Package evaluation to test StochasticGene on Julia 1.14.0-DEV.1871 (50d44f5be7*) started at 2026-03-09T03:32:06.888 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.42s ################################################################################ # Installation # Installing StochasticGene... Resolving package versions... Installed CommonWorldInvalidations ──────────── v1.0.0 Installed MKL_jll ───────────────────────────── v2025.2.0+0 Installed FastPower ─────────────────────────── v1.3.1 Installed SIMDTypes ─────────────────────────── v0.1.0 Installed OrderedCollections ────────────────── v1.8.1 Installed InlineStrings ─────────────────────── v1.4.5 Installed MultivariateStats ─────────────────── v0.10.4 Installed PreallocationTools ────────────────── v1.1.2 Installed OrdinaryDiffEqExponentialRK ───────── v1.13.0 Installed Optim ─────────────────────────────── v1.13.3 Installed EnzymeCore ────────────────────────── v0.8.18 Installed NonlinearSolveSpectralMethods ─────── v1.6.0 Installed OrdinaryDiffEqRosenbrock ──────────── v1.25.0 Installed CpuId ─────────────────────────────── v0.3.1 Installed SentinelArrays ────────────────────── v1.4.9 Installed Compiler ──────────────────────────── v0.1.1 Installed NaNMath ───────────────────────────── v1.1.3 Installed QuadGK ────────────────────────────── v2.11.2 Installed StaticArrayInterface ──────────────── v1.9.0 Installed OrdinaryDiffEqFIRK ────────────────── v1.23.0 Installed OpenSpecFun_jll ───────────────────── v0.5.6+0 Installed Revise ────────────────────────────── v3.13.2 Installed OrdinaryDiffEqQPRK ────────────────── v1.8.0 Installed FastBroadcast ─────────────────────── v0.3.5 Installed Tables ────────────────────────────── v1.12.1 Installed NLSolversBase ─────────────────────── v7.10.0 Installed OrdinaryDiffEqLowOrderRK ──────────── v1.10.0 Installed EnumX ─────────────────────────────── v1.0.7 Installed Arpack ────────────────────────────── v0.5.4 Installed LinearSolve ───────────────────────── v3.64.0 Installed DiffEqBase ────────────────────────── v6.210.1 Installed Reexport ──────────────────────────── v1.2.2 Installed InverseFunctions ──────────────────── v0.1.17 Installed LoweredCodeUtils ──────────────────── v3.5.1 Installed Jieko ─────────────────────────────── v0.2.1 Installed NonlinearSolveBase ────────────────── v2.15.0 Installed BracketingNonlinearSolve ──────────── v1.11.0 Installed Missings ──────────────────────────── v1.2.0 Installed RegistryInstances ─────────────────── v0.1.0 Installed TableTraits ───────────────────────── v1.0.1 Installed Static ────────────────────────────── v1.3.1 Installed MaybeInplace ──────────────────────── v0.1.4 Installed Preferences ───────────────────────── v1.5.2 Installed SortingAlgorithms ─────────────────── v1.2.2 Installed OrdinaryDiffEqNordsieck ───────────── v1.9.0 Installed LaTeXStrings ──────────────────────── v1.4.0 Installed OrdinaryDiffEqAdamsBashforthMoulton ─ v1.9.0 Installed Crayons ───────────────────────────── v4.1.1 Installed NonlinearSolve ────────────────────── v4.16.0 Installed OrdinaryDiffEqLinear ──────────────── v1.10.0 Installed OpenSSH_jll ───────────────────────── v10.2.1+0 Installed UnPack ────────────────────────────── v1.0.2 Installed ADTypes ───────────────────────────── v1.21.0 Installed MacroTools ────────────────────────── v0.5.16 Installed GenericSchur ──────────────────────── v0.5.6 Installed DataStructures ────────────────────── v0.19.3 Installed RecursiveArrayTools ───────────────── v3.48.0 Installed DiffResults ───────────────────────── v1.1.0 Installed ManualMemory ──────────────────────── v0.1.8 Installed oneTBB_jll ────────────────────────── v2022.0.0+1 Installed FillArrays ────────────────────────── v1.16.0 Installed AbstractTrees ─────────────────────── v0.4.5 Installed DelimitedFiles ────────────────────── v1.9.1 Installed StatsBase ─────────────────────────── v0.34.10 Installed CodecZlib ─────────────────────────── v0.7.8 Installed ExprTools ─────────────────────────── v0.1.10 Installed IntelOpenMP_jll ───────────────────── v2025.2.0+0 Installed SciMLJacobianOperators ────────────── v0.1.12 Installed DataValueInterfaces ───────────────── v1.0.0 Installed CommonSubexpressions ──────────────── v0.3.1 Installed Expat_jll ─────────────────────────── v2.7.3+0 Installed IrrationalConstants ───────────────── v0.2.6 Installed TruncatedStacktraces ──────────────── v1.4.0 Installed LoggingExtras ─────────────────────── v1.2.0 Installed LayoutPointers ────────────────────── v0.1.17 Installed ConcreteStructs ───────────────────── v0.2.3 Installed ArrayInterface ────────────────────── v7.23.0 Installed SparseMatrixColorings ─────────────── v0.4.24 Installed LSODA_jll ─────────────────────────── v0.1.2+0 Installed IOCapture ─────────────────────────── v1.0.0 Installed GPUArraysCore ─────────────────────── v0.2.0 Installed OrdinaryDiffEqStabilizedIRK ───────── v1.11.0 Installed OrdinaryDiffEqPRK ─────────────────── v1.8.0 Installed PooledArrays ──────────────────────── v1.4.3 Installed OrdinaryDiffEqExtrapolation ───────── v1.16.0 Installed PDMats ────────────────────────────── v0.11.37 Installed OrdinaryDiffEqRKN ─────────────────── v1.10.0 Installed Setfield ──────────────────────────── v1.1.2 Installed Moshi ─────────────────────────────── v0.3.7 Installed NonlinearSolveQuasiNewton ─────────── v1.12.0 Installed WorkerUtilities ───────────────────── v1.6.1 Installed OrdinaryDiffEqHighOrderRK ─────────── v1.9.0 Installed CompositionsBase ──────────────────── v0.1.2 Installed CommonSolve ───────────────────────── v0.2.6 Installed DocStringExtensions ───────────────── v0.9.5 Installed DifferentiationInterface ──────────── v0.7.16 Installed Rmath_jll ─────────────────────────── v0.5.1+0 Installed VersionParsing ────────────────────── v1.3.0 Installed ZMQ ───────────────────────────────── v1.5.1 Installed ForwardDiff ───────────────────────── v1.3.2 Installed AliasTables ───────────────────────── v1.1.3 Installed OrdinaryDiffEq ────────────────────── v6.108.0 Installed OrdinaryDiffEqStabilizedRK ────────── v1.8.0 Installed BitTwiddlingConvenienceFunctions ──── v0.1.6 Installed IteratorInterfaceExtensions ───────── v1.0.0 Installed LineSearch ────────────────────────── v0.1.6 Installed CSV ───────────────────────────────── v0.10.16 Installed FunctionWrappersWrappers ──────────── v0.1.3 Installed RecipesBase ───────────────────────── v1.3.4 Installed SciMLOperators ────────────────────── v1.15.1 Installed Git_LFS_jll ───────────────────────── v3.7.0+0 Installed Krylov ────────────────────────────── v0.10.5 Installed