Package evaluation to test PlantSimEngine on Julia 1.14.0-DEV.2071 (559ec66647*) started at 2026-04-24T01:23:59.910 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.76s ################################################################################ # Installation # Installing PlantSimEngine... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [9a576370] + PlantSimEngine v0.14.0 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 [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 [8f5d6c58] + EzXML v1.2.3 [cc61a311] + FLoops v0.2.2 [b9860ae5] + FLoopsBase v0.1.1 [48062228] + FilePathsBase v0.9.24 [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 v1.7.1 [682c06a0] + JSON v1.5.0 [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 v0.15.3 [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 v2.8.3 [4630fe09] + PlantMeteo v0.8.3 [9a576370] + PlantSimEngine v0.14.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [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 v2.8.0 [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 v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 ⌅ [fdbf4ff8] + XLSX v0.10.4 [ddb6d928] + YAML v0.4.16 [49080126] + ZipArchives v2.6.0 [a5390f91] + ZipFile v0.10.1 [94ce4f54] + Libiconv_jll v1.18.0+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [02c8fc9c] + XML2_jll v2.15.1+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 v1.0.0 [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 v1.3.0+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+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 4.98s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 52.5 s ✓ PlantSimEngine 1 dependency successfully precompiled in 57 seconds. 167 already precompiled. Precompilation completed after 75.86s ################################################################################ # Testing # Testing PlantSimEngine Status `/tmp/jl_fMmHmp/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 [dd4a991b] MultiScaleTreeGraph v0.15.3 [4630fe09] PlantMeteo v0.8.3 [9a576370] PlantSimEngine v0.14.0 [10745b16] Statistics v1.11.1 [bd369af6] Tables v1.12.1 [ade2ca70] Dates v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_fMmHmp/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] CodecZlib v0.7.8 [34da2185] 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v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.30+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/Ih7fa/Project.toml". │ SHA is a non-upgradable standard library with version 1.0.0 in the current Julia version. │ Fix by setting compat to "0.7.0, 1" to mark support of the current version 1.0.0. └ @ 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/Ih7fa/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/Ih7fa/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/Ih7fa/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:607 └ @ PlantSimEngine ~/.julia/packages/PlantSimEngine/Ih7fa/src/run.jl:607 [ 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/Ih7fa/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/Ih7fa/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/Ih7fa/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/Ih7fa/src/run.jl:193 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = #run!#311 at run.jl:193 [inlined] └ @ Core ~/.julia/packages/PlantSimEngine/Ih7fa/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/Ih7fa/src/run.jl:262 ┌ Warning: `run!` with a collection of `ModelList` is deprecated. Use a collection of `ModelMapping` objects instead. │ caller = #run!#311 at run.jl:193 [inlined] └ @ Core ~/.julia/packages/PlantSimEngine/Ih7fa/src/run.jl:193 Issue in function #229 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/Ih7fa/src/run.jl:376 Issue in function #229 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/Ih7fa/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/Ih7fa/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/Ih7fa/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/Ih7fa/src/mtg/initialisation.jl:130 Issue in function #229 for node #3. Issue in function #229 for node #5. Cyclic dependency -> error: Test Failed at /home/pkgeval/.julia/packages/PlantSimEngine/Ih7fa/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/Ih7fa/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/Ih7fa/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/Ih7fa/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/Ih7fa/src/mtg/mapping/mapping.jl:537 [3] _check_multiscale_mapping! @ ~/.julia/packages/PlantSimEngine/Ih7fa/src/mtg/mapping/mapping.jl:514 [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/Ih7fa/src/mtg/mapping/mapping.jl:333 [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/Ih7fa/src/mtg/mapping/mapping.jl:331 [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, check::Bool, processes::@Kwargs{}) @ PlantSimEngine ~/.julia/packages/PlantSimEngine/Ih7fa/src/mtg/mapping/mapping.jl:380 [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/Ih7fa/src/mtg/mapping/mapping.jl:350 [8] top-level scope @ ~/.julia/packages/PlantSimEngine/Ih7fa/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/Ih7fa/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/Ih7fa/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/Ih7fa/test/runtests.jl:80 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [16] macro expansion @ ~/.julia/packages/PlantSimEngine/Ih7fa/test/runtests.jl:80 [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:318 [21] _start() @ Base ./client.jl:593 ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/utilities/utilities.jl:719 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. ┌ Error: doctest failure in ../src/mtg/mapping/reverse_mapping.jl │ │ ```jldoctest mylabel │ julia> mapping = ModelMapping( :Plant => MultiScaleModel( model=ToyCAllocationModel(), mapped_variables=[ :carbon_assimilation => [:Leaf], :carbon_demand => [:Leaf, :Internode], :carbon_allocation => [:Leaf, :Internode] ], ), :Internode => ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0), :Leaf => ( MultiScaleModel( model=ToyAssimModel(), mapped_variables=[:soil_water_content => :Soil => :soil_water_content,], ), ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0), Status(aPPFD=1300.0, TT=10.0), ), :Soil => ( ToySoilWaterModel(), ), ); │ ``` │ │ Subexpression: │ │ mapping = ModelMapping( :Plant => MultiScaleModel( model=ToyCAllocationModel(), mapped_variables=[ :carbon_assimilation => [:Leaf], :carbon_demand => [:Leaf, :Internode], :carbon_allocation => [:Leaf, :Internode] ], ), :Internode => ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0), :Leaf => ( MultiScaleModel( model=ToyAssimModel(), mapped_variables=[:soil_water_content => :Soil => :soil_water_content,], ), ToyCDemandModel(optimal_biomass=10.0, development_duration=200.0), Status(aPPFD=1300.0, TT=10.0), ), :Soil => ( ToySoilWaterModel(), ), ); │ │ Evaluated output: │ │ ┌ 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/Ih7fa/src/mtg/mapping/compute_mapping.jl:28 │ │ Expected output: │ │ │ │ diff = │ Warning: Diff output requires color. │ ┌ 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/Ih7fa/src/mtg/mapping/compute_mapping.jl:28 └ @ Documenter ~/.julia/packages/PlantSimEngine/Ih7fa/src/mtg/mapping/reverse_mapping.jl ┌ Error: doctest failure in ../src/mtg/mapping/reverse_mapping.jl:63-71 │ │ ```jldoctest mylabel │ julia> rm = PlantSimEngine.reverse_mapping(mapping); │ │ julia> Set(keys(rm)) == Set([:Soil, :Internode, :Leaf]) │ true │ │ julia> rm[:Soil][:Leaf][:soil_water_content] == :soil_water_content │ true │ ``` │ │ Subexpression: │ │ rm = PlantSimEngine.reverse_mapping(mapping); │ │ Evaluated output: │ │ ┌ 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/Ih7fa/src/mtg/mapping/compute_mapping.jl:28 │ │ Expected output: │ │ │ │ diff = │ Warning: Diff output requires color. │ ┌ 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/Ih7fa/src/mtg/mapping/compute_mapping.jl:28 └ @ Documenter ~/.julia/packages/PlantSimEngine/Ih7fa/src/mtg/mapping/reverse_mapping.jl:63 ┌ Error: Doctesting failed │ exception = │ `makedocs` encountered a doctest error. Terminating build │ Stacktrace: │ [1] error(s::String) │ @ Base ./error.jl:56 │ [2] runner(::Type{Documenter.Builder.Doctest}, doc::Documenter.Document) │ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/builder_pipeline.jl:213 │ [3] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document) │ @ Documenter.Selectors ~/.julia/packages/Documenter/AXNMp/src/utilities/Selectors.jl:170 │ [4] delete!(::Base.EnvDict, k::String) │ @ Base ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:283 [inlined] │ [5] withenv(::Documenter.var"#95#96"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}}) │ @ Base ./env.jl:265 │ [6] #93 │ @ ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:282 [inlined] │ [7] cd(f::Documenter.var"#93#94"{Documenter.Document}, dir::String) │ @ Base.Filesystem ./file.jl:112 │ [8] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{root::String, source::String, sitename::String, doctest::Symbol, modules::Vector{Module}, doctestfilters::Vector{Regex}, remotes::Nothing, plugins::Vector{Documenter.Plugin}}) │ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:281 │ [9] (::Documenter.var"#all_doctests#147"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Vector{Module}})() │ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:85 │ [10] macro expansion │ @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined] │ [11] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] │ [12] macro expansion │ @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined] │ [13] get_testset() │ @ Test /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] │ [14] doctest(source::Nothing, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) │ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 │ [15] doctest │ @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:69 [inlined] │ [16] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{}) │ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:37 │ [17] top-level scope │ @ ~/.julia/packages/PlantSimEngine/Ih7fa/test/runtests.jl:18 │ [18] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] │ [19] macro expansion │ @ ~/.julia/packages/PlantSimEngine/Ih7fa/test/runtests.jl:90 [inlined] │ [20] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] │ [21] macro expansion │ @ ~/.julia/packages/PlantSimEngine/Ih7fa/test/runtests.jl:93 [inlined] │ [22] include(mapexpr::Function, mod::Module, _path::String) │ @ Base ./Base.jl:327 │ [23] top-level scope │ @ none:6 │ [24] eval(m::Module, e::Any) │ @ Core ./boot.jl:517 │ [25] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:318 │ [26] _start() │ @ Base ./client.jl:593 └ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:99 Doctests: PlantSimEngine: Test Failed at /home/pkgeval/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 Expression: all_doctests() Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] macro expansion @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [4] doctest(source::Nothing, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin}) @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 Test Summary: | Pass Fail Error Total Time Testing PlantSimEngine | 1599 2 1 1602 38m05.9s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.3s Stale dependencies | 1 1 27.0s Compat bounds | 4 4 0.8s Piracy | 1 1 25.1s Persistent tasks | 1 1 1m24.3s ModelMapping: single scale | 342 342 7m54.5s ModelMapping: multi scale | 61 61 2m42.2s Multi-rate scaffolding | 36 36 4.5s Multi-rate runtime | 152 152 7m29.7s Multi-rate output export | 13 13 40.9s MultiScaleModel | 26 26 2.6s Status | 32 32 4.0s TimeStepTable | 27 27 8.9s Dimensions | 6 6 1.6s Simulations | 402 402 4m57.1s Statistics | 4 4 2.4s Fitting | 1 1 9.2s Toy models | 26 26 40.2s MTG with multiscale mapping | 210 1 211 4m04.3s MTG initialisation | 4 4 5.1s Multiscale dependency graph | 10 10 0.6s inputs and outputs of a mapping | 12 12 0.3s Status initialisation | 18 18 8.1s Multiscale initialisations and outputs | 19 19 4.9s Mapping: missing initialisation | 8 8 11.0s Mapping: missing organ in mapping (Soil) | 1 1 0.2s Mapping: missing model at other scale (soil_water_content) + missing init + var1 from MTG | 1 1 0.1s Mapping: missing init + var1 from MTG | 4 4 3.0s run! on MTG: simple mapping | 12 12 10.5s run! on MTG with complete mapping (missing init) | 10 10 8.0s run! on MTG with complete mapping (with init) | 26 26 1.1s MTG initialisation | 5 5 4.0s MTG with complex mapping | 6 6 17.4s MTG with dynamic output variables | 21 21 3.6s MTG with dynamic growth | 8 8 0.8s MTG with mixed daily/hourly clocks (2 leaves) | 14 14 43.4s Cyclic dependency -> error | 2 1 3 23.2s Cyclic dependency -> fixed with `PreviousTimeStep` | 6 6 19.8s Mutiscale simulation -> cyclic dependency | 23 23 1m11.4s Multiscale corner-cases | 18 1 19 2m14.9s Multiscale nested hard dependencies | 4 4 1m08.2s Soft dependency whose parent is a hard dependency of a parent at a different scale | 1 1 4.6s Process/model reuse at different scales | 7 7 49.6s Issue 105 : no outputs when simulating a mapping with one meteo timestep | 3 3 2.8s Issue 111 : Multiscale : outputs not saved when dependency graph only has one depth level | 2 2 0.0s Issue #86 : BoundsError with a single model and several Weather timesteps | 2 2 8.9s Multithreading | 232 232 2m20.9s Doctests | 1 1 1m12.2s Doctests: PlantSimEngine | 1 1 1m07.9s RNG of the outermost testset: Random.Xoshiro(0x99f5012944a5ae59, 0xf179d512c1239a86, 0xe6fcf7666de28783, 0xd01f17713c5e6289, 0xa22cf97a5411d539) ERROR: LoadError: Some tests did not pass: 1599 passed, 2 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PlantSimEngine/Ih7fa/test/runtests.jl:17 Testing failed after 2312.97s ERROR: LoadError: Package PlantSimEngine errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3162 [3] Cmd(cmd::Cmd) @ Base /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3025 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [7] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [8] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [10] include(mod::Module, _path::String) @ Base ./Base.jl:326 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:352 [12] _start() @ Base ./client.jl:593 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 2462.96s: package tests unexpectedly errored