Package evaluation of SBMLImporter on Julia 1.13.0-DEV.880 (5ebc5b463e*) started at 2025-07-21T03:52:52.857 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.9s ################################################################################ # Installation # Installing SBMLImporter... Resolving package versions... Installed MKL_jll ────────────────────────── v2025.2.0+0 Installed Glob ───────────────────────────── v1.3.1 Installed SIMDTypes ──────────────────────── v0.1.0 Installed CommonWorldInvalidations ───────── v1.0.0 Installed OrderedCollections ─────────────── v1.8.1 Installed CpuId ──────────────────────────── v0.3.1 Installed NonlinearSolveSpectralMethods ──── v1.2.0 Installed EnzymeCore ─────────────────────── v0.8.12 Installed FastPower ──────────────────────── v1.1.3 Installed SymbolicUtils ──────────────────── v3.29.0 Installed Functors ───────────────────────── v0.5.2 Installed Optim ──────────────────────────── v1.13.2 Installed QuadGK ─────────────────────────── v2.11.2 Installed NaNMath ────────────────────────── v1.1.3 Installed StaticArrayInterface ───────────── v1.8.0 Installed DiffEqCallbacks ────────────────── v4.8.0 Installed DispatchDoctor ─────────────────── v0.4.26 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed SBML_jll ───────────────────────── v5.20.1+0 Installed DynamicQuantities ──────────────── v1.8.0 Installed FastBroadcast ──────────────────── v0.3.5 Installed NonlinearSolveBase ─────────────── v1.13.0 Installed EnumX ──────────────────────────── v1.0.5 Installed Tables ─────────────────────────── v1.12.1 Installed LinearSolve ────────────────────── v3.20.0 Installed SCCNonlinearSolve ──────────────── v1.4.0 Installed JuliaFormatter ─────────────────── v2.1.2 Installed DiffEqBase ─────────────────────── v6.177.2 Installed BracketingNonlinearSolve ───────── v1.3.0 Installed Jieko ──────────────────────────── v0.2.1 Installed NLSolversBase ──────────────────── v7.10.0 Installed InverseFunctions ───────────────── v0.1.17 Installed Reexport ───────────────────────── v1.2.2 Installed JumpProcesses ──────────────────── v9.16.1 Installed Missings ───────────────────────── v1.2.0 Installed Preferences ────────────────────── v1.4.3 Installed TableTraits ────────────────────── v1.0.1 Installed NonlinearSolve ─────────────────── v4.10.0 Installed Static ─────────────────────────── v1.2.0 Installed LaTeXStrings ───────────────────── v1.4.0 Installed Crayons ────────────────────────── v4.1.1 Installed SortingAlgorithms ──────────────── v1.2.1 Installed Format ─────────────────────────── v1.3.7 Installed UnPack ─────────────────────────── v1.0.2 Installed MaybeInplace ───────────────────── v0.1.4 Installed Catalyst ───────────────────────── v15.0.8 Installed Inflate ────────────────────────── v0.1.5 Installed MacroTools ─────────────────────── v0.5.16 Installed DataStructures ─────────────────── v0.18.22 Installed URIs ───────────────────────────── v1.6.1 Installed RecursiveArrayTools ────────────── v3.34.1 Installed DiffResults ────────────────────── v1.1.0 Installed ADTypes ────────────────────────── v1.15.0 Installed ManualMemory ───────────────────── v0.1.8 Installed MLStyle ────────────────────────── v0.4.17 Installed SBMLImporter ───────────────────── v3.0.3 Installed TermInterface ──────────────────── v2.0.0 Installed FillArrays ─────────────────────── v1.13.0 Installed oneTBB_jll ─────────────────────── v2022.0.0+0 Installed AbstractTrees ──────────────────── v0.4.5 Installed Tricks ─────────────────────────── v0.1.10 Installed ArnoldiMethod ──────────────────── v0.4.0 Installed IntelOpenMP_jll ────────────────── v2025.2.0+0 Installed DataValueInterfaces ────────────── v1.0.0 Installed ExprTools ──────────────────────── v0.1.10 Installed StatsBase ──────────────────────── v0.34.5 Installed SparseMatrixColorings ──────────── v0.4.21 Installed ArrayInterface ─────────────────── v7.19.0 Installed CommonSubexpressions ───────────── v0.3.1 Installed IrrationalConstants ────────────── v0.2.4 Installed TruncatedStacktraces ───────────── v1.4.0 Installed LayoutPointers ─────────────────── v0.1.17 Installed ConcreteStructs ────────────────── v0.2.3 Installed SciMLJacobianOperators ─────────── v0.1.7 Installed