DataAPI ───────────────────────────── v1.16.0 Installed InvertedIndices ───────────────────── v1.3.1 Installed OrdinaryDiffEqSymplecticRK ────────── v1.11.0 Installed Conda ─────────────────────────────── v1.10.3 Installed OrdinaryDiffEqBDF ─────────────────── v1.22.0 Installed SciMLStructures ───────────────────── v1.10.0 Installed LSODA ─────────────────────────────── v0.7.5 Installed StaticArraysCore ──────────────────── v1.4.4 Installed FastGaussQuadrature ───────────────── v1.1.0 Installed StaticArrays ──────────────────────── v1.9.17 Installed Documenter ────────────────────────── v1.17.0 Installed OrdinaryDiffEqLowStorageRK ────────── v1.12.0 Installed CodeTracking ──────────────────────── v3.0.0 Installed SciMLPublic ───────────────────────── v1.0.1 Installed AbstractFFTs ──────────────────────── v1.5.0 Installed FunctionWrappers ──────────────────── v1.1.3 Installed DiffRules ─────────────────────────── v1.15.1 Installed OrdinaryDiffEqDifferentiation ─────── v2.2.1 Installed Requires ──────────────────────────── v1.3.1 Installed LogExpFunctions ───────────────────── v0.3.29 Installed OrdinaryDiffEqNonlinearSolve ──────── v1.23.0 Installed StringManipulation ────────────────── v0.4.4 Installed Git_jll ───────────────────────────── v2.53.0+0 Installed Distributions ─────────────────────── v0.25.123 Installed JuliaInterpreter ──────────────────── v0.10.10 Installed JSON ──────────────────────────────── v0.21.4 Installed OrdinaryDiffEqCore ────────────────── v3.17.0 Installed Rmath ─────────────────────────────── v0.9.0 Installed PrettyTables ──────────────────────── v3.2.3 Installed SciMLBase ─────────────────────────── v2.148.0 Installed OrdinaryDiffEqExplicitRK ──────────── v1.9.0 Installed Parsers ───────────────────────────── v2.8.3 Installed NonlinearSolveFirstOrder ──────────── v2.0.0 Installed FastClosures ──────────────────────── v0.3.2 Installed Arpack_jll ────────────────────────── v3.5.2+0 Installed FiniteDiff ────────────────────────── v2.29.0 Installed CloseOpenIntervals ────────────────── v0.1.13 Installed StatsFuns ─────────────────────────── v1.5.2 Installed libsodium_jll ─────────────────────── v1.0.21+0 Installed Polyester ─────────────────────────── v0.7.19 Installed OrdinaryDiffEqFeagin ──────────────── v1.8.0 Installed OrdinaryDiffEqIMEXMultistep ───────── v1.12.0 Installed WeakRefStrings ────────────────────── v1.4.2 Installed JLLWrappers ───────────────────────── v1.7.1 Installed IJulia ────────────────────────────── v1.34.4 Installed DataFrames ────────────────────────── v1.8.1 Installed OrdinaryDiffEqSSPRK ───────────────── v1.11.0 Installed OrdinaryDiffEqPDIRK ───────────────── v1.11.0 Installed OrdinaryDiffEqSDIRK ───────────────── v1.12.0 Installed ThreadingUtilities ────────────────── v0.5.5 Installed ZeroMQ_jll ────────────────────────── v4.3.6+0 Installed Accessors ─────────────────────────── v0.1.43 Installed OrdinaryDiffEqVerner ──────────────── v1.11.0 Installed ExponentialUtilities ──────────────── v1.30.0 Installed RuntimeGeneratedFunctions ─────────── v0.5.17 Installed OrdinaryDiffEqDefault ─────────────── v1.13.0 Installed ConstructionBase ──────────────────── v1.6.0 Installed HypergeometricFunctions ───────────── v0.3.28 Installed Adapt ─────────────────────────────── v4.5.0 Installed FilePathsBase ─────────────────────── v0.9.24 Installed SymbolicIndexingInterface ─────────── v0.3.46 Installed TranscodingStreams ────────────────── v0.11.3 Installed Compat ────────────────────────────── v4.18.1 Installed Statistics ────────────────────────── v1.11.1 Installed PositiveFactorizations ────────────── v0.2.4 Installed StatsAPI ──────────────────────────── v1.8.0 Installed ExproniconLite ────────────────────── v0.10.14 Installed StrideArraysCore ──────────────────── v0.5.8 Installed TimerOutputs ──────────────────────── v0.5.29 Installed CPUSummary ────────────────────────── v0.2.7 Installed PrecompileTools ───────────────────── v1.3.3 Installed ChainRulesCore ────────────────────── v1.26.0 Installed MarkdownAST ───────────────────────── v0.1.3 Installed Parameters ────────────────────────── v0.12.3 Installed IfElse ────────────────────────────── v0.1.1 Installed MuladdMacro ───────────────────────── v0.2.4 Installed LazilyInitializedFields ───────────── v1.3.0 Installed FFTW_jll ──────────────────────────── v3.3.11+0 Installed SpecialFunctions ──────────────────── v2.7.1 Installed FFTW ──────────────────────────────── v1.10.0 Installed SciMLLogging ──────────────────────── v1.9.1 Installed PtrArrays ─────────────────────────── v1.4.0 Installed Git ───────────────────────────────── v1.5.0 Installed SimpleNonlinearSolve ──────────────── v2.11.0 Installed Libiconv_jll ──────────────────────── v1.18.0+0 Installed OrdinaryDiffEqTsit5 ───────────────── v1.9.0 Installed OrdinaryDiffEqFunctionMap ─────────── v1.9.0 Installed PolyesterWeave ────────────────────── v0.2.2 Installed ANSIColoredPrinters ───────────────── v0.0.1 Installed LineSearches ──────────────────────── v7.5.1 Installed StochasticGene ────────────────────── v1.7.2 Installing 13 artifacts Installed artifact Rmath 121.9 KiB Installed artifact LSODA 24.9 KiB Installed artifact ZeroMQ 316.1 KiB Installed artifact Arpack 138.3 KiB Installed artifact libsodium 1.6 MiB Installed artifact FFTW 2.2 MiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Expat 283.3 KiB Installed artifact OpenSSH 4.3 MiB Installed artifact Git_LFS 9.6 MiB Installed artifact testfiles 6.2 MiB Installed artifact Git 49.5 MiB Updating `~/.julia/environments/v1.14/Project.toml` [a2598c62] + StochasticGene v1.7.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] 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[864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [2b5f629d] + DiffEqBase v6.210.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.16 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [e30172f5] + Documenter v1.17.0 [4e289a0a] + EnumX v1.0.7 [f151be2c] + EnzymeCore v0.8.18 [d4d017d3] + ExponentialUtilities v1.30.0 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [7a1cc6ca] + FFTW v1.10.0 [7034ab61] + FastBroadcast v0.3.5 [9aa1b823] + FastClosures v0.3.2 [442a2c76] + FastGaussQuadrature v1.1.0 [a4df4552] + FastPower v1.3.