎ ╎ ╎ ╎ 1 @PlantMeteo/…l:56 TimeStepTable{Atmosphere}(t… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ray.jl:843 collect(itr::Base.Generato… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:869 collect_to_with_first!(des… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:914 collect_to!(dest::Vector{… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…or.jl:45 iterate(g::Base.Generator… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Tables/….jl:83 iterate(rows::Tables.Nam… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…le.jl:454 Tuple(itr::Base.Genera… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…le.jl:488 _totuple(::Type{Tuple… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:843 collect(itr::Base.Ge… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:869 collect_to_with_fir… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:922 collect_to!(dest::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:922 collect_to!(dest:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 1 @Base/…ay.jl:914 iterate(g::Base.G… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 1 @Base/…or.jl:48 iterate ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 none:? #38 ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @PlantMeteo/…:430 getcolumn ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @PlantMeteo/…:161 getindex ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457:34 wait at ./task.jl:1246:44 wait_forever at ./task.jl:1168:5 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4127:23 [inlined] ijl_apply_generic at /source/src/gf.c:4353:12 jl_apply at /source/src/julia.h:2328:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007853716e55a0 Total snapshots: 585. Utilization: 0% ╎585 @Base/task.jl:1168 wait_forever() 584╎ 585 @Base/task.jl:1246 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457:34 PkgEval terminated after 2722.15s: test duration exceeded the time limit