GPUArraysCore ──────────────────── v0.2.0 Installed RandomNumbers ──────────────────── v1.6.0 Installed SimpleTraits ───────────────────── v0.9.4 Installed IntegerMathUtils ───────────────── v0.1.3 Installed CompositeTypes ─────────────────── v0.1.4 Installed Setfield ───────────────────────── v1.1.2 Installed BlockArrays ────────────────────── v1.7.0 Installed WeakValueDicts ─────────────────── v0.1.0 Installed PDMats ─────────────────────────── v0.11.35 Installed NonlinearSolveQuasiNewton ──────── v1.6.0 Installed ArrayLayouts ───────────────────── v1.11.1 Installed DocStringExtensions ────────────── v0.9.5 Installed CompositionsBase ───────────────── v0.1.2 Installed ForwardDiff ────────────────────── v0.10.38 Installed CommonSolve ────────────────────── v0.2.4 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed FindFirstFunctions ─────────────── v1.4.1 Installed ResettableStacks ───────────────── v1.1.1 Installed Unityper ───────────────────────── v0.1.6 Installed AliasTables ────────────────────── v1.1.3 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed Bijections ─────────────────────── v0.2.2 Installed Moshi ──────────────────────────── v0.3.7 Installed Combinatorics ──────────────────── v1.0.3 Installed LineSearch ─────────────────────── v0.1.4 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed DynamicPolynomials ─────────────── v0.6.2 Installed DifferentiationInterface ───────── v0.6.54 Installed FunctionWrappersWrappers ───────── v0.1.3 Installed RecipesBase ────────────────────── v1.3.4 Installed DataAPI ────────────────────────── v1.16.0 Installed Krylov ─────────────────────────── v0.10.1 Installed ComponentArrays ────────────────── v0.15.28 Installed SciMLOperators ─────────────────── v1.3.1 Installed DomainSets ─────────────────────── v0.7.15 Installed SciMLStructures ────────────────── v1.7.0 Installed StaticArraysCore ───────────────── v1.4.3 Installed Requires ───────────────────────── v1.3.1 Installed StringManipulation ─────────────── v0.4.1 Installed StaticArrays ───────────────────── v1.9.14 Installed MultivariatePolynomials ────────── v0.5.9 Installed FunctionWrappers ───────────────── v1.1.3 Installed Latexify ───────────────────────── v0.16.8 Installed TaskLocalValues ────────────────── v0.1.3 Installed Symbolics ──────────────────────── v6.45.0 Installed LogExpFunctions ────────────────── v0.3.29 Installed DiffRules ──────────────────────── v1.15.1 Installed PrettyTables ───────────────────── v2.4.0 Installed NonlinearSolveFirstOrder ───────── v1.5.0 Installed Rmath ──────────────────────────── v0.8.0 Installed JuliaSyntax ────────────────────── v0.4.10 Installed SciMLBase ──────────────────────── v2.104.0 Installed FastClosures ───────────────────── v0.3.2 Installed FiniteDiff ─────────────────────── v2.27.0 Installed Distributions ──────────────────── v0.25.120 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed StatsFuns ──────────────────────── v1.5.0 Installed Polyester ──────────────────────── v0.7.18 Installed Unitful ────────────────────────── v1.23.1 Installed TestItems ──────────────────────── v1.0.0 Installed JLLWrappers ────────────────────── v1.7.0 Installed MutableArithmetics ─────────────── v1.6.4 Installed Primes ─────────────────────────── v0.5.7 Installed ThreadingUtilities ─────────────── v0.5.5 Installed SymbolicLimits ─────────────────── v0.2.2 Installed Accessors ──────────────────────── v0.1.42 Installed Graphs ─────────────────────────── v1.13.0 Installed Adapt ──────────────────────────── v4.3.0 Installed HypergeometricFunctions ────────── v0.3.28 Installed RuntimeGeneratedFunctions ──────── v0.5.15 Installed ConstructionBase ───────────────── v1.6.0 Installed SBML ───────────────────────────── v1.6.0 Installed PoissonRandom ──────────────────── v0.4.5 Installed Compat ─────────────────────────── v4.17.0 Installed Random123 ──────────────────────── v1.7.1 Installed StrideArraysCore ───────────────── v0.5.7 Installed ModelingToolkit ────────────────── v9.82.0 Installed Statistics ─────────────────────── v1.11.1 Installed StatsAPI ───────────────────────── v1.7.1 Installed SymbolicIndexingInterface ──────── v0.3.42 Installed PrecompileTools ────────────────── v1.3.2 Installed LazyArrays ─────────────────────── v2.6.1 Installed TimerOutputs ───────────────────── v0.5.29 Installed PositiveFactorizations ─────────── v0.2.4 Installed OffsetArrays ───────────────────── v1.17.0 Installed CPUSummary ─────────────────────── v0.2.6 Installed Parameters ─────────────────────── v0.12.3 Installed ChainRulesCore ─────────────────── v1.25.2 Installed IfElse ─────────────────────────── v0.1.1 Installed ReactionNetworkImporters ───────── v0.16.1 Installed PtrArrays ──────────────────────── v1.3.0 Installed ExproniconLite ─────────────────── v0.10.14 Installed MuladdMacro ────────────────────── v0.2.4 Installed XML2_jll ───────────────────────── v2.13.6+1 Installed DiffEqNoiseProcess ─────────────── v5.24.1 Installed IntervalSets ───────────────────── v0.7.11 Installed SpecialFunctions ───────────────── v2.5.1 Installed SimpleNonlinearSolve ───────────── v2.6.0 Installed LineSearches ───────────────────── v7.4.0 Installed Libiconv_jll ───────────────────── v1.18.0+0 Installed PolyesterWeave ─────────────────── v0.2.2 Installed CommonMark ─────────────────────── v0.9.1 Installing 6 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact oneTBB 435.6 KiB Installed artifact XML2 2.5 MiB Installed artifact Libiconv 1.9 MiB Installed artifact SBML 5.8 MiB Updating `~/.julia/environments/v1.13/Project.toml` [210efffb] + SBMLImporter v3.0.3 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.19.0 [4c555306] + ArrayLayouts v1.11.1 [e2ed5e7c] + Bijections v0.2.2 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [8e7c35d0] + BlockArrays v1.7.0 [70df07ce] + BracketingNonlinearSolve v1.3.0 [2a0fbf3d] + CPUSummary v0.2.6 [479239e8] + Catalyst v15.0.8 [d360d2e6] + ChainRulesCore v1.25.2 [fb6a15b2] + CloseOpenIntervals v0.1.13 [861a8166] + Combinatorics v1.0.3 [a80b9123] + CommonMark v0.9.1 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.17.0 [b0b7db55] + ComponentArrays v0.15.28 [b152e2b5] + CompositeTypes v0.1.4 [a33af91c] + CompositionsBase v0.1.2 [2569d6c7] + ConcreteStructs v0.2.3 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [2b5f629d] + DiffEqBase v6.177.2 [459566f4] + DiffEqCallbacks v4.8.0 [77a26b50] + DiffEqNoiseProcess v5.24.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 ⌅ [a0c0ee7d] + DifferentiationInterface v0.6.54 [8d63f2c5] + DispatchDoctor v0.4.26 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [5b8099bc] + DomainSets v0.7.15 [7c1d4256] + DynamicPolynomials v0.6.2 [06fc5a27] + DynamicQuantities v1.8.0 [4e289a0a] + EnumX v1.0.5 [f151be2c] + EnzymeCore v0.8.12 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [7034ab61] + FastBroadcast v0.3.5 [9aa1b823] + FastClosures v0.3.2 [a4df4552] + FastPower v1.1.3 [1a297f60] + FillArrays v1.13.0 [64ca27bc] + FindFirstFunctions v1.4.1 [6a86dc24] + FiniteDiff v2.27.0 [1fa38f19] + Format v1.3.7 ⌅ [f6369f11] + ForwardDiff v0.10.38 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 [d9f16b24] + Functors v0.5.2 [46192b85] + GPUArraysCore v0.2.0 [c27321d9] + Glob v1.3.1 [86223c79] + Graphs v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [d25df0c9] + Inflate v0.1.5 [18e54dd8] + IntegerMathUtils v0.1.3 [8197267c] + IntervalSets v0.7.11 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [ae98c720] + Jieko v0.2.1 [98e50ef6] + JuliaFormatter v2.1.2 ⌅ [70703baa] + JuliaSyntax v0.4.10 [ccbc3e58] + JumpProcesses v9.16.1 [ba0b0d4f] + Krylov v0.10.1 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.8 [10f19ff3] + LayoutPointers v0.1.17 [5078a376] + LazyArrays v2.6.1 [87fe0de2] + LineSearch v0.1.4 [d3d80556] + LineSearches v7.4.0 [7ed4a6bd] + LinearSolve v3.20.