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.29.0 [f6369f11] + ForwardDiff v1.3.2 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 [46192b85] + GPUArraysCore v0.2.0 [c145ed77] + GenericSchur v0.5.6 [d7ba0133] + Git v1.5.0 [34004b35] + HypergeometricFunctions v0.3.28 [7073ff75] + IJulia v1.34.4 [b5f81e59] + IOCapture v1.0.0 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [ae98c720] + Jieko v0.2.1 [aa1ae85d] + JuliaInterpreter v0.10.10 [ba0b0d4f] + Krylov v0.10.5 [7f56f5a3] + LSODA v0.7.5 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [0e77f7df] + LazilyInitializedFields v1.3.0 [87fe0de2] + LineSearch v0.1.6 ⌃ [d3d80556] + LineSearches v7.5.1 [7ed4a6bd] + LinearSolve v3.64.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [6f1432cf] + LoweredCodeUtils v3.5.1 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [d0879d2d] + MarkdownAST v0.1.3 [bb5d69b7] + MaybeInplace v0.1.4 [e1d29d7a] + Missings v1.2.0 [2e0e35c7] + Moshi v0.3.7 [46d2c3a1] + MuladdMacro v0.2.4 [6f286f6a] + MultivariateStats v0.10.4 ⌅ [d41bc354] + NLSolversBase v7.10.0 [77ba4419] + NaNMath v1.1.3 [8913a72c] + NonlinearSolve v4.16.0 [be0214bd] + NonlinearSolveBase v2.15.0 [5959db7a] + NonlinearSolveFirstOrder v2.0.0 [9a2c21bd] + NonlinearSolveQuasiNewton v1.12.0 [26075421] + NonlinearSolveSpectralMethods v1.6.0 ⌅ [429524aa] + Optim v1.13.3 [bac558e1] + OrderedCollections v1.8.1 [1dea7af3] + OrdinaryDiffEq v6.108.0 [89bda076] + OrdinaryDiffEqAdamsBashforthMoulton v1.9.0 [6ad6398a] + OrdinaryDiffEqBDF v1.22.0 [bbf590c4] + OrdinaryDiffEqCore v3.17.0 [50262376] + OrdinaryDiffEqDefault v1.13.0 [4302a76b] + OrdinaryDiffEqDifferentiation v2.2.1 [9286f039] + OrdinaryDiffEqExplicitRK v1.9.0 [e0540318] + OrdinaryDiffEqExponentialRK v1.13.0 [becaefa8] + OrdinaryDiffEqExtrapolation v1.16.0 [5960d6e9] + OrdinaryDiffEqFIRK v1.23.0 [101fe9f7] + OrdinaryDiffEqFeagin v1.8.0 [d3585ca7] + OrdinaryDiffEqFunctionMap v1.9.0 [d28bc4f8] + OrdinaryDiffEqHighOrderRK v1.9.0 [9f002381] + OrdinaryDiffEqIMEXMultistep v1.12.0 [521117fe] + OrdinaryDiffEqLinear v1.10.0 [1344f307] + OrdinaryDiffEqLowOrderRK v1.10.0 [b0944070] + OrdinaryDiffEqLowStorageRK v1.12.0 [127b3ac7] + OrdinaryDiffEqNonlinearSolve v1.23.0 [c9986a66] + OrdinaryDiffEqNordsieck v1.9.0 [5dd0a6cf] + OrdinaryDiffEqPDIRK v1.11.0 [5b33eab2] + OrdinaryDiffEqPRK v1.8.0 [04162be5] + OrdinaryDiffEqQPRK v1.8.0 [af6ede74] + OrdinaryDiffEqRKN v1.10.0 [43230ef6] + OrdinaryDiffEqRosenbrock v1.25.0 [2d112036] + OrdinaryDiffEqSDIRK v1.12.0 [669c94d9] + OrdinaryDiffEqSSPRK v1.11.0 [e3e12d00] + OrdinaryDiffEqStabilizedIRK v1.11.0 [358294b1] + OrdinaryDiffEqStabilizedRK v1.8.0 [fa646aed] + OrdinaryDiffEqSymplecticRK v1.11.0 [b1df2697] + OrdinaryDiffEqTsit5 v1.9.0 [79d7bb75] + OrdinaryDiffEqVerner v1.11.0 [90014a1f] + PDMats v0.11.37 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [f517fe37] + Polyester v0.7.19 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [d236fae5] + PreallocationTools v1.1.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v3.48.0 [189a3867] + Reexport v1.2.2 [2792f1a3] + RegistryInstances v0.1.0 [ae029012] + Requires v1.3.1 [295af30f] + Revise v3.13.2 [79098fc4] + Rmath v0.9.0 [7e49a35a] + RuntimeGeneratedFunctions v0.5.17 [94e857df] + SIMDTypes v0.1.0 [0bca4576] + SciMLBase v2.148.0 [19f34311] + SciMLJacobianOperators v0.1.12 [a6db7da4] + SciMLLogging v1.9.1 [c0aeaf25] + SciMLOperators v1.15.1 [431bcebd] + SciMLPublic v1.0.1 [53ae85a6] + SciMLStructures v1.10.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [727e6d20] + SimpleNonlinearSolve v2.11.0 [a2af1166] + SortingAlgorithms v1.2.2 [0a514795] + SparseMatrixColorings v0.4.24 [276daf66] + SpecialFunctions v2.7.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.9.0 [90137ffa] + StaticArrays v1.9.17 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [a2598c62] + StochasticGene v1.7.2 [7792a7ef] + StrideArraysCore v0.5.8 [892a3eda] + StringManipulation v0.4.4 [2efcf032] + SymbolicIndexingInterface v0.3.46 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 [a759f4b9] + TimerOutputs v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 [781d530d] + TruncatedStacktraces v1.4.0 [3a884ed6] + UnPack v1.0.2 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [c2297ded] + ZMQ v1.5.1 ⌅ [68821587] + Arpack_jll v3.5.2+0 [2e619515] + Expat_jll v2.7.3+0 [f5851436] + FFTW_jll v3.3.11+0 [020c3dae] + Git_LFS_jll v3.7.0+0 [f8c6e375] + Git_jll v2.53.0+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aae0fff6] + LSODA_jll v0.1.2+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [856f044c] + MKL_jll v2025.2.0+0 [9bd350c2] + OpenSSH_jll v10.2.1+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [8f1865be] + ZeroMQ_jll v4.3.6+0 [a9144af2] + libsodium_jll v1.0.21+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 v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v8.18.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.12.2 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.5+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+0 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` Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/8f06b0cfa4c514c7b9546756dbae91fcfbc92dc9/build.log` Building IJulia → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/102656c4efc9737f892e1bca7e66ae374c650740/build.log` Installation completed after 73.4s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4799.5 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4394.1 ms ✓ MacroTools 1688.5 ms ✓ InlineStrings 784.1 ms ✓ Reexport 1240.9 ms ✓ ConstructionBase 2067.6 ms ✓ IrrationalConstants 801.5 ms ✓ DataValueInterfaces 884.1 ms ✓ StatsAPI 871.6 ms ✓ LazilyInitializedFields 937.7 ms ✓ VersionParsing 774.3 ms ✓ CommonSolve 1284.5 ms ✓ TranscodingStreams 841.7 ms ✓ LaTeXStrings 1120.9 ms ✓ Statistics 990.4 ms ✓ StaticArraysCore 1286.7 ms ✓ EnzymeCore 796.2 ms ✓ IfElse 886.6 ms ✓ PtrArrays 1037.5 ms ✓ ANSIColoredPrinters 919.9 ms ✓ ManualMemory 940.7 ms ✓ PositiveFactorizations 874.5 ms ✓ DataAPI 917.0 ms ✓ SciMLPublic 3633.6 ms ✓ ExproniconLite 817.0 ms ✓ CommonWorldInvalidations 805.4 ms ✓ FastPower 847.2 ms ✓ InvertedIndices 926.6 ms ✓ InverseFunctions 837.9 ms ✓ CompositionsBase 1150.6 ms ✓ AbstractTrees 842.8 ms ✓ MuladdMacro 1080.5 ms ✓ AbstractFFTs 897.8 ms ✓ EnumX 1013.5 ms ✓ WorkerUtilities 2236.5 ms ✓ FillArrays 905.2 ms ✓ ExprTools 861.6 ms ✓ UnPack 1213.8 ms ✓ ConcreteStructs 1395.8 ms ✓ OrderedCollections 1524.3 ms ✓ FunctionWrappers 1408.6 ms ✓ ADTypes 1117.1 ms ✓ DocStringExtensions 847.8 ms ✓ FastClosures 1673.6 ms ✓ Compiler 801.1 ms ✓ SIMDTypes 797.5 ms ✓ IteratorInterfaceExtensions 1918.8 ms ✓ Crayons 865.5 ms ✓ IOCapture 985.1 ms ✓ DelimitedFiles 15164.8 ms ✓ Krylov 2515.4 ms ✓ GenericSchur 1072.6 ms ✓ NaNMath 1278.3 ms ✓ Requires 1846.5 ms ✓ CpuId 2128.3 ms ✓ PDMats 2433.2 ms ✓ SentinelArrays 1524.1 ms ✓ LoggingExtras 1583.3 ms ✓ CodeTracking 1202.7 ms ✓ Compat 1466.4 ms ✓ Preferences 1814.2 ms ✓ CommonSubexpressions 849.1 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 5892.6 ms ✓ RegistryInstances 1089.7 ms ✓ CodecZlib 1524.3 ms ✓ Statistics → SparseArraysExt 888.5 ms ✓ DiffResults 999.3 ms ✓ AliasTables 1869.7 ms ✓ ThreadingUtilities 994.7 ms ✓ Missings 1072.7 ms ✓ PooledArrays 3284.9 ms ✓ Jieko 1258.6 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1714.9 ms ✓ InverseFunctions → InverseFunctionsTestExt 866.5 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 2110.8 ms ✓ MarkdownAST 4564.4 ms ✓ AbstractFFTs → AbstractFFTsTestExt 1734.7 ms ✓ FillArrays → FillArraysSparseArraysExt 1094.4 ms ✓ FillArrays → FillArraysStatisticsExt 3447.1 ms ✓ TimerOutputs 966.3 ms ✓ RuntimeGeneratedFunctions 1114.6 ms ✓ Parameters 3864.0 ms ✓ DataStructures 849.9 ms ✓ FunctionWrappersWrappers 803.9 ms ✓ ADTypes → ADTypesConstructionBaseExt 1936.1 ms ✓ DifferentiationInterface 798.5 ms ✓ ADTypes → ADTypesEnzymeCoreExt 1407.7 ms ✓ LogExpFunctions 785.6 ms ✓ TableTraits 968.9 ms ✓ Adapt 1740.6 ms ✓ FillArrays → FillArraysPDMatsExt 10321.6 ms ✓ JuliaInterpreter 855.6 ms ✓ Compat → CompatLinearAlgebraExt 1225.7 ms ✓ PrecompileTools 1564.4 ms ✓ JLLWrappers 2372.5 ms ✓ TruncatedStacktraces 2266.1 ms ✓ SciMLLogging 3051.1 ms ✓ Setfield 16723.4 ms ✓ Moshi 5479.4 ms ✓ Accessors 1181.4 ms ✓ SortingAlgorithms 2372.4 ms ✓ QuadGK 1476.8 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 822.3 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1886.2 ms ✓ Tables 1161.6 ms ✓ ArrayInterface 1489.8 ms ✓ Adapt → AdaptSparseArraysExt 1221.1 ms ✓ GPUArraysCore 783.6 ms ✓ EnzymeCore → AdaptExt 18972.6 ms ✓ LoweredCodeUtils 2756.6 ms ✓ ChainRulesCore 2417.7 ms ✓ FilePathsBase 3830.3 ms ✓ StringManipulation 14075.6 ms ✓ StaticArrays 3661.9 ms ✓ RecipesBase 16719.9 ms ✓ Parsers 7862.4 ms ✓ Static 12009.8 ms ✓ SparseMatrixColorings 2295.8 ms ✓ libsodium_jll 2308.6 ms ✓ Rmath_jll 2275.7 ms ✓ OpenSpecFun_jll 5668.0 ms ✓ IntelOpenMP_jll 5611.6 ms ✓ oneTBB_jll 2335.0 ms ✓ Arpack_jll 2297.9 ms ✓ Git_LFS_jll 2312.7 ms ✓ FFTW_jll 2362.0 ms ✓ OpenSSH_jll 2301.5 ms ✓ LSODA_jll 2320.0 ms ✓ Libiconv_jll 2322.9 ms ✓ Expat_jll 2215.8 ms ✓ Accessors → TestExt 2895.5 ms ✓ Accessors → LinearAlgebraExt 4806.7 ms ✓ StatsBase 810.7 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 2142.4 ms ✓ MaybeInplace 1514.8 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 2116.8 ms ✓ SciMLStructures 3119.3 ms ✓ PreallocationTools 856.0 ms ✓ DifferentiationInterface → DifferentiationInterfaceGPUArraysCoreExt 854.4 ms ✓ ArrayInterface → ArrayInterfaceGPUArraysCoreExt 13220.0 ms ✓ Revise 1528.0 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 1359.4 ms ✓ EnzymeCore → EnzymeCoreChainRulesCoreExt 986.1 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 946.5 ms ✓ ADTypes → ADTypesChainRulesCoreExt 992.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceChainRulesCoreExt 3529.0 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 896.1 ms ✓ ArrayInterface → ArrayInterfaceChainRulesCoreExt 3250.4 ms ✓ FilePathsBase → FilePathsBaseTestExt 1321.1 ms ✓ FilePathsBase → FilePathsBaseMmapExt 41767.3 ms ✓ PrettyTables 1853.3 ms ✓ StaticArrays → StaticArraysStatisticsExt 1951.7 ms ✓ StaticArrays → StaticArraysChainRulesCoreExt 1876.7 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 2006.0 ms ✓ FillArrays → FillArraysStaticArraysExt 1862.8 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1852.1 ms ✓ Adapt → AdaptStaticArraysExt 1964.9 ms ✓ Accessors → StaticArraysExt 4130.9 ms ✓ JSON 1347.8 ms ✓ InlineStrings → ParsersExt 1274.6 ms ✓ BitTwiddlingConvenienceFunctions 3062.3 ms ✓ CPUSummary 8400.9 ms ✓ StaticArrayInterface 2036.1 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseMatrixColoringsExt 2174.1 ms ✓ ZeroMQ_jll 1862.7 ms ✓ Rmath 5035.1 ms ✓ SpecialFunctions  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB 10692.8 ms ✓ MKL_jll 1713.2 ms ✓ Arpack 2229.3 ms ✓ Git_jll 4708.1 ms ✓ SciMLOperators 1445.3 ms ✓ PDMats → StatsBaseExt 1263.6 ms ✓ FiniteDiff 3633.9 ms ✓ SymbolicIndexingInterface 1339.2 ms ✓ MaybeInplace → MaybeInplaceSparseArraysExt 38509.0 ms ✓ ExponentialUtilities 4458.0 ms ✓ Revise → DistributedExt 82320.9 ms ✓ DataFrames 1993.6 ms ✓ Conda 2901.2 ms ✓ WeakRefStrings 2040.2 ms ✓ PolyesterWeave 1981.4 ms ✓ StaticArrayInterface → StaticArrayInterfaceStaticArraysExt 1456.4 ms ✓ CloseOpenIntervals 1613.9 ms ✓ LayoutPointers 5853.5 ms ✓ ZMQ 4456.1 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 5111.8 ms ✓ FastGaussQuadrature 2598.9 ms ✓ HypergeometricFunctions 1354.1 ms ✓ DiffRules 7494.5 ms ✓ FFTW 1298.3 ms ✓ Git 1391.9 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1952.1 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 1810.2 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 1464.2 ms ✓ FiniteDiff → FiniteDiffSparseArraysExt 1053.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceFiniteDiffExt 3869.9 ms ✓ SymbolicIndexingInterface → SymbolicIndexingInterfacePrettyTablesExt 8372.4 ms ✓ RecursiveArrayTools 7125.2 ms ✓ ExponentialUtilities → ExponentialUtilitiesStaticArraysExt 26770.7 ms ✓ CSV 2465.7 ms ✓ StrideArraysCore 17258.6 ms ✓ IJulia 3186.6 ms ✓ StatsFuns 7723.9 ms ✓ ForwardDiff 46468.3 ms ✓ Documenter 2381.1 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1749.4 ms ✓ RecursiveArrayTools → RecursiveArrayToolsTablesExt 1765.7 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 2637.1 ms ✓ Polyester 21388.8 ms ✓ IJulia → IJuliaReviseExt 3994.7 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 1510.3 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9757.0 ms ✓ Distributions 2165.7 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1492.6 ms ✓ FastPower → FastPowerForwardDiffExt 1734.4 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 2999.9 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 1825.0 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 30397.0 ms ✓ SciMLBase 2368.6 ms ✓ FastBroadcast 3826.0 ms ✓ Distributions → DistributionsTestExt 3314.9 ms ✓ Distributions → DistributionsChainRulesCoreExt 3737.9 ms ✓ MultivariateStats 2175.3 ms ✓ NLSolversBase 4269.1 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 4348.1 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 3535.6 ms ✓ SciMLBase → SciMLBaseDifferentiationInterfaceExt 4849.2 ms ✓ SciMLBase → SciMLBaseDistributionsExt 2767.8 ms ✓ RecursiveArrayTools → RecursiveArrayToolsFastBroadcastExt 2580.5 ms ✓ LineSearches 20979.8 ms ✓ LinearSolve 8243.6 ms ✓ SciMLJacobianOperators 6677.0 ms ✓ Optim 10081.2 ms ✓ LinearSolve → LinearSolveSparseArraysExt 8207.2 ms ✓ LinearSolve → LinearSolveForwardDiffExt 12872.1 ms ✓ LineSearch 19410.1 ms ✓ NonlinearSolveBase 4844.7 ms ✓ LinearSolve → LinearSolveEnzymeExt 3698.9 ms ✓ LineSearch → LineSearchLineSearchesExt 4711.1 ms ✓ NonlinearSolveBase → NonlinearSolveBaseSparseMatrixColoringsExt 4529.2 ms ✓ NonlinearSolveBase → NonlinearSolveBaseSparseArraysExt 4181.9 ms ✓ NonlinearSolveBase → NonlinearSolveBaseChainRulesCoreExt 5165.2 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLinearSolveExt 3952.4 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLineSearchExt 5136.9 ms ✓ NonlinearSolveBase → NonlinearSolveBaseForwardDiffExt 9513.7 ms ✓ BracketingNonlinearSolve 29438.8 ms ✓ NonlinearSolveQuasiNewton 18656.5 ms ✓ NonlinearSolveSpectralMethods 55980.0 ms ✓ NonlinearSolveFirstOrder 4473.9 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveForwardDiffExt 8422.1 ms ✓ DiffEqBase 6389.2 ms ✓ NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt 4898.4 ms ✓ NonlinearSolveSpectralMethods → NonlinearSolveSpectralMethodsForwardDiffExt 3824.0 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveChainRulesCoreExt 20810.2 ms ✓ SimpleNonlinearSolve 5083.9 ms ✓ DiffEqBase → DiffEqBaseSparseArraysExt 4279.1 ms ✓ DiffEqBase → DiffEqBaseChainRulesCoreExt 4990.6 ms ✓ DiffEqBase → DiffEqBaseForwardDiffExt 7174.6 ms ✓ LSODA 13992.7 ms ✓ OrdinaryDiffEqCore 4741.2 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveChainRulesCoreExt 5539.1 ms ✓ OrdinaryDiffEqCore → OrdinaryDiffEqCoreSparseArraysExt 8396.1 ms ✓ OrdinaryDiffEqStabilizedRK 5835.5 ms ✓ OrdinaryDiffEqFunctionMap 62259.4 ms ✓ OrdinaryDiffEqVerner 6614.2 ms ✓ OrdinaryDiffEqQPRK 7225.8 ms ✓ OrdinaryDiffEqSymplecticRK 9963.2 ms ✓ OrdinaryDiffEqLowOrderRK 7570.6 ms ✓ OrdinaryDiffEqFeagin 9564.4 ms ✓ OrdinaryDiffEqSSPRK 7545.1 ms ✓ OrdinaryDiffEqRKN 7663.2 ms ✓ OrdinaryDiffEqHighOrderRK 6986.9 ms ✓ OrdinaryDiffEqExplicitRK 14836.7 ms ✓ OrdinaryDiffEqTsit5 6940.9 ms ✓ OrdinaryDiffEqPRK 9878.2 ms ✓ OrdinaryDiffEqLowStorageRK 40393.5 ms ✓ NonlinearSolve 10981.0 ms ✓ OrdinaryDiffEqLinear 12777.7 ms ✓ OrdinaryDiffEqDifferentiation 7209.0 ms ✓ OrdinaryDiffEqAdamsBashforthMoulton 6872.7 ms ✓ OrdinaryDiffEqNordsieck 7491.9 ms ✓ OrdinaryDiffEqDifferentiation → OrdinaryDiffEqDifferentiationSparseArraysExt 13834.4 ms ✓ OrdinaryDiffEqExtrapolation 46546.3 ms ✓ OrdinaryDiffEqRosenbrock 15334.1 ms ✓ OrdinaryDiffEqExponentialRK 14719.8 ms ✓ OrdinaryDiffEqNonlinearSolve 13819.5 ms ✓ OrdinaryDiffEqIMEXMultistep 14270.6 ms ✓ OrdinaryDiffEqStabilizedIRK 14307.7 ms ✓ OrdinaryDiffEqPDIRK 11296.8 ms ✓ OrdinaryDiffEqSDIRK 45541.2 ms ✓ OrdinaryDiffEqFIRK 29193.1 ms ✓ OrdinaryDiffEqBDF 65018.9 ms ✓ OrdinaryDiffEqDefault 23757.0 ms ✓ OrdinaryDiffEq 51292.2 ms ✓ StochasticGene 293 dependencies successfully precompiled in 1843 seconds. 40 already precompiled. 1 dependency had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ Precompilation completed after 1861.88s ################################################################################ # Testing # Testing StochasticGene Status `/tmp/jl_14fLSI/Project.toml` [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.123 [e30172f5] Documenter v1.17.0 [7a1cc6ca] FFTW v1.10.0 [7073ff75] IJulia v1.34.4 ⌅ [682c06a0] JSON v0.21.4 [7f56f5a3] LSODA v0.7.5 [6f286f6a] MultivariateStats v0.10.4 ⌅ [429524aa] Optim v1.13.3 [1dea7af3] OrdinaryDiffEq v6.108.0 [295af30f] Revise v3.13.2 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.10 [a2598c62] StochasticGene v1.7.2 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_14fLSI/Manifest.toml` [47edcb42] ADTypes v1.21.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.5.0 [66dad0bd] AliasTables v1.1.3 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.23.0 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [70df07ce] BracketingNonlinearSolve v1.11.0 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.16 [d360d2e6] ChainRulesCore v1.26.0 [fb6a15b2] CloseOpenIntervals v0.1.13 [da1fd8a2] CodeTracking v3.0.0 [944b1d66] CodecZlib v0.7.8 [38540f10] CommonSolve v0.2.6 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [807dbc54] Compiler v0.1.1 [a33af91c] CompositionsBase v0.1.2 [2569d6c7] ConcreteStructs v0.2.3 [8f4d0f93] Conda v1.10.3 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [2b5f629d] DiffEqBase v6.210.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.16 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 [4e289a0a] EnumX v1.0.7 [f151be2c] EnzymeCore v0.8.18 [d4d017d3] ExponentialUtilities v1.30.0 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [7a1cc6ca] FFTW v1.10.0 [7034ab61] FastBroadcast v0.3.5 [9aa1b823] FastClosures v0.3.2 [442a2c76] FastGaussQuadrature v1.1.0 [a4df4552] FastPower v1.3.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [6a86dc24] FiniteDiff v2.29.0 [f6369f11] ForwardDiff v1.3.2 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [46192b85] GPUArraysCore v0.2.0 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v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [4536629a] OpenBLAS_jll v0.3.30+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.5+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Warmup Sampling Histogram count: 6774.0 Warmup ┌ Info: Updated proposal covariance (scaled) │ proposalcv = │ 3×3 Matrix{Float64}: │ 0.131522 0.270332 0.135642 │ 0.270332 2.58036 2.26468 └ 0.135642 2.26468 2.1288 Sampling Sampling Warmup Sampling Warmup Sampling 0.21175950486295314 initial: [0.01, 0.01, 0.1, 0.15, 0.1, 1.0, 50.0, 5.0, 50.0, 5.0] Warmup Sampling 454 946 No rate file, set rate to prior Warmup Sampling ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 1168 running 1 of 1 signal (10): User defined signal 1 _mapreduce at ./reduce.jl:440 [inlined] _mapreduce_dim at ./reducedim.jl:338 [inlined] #mapreduce#726 at ./reducedim.jl:330 [inlined] mapreduce at ./reducedim.jl:330 [inlined] #_sum#736 at ./reducedim.jl:988 [inlined] _sum at ./reducedim.jl:988 [inlined] #_sum#735 at ./reducedim.jl:987 [inlined] _sum at ./reducedim.jl:987 [inlined] #sum#733 at ./reducedim.jl:983 [inlined] sum at ./reducedim.jl:983 [inlined] forward at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:973 forward at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:1059 [inlined] _ll_hmm at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:1684 unknown function (ip: 0x76ecd991e435) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 ll_hmm at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:1862 unknown function (ip: 0x76ecd9918eac) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 