Package evaluation to test SBMLToolkit on Julia 1.11.7 (58327cce5e*) started at 2025-10-29T07:34:55.440 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.28s ################################################################################ # Installation # Installing SBMLToolkit... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [86080e66] + SBMLToolkit v0.1.31 Updating `~/.julia/environments/v1.11/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [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 [8e7c35d0] + BlockArrays v1.9.0 [70df07ce] + BracketingNonlinearSolve v1.5.0 [2a0fbf3d] + CPUSummary v0.2.7 [00ebfdb7] + CSTParser v3.4.3 ⌃ [479239e8] + Catalyst v14.4.1 [d360d2e6] + ChainRulesCore v1.26.0 [fb6a15b2] + CloseOpenIntervals v0.1.13 ⌅ [861a8166] + Combinatorics v1.0.2 ⌅ [a80b9123] + CommonMark v0.8.16 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [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 [2b5f629d] + DiffEqBase v6.190.2 [459566f4] + DiffEqCallbacks v4.10.1 [77a26b50] + DiffEqNoiseProcess v5.24.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.9 [8d63f2c5] + DispatchDoctor v0.4.26 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [5b8099bc] + DomainSets v0.7.16 ⌃ [7c1d4256] + DynamicPolynomials v0.6.3 [06fc5a27] + DynamicQuantities v1.10.0 [4e289a0a] + EnumX v1.0.5 [f151be2c] + EnzymeCore v0.8.15 [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 v1.14.0 [64ca27bc] + FindFirstFunctions v1.4.2 [6a86dc24] + FiniteDiff v2.29.0 [1fa38f19] + Format v1.3.7 ⌅ [f6369f11] + ForwardDiff v0.10.39 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 [46192b85] + GPUArraysCore v0.2.0 [c27321d9] + Glob v1.3.1 [86223c79] + Graphs v1.13.1 [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 v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [ae98c720] + Jieko v0.2.1 ⌅ [98e50ef6] + JuliaFormatter v1.0.62 [ccbc3e58] + JumpProcesses v9.19.1 [ba0b0d4f] + Krylov v0.10.2 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.10 [10f19ff3] + LayoutPointers v0.1.17 [5078a376] + LazyArrays v2.8.0 [87fe0de2] + LineSearch v0.1.4 [d3d80556] + LineSearches v7.4.0 [7ed4a6bd] + LinearSolve v3.45.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [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 v9.68.1 [2e0e35c7] + Moshi v0.3.7 [46d2c3a1] + MuladdMacro v0.2.4 ⌃ [102ac46a] + MultivariatePolynomials v0.5.9 [d8a4904e] + MutableArithmetics v1.6.7 [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [8913a72c] + NonlinearSolve v4.12.0 [be0214bd] + NonlinearSolveBase v2.0.0 [5959db7a] + NonlinearSolveFirstOrder v1.9.0 [9a2c21bd] + NonlinearSolveQuasiNewton v1.10.0 [26075421] + NonlinearSolveSpectralMethods v1.5.0 [6fe1bfb0] + OffsetArrays v1.17.0 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [d96e819e] + Parameters v0.12.3 [e409e4f3] + PoissonRandom v0.4.7 [f517fe37] + Polyester v0.7.18 [1d0040c9] + PolyesterWeave v0.2.2 [85a6dd25] + PositiveFactorizations v0.2.4 [d236fae5] + PreallocationTools v0.4.34 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.5.0 [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 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.39.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [ae5879a3] + ResettableStacks v1.1.1 [79098fc4] + Rmath v0.9.0 [7e49a35a] + RuntimeGeneratedFunctions v0.5.15 [e5567a89] + SBML v1.6.0 [86080e66] + SBMLToolkit v0.1.31 [9dfe8606] + SCCNonlinearSolve v1.6.0 [94e857df] + SIMDTypes v0.1.0 [0bca4576] + SciMLBase v2.124.0 [19f34311] + SciMLJacobianOperators v0.1.11 [a6db7da4] + SciMLLogging v1.3.1 [c0aeaf25] + SciMLOperators v1.9.0 [431bcebd] + SciMLPublic v1.0.0 [53ae85a6] + SciMLStructures v1.7.0 [efcf1570] + Setfield v1.1.2 [727e6d20] + SimpleNonlinearSolve v2.9.0 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [7792a7ef] + StrideArraysCore v0.5.8 [2efcf032] + SymbolicIndexingInterface v0.3.46 ⌃ [19f23fe9] + SymbolicLimits v0.2.3 ⌅ [d1185830] + SymbolicUtils v3.32.0 [0c5d862f] + Symbolics v6.57.0 [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 [0796e94c] + Tokenize v0.5.29 [410a4b4d] + Tricks v0.1.12 [781d530d] + TruncatedStacktraces v1.4.0 