Package evaluation to test AlgebraicPetri on Julia 1.11.7 (58327cce5e*) started at 2025-10-29T01:23:59.253 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.79s ################################################################################ # Installation # Installing AlgebraicPetri... Resolving package versions... ┌ Warning: tarball content does not match git-tree-sha1 └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:680 Cloning [227ef7b5-1206-438b-ac65-934d6da304b8] ACSets from https://github.com/AlgebraicJulia/ACSets.jl.git Installed ACSets ─ v0.2.25 Updating `~/.julia/environments/v1.11/Project.toml` [4f99eebe] + AlgebraicPetri v0.10.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [227ef7b5] + ACSets v0.2.25 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [23cfdc9f] + AlgebraicInterfaces v0.1.4 [4f99eebe] + AlgebraicPetri v0.10.0 [4fba245c] + ArrayInterface v7.22.0 [134e5e36] + Catlab v0.17.2 [d360d2e6] + ChainRulesCore v1.26.0 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [861a8166] + Combinatorics v1.0.3 [bbf7d656] + CommonSubexpressions v0.3.1 [0fb5dd42] + CompTime v0.1.2 [34da2185] + Compat v4.18.1 [a81c6b42] + Compose v0.9.6 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [53c48c17] + FixedPointNumbers v0.8.5 [f6369f11] + ForwardDiff v1.2.2 [f0ffcf3b] + GATlab v0.2.1 [46192b85] + GPUArraysCore v0.2.0 [6b9d7cbe] + GeneralizedGenerated v0.3.3 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b14d175d] + JuliaVariables v0.2.4 [b964fa9f] + LaTeXStrings v1.4.0 [2ee39098] + LabelledArrays v1.16.1 [9c8b4983] + LightXML v0.9.3 [2ab3a3ac] + LogExpFunctions v0.3.29 [d8e11817] + MLStyle v0.4.17 [1914dd2f] + MacroTools v0.5.16 [442fdcdd] + Measures v0.3.2 [77ba4419] + NaNMath v1.1.3 [71a1bf82] + NameResolution v0.1.5 [bac558e1] + OrderedCollections v1.8.1 [12d937ae] + PEG v1.0.4 [69de0a69] + Parsers v2.8.3 [2ae35dd2] + Permutations v0.4.23 [d236fae5] + PreallocationTools v0.4.34 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.0 [8162dcfd] + PrettyPrint v0.2.0 ⌅ [08abe8d2] + PrettyTables v2.4.0 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.39.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.15 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [892a3eda] + StringManipulation v0.4.1 [6ec83bb0] + StructEquality v2.1.0 [856f2bd8] + StructTypes v1.11.0 ⌃ [2efcf032] + SymbolicIndexingInterface v0.3.44 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [94ce4f54] + Libiconv_jll v1.18.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [02c8fc9c] + XML2_jll v2.15.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 11.84s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:76 Precompiling package dependencies... Precompilation completed after 2298.79s ################################################################################ # Testing # Testing AlgebraicPetri ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1924 Status `/tmp/jl_nBOA9g/Project.toml` ⌃ [4f99eebe] AlgebraicPetri v0.8.10 [479239e8] Catalyst v15.0.8 ⌅ [134e5e36] Catlab v0.14.17 [2ee39098] LabelledArrays v1.16.1 ⌅ [961ee093] ModelingToolkit v9.83.0 [1dea7af3] OrdinaryDiffEq v6.103.0 [bd369af6] Tables v1.12.1 [8dfed614] Test v1.11.0 Status `/tmp/jl_nBOA9g/Manifest.toml` [47edcb42] ADTypes v1.18.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 ⌃ [4f99eebe] AlgebraicPetri v0.8.10 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [4c555306] ArrayLayouts v1.12.0 [e2ed5e7c] Bijections v0.2.2 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling AlgebraicPetri... 60266.0 ms ✓ AlgebraicPetri 1 dependency successfully precompiled in 63 seconds. 127 already precompiled. Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:61 Test threw exception Expression: to_graphviz(sir_petri) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::AlgebraicPetri.PetriNet) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:61 Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:62 Test threw exception Expression: to_graphviz(sir_lpetri) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::AlgebraicPetri.LabelledPetriNet) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:62 Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:63 Test threw exception Expression: to_graphviz(sir_rxn) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::AlgebraicPetri.ReactionNet{Function, Int64}) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:63 Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:64 Test threw exception Expression: to_graphviz(open_sir_rxn) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::Catlab.CategoricalAlgebra.StructuredCospans.StructuredCospan{Catlab.CategoricalAlgebra.StructuredCospans.DiscreteACSet{Catlab.DenseACSets.AnonACSet{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:S}, Tuple{}, Tuple{:Rate, :Concentration}, Tuple{(:concentration, :S, :Concentration)}}, Tuple{Function, Int64}, Catlab.LVectors.LVector{(:S,), Int64}, @NamedTuple{concentration::Catlab.ColumnImplementations.DenseColumn{Int64, Vector{Int64}}}}, AlgebraicPetri.ReactionNet{Function, Int64}}, Catlab.CategoricalAlgebra.FreeDiagrams.Multicospan{AlgebraicPetri.ReactionNet{Function, Int64}, Catlab.CategoricalAlgebra.CSets.StructTightACSetTransformation{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:T, :S, :I, :O}, Tuple{(:it, :I, :T), (:is, :I, :S), (:ot, :O, :T), (:os, :O, :S)}, Tuple{:Rate, :Concentration}, Tuple{(:rate, :T, :Rate), (:concentration, :S, :Concentration)}}, @NamedTuple{T::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, S::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, Vector{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, I::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, O::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}}, AlgebraicPetri.ReactionNet{Function, Int64}, AlgebraicPetri.ReactionNet{Function, Int64}}, StaticArraysCore.SVector{2, Catlab.CategoricalAlgebra.CSets.StructTightACSetTransformation{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:T, :S, :I, :O}, Tuple{(:it, :I, :T), (:is, :I, :S), (:ot, :O, :T), (:os, :O, :S)}, Tuple{:Rate, :Concentration}, Tuple{(:rate, :T, :Rate), (:concentration, :S, :Concentration)}}, @NamedTuple{T::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, S::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, Vector{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, I::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, O::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}}, AlgebraicPetri.ReactionNet{Function, Int64}, AlgebraicPetri.ReactionNet{Function, Int64}}}}, StaticArraysCore.SVector{2, Catlab.DenseACSets.AnonACSet{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:S}, Tuple{}, Tuple{:Rate, :Concentration}, Tuple{(:concentration, :S, :Concentration)}}, Tuple{Function, Int64}, Catlab.LVectors.LVector{(:S,), Int64}, @NamedTuple{concentration::Catlab.ColumnImplementations.DenseColumn{Int64, Vector{Int64}}}}}}) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:64 Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:65 Test threw exception Expression: to_graphviz(sir_lrxn) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::AlgebraicPetri.LabelledReactionNet{Number, Int64}) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:65 Types: Error During Test at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:66 Test threw exception Expression: to_graphviz(open_sir_lrxn) isa Graphics.Graphviz.Graph MethodError: no method matching to_graphviz(::Catlab.CategoricalAlgebra.StructuredCospans.StructuredCospan{Catlab.CategoricalAlgebra.StructuredCospans.DiscreteACSet{Catlab.DenseACSets.AnonACSet{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:S}, Tuple{}, Tuple{:Rate, :Concentration, :Name}, Tuple{(:concentration, :S, :Concentration), (:sname, :S, :Name)}}, Tuple{Number, Int64, Symbol}, Catlab.LVectors.LVector{(:S,), Int64}, @NamedTuple{concentration::Catlab.ColumnImplementations.DenseColumn{Int64, Vector{Int64}}, sname::Catlab.ColumnImplementations.DenseColumn{Symbol, Vector{Symbol}}}}, AlgebraicPetri.LabelledReactionNet{Number, Int64}}, Catlab.CategoricalAlgebra.FreeDiagrams.Multicospan{AlgebraicPetri.LabelledReactionNet{Number, Int64}, Catlab.CategoricalAlgebra.CSets.StructTightACSetTransformation{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:T, :S, :I, :O}, Tuple{(:it, :I, :T), (:is, :I, :S), (:ot, :O, :T), (:os, :O, :S)}, Tuple{:Rate, :Concentration, :Name}, Tuple{(:rate, :T, :Rate), (:concentration, :S, :Concentration), (:tname, :T, :Name), (:sname, :S, :Name)}}, @NamedTuple{T::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, S::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, Vector{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, I::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