ll_hmm_trace at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/likelihoods.jl:530 loglikelihood at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/likelihoods.jl:535 [inlined] mhstep at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:584 unknown function (ip: 0x76ecd9930a9a) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 sample at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:478 sample at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:468 unknown function (ip: 0x76ecd9922a01) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 metropolis_hastings at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:322 #run_chains##0 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/macros.jl:43 unknown function (ip: 0x76ecd990e7a1) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] jl_f_invokelatest at /source/src/builtins.c:910 #local_remotecall_thunk##0 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:425 [inlined] run_work_thunk at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:70 unknown function (ip: 0x76ecd990e574) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 run_work_thunk_remotevalue at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:79 #schedule_call##2 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:88 unknown function (ip: 0x76ecd990dd98) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== Warmup ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== 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:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000072eaf54ed780 Total snapshots: 452. Utilization: 0% ╎452 @Base/task.jl:1168 wait_forever() 451╎ 452 @Base/task.jl:1246 wait() Sampling┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000076ecd81ce680 Total snapshots: 665. Utilization: 100% ╎665 @Distributed/…essages.jl:88 (::Distributed.var"#schedule_call##2#sched… ╎ 665 @Distributed/…ssages.jl:79 run_work_thunk_remotevalue(rv::Distributed… ╎ 665 @Distributed/…ssages.jl:70 run_work_thunk(thunk::Distributed.var"#lo… ╎ 665 @Distributed/…ecall.jl:425 #local_remotecall_thunk##0 ╎ 665 @Distributed/…acros.jl:43 (::StochasticGene.var"#run_chains##0#run… ╎ 665 @StochasticGene/…s.jl:322 metropolis_hastings(data::TraceData{Str… ╎ ╎ 665 @StochasticGene/…s.jl:468 sample(logpredictions::Vector{Float64}… ╎ ╎ 665 @StochasticGene/….jl:478 sample(logpredictions::Vector{Float64}… ╎ ╎ 665 @StochasticGene/….jl:584 mhstep(logpredictions::Vector{Float64… ╎ ╎ 665 @StochasticGene/….jl:535 loglikelihood ╎ ╎ 665 @StochasticGene/…jl:530 ll_hmm_trace(param::Vector{Float64},… ╎ ╎ ╎ 3 @StochasticGene/…l:1860 ll_hmm(r::Tuple{Vector{Vector{Float… ╎ ╎ ╎ 3 @StochasticGene/…l:457 make_ap ╎ ╎ ╎ 3 @StochasticGene/…l:79 kolmogorov_forward ╎ ╎ ╎ 3 @StochasticGene/…l:81 kolmogorov_forward(Q::LinearAlgebr… ╎ ╎ ╎ 3 @DiffEqBase/…e.jl:575 kwcall(::@NamedTuple{save_everyst… ╎ ╎ ╎ ╎ 3 @DiffEqBase/…e.jl:587 solve(prob::SciMLBase.ODEProblem… ╎ ╎ ╎ ╎ 3 @DiffEqBase/….jl:603 solve_up ╎ ╎ ╎ ╎ 2 @DiffEqBase/….jl:624 solve_up(prob::SciMLBase.ODEPro… ╎ ╎ ╎ ╎ 2 @DiffEqBase/….jl:665 get_concrete_problem ╎ ╎ ╎ ╎ 1 @DiffEqBase/…jl:673 get_concrete_problem(prob::Sci… ╎ ╎ ╎ ╎ ╎ 1 @SciMLBase/….jl:164 get_concrete_u0(prob::SciMLBa… ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:897 materialize ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:922 copy ╎ ╎ ╎ ╎ ╎ 1 @Base/…cast.jl:950 copyto! ╎ ╎ ╎ ╎ ╎ 1 @Base/…ast.jl:997 copyto! ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…oop.jl:77 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:998 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:615 getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:619 _getindex ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:674 _broadcast_getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:699 _getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…st.jl:668 _broadcast_getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…al.jl:772 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ay.jl:963 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1026 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @DiffEqBase/…jl:687 get_concrete_problem(prob::Sci… ╎ ╎ ╎ ╎ 1 @DiffEqBase/….jl:630 solve_up(prob::SciMLBase.ODEPro… ╎ ╎ ╎ ╎ 1 @DiffEqBase/….jl:137 kwcall(::@NamedTuple{save_ever… ╎ ╎ ╎ ╎ 1 @DiffEqBase/…jl:172 #solve_call#22 ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:1 __solve ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:9 #__solve#58 ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:19 __init ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:19 __init ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:37 #__init#59 ╎ ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:47 _ode_init ╎ ╎ ╎ ╎ ╎ ╎ 1 @OrdinaryDiffEqCore/…:778 _ode_init(prob::S… ╎ ╎ ╎ ╎ ╎ ╎ 1 @RecursiveArrayTools/…:251 copyat_or_push! 1╎ ╎ ╎ ╎ ╎ ╎ 1 @RecursiveArrayTools/…:27 recursivecopy(a… ╎ ╎ ╎ 661 @StochasticGene/…l:1862 ll_hmm(r::Tuple{Vector{Vector{Float… 5╎ ╎ ╎ 309 @StochasticGene/…l:1683 _ll_hmm(noiseparams::Vector{Vector… 1╎ ╎ ╎ 1 @Base/…sentials.jl:0 set_b(trace::Vector{Float64}, d::Vec… 4╎ ╎ ╎ 8 @StochasticGene/…l:0 set_b(trace::Vector{Float64}, d::Vec… 4╎ ╎ ╎ 4 @Base/…sentials.jl:0 iterate ╎ ╎ ╎ 4 @StochasticGene/…l:690 set_b(trace::Vector{Float64}, d::V… ╎ ╎ ╎ 4 @Base/boot.jl:718 Array ╎ ╎ ╎ 4 @Base/boot.jl:671 new_as_memoryref 4╎ ╎ ╎ ╎ 4 @Base/boot.jl:654 GenericMemory 136╎ ╎ ╎ 282 @StochasticGene/…l:693 set_b(trace::Vector{Float64}, d::V… 1╎ ╎ ╎ 1 @Base/array.jl:0 setindex! 4╎ ╎ ╎ 4 @Base/array.jl:1030 setindex! ╎ ╎ ╎ 10 @Base/array.jl:1031 setindex! ╎ ╎ ╎ 3 @Base/array.jl:1036 _setindex! ╎ ╎ ╎ ╎ 3 @Base/…entials.jl:385 checkbounds ╎ ╎ ╎ ╎ 3 @Base/…tarray.jl:684 checkbounds ╎ ╎ ╎ ╎ 3 @Base/…tarray.jl:724 checkbounds_indices ╎ ╎ ╎ ╎ 3 @Base/…tarray.jl:753 checkindex 2╎ ╎ ╎ ╎ 3 @Base/int.jl:559 < 7╎ ╎ ╎ 7 @Base/array.jl:1037 _setindex! 