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [d8e11817] + MLStyle v0.4.17 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [bb5d69b7] + MaybeInplace v0.1.4 [e1d29d7a] + Missings v1.2.0 ⌅ [961ee093] + ModelingToolkit v9.82.0 [2e0e35c7] + Moshi v0.3.7 [46d2c3a1] + MuladdMacro v0.2.4 [102ac46a] + MultivariatePolynomials v0.5.9 [d8a4904e] + MutableArithmetics v1.6.4 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [8913a72c] + NonlinearSolve v4.10.0 [be0214bd] + NonlinearSolveBase v1.13.0 [5959db7a] + NonlinearSolveFirstOrder v1.5.0 [9a2c21bd] + NonlinearSolveQuasiNewton v1.6.0 [26075421] + NonlinearSolveSpectralMethods v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [e409e4f3] + PoissonRandom v0.4.5 [f517fe37] + Polyester v0.7.18 [1d0040c9] + PolyesterWeave v0.2.2 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [27ebfcd6] + Primes v0.5.7 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [74087812] + Random123 v1.7.1 [e6cf234a] + RandomNumbers v1.6.0 [b4db0fb7] + ReactionNetworkImporters v0.16.1 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.34.1 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [ae5879a3] + ResettableStacks v1.1.1 [79098fc4] + Rmath v0.8.0 [7e49a35a] + RuntimeGeneratedFunctions v0.5.15 [e5567a89] + SBML v1.6.0 [210efffb] + SBMLImporter v3.0.3 [9dfe8606] + SCCNonlinearSolve v1.4.0 [94e857df] + SIMDTypes v0.1.0 [0bca4576] + SciMLBase v2.104.0 [19f34311] + SciMLJacobianOperators v0.1.7 [c0aeaf25] + SciMLOperators v1.3.1 [53ae85a6] + SciMLStructures v1.7.0 [efcf1570] + Setfield v1.1.2 [727e6d20] + SimpleNonlinearSolve v2.6.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [0a514795] + SparseMatrixColorings v0.4.21 [276daf66] + SpecialFunctions v2.5.1 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [7792a7ef] + StrideArraysCore v0.5.7 [892a3eda] + StringManipulation v0.4.1 [2efcf032] + SymbolicIndexingInterface v0.3.42 [19f23fe9] + SymbolicLimits v0.2.2 [d1185830] + SymbolicUtils v3.29.0 [0c5d862f] + Symbolics v6.45.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [ed4db957] + TaskLocalValues v0.1.3 [8ea1fca8] + TermInterface v2.0.0 [1c621080] + TestItems v1.0.0 [8290d209] + ThreadingUtilities v0.5.5 [a759f4b9] + TimerOutputs v0.5.29 [410a4b4d] + Tricks v0.1.10 [781d530d] + TruncatedStacktraces v1.4.0 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.23.1 [a7c27f48] + Unityper v0.1.6 [897b6980] + WeakValueDicts v0.1.0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [bb12108a] + SBML_jll v5.20.1+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [1317d2d5] + oneTBB_jll v2022.0.0+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 [4af54fe1] + LazyArtifacts v1.11.0 [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 v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [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 v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 15.72s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4777.1 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... ERROR: LoadError: The following 2 direct dependencies failed to precompile: SBMLImporterForwardDiffExt Failed to precompile SBMLImporterForwardDiffExt [21714604-6a7c-57b9-a063-59b01068f571] to "/home/pkgeval/.julia/compiled/v1.13/SBMLImporterForwardDiffExt/jl_N0SbaC" (ProcessExited(1)). ERROR: LoadError: UndefVarError: `t` not defined in `SBMLImporter` The binding may be too new: running in world age 39728, while current world is 39752. Stacktrace: [1] _get_reaction_system(model_SBML_sys::SBMLImporter.ModelSBMLSystem, model_SBML::SBMLImporter.ModelSBML) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/system.jl:43 [2] load_SBML(path::String; massaction::Bool, complete::Bool, ifelse_to_callback::Bool, write_to_file::Bool, inline_assignment_rules::Bool, inline_kineticlaw_parameters::Bool, model_as_string::Bool) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:84 [3] load_SBML(path::String) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:74 [4] macro expansion @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:52 [inlined] [5] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined] [6] top-level scope @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:118 [7] include(mod::Module, _path::String) @ Base ./Base.jl:309 [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:3002 [9] top-level scope @ stdin:5 [10] eval(m::Module, e::Any) @ Core ./boot.jl:489 [11] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [12] include_string @ ./loading.jl:2858 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [14] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile SBMLImporter [210efffb-c3c8-456d-a807-6f55560b12fe] to "/home/pkgeval/.julia/compiled/v1.13/SBMLImporter/jl_Mqv89w" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3289 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2654 