Package evaluation to test PlantSimEngine on Julia 1.12.7-DEV.5 (decd03c4f0*) started at 2026-06-20T01:12:30.186 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.04s ################################################################################ # Installation # Installing PlantSimEngine... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [9a576370] + PlantSimEngine v0.14.1 Updating `~/.julia/environments/v1.12/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 v0.1.10 [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 v0.19.5 [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 v0.8.6 [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 v1.6.1 [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 v1.8.2 ⌅ [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.6 [4630fe09] + PlantMeteo v0.8.4 [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 v1.4.10 [efcf1570] + Setfield v1.1.2 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.6 [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 v0.11.10 [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 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [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 v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [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 v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [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 6.41s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 23.18s ################################################################################ # Testing # Testing PlantSimEngine Status `/tmp/jl_iX9aGb/Project.toml` [4c88cf16] Aqua v0.8.16 [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 v0.8.4 [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_iX9aGb/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.44 [4c88cf16] Aqua v0.8.16 [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 v0.1.10 [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 v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [244e2a9f] DefineSingletons v0.1.2 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 [460bff9d] ExceptionUnwrapping v0.1.11 [cc61a311] FLoops v0.2.2 [b9860ae5] FLoopsBase v0.1.1 [48062228] FilePathsBase v0.9.24 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [d7ba0133] Git v1.5.0 [86223c79] Graphs v1.14.0 ⌅ [cd3eb016] HTTP v1.11.0 ⌅ [eafb193a] Highlights v0.5.3 [b5f81e59] IOCapture v1.0.0 [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 v1.6.1 [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 v1.8.2 ⌅ [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.6 [4630fe09] PlantMeteo v0.8.4 [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 [2792f1a3] RegistryInstances v0.1.0 [91c51154] SentinelArrays v1.4.10 [efcf1570] Setfield v1.1.2 [777ac1f9] SimpleBufferStream v1.2.0 [699a6c99] SimpleTraits v0.9.6 [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 v0.11.10 [72c71f33] XML v0.3.8 [ddb6d928] YAML v0.4.16 [49080126] ZipArchives v2.6.0 [2e619515] Expat_jll v2.8.1+0 [020c3dae] Git_LFS_jll v3.7.1+0 [f8c6e375] Git_jll v2.54.0+0 [94ce4f54] Libiconv_jll v1.18.0+0 [c8ffd9c3] MbedTLS_jll v2.28.1010+0 [9bd350c2] OpenSSH_jll v10.3.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.1 [de0858da] Printf v1.11.0 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ 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: 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 └ @ Core ~/.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!#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:461 ┌ 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: `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 [ Info: Listening on: 127.0.0.1:40895, thread id: 1 Warning: detected a stack overflow; program state may be corrupted, so further execution might be unreliable. [ Info: Server on 127.0.0.1:40895 closing [ Info: Listening on: 127.0.0.1:46839, 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 127.0.0.1:46839 closing [ Info: Listening on: 127.0.0.1:37265, 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 127.0.0.1:37265 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. ┌ 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. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Total Time Testing PlantSimEngine | 1755 1755 42m23.5s Testing PlantSimEngine tests passed Testing completed after 2561.07s PkgEval succeeded after 2641.75s