8╎ ╎ ╎ 8 @Base/…entials.jl:1027 getindex 4╎ ╎ ╎ 123 @Distributions/…l:644 pdf(d::Distributions.Normal{Float6… ╎ ╎ ╎ 7 @StatsFuns/…orm.jl:15 normpdf ╎ ╎ ╎ ╎ 7 @Base/number.jl:44 iszero 7╎ ╎ ╎ ╎ 7 @Base/float.jl:621 == ╎ ╎ ╎ 12 @StatsFuns/…orm.jl:23 normpdf ╎ ╎ ╎ ╎ 12 @StatsFuns/…rm.jl:10 zval 1╎ ╎ ╎ ╎ 1 @Base/float.jl:493 - 11╎ ╎ ╎ ╎ 11 @Base/float.jl:495 / 17╎ ╎ ╎ 100 @StatsFuns/…orm.jl:25 normpdf 13╎ ╎ ╎ ╎ 13 @Base/float.jl:495 / 6╎ ╎ ╎ ╎ 70 @StatsFuns/…rm.jl:13 normpdf ╎ ╎ ╎ ╎ 5 @Base/…motion.jl:436 / 5╎ ╎ ╎ ╎ 5 @Base/float.jl:495 / 4╎ ╎ ╎ ╎ 59 @Base/…al/exp.jl:329 exp(x::Float64) ╎ ╎ ╎ ╎ 1 @Base/…al/exp.jl:209 exp_impl 1╎ ╎ ╎ ╎ 1 @Base/float.jl:497 muladd ╎ ╎ ╎ ╎ 1 @Base/…al/exp.jl:211 exp_impl 1╎ ╎ ╎ ╎ 1 @Base/float.jl:493 - ╎ ╎ ╎ ╎ 4 @Base/…al/exp.jl:213 exp_impl 4╎ ╎ ╎ ╎ 4 @Base/float.jl:497 muladd ╎ ╎ ╎ ╎ 2 @Base/…al/exp.jl:214 exp_impl ╎ ╎ ╎ ╎ 2 @Base/int.jl:580 >> 2╎ ╎ ╎ ╎ 2 @Base/int.jl:573 >> ╎ ╎ ╎ ╎ 20 @Base/…al/exp.jl:215 exp_impl ╎ ╎ ╎ ╎ 3 @Base/…al/exp.jl:179 table_unpack ╎ ╎ ╎ ╎ 3 @Base/int.jl:1058 & 3╎ ╎ ╎ ╎ ╎ 3 @Base/int.jl:393 & 11╎ ╎ ╎ ╎ 11 @Base/…al/exp.jl:180 table_unpack ╎ ╎ ╎ ╎ 6 @Base/…al/exp.jl:182 table_unpack 3╎ ╎ ╎ ╎ 3 @Base/…tials.jl:779 reinterpret ╎ ╎ ╎ ╎ 2 @Base/int.jl:580 >> 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:574 >> 1╎ ╎ ╎ ╎ 1 @Base/int.jl:418 | ╎ ╎ ╎ ╎ 18 @Base/…al/exp.jl:216 exp_impl 2╎ ╎ ╎ ╎ 2 @Base/float.jl:492 + 6╎ ╎ ╎ ╎ 6 @Base/float.jl:497 muladd ╎ ╎ ╎ ╎ 10 @Base/…al/exp.jl:78 expm1b_kernel ╎ ╎ ╎ ╎ 10 @Base/math.jl:96 evalpoly ╎ ╎ ╎ ╎ ╎ 10 @Base/math.jl:97 macro expansion 10╎ ╎ ╎ ╎ ╎ 10 @Base/float.jl:497 muladd ╎ ╎ ╎ ╎ 3 @Base/…al/exp.jl:218 exp_impl 3╎ ╎ ╎ ╎ 3 @Base/float.jl:698 abs ╎ ╎ ╎ ╎ 6 @Base/…al/exp.jl:230 exp_impl 5╎ ╎ ╎ ╎ 5 @Base/…tials.jl:1213 + 1╎ ╎ ╎ ╎ 1 @Base/…tials.jl:779 reinterpret ╎ ╎ ╎ 6 @StochasticGene/…l:694 set_b(trace::Vector{Float64}, d::V… ╎ ╎ ╎ 6 @Base/range.jl:925 iterate 6╎ ╎ ╎ 6 @Base/…omotion.jl:637 == ╎ ╎ ╎ 3 @StochasticGene/…l:695 set_b(trace::Vector{Float64}, d::V… ╎ ╎ ╎ 1 @Base/iterators.jl:197 iterate ╎ ╎ ╎ 1 @Base/…ctarray.jl:1241 iterate 1╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1248 _iterate_abstractarray ╎ ╎ ╎ 2 @Base/iterators.jl:199 iterate 2╎ ╎ ╎ 2 @Base/…entials.jl:1213 + ╎ ╎ ╎ 342 @StochasticGene/…l:1684 _ll_hmm(noiseparams::Vector{Vector… 1╎ ╎ ╎ 342 @StochasticGene/…l:1059 forward 1╎ ╎ ╎ 1 @Base/array.jl:0 forward(a::Matrix{Float64}, b::Matrix{F… 1╎ ╎ ╎ 1 @Base/reduce.jl:0 forward(a::Matrix{Float64}, b::Matrix{… 4╎ ╎ ╎ 4 @StochasticGene/…l:0 forward(a::Matrix{Float64}, b::Matr… ╎ ╎ ╎ 6 @StochasticGene/…l:962 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 6 @Base/array.jl:621 zeros ╎ ╎ ╎ ╎ 6 @Base/array.jl:623 zeros ╎ ╎ ╎ ╎ 3 @Base/array.jl:626 zeros ╎ ╎ ╎ ╎ 3 @Base/boot.jl:728 Array ╎ ╎ ╎ ╎ 3 @Base/boot.jl:718 Array ╎ ╎ ╎ ╎ 3 @Base/boot.jl:671 new_as_memoryref 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:654 GenericMemory ╎ ╎ ╎ ╎ 3 @Base/array.jl:627 zeros ╎ ╎ ╎ ╎ 3 @Base/array.jl:359 fill! ╎ ╎ ╎ ╎ 3 @Base/array.jl:363 _fill! ╎ ╎ ╎ ╎ 3 @Base/array.jl:1020 setindex! 3╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:1025 _setindex! ╎ ╎ ╎ 5 @StochasticGene/…l:963 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 5 @Base/boot.jl:714 Array 5╎ ╎ ╎ ╎ 5 @Base/boot.jl:654 GenericMemory 1╎ ╎ ╎ 1 @StochasticGene/…l:969 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 135 @StochasticGene/…l:970 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 135 @StochasticGene/…:932 forward_inner_operation! 1╎ ╎ ╎ ╎ 2 @Base/array.jl:962 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds ╎ ╎ ╎ ╎ 66 @Base/array.jl:963 getindex 11╎ ╎ ╎ ╎ 11 @Base/…ntials.jl:0 getindex ╎ ╎ ╎ ╎ 15 @Base/…ntials.jl:1026 getindex 13╎ ╎ ╎ ╎ 15 @Base/…ntials.jl:385 checkbounds 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:381 checkbounds 40╎ ╎ ╎ ╎ 40 @Base/…ntials.jl:1027 getindex ╎ ╎ ╎ ╎ 7 @Base/array.jl:1031 setindex! 7╎ ╎ ╎ ╎ 7 @Base/array.jl:1037 _setindex! 6╎ ╎ ╎ ╎ 6 @Base/…ntials.jl:0 getindex 31╎ ╎ ╎ ╎ 31 @Base/float.jl:492 + ╎ ╎ ╎ ╎ 23 @Base/…rators.jl:650 * 23╎ ╎ ╎ ╎ 23 @Base/float.jl:494 * 5╎ ╎ ╎ 32 @StochasticGene/…l:971 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 27 @Base/range.jl:925 iterate 27╎ ╎ ╎ ╎ 27 @Base/…omotion.jl:637 == ╎ ╎ ╎ 5 @StochasticGene/…l:972 forward(a::Matrix{Float64}, b::Ma… 5╎ ╎ ╎ 5 @Base/range.jl:925 iterate ╎ ╎ ╎ 59 @StochasticGene/…l:973 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 49 @Base/…ctarray.jl:1356 getindex ╎ ╎ ╎ ╎ 49 @Base/…nsional.jl:984 _getindex ╎ ╎ ╎ ╎ 27 @Base/…sional.jl:996 _unsafe_getindex ╎ ╎ ╎ ╎ 27 @Base/…tarray.jl:821 similar ╎ ╎ ╎ ╎ 27 @Base/…tarray.jl:832 similar ╎ ╎ ╎ ╎ 27 @Base/array.jl:407 similar ╎ ╎ ╎ ╎ ╎ 27 @Base/boot.jl:727 Array ╎ ╎ ╎ ╎ ╎ 9 @Base/boot.jl:714 Array 9╎ ╎ ╎ ╎ ╎ 9 @Base/boot.jl:654 GenericMemory 18╎ ╎ ╎ ╎ ╎ 18 @Base/boot.jl:715 Array ╎ ╎ ╎ ╎ 22 @Base/…sional.jl:998 _unsafe_getindex ╎ ╎ ╎ ╎ 22 @Base/…sional.jl:1007 _unsafe_getindex! ╎ ╎ ╎ ╎ 18 @Base/…tesian.jl:65 macro expansion ╎ ╎ ╎ ╎ 18 @Base/…ional.jl:1009 macro expansion ╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:962 getindex 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:963 getindex 4╎ ╎ ╎ ╎ ╎ 4 @Base/…ials.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ 10 @Base/array.jl:1020 setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:0 _setindex! 8╎ ╎ ╎ ╎ ╎ 8 @Base/array.jl:1025 _setindex! 2╎ ╎ ╎ ╎ ╎ 2 @Base/…ials.jl:0 getindex ╎ ╎ ╎ ╎ 4 @Base/…tesian.jl:67 macro expansion ╎ ╎ ╎ ╎ 4 @Base/…dices.jl:399 iterate ╎ ╎ ╎ ╎ ╎ 4 @Base/range.jl:925 iterate 4╎ ╎ ╎ ╎ ╎ 4 @Base/…tion.jl:637 == ╎ ╎ ╎ 5 @Base/array.jl:1020 setindex! 5╎ ╎ ╎ ╎ 5 @Base/array.jl:1025 _setindex! ╎ ╎ ╎ 5 @Base/…ducedim.jl:983 sum ╎ ╎ ╎ ╎ 5 @Base/…ducedim.jl:983 #sum#733 ╎ ╎ ╎ ╎ 5 @Base/…ucedim.jl:987 _sum ╎ ╎ ╎ ╎ 5 @Base/…ucedim.jl:987 #_sum#735 ╎ ╎ ╎ ╎ 5 @Base/…ucedim.jl:988 _sum ╎ ╎ ╎ ╎ 5 @Base/…cedim.jl:988 #_sum#736 ╎ ╎ ╎ ╎ ╎ 5 @Base/…cedim.jl:330 mapreduce ╎ ╎ ╎ ╎ ╎ 5 @Base/…edim.jl:330 #mapreduce#726 ╎ ╎ ╎ ╎ ╎ 5 @Base/…edim.jl:338 _mapreduce_dim ╎ ╎ ╎ ╎ ╎ 1 @Base/…duce.jl:437 _mapreduce 1╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:1027 getindex 3╎ ╎ ╎ ╎ ╎ 4 @Base/…duce.jl:440 _mapreduce 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ 92 @StochasticGene/…l:974 forward(a::Matrix{Float64}, b::Ma… ╎ ╎ ╎ 43 @Base/…ctarray.jl:1356 getindex ╎ ╎ ╎ ╎ 43 @Base/…nsional.jl:984 _getindex ╎ ╎ ╎ ╎ 26 @Base/…sional.jl:996 _unsafe_getindex ╎ ╎ ╎ ╎ 26 @Base/…tarray.jl:821 similar ╎ ╎ ╎ ╎ 26 @Base/…tarray.jl:832 similar ╎ ╎ ╎ ╎ 26 @Base/array.jl:407 similar ╎ ╎ ╎ ╎ ╎ 26 @Base/boot.jl:727 Array ╎ ╎ ╎ ╎ ╎ 10 @Base/boot.jl:714 Array 10╎ ╎ ╎ ╎ ╎ 10 @Base/boot.jl:654 GenericMemory 16╎ ╎ ╎ ╎ ╎ 16 @Base/boot.jl:715 Array ╎ ╎ ╎ ╎ 17 @Base/…sional.jl:998 _unsafe_getindex ╎ ╎ ╎ ╎ 17 @Base/…sional.jl:1007 _unsafe_getindex! ╎ ╎ ╎ ╎ 13 @Base/…tesian.jl:65 macro expansion ╎ ╎ ╎ ╎ 13 @Base/…ional.jl:1009 macro expansion ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:962 getindex 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:385 checkbounds ╎ ╎ ╎ ╎ ╎ 4 @Base/array.jl:963 getindex 4╎ ╎ ╎ ╎ ╎ 4 @Base/…ials.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ 8 @Base/array.jl:1020 setindex! 