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [7] #invokelatest_gr#236 @ ./reflection.jl:1333 [inlined] [8] invokelatest_gr @ ./reflection.jl:1325 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3860 [10] maybe_cachefile_lock @ ./loading.jl:3857 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2640 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2468 [13] macro expansion @ ./loading.jl:2396 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2360 [16] require @ ./loading.jl:2336 [inlined] [17] eval_import_path @ ./module.jl:36 [inlined] [18] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [19] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [20] top-level scope @ ~/.julia/packages/SBMLImporter/yj2XS/ext/SBMLImporterForwardDiffExt.jl:4 [21] include(mod::Module, _path::String) @ Base ./Base.jl:309 [22] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3002 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [26] include_string @ ./loading.jl:2858 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [28] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/SBMLImporter/yj2XS/ext/SBMLImporterForwardDiffExt.jl:1 in expression starting at stdin:5 SBMLImporter Failed to precompile SBMLImporter [210efffb-c3c8-456d-a807-6f55560b12fe] to "/home/pkgeval/.julia/compiled/v1.13/SBMLImporter/jl_zygDM6" (ProcessExited(1)). ERROR: LoadError: UndefVarError: `t` not defined in `SBMLImporter` The binding may be too new: running in world age 39728, while current world is 39752. Stacktrace: [1] _get_reaction_system(model_SBML_sys::SBMLImporter.ModelSBMLSystem, model_SBML::SBMLImporter.ModelSBML) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/system.jl:43 [2] load_SBML(path::String; massaction::Bool, complete::Bool, ifelse_to_callback::Bool, write_to_file::Bool, inline_assignment_rules::Bool, inline_kineticlaw_parameters::Bool, model_as_string::Bool) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:84 [3] load_SBML(path::String) @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:74 [4] macro expansion @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:52 [inlined] [5] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined] [6] top-level scope @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:118 [7] include(mod::Module, _path::String) @ Base ./Base.jl:309 [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3002 [9] top-level scope @ stdin:5 [10] eval(m::Module, e::Any) @ Core ./boot.jl:489 [11] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [12] include_string @ ./loading.jl:2858 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [14] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:1 in expression starting at stdin:5 in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 2455.48s ################################################################################ # Testing # Testing SBMLImporter Status `/tmp/jl_KUrqQn/Project.toml` [4c88cf16] Aqua v0.8.13 [336ed68f] CSV v0.10.15 [479239e8] Catalyst v15.0.8 [b0b7db55] ComponentArrays v0.15.28 [a93c6f00] DataFrames v1.7.0 [2b5f629d] DiffEqBase v6.177.2 [ccbc3e58] JumpProcesses v9.16.1 ⌅ [961ee093] ModelingToolkit v9.82.0 [6ad6398a] OrdinaryDiffEqBDF v1.6.0 [43230ef6] OrdinaryDiffEqRosenbrock v1.11.0 [aea7be01] PrecompileTools v1.3.2 [b4db0fb7] ReactionNetworkImporters v0.16.1 [7e49a35a] RuntimeGeneratedFunctions v0.5.15 [e5567a89] SBML v1.6.0 [210efffb] SBMLImporter v3.0.3 [1bc83da4] SafeTestsets v0.1.0 [0bca4576] SciMLBase v2.104.0 [efcf1570] Setfield v1.1.2 [276daf66] SpecialFunctions v2.5.1 [f43a241f] Downloads v1.7.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_KUrqQn/Manifest.toml` [47edcb42] ADTypes v1.15.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.19.0 [4c555306] ArrayLayouts v1.11.1 [e2ed5e7c] Bijections v0.2.2 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [8e7c35d0] BlockArrays v1.7.0 [70df07ce] BracketingNonlinearSolve v1.3.0 [2a0fbf3d] CPUSummary v0.2.6 [336ed68f] CSV v0.10.15 [479239e8] Catalyst v15.0.8 [d360d2e6] ChainRulesCore v1.25.2 [fb6a15b2] CloseOpenIntervals v0.1.13 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [a80b9123] CommonMark v0.9.1 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.17.0 [b0b7db55] ComponentArrays v0.15.28 [b152e2b5] CompositeTypes v0.1.4 [a33af91c] CompositionsBase v0.1.2 [2569d6c7] ConcreteStructs v0.2.3 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [2b5f629d] DiffEqBase v6.177.2 [459566f4] DiffEqCallbacks v4.8.0 [77a26b50] DiffEqNoiseProcess v5.24.