, O::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}}, AlgebraicPetri.LabelledReactionNet{Number, Int64}, AlgebraicPetri.LabelledReactionNet{Number, Int64}}, StaticArraysCore.SVector{2, Catlab.CategoricalAlgebra.CSets.StructTightACSetTransformation{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:T, :S, :I, :O}, Tuple{(:it, :I, :T), (:is, :I, :S), (:ot, :O, :T), (:os, :O, :S)}, Tuple{:Rate, :Concentration, :Name}, Tuple{(:rate, :T, :Rate), (:concentration, :S, :Concentration), (:tname, :T, :Name), (:sname, :S, :Name)}}, @NamedTuple{T::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, S::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, Vector{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, I::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}, O::Catlab.CategoricalAlgebra.FinSets.FinDomFunctionVector{Int64, UnitRange{Int64}, Catlab.CategoricalAlgebra.FinSets.FinSetInt}}, AlgebraicPetri.LabelledReactionNet{Number, Int64}, AlgebraicPetri.LabelledReactionNet{Number, Int64}}}}, StaticArraysCore.SVector{2, Catlab.DenseACSets.AnonACSet{Catlab.Schemas.TypeLevelBasicSchema{Symbol, Tuple{:S}, Tuple{}, Tuple{:Rate, :Concentration, :Name}, Tuple{(:concentration, :S, :Concentration), (:sname, :S, :Name)}}, Tuple{Number, Int64, Symbol}, Catlab.LVectors.LVector{(:S,), Int64}, @NamedTuple{concentration::Catlab.ColumnImplementations.DenseColumn{Int64, Vector{Int64}}, sname::Catlab.ColumnImplementations.DenseColumn{Symbol, Vector{Symbol}}}}}}) The function `to_graphviz` exists, but no method is defined for this combination of argument types. Closest candidates are: to_graphviz(!Matched::Catlab.WiringDiagrams.CPortGraphs.CPortGraph; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:658 to_graphviz(!Matched::Catlab.WiringDiagrams.DirectedWiringDiagrams.WiringDiagram; graph_name, orientation, node_labels, labels, label_attr, port_size, junction_size, outer_ports, anchor_outer_ports, graph_attrs, node_attrs, title, node_colors, edge_attrs, cell_attrs) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:81 to_graphviz(!Matched::Catlab.Theories.HomExpr; kw...) @ Catlab ~/.julia/packages/Catlab/NhhmR/src/graphics/GraphvizWiringDiagrams.jl:159 ... Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:677 [inlined] [2] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/types.jl:66 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 803 running 1 of 1 signal (10): User defined signal 1 __libc_free at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: (nil)) ============================================================== Profile collected. A report will print at the next yield point ============================================================== Petri: Error During Test ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== 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:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 #wait#733 at ./condition.jl:130 wait at ./condition.jl:125 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 unknown function (ip: 0x74d3a8f81932) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 subprocess_handler at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2146 #131 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2086 withenv at ./env.jl:265 #118 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1935 with_temp_env at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1793 #116 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1902 #mktempdir#28 at ./file.jl:819 unknown function (ip: 0x74d3a8f759fd) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 mktempdir at ./file.jl:815 mktempdir at ./file.jl:815 [inlined] #sandbox#115 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1849 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1841 unknown function (ip: 0x74d3a8f69f86) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #test#128 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2067 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined] #test#146 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:460 unknown function (ip: 0x74d3a8f69c8d) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #test#77 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 unknown function (ip: 0x74d3a8f6965d) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:148 #test#75 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] #test#74 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 unknown function (ip: 0x74d3a8f65af6) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 eval_body at /source/src/interpreter.c:539 eval_body at /source/src/interpreter.c:539 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2775 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _include at ./loading.jl:2835 include at ./Base.jl:562 jfptr_include_47022.