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [1986cc42] + Unitful v1.25.1 [a7c27f48] + Unityper v0.1.6 [61579ee1] + Ghostscript_jll v9.55.1+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aacddb02] + JpegTurbo_jll v3.1.3+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 v2.13.9+0 [1317d2d5] + oneTBB_jll v2022.0.0+1 [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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts 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 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays 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 v1.1.1+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 9.15s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 1101.73s ################################################################################ # Testing # Testing SBMLToolkit Status `/tmp/jl_JDleSw/Project.toml` [4c88cf16] Aqua v0.8.14 [336ed68f] CSV v0.10.15 ⌃ [479239e8] Catalyst v14.4.1 [a93c6f00] DataFrames v1.8.1 ⌅ [961ee093] ModelingToolkit v9.68.1 [1dea7af3] OrdinaryDiffEq v6.103.0 [91a5bcdd] Plots v1.41.1 [e5567a89] SBML v1.6.0 [86080e66] SBMLToolkit v0.1.31 ⌅ [792e603a] SBMLToolkitTestSuite v0.0.4 [1bc83da4] SafeTestsets v0.1.0 ⌅ [c3572dad] Sundials v4.28.0 ⌅ [d1185830] SymbolicUtils v3.32.0 [f43a241f] Downloads v1.6.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_JDleSw/Manifest.toml` [47edcb42] ADTypes v1.18.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.22.0 [4c555306] ArrayLayouts v1.12.0 [e2ed5e7c] Bijections v0.2.2 [d1d4a3ce] BitFlags v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [8e7c35d0] BlockArrays v1.9.0 [70df07ce] BracketingNonlinearSolve v1.5.0 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.7 [00ebfdb7] CSTParser v3.4.3 [336ed68f] CSV v0.10.15 ⌃ [479239e8] Catalyst v14.4.1 [d360d2e6] ChainRulesCore v1.26.0 [fb6a15b2] CloseOpenIntervals v0.1.13 [944b1d66] CodecZlib v0.7.8 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 ⌅ [861a8166] Combinatorics v1.0.2 ⌅ [a80b9123] CommonMark v0.8.16 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [b152e2b5] CompositeTypes v0.1.4 [a33af91c] CompositionsBase v0.1.2 [2569d6c7] ConcreteStructs v0.2.3 [f0e56b4a] ConcurrentUtilities v2.5.0 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [2b5f629d] DiffEqBase v6.190.2 [459566f4] DiffEqCallbacks v4.10.1 [77a26b50] DiffEqNoiseProcess v5.24.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.9 [8d63f2c5] DispatchDoctor v0.4.26 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [5b8099bc] DomainSets v0.7.16 ⌃ [7c1d4256] DynamicPolynomials v0.6.3 [06fc5a27] DynamicQuantities v1.10.0 [4e289a0a] EnumX v1.0.5 [f151be2c] EnzymeCore v0.8.15 [460bff9d] ExceptionUnwrapping v0.1.11 [d4d017d3] ExponentialUtilities v1.27.0 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [c87230d0] FFMPEG v0.4.5 [7034ab61] FastBroadcast v0.3.5 [9aa1b823] FastClosures v0.3.2 [442a2c76] FastGaussQuadrature v1.1.0 [a4df4552] FastPower v1.1.3 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [64ca27bc] FindFirstFunctions v1.4.2 [6a86dc24] FiniteDiff v2.29.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 ⌅ [f6369f11] ForwardDiff v0.10.39 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 [28b8d3ca] GR v0.73.17 [c145ed77] GenericSchur v0.5.6 [c27321d9] Glob v1.3.1 [86223c79] Graphs v1.13.1 [42e2da0e] Grisu v1.0.2 [cd3eb016] HTTP v1.10.19 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [18e54dd8] IntegerMathUtils v0.1.3 [8197267c] IntervalSets v0.7.11 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [1019f520] JLFzf v0.1.11 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.2.0 [ae98c720] Jieko v0.2.1 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [ccbc3e58] JumpProcesses v9.19.1 [ba0b0d4f] Krylov v0.10.2 [b964fa9f] LaTeXStrings v1.4.0 [23fbe1c1] Latexify v0.16.10 [10f19ff3] LayoutPointers v0.1.17 [5078a376] LazyArrays v2.8.0 [87fe0de2] LineSearch v0.1.4 [d3d80556] LineSearches v7.4.0 [7ed4a6bd] LinearSolve v3.45.