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 ⌅ [a0c0ee7d] DifferentiationInterface v0.6.54 [8d63f2c5] DispatchDoctor v0.4.26 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [5b8099bc] DomainSets v0.7.15 [7c1d4256] DynamicPolynomials v0.6.2 [06fc5a27] DynamicQuantities v1.8.0 [4e289a0a] EnumX v1.0.5 [f151be2c] EnzymeCore v0.8.12 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [7034ab61] FastBroadcast v0.3.5 [9aa1b823] FastClosures v0.3.2 [a4df4552] FastPower v1.1.3 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [64ca27bc] FindFirstFunctions v1.4.1 [6a86dc24] FiniteDiff v2.27.0 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.38 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [d9f16b24] Functors v0.5.2 [46192b85] GPUArraysCore v0.2.0 [c27321d9] Glob v1.3.1 [86223c79] Graphs v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.4 [18e54dd8] IntegerMathUtils v0.1.3 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] 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v2.13.6+1 [1317d2d5] oneTBB_jll v2022.0.0+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 [4af54fe1] LazyArtifacts v1.11.0 [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 v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... Info Given SBMLImporter was explicitly requested, output will be shown live  ERROR: LoadError: UndefVarError: `t` not defined in `SBMLImporter` The binding may be too new: running in world age 39728, while current world is 39752. Stacktrace:  [1] _get_reaction_system(model_SBML_sys::SBMLImporter.ModelSBMLSystem, model_SBML::SBMLImporter.ModelSBML)  @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/system.jl:43  [2] load_SBML(path::String; massaction::Bool, complete::Bool, ifelse_to_callback::Bool, write_to_file::Bool, inline_assignment_rules::Bool, inline_kineticlaw_parameters::Bool, model_as_string::Bool)  @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:84  [3] load_SBML(path::String)  @ SBMLImporter ~/.julia/packages/SBMLImporter/yj2XS/src/load.jl:74  [4] macro expansion  @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:52 [inlined]  [5] macro expansion  @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:121 [inlined]  [6] top-level scope  @ ~/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:118  [7] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [8] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3002  [9] top-level scope  @ stdin:5  [10] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [11] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2848  [12] include_string  @ ./loading.jl:2858 [inlined]  [13] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:318  [14] _start()  @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/SBMLImporter/yj2XS/src/SBMLImporter.jl:1 in expression starting at stdin:5 ✗ SBMLImporter ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1465 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 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000719595625000 Total snapshots: 438. Utilization: 0% ╎438 @Base/task.jl:1129 wait_forever() 437╎ 438 @Base/task.jl:1192 wait() ====================================================================================== 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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007d9beae03580 Total snapshots: 479. Utilization: 0% ╎479 @Base/task.jl:1129 wait_forever() 478╎ 479 @Base/task.jl:1192 wait() [1465] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/SBMLImporter/yj2XS/test/aqua.jl:2 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 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 2265379 (Pool: 2265141; Big: 238); GC: 5 [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:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 28705481 (Pool: 28704572; Big: 909); GC: 42 PkgEval terminated after 2745.31s: test duration exceeded the time limit