8╎ ╎ ╎ ╎ ╎ 8 @Base/array.jl:1025 _setindex! ╎ ╎ ╎ ╎ 4 @Base/…tesian.jl:67 macro expansion ╎ ╎ ╎ ╎ 4 @Base/…dices.jl:399 iterate ╎ ╎ ╎ ╎ ╎ 4 @Base/range.jl:925 iterate 4╎ ╎ ╎ ╎ ╎ 4 @Base/…tion.jl:637 == ╎ ╎ ╎ 27 @Base/…ctarray.jl:1457 setindex! 6╎ ╎ ╎ ╎ 27 @Base/…sional.jl:1036 _setindex! ╎ ╎ ╎ ╎ 18 @Base/…sional.jl:1048 _unsafe_setindex!(::IndexLinear… 1╎ ╎ ╎ ╎ 1 @Base/…tesian.jl:0 macro expansion ╎ ╎ ╎ ╎ 11 @Base/…tesian.jl:65 macro expansion 2╎ ╎ ╎ ╎ 11 @Base/…ional.jl:1050 macro expansion ╎ ╎ ╎ ╎ 1 @Base/array.jl:1031 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1037 _setindex! ╎ ╎ ╎ ╎ 5 @Base/…tials.jl:1026 getindex 5╎ ╎ ╎ ╎ ╎ 5 @Base/…tials.jl:385 checkbounds 3╎ ╎ ╎ ╎ 3 @Base/…tials.jl:1027 getindex 6╎ ╎ ╎ ╎ 6 @Base/…tesian.jl:67 macro expansion 3╎ ╎ ╎ ╎ 3 @Base/…sional.jl:1065 _unsafe_setindex!(::IndexLinear… ╎ ╎ ╎ 22 @Base/…raymath.jl:57 * ╎ ╎ ╎ ╎ 22 @Base/…raymath.jl:28 _broadcast_preserving_zero_d ╎ ╎ ╎ ╎ 22 @Base/…tarray.jl:3386 map ╎ ╎ ╎ ╎ 22 @Base/array.jl:763 collect_similar ╎ ╎ ╎ ╎ 1 @Base/array.jl:848 _collect 1╎ ╎ ╎ ╎ 1 @Base/…erator.jl:46 iterate ╎ ╎ ╎ ╎ 9 @Base/array.jl:853 _collect ╎ ╎ ╎ ╎ 9 @Base/array.jl:695 _similar_for ╎ ╎ ╎ ╎ ╎ 9 @Base/…array.jl:832 similar ╎ ╎ ╎ ╎ ╎ 9 @Base/array.jl:407 similar ╎ ╎ ╎ ╎ ╎ 9 @Base/boot.jl:727 Array ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:714 Array 6╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:654 GenericMemory 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:715 Array ╎ ╎ ╎ ╎ 12 @Base/array.jl:858 _collect ╎ ╎ ╎ ╎ 12 @Base/array.jl:864 collect_to_with_first! ╎ ╎ ╎ ╎ ╎ 11 @Base/array.jl:886 collect_to! ╎ ╎ ╎ ╎ ╎ 11 @Base/…rator.jl:45 iterate ╎ ╎ ╎ ╎ ╎ 11 @Base/…rray.jl:1241 iterate ╎ ╎ ╎ ╎ ╎ 11 @Base/…ray.jl:1249 _iterate_abstractarray 7╎ ╎ ╎ ╎ ╎ 7 @Base/…als.jl:1213 + 4╎ ╎ ╎ ╎ ╎ 4 @Base/…als.jl:1027 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:890 collect_to! ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1020 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1025 _setindex! ╎ ╎ ╎ 10 @StochasticGene/…l:1685 _ll_hmm(noiseparams::Vector{Vector… ╎ ╎ ╎ 8 @Base/broadcast.jl:897 materialize ╎ ╎ ╎ 8 @Base/broadcast.jl:922 copy ╎ ╎ ╎ 8 @Base/…oadcast.jl:950 copyto! ╎ ╎ ╎ ╎ 8 @Base/…oadcast.jl:997 copyto! ╎ ╎ ╎ ╎ 8 @Base/simdloop.jl:77 macro expansion ╎ ╎ ╎ ╎ 8 @Base/…adcast.jl:998 macro expansion ╎ ╎ ╎ ╎ 8 @Base/…adcast.jl:615 getindex ╎ ╎ ╎ ╎ 8 @Base/…dcast.jl:619 _getindex ╎ ╎ ╎ ╎ ╎ 8 @Base/…dcast.jl:675 _broadcast_getindex ╎ ╎ ╎ ╎ ╎ 8 @Base/…cast.jl:702 _broadcast_getindex_evalf 1╎ ╎ ╎ ╎ ╎ 8 @Base/…/log.jl:261 log(x::Float64) 1╎ ╎ ╎ ╎ ╎ 1 @Base/…/log.jl:277 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…/log.jl:287 _log 1╎ ╎ ╎ ╎ ╎ 1 @Base/…oat.jl:493 - ╎ ╎ ╎ ╎ ╎ 5 @Base/…/log.jl:289 _log ╎ ╎ ╎ ╎ ╎ 1 @Base/…log.jl:159 log_proc1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…oat.jl:417 unsafe_trunc ╎ ╎ ╎ ╎ ╎ 1 @Base/…log.jl:163 log_proc1 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…oat.jl:492 + ╎ ╎ ╎ ╎ ╎ 3 @Base/…log.jl:186 log_proc1 3╎ ╎ ╎ ╎ ╎ ╎ 3 @Base/…ncs.jl:360 fma ╎ ╎ ╎ 2 @Base/reducedim.jl:983 sum ╎ ╎ ╎ 2 @Base/reducedim.jl:983 #sum#733 ╎ ╎ ╎ 2 @Base/…ducedim.jl:987 _sum ╎ ╎ ╎ ╎ 2 @Base/…ducedim.jl:987 #_sum#735 ╎ ╎ ╎ ╎ 2 @Base/…ucedim.jl:988 _sum ╎ ╎ ╎ ╎ 2 @Base/…ucedim.jl:988 #_sum#736 ╎ ╎ ╎ ╎ 2 @Base/…ucedim.jl:330 mapreduce ╎ ╎ ╎ ╎ 2 @Base/…cedim.jl:330 #mapreduce#726 ╎ ╎ ╎ ╎ ╎ 2 @Base/…cedim.jl:338 _mapreduce_dim ╎ ╎ ╎ ╎ ╎ 2 @Base/…duce.jl:446 _mapreduce ╎ ╎ ╎ ╎ ╎ 2 @Base/…duce.jl:275 mapreduce_impl ╎ ╎ ╎ ╎ ╎ 2 @Base/…duce.jl:261 mapreduce_impl(f::typeof(id… ╎ ╎ ╎ ╎ ╎ 2 @Base/…loop.jl:77 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…uce.jl:262 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1026 getindex 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:385 checkbounds 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ls.jl:1027 getindex ╎ ╎ ╎ 1 @StochasticGene/…l:1867 ll_hmm(r::Tuple{Vector{Vector{Float… 1╎ ╎ ╎ 1 @StochasticGene/…l:1815 ll_hierarchy(pindividual::Vector{S… [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 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:1246 wait_forever at ./task.jl:1168 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) Allocations: 31297534 (Pool: 31296382; Big: 1152); GC: 35 [1168] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/StochasticGene/586ID/test/runtests.jl:11 set_b at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:693 unknown function (ip: 0x76ecd9db4036) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 _ll_hmm at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:1683 unknown function (ip: 0x76ecd991e435) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 ll_hmm at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/hmm.jl:1862 unknown function (ip: 0x76ecd9918eac) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 ll_hmm_trace at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/likelihoods.jl:530 loglikelihood at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/likelihoods.jl:535 [inlined] mhstep at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:584 unknown function (ip: 0x76ecd9930a9a) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 sample at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:478 sample at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:468 unknown function (ip: 0x76ecd9922a01) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 metropolis_hastings at /home/pkgeval/.julia/packages/StochasticGene/586ID/src/metropolis_hastings.jl:322 #run_chains##0 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/macros.jl:43 unknown function (ip: 0x76ecd990e7a1) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] jl_f_invokelatest at /source/src/builtins.c:910 #local_remotecall_thunk##0 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/remotecall.jl:425 [inlined] run_work_thunk at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:70 unknown function (ip: 0x76ecd990e574) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 run_work_thunk_remotevalue at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:79 #schedule_call##2 at /source/usr/share/julia/stdlib/v1.14/Distributed/src/process_messages.jl:88 unknown function (ip: 0x76ecd990dd98) at (unknown file) _jl_invoke at /source/src/gf.c:4113 [inlined] ijl_apply_generic at /source/src/gf.c:4339 jl_apply at /source/src/julia.h:2300 [inlined] start_task at /source/src/task.c:1275 unknown function (ip: (nil)) at (unknown file) Allocations: 3916079913 (Pool: 3916078555; Big: 1358); GC: 3529 PkgEval terminated after 2723.46s: test duration exceeded the time limit