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [d8e11817] MLStyle v0.4.17 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [bb5d69b7] MaybeInplace v0.1.4 [739be429] MbedTLS v1.1.9 [442fdcdd] Measures v0.3.2 [e1d29d7a] Missings v1.2.0 ⌅ [961ee093] ModelingToolkit v9.68.1 [2e0e35c7] Moshi v0.3.7 [46d2c3a1] MuladdMacro v0.2.4 ⌃ [102ac46a] MultivariatePolynomials v0.5.9 [d8a4904e] MutableArithmetics v1.6.7 [d41bc354] NLSolversBase v7.10.0 [77ba4419] NaNMath v1.1.3 [8913a72c] NonlinearSolve v4.12.0 [be0214bd] NonlinearSolveBase v2.0.0 [5959db7a] NonlinearSolveFirstOrder v1.9.0 [9a2c21bd] NonlinearSolveQuasiNewton v1.10.0 [26075421] NonlinearSolveSpectralMethods v1.5.0 [6fe1bfb0] OffsetArrays v1.17.0 [4d8831e6] OpenSSL v1.5.0 [429524aa] Optim v1.13.2 [bac558e1] OrderedCollections v1.8.1 [1dea7af3] OrdinaryDiffEq v6.103.0 [89bda076] OrdinaryDiffEqAdamsBashforthMoulton v1.5.0 [6ad6398a] OrdinaryDiffEqBDF v1.10.1 [bbf590c4] OrdinaryDiffEqCore v1.36.0 [50262376] OrdinaryDiffEqDefault v1.8.0 [4302a76b] OrdinaryDiffEqDifferentiation v1.16.1 [9286f039] OrdinaryDiffEqExplicitRK v1.4.0 [e0540318] OrdinaryDiffEqExponentialRK v1.8.0 [becaefa8] OrdinaryDiffEqExtrapolation v1.9.0 [5960d6e9] OrdinaryDiffEqFIRK v1.16.0 [101fe9f7] OrdinaryDiffEqFeagin v1.4.0 [d3585ca7] OrdinaryDiffEqFunctionMap v1.5.0 [d28bc4f8] OrdinaryDiffEqHighOrderRK v1.5.0 [9f002381] OrdinaryDiffEqIMEXMultistep v1.7.0 [521117fe] OrdinaryDiffEqLinear v1.6.0 [1344f307] OrdinaryDiffEqLowOrderRK v1.6.0 [b0944070] OrdinaryDiffEqLowStorageRK v1.7.0 [127b3ac7] OrdinaryDiffEqNonlinearSolve v1.15.0 [c9986a66] OrdinaryDiffEqNordsieck v1.4.0 [5dd0a6cf] OrdinaryDiffEqPDIRK v1.6.0 [5b33eab2] OrdinaryDiffEqPRK v1.4.0 [04162be5] OrdinaryDiffEqQPRK v1.4.0 [af6ede74] OrdinaryDiffEqRKN v1.5.0 [43230ef6] OrdinaryDiffEqRosenbrock v1.18.1 [2d112036] OrdinaryDiffEqSDIRK v1.7.0 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... ┌ Warning: `istree` is deprecated, use `iscall` instead. │ caller = (::SBMLToolkit.var"#check_args#18")(x::SymbolicUtils.BasicSymbolic{Real}) at reactions.jl:166 └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/reactions.jl:166 Systems: Test Failed at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:53 Expression: issetequal(Catalyst.get_ps(rs), [k1, c1]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:516 [3] include(mod::Module, _path::String) @ Base ./Base.jl:562 [4] include(x::String) @ Main.var"##SBMLToolkit.jl#232".var"##Systems#234" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [5] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [8] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [9] eval(m::Module, e::Any) @ Core ./boot.jl:430 [10] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [11] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:7 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:4 [inlined] [14] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 Systems: Test Failed at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:63 Expression: issetequal(Catalyst.get_ps(rs), [k1, c1]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:516 [3] include(mod::Module, _path::String) @ Base ./Base.jl:562 [4] include(x::String) @ Main.var"##SBMLToolkit.jl#232".var"##Systems#234" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [5] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [8] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [9] eval(m::Module, e::Any) @ Core ./boot.jl:430 [10] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [11] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:7 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:4 [inlined] [14] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 Systems: Test Failed at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:75 Expression: issetequal(Catalyst.get_ps(rs), [k1, c1]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:516 [3] include(mod::Module, _path::String) @ Base ./Base.jl:562 [4] include(x::String) @ Main.var"##SBMLToolkit.jl#232".var"##Systems#234" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [5] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [8] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [9] eval(m::Module, e::Any) @ Core ./boot.jl:430 [10] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [11] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:7 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:4 [inlined] [14] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 Systems: Test Failed at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:86 Expression: issetequal(ModelingToolkit.parameters_toplevel(odesys), [k1, c1]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:516 [3] include(mod::Module, _path::String) @ Base ./Base.jl:562 [4] include(x::String) @ Main.var"##SBMLToolkit.jl#232".var"##Systems#234" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [5] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [8] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [9] eval(m::Module, e::Any) @ Core ./boot.jl:430 [10] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [11] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:7 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:4 [inlined] [14] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 Systems: Test Failed at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:103 Expression: issetequal(ModelingToolkit.parameters_toplevel(odesys), [k1, c1]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:680 [inlined] [2] top-level scope @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/systems.jl:516 [3] include(mod::Module, _path::String) @ Base ./Base.jl:562 [4] include(x::String) @ Main.var"##SBMLToolkit.jl#232".var"##Systems#234" ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [5] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [7] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:8 [inlined] [8] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 [9] eval(m::Module, e::Any) @ Core ./boot.jl:430 [10] macro expansion @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 [inlined] [11] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:7 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1709 [inlined] [13] macro expansion @ ~/.julia/packages/SBMLToolkit/7Hd7h/test/runtests.jl:4 [inlined] [14] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:30 ┌ Warning: Cannot separate bidirectional kineticLaw `k1 - s1s2(t) - k1*s2(t)` to forward and reverse part. Setting forward to `k1 - s1s2(t) - k1*s2(t)` and reverse to `0`. Stochastic simulations will be inexact. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/reactions.jl:49 ┌ Warning: Cannot separate bidirectional kineticLaw `k1` to forward and reverse part. Setting forward to `k1` and reverse to `0`. Stochastic simulations will be inexact. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/reactions.jl:35 ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: `convert_simplify_math` is deprecated, use `convert_promotelocals_expandfuns` instead. │ caller = #16 at SBMLToolkitTestSuite.jl:104 [inlined] └ @ Core ~/.julia/packages/SBMLToolkitTestSuite/QDNw7/src/SBMLToolkitTestSuite.jl:104 [ Info: Case 00007 done with a code 6 and error msg: [ Info: ("00007", false, true, "", 6, SciMLBase.ReturnCode.Success) [ Info: Case 00022 done with a code 6 and error msg: [ Info: ("00022", false, true, "", 6, SciMLBase.ReturnCode.Success) [ Info: Case 00023 done with a code 6 and error msg: [ Info: ("00023", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 [ Info: Case 00041 done with a code 6 and error msg: [ Info: ("00041", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: Initialization system is overdetermined. 1 equations for 0 unknowns. Initialization will default to using least squares. `SCCNonlinearProblem` can only be used for initialization of fully determined systems and hence will not be used here. To suppress this warning pass warn_initialize_determined = false. To make this warning into an error, pass fully_determined = true └ @ ModelingToolkit ~/.julia/packages/ModelingToolkit/S1kqK/src/systems/diffeqs/abstractodesystem.jl:1446 [ Info: Case 00140 done with a code 6 and error msg: [ Info: ("00140", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: Initialization system is overdetermined. 