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 exec_options at ./client.jl:316 _start at ./client.jl:524 jfptr__start_73678.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x74d3aa424249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ 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/v1.11/Profile/src/Profile.jl:1240 Overhead ╎ [+additional indent] Count File:Line; Function ========================================================= Thread 1 Task 0x000074d39d5fc010 Total snapshots: 34. Utilization: 0% ╎34 @Base/client.jl:524; _start() ╎ 34 @Base/client.jl:316; exec_options(opts::Base.JLOptions) ╎ 34 @Base/Base.jl:562; include(mod::Module, _path::String) ╎ 34 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, _path:… ╎ 34 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity), mod:… ╎ 34 @Base/boot.jl:430; eval ╎ ╎ 34 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typeo… ╎ ╎ 34 @Pkg/src/API.jl:146; #test#74 ╎ ╎ 34 @Pkg/src/API.jl:147; test ╎ ╎ 34 @Pkg/src/API.jl:147; #test#75 ╎ ╎ 34 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, ::t… ╎ ╎ ╎ 34 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec};… ╎ ╎ ╎ 34 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, io… ╎ ╎ ╎ 34 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Vect… ╎ ╎ ╎ 34 …src/Operations.jl:2011; test ╎ ╎ ╎ 34 …src/Operations.jl:2067; test(ctx::Pkg.Types.Context, pkgs… ╎ ╎ ╎ ╎ 34 …rc/Operations.jl:1841; kwcall(::@NamedTuple{preferences:… ╎ ╎ ╎ ╎ 34 …rc/Operations.jl:1849; #sandbox#115 ╎ ╎ ╎ ╎ 34 @Base/file.jl:815; mktempdir ╎ ╎ ╎ ╎ 34 @Base/file.jl:815; mktempdir(fn::Function, parent::Str… ╎ ╎ ╎ ╎ 34 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var"#… ╎ ╎ ╎ ╎ ╎ 34 …/Operations.jl:1902; (::Pkg.Operations.var"#116#121… ╎ ╎ ╎ ╎ ╎ 34 …/Operations.jl:1793; with_temp_env(fn::Pkg.Operati… ╎ ╎ ╎ ╎ ╎ 34 …Operations.jl:1935; (::Pkg.Operations.var"#118#12… ╎ ╎ ╎ ╎ ╎ 34 @Base/env.jl:265; withenv(::Pkg.Operations.var"#1… ╎ ╎ ╎ ╎ ╎ 34 …Operations.jl:2086; (::Pkg.Operations.var"#131#… ╎ ╎ ╎ ╎ ╎ ╎ 34 …perations.jl:2146; subprocess_handler(cmd::Cmd… ╎ ╎ ╎ ╎ ╎ ╎ 34 …e/process.jl:687; wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 34 …e/process.jl:694; wait(x::Base.Process, sync… ╎ ╎ ╎ ╎ ╎ ╎ 34 …ondition.jl:125; wait ╎ ╎ ╎ ╎ ╎ ╎ 34 …ondition.jl:130; wait(c::Base.GenericCondi… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 34 …ase/task.jl:1021; wait() 33╎ ╎ ╎ ╎ ╎ ╎ ╎ 34 …ase/task.jl:1012; poptask(W::Base.Intrus… [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 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:522 [803] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/AlgebraicPetri.jl:11 has_free_typevars at /source/src/jltypes.c:156 has_free_typevars at /source/src/jltypes.c:134 has_free_typevars at /source/src/jltypes.c:140 has_free_typevars at /source/src/jltypes.c:119 ijl_type_union at /source/src/jltypes.c:621 inst_type_w_ at /source/src/jltypes.c:2526 inst_type_w_ at /source/src/jltypes.c:2506 ijl_instantiate_unionall at /source/src/jltypes.c:1487 ijl_apply_type at /source/src/jltypes.c:1421 _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] do_apply at /source/src/builtins.c:831 poptask at ./task.jl:1012 make_typealias at ./show.jl:644 wait at ./task.jl:1021 show_typealias at ./show.jl:805 _show_type at ./show.jl:970 show at ./show.jl:965 unknown function (ip: 0x7dd3e71e9606) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #wait#733 at ./condition.jl:130 show_typeparams at ./show.jl:722 show_datatype at ./show.jl:1181 show_datatype at ./show.jl:1089 [inlined] _show_type at ./show.jl:973 show at ./show.jl:965 unknown function (ip: 0x7dd3e71e9606) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 show_at_namedtuple at ./show.jl:1194 unknown function (ip: 0x7dd3e598279d) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 show_datatype at ./show.jl:1167 show_datatype at ./show.jl:1089 [inlined] _show_type at ./show.jl:973 show at ./show.jl:965 unknown function (ip: 0x7dd3e71e9606) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 wait at ./condition.jl:125 [inlined] _trywait at ./asyncevent.jl:145 show_typeparams at ./show.jl:722 show_datatype at ./show.jl:1181 show_datatype at ./show.jl:1089 [inlined] _show_type at ./show.jl:973 show at ./show.jl:965 unknown function (ip: 0x7dd3e71e9606) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #sprint#594 at ./strings/io.jl:112 sprint at ./strings/io.jl:107 [inlined] #print_type_bicolor#659 at ./show.jl:2718 [inlined] print_type_bicolor at ./show.jl:2717 unknown function (ip: 0x7dd3e71e77bd) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 profile_printing_listener at ./Base.jl:582 #show_tuple_as_call#653 at ./show.jl:2585 #1192 at ./Base.jl:622 show_tuple_as_call at ./show.jl:2552 [inlined] show_spec_sig at ./stacktraces.jl:265 jfptr_YY.1192_76252.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] start_task at /source/src/task.c:1202 unknown function (ip: (nil)) Allocations: 31141223 (Pool: 31140328; Big: 895); GC: 36 show_spec_linfo at ./stacktraces.jl:232 jfptr_show_spec_linfo_50362.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") #sprint#594 at ./strings/io.jl:114 sprint at ./strings/io.jl:107 [inlined] tree_format at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:925 error at ./error.jl:35 print_tree at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:1120 tree at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:1170 print_group at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:355 #print#5 at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:304 print at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:244 [inlined] print at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:244 [inlined] print at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:244 [inlined] _peek_report at /source/usr/share/julia/stdlib/v1.11/Profile/src/Profile.jl:70 unknown function (ip: 0x7dd3e597f5cf) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] jl_f__call_latest at /source/src/builtins.c:875 #schedule#763 at ./task.jl:884 #invokelatest#2 at ./essentials.jl:1055 [inlined] invokelatest at ./essentials.jl:1052 [inlined] profile_printing_listener at ./Base.jl:584 schedule at ./task.jl:876 [inlined] uv_writecb_task at ./stream.jl:1200 #1192 at ./Base.jl:622 jfptr_uv_writecb_task_67129.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jfptr_YY.1192_76252.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] start_task at /source/src/task.c:1202 unknown function (ip: (nil)) Allocations: 118179515 (Pool: 118176587; Big: 2928); GC: 65 jlcapi_uv_writecb_task_67593.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420 ijl_task_get_next at /source/src/scheduler.c:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 uv_write at ./stream.jl:1081 unsafe_write at ./stream.jl:1154 write at ./strings/io.jl:248 [inlined] print at ./strings/io.jl:250 jfptr_print_48479.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 showerror at ./errorshow.jl:152 unknown function (ip: 0x74d3a8f84056) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 _atexit at ./initdefs.jl:454 jfptr__atexit_69637.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 jl_apply at /source/src/julia.h:2157 [inlined] ijl_atexit_hook at /source/src/init.c:271 jl_exit_thread0_cb at /source/src/signals-unix.c:517 at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/AlgebraicPetri.jl:11 Got exception outside of a @test LoadError: UndefVarError: `⋅` not defined in `Main.TestPetri` Stacktrace: [1] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/petri.jl:12 [2] include(fname::String) @ Main ./sysimg.jl:38 [3] macro expansion @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/AlgebraicPetri.jl:12 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [5] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/AlgebraicPetri.jl:12 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] macro expansion @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/runtests.jl:4 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [9] top-level scope @ ~/.julia/packages/AlgebraicPetri/Oxc0f/test/runtests.jl:4 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 in expression starting at /home/pkgeval/.julia/packages/AlgebraicPetri/Oxc0f/test/algebraicpetri/petri.jl:1 PkgEval terminated after 2731.96s: test duration exceeded the time limit