3 equations for 0 unknowns. Initialization will default to using least squares. `SCCNonlinearProblem` can only be used for initialization of fully determined systems and hence will not be used here. To suppress this warning pass warn_initialize_determined = false. To make this warning into an error, pass fully_determined = true └ @ ModelingToolkit ~/.julia/packages/ModelingToolkit/S1kqK/src/systems/diffeqs/abstractodesystem.jl:1446 [ Info: Case 00170 done with a code 6 and error msg: [ Info: ("00170", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: Initialization system is overdetermined. 2 equations for 0 unknowns. Initialization will default to using least squares. `SCCNonlinearProblem` can only be used for initialization of fully determined systems and hence will not be used here. To suppress this warning pass warn_initialize_determined = false. To make this warning into an error, pass fully_determined = true └ @ ModelingToolkit ~/.julia/packages/ModelingToolkit/S1kqK/src/systems/diffeqs/abstractodesystem.jl:1446 [ Info: Case 00325 done with a code 6 and error msg: [ Info: ("00325", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: Initialization system is overdetermined. 1 equations for 0 unknowns. Initialization will default to using least squares. `SCCNonlinearProblem` can only be used for initialization of fully determined systems and hence will not be used here. To suppress this warning pass warn_initialize_determined = false. To make this warning into an error, pass fully_determined = true └ @ ModelingToolkit ~/.julia/packages/ModelingToolkit/S1kqK/src/systems/diffeqs/abstractodesystem.jl:1446 [ Info: Case 00679 done with a code 6 and error msg: [ Info: ("00679", false, true, "", 6, SciMLBase.ReturnCode.Success) ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 ┌ Warning: SBMLToolkit currently fires events regardless of uppass or downpass trigger. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/events.jl:31 [ Info: Case 00944 done with a code 6 and error msg: [ Info: ("00944", false, true, "", 6, SciMLBase.ReturnCode.Success) 9×6 DataFrame Row │ case expected_err res error k diffeq_retcode │ String Bool Bool String Int64 Any ─────┼─────────────────────────────────────────────────────────── 1 │ 00007 false true 6 Success 2 │ 00022 false true 6 Success 3 │ 00023 false true 6 Success 4 │ 00041 false true 6 Success 5 │ 00140 false true 6 Success 6 │ 00170 false true 6 Success 7 │ 00325 false true 6 Success 8 │ 00679 false true 6 Success 9 │ 00944 false true 6 Success┌ Warning: SBML SpeciesReferences does not contain stoichiometries. Assuming stoichiometry of 1. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/reactions.jl:92 ┌ Warning: Stoichiometries of SpeciesReferences are not defined. Setting to 1. └ @ SBMLToolkit ~/.julia/packages/SBMLToolkit/7Hd7h/src/reactions.jl:117 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 175 running 1 of 1 signal (10): User defined signal 1 _ZNK4llvm12DenseMapBaseINS_8DenseMapIPNS_10BasicBlockESt10unique_ptrINS_15DomTreeNodeBaseIS2_EESt14default_deleteIS6_EENS_12DenseMapInfoIS3_vEENS_6detail12DenseMapPairIS3_S9_EEEES3_S9_SB_SE_E4findEPKS2_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZNK4llvm17DominatorTreeBaseINS_10BasicBlockELb0EE7getNodeEPKS1_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZNK4llvm17DominatorTreeBaseINS_10BasicBlockELb0EE9dominatesEPKS1_S4_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass10findLeaderEPKNS_10BasicBlockEj at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass18processInstructionEPNS_11InstructionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass12processBlockEPNS_10BasicBlockE.part.0 at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass17iterateOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass7runImplERNS_8FunctionERNS_15AssumptionCacheERNS_13DominatorTreeERKNS_17TargetLibraryInfoERNS_9AAResultsEPNS_23MemoryDependenceResultsEPNS_8LoopInfoEPNS_25OptimizationRemarkEmitterEPNS_9MemorySSAE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 run at /source/usr/include/llvm/IR/PassManager.h:517 [inlined] run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/src/pipeline.cpp:777 operator() at /source/src/jitlayers.cpp:1298 withModuleDo<(anonymous namespace)::OptimizerT::operator()(llvm::orc::ThreadSafeModule, llvm::orc::MaterializationResponsibility&) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1259 [inlined] CallImpl<(anonymous namespace)::OptimizerT<4> > at /source/usr/include/llvm/ADT/FunctionExtras.h:221 _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm6detail18UniqueFunctionBaseIvJSt10unique_ptrINS_3orc4TaskESt14default_deleteIS4_EEEE8CallImplIPFvS7_EEEvPvRS7_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISI_vEEEENSJ_IS5_vEENS_6detail12DenseMapPairIS5_SL_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) addModule at /source/src/jitlayers.cpp:1875 jl_add_to_ee at /source/src/jitlayers.cpp:2306 _jl_compile_codeinst at /source/src/jitlayers.cpp:277 jl_generate_fptr_impl at /source/src/jitlayers.cpp:536 jl_compile_method_internal at /source/src/gf.c:2538 [inlined] jl_compile_method_internal at /source/src/gf.c:2425 gen_cfun_wrapper at /source/src/codegen.cpp:6762 emit_cfunction at /source/src/codegen.cpp:7404 [inlined] emit_expr at /source/src/codegen.cpp:6219 emit_ssaval_assign at /source/src/codegen.cpp:5747 emit_stmtpos at /source/src/codegen.cpp:6025 [inlined] emit_function at /source/src/codegen.cpp:9215 jl_emit_code at /source/src/codegen.cpp:9549 jl_emit_codeinst at /source/src/codegen.cpp:9635 _jl_compile_codeinst at /source/src/jitlayers.cpp:221 jl_generate_fptr_impl at /source/src/jitlayers.cpp:536 jl_compile_method_internal at /source/src/gf.c:2538 [inlined] jl_compile_method_internal at /source/src/gf.c:2425 _jl_invoke at /source/src/gf.c:2943 [inlined] ijl_apply_generic at /source/src/gf.c:3128 #4 at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/ext/DiffEqBaseForwardDiffExt.jl:63 unknown function (ip: 0x7d5d28b56ea6) _jl_invoke at /source/src/gf.c:2951 [inlined] ijl_apply_generic at /source/src/gf.c:3128 map at ./tuple.jl:386 [inlined] wrapfun_iip at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/ext/DiffEqBaseForwardDiffExt.jl:62 promote_f at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:696 [inlined] #get_concrete_problem#46 at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:605 get_concrete_problem at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:594 [inlined] #solve_up#39 at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:557 solve_up at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:540 [inlined] #solve#38 at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:530 solve at /home/pkgeval/.julia/packages/DiffEqBase/p82Yh/src/solve.jl:520 unknown function (ip: 0x7d5d28b56dd6) _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 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 jl_apply at /source/src/julia.h:2157 [inlined] jl_f__call_latest at /source/src/builtins.c:875 include at /home/pkgeval/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:28 unknown function (ip: 0x7d5d28aec0b2) _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_eval_module_expr at /source/src/toplevel.c:215 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:743 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 jfptr_eval_28355.1 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] 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_eval_module_expr at /source/src/toplevel.c:215 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:743 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 jfptr_eval_28355.1 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] 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 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 ./sysimg.jl:38 unknown function (ip: 0x7d5d91e83082) _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 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] exec_options at ./client.jl:289 _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: 0x7d5d93388249) __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 ============================================================== ====================================================================================== 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: 0x712e3af66f52) _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: 0x712e3af5f6ad) _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: 0x712e3af53c3a) _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: 0x712e3af5393d) _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: 0x712e3af5330d) _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: 0x712e3af4f786) _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: 0x712e3c44c249) __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 0x0000712e2f5fc010 Total snapshots: 250. Utilization: 0% ╎250 @Base/client.jl:524; _start() ╎ 250 @Base/client.jl:316; exec_options(opts::Base.JLOptions) ╎ 250 @Base/Base.jl:562; include(mod::Module, _path::String) ╎ 250 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, _pat… ╎ 250 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity), mo… ╎ 250 @Base/boot.jl:430; eval ╎ ╎ 250 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 250 @Pkg/src/API.jl:146; #test#74 ╎ ╎ 250 @Pkg/src/API.jl:147; test ╎ ╎ 250 @Pkg/src/API.jl:147; #test#75 ╎ ╎ 250 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 250 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec… ╎ ╎ ╎ 250 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 250 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 250 …rc/Operations.jl:2011; test ╎ ╎ ╎ 250 …rc/Operations.jl:2067; test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 250 …c/Operations.jl:1841; kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 250 …c/Operations.jl:1849; #sandbox#115 ╎ ╎ ╎ ╎ 250 @Base/file.jl:815; mktempdir ╎ ╎ ╎ ╎ 250 @Base/file.jl:815; mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 250 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 250 …Operations.jl:1902; (::Pkg.Operations.var"#116#12… ╎ ╎ ╎ ╎ ╎ 250 …Operations.jl:1793; with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 250 …Operations.jl:1935; (::Pkg.Operations.var"#118#… ╎ ╎ ╎ ╎ ╎ 250 @Base/env.jl:265; withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 250 …perations.jl:2086; (::Pkg.Operations.var"#131… ╎ ╎ ╎ ╎ ╎ ╎ 250 …erations.jl:2146; subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 250 …/process.jl:687; wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 250 …/process.jl:694; wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 250 …ondition.jl:125; wait ╎ ╎ ╎ ╎ ╎ ╎ 250 …ondition.jl:130; wait(c::Base.GenericCon… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 250 …ase/task.jl:1021; wait() 249╎ ╎ ╎ ╎ ╎ ╎ ╎ 250 …ase/task.jl:1012; poptask(W::Base.Intr… [175] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/SBMLToolkit/7Hd7h/test/wuschel.jl:19 _ZNK4llvm17DominatorTreeBaseINS_10BasicBlockELb0EE9dominatesEPKNS_15DomTreeNodeBaseIS1_EES6_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass10findLeaderEPKNS_10BasicBlockEj at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass18processInstructionEPNS_11InstructionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass12processBlockEPNS_10BasicBlockE.part.0 at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass17iterateOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass7runImplERNS_8FunctionERNS_15AssumptionCacheERNS_13DominatorTreeERKNS_17TargetLibraryInfoERNS_9AAResultsEPNS_23MemoryDependenceResultsEPNS_8LoopInfoEPNS_25OptimizationRemarkEmitterEPNS_9MemorySSAE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm7GVNPass3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 run at /source/usr/include/llvm/IR/PassManager.h:517 [inlined] run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/src/pipeline.cpp:777 operator() at /source/src/jitlayers.cpp:1298 withModuleDo<(anonymous namespace)::OptimizerT::operator()(llvm::orc::ThreadSafeModule, llvm::orc::MaterializationResponsibility&) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1259 [inlined] CallImpl<(anonymous namespace)::OptimizerT<4> > at /source/usr/include/llvm/ADT/FunctionExtras.h:221 _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) PkgEval terminated after 2724.05s: test duration exceeded the time limit