Package evaluation of StochasticGene on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T10:44:06.404


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# Set-up
#


Set-up completed after 0.25s


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# Installation
#

Installing StochasticGene...
   Resolving package versions...
   Installed Conda ── v1.10.2
   Installed IJulia ─ v1.27.0
    Updating `~/.julia/environments/v1.13/Project.toml`
  [a2598c62] + StochasticGene v1.4.0
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [47edcb42] + ADTypes v1.14.0
  [621f4979] + AbstractFFTs v1.5.0
  [7d9f7c33] + Accessors v0.1.42
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [7d9fca2a] + Arpack v0.5.4
  [4fba245c] + ArrayInterface v7.18.0
  [4c555306] + ArrayLayouts v1.11.1
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.6
  [70df07ce] + BracketingNonlinearSolve v1.2.0
  [2a0fbf3d] + CPUSummary v0.2.6
  [336ed68f] + CSV v0.10.15
  [d360d2e6] + ChainRulesCore v1.25.1
  [fb6a15b2] + CloseOpenIntervals v0.1.13
  [da1fd8a2] + CodeTracking v1.3.9
  [944b1d66] + CodecZlib v0.7.8
  [38540f10] + CommonSolve v0.2.4
  [bbf7d656] + CommonSubexpressions v0.3.1
  [f70d9fcc] + CommonWorldInvalidations v1.0.0
  [34da2185] + Compat v4.16.0
  [a33af91c] + CompositionsBase v0.1.2
  [2569d6c7] + ConcreteStructs v0.2.3
  [8f4d0f93] + Conda v1.10.2
  [187b0558] + ConstructionBase v1.5.8
  [adafc99b] + CpuId v0.3.1
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.7.0
  [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [2b5f629d] + DiffEqBase v6.170.1
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [a0c0ee7d] + DifferentiationInterface v0.6.52
  [31c24e10] + Distributions v0.25.119
  [ffbed154] + DocStringExtensions v0.9.4
  [4e289a0a] + EnumX v1.0.5
  [f151be2c] + EnzymeCore v0.8.8
  [d4d017d3] + ExponentialUtilities v1.27.0
  [e2ba6199] + ExprTools v0.1.10
  [55351af7] + ExproniconLite v0.10.14
  [7a1cc6ca] + FFTW v1.8.1
  [7034ab61] + FastBroadcast v0.3.5
  [9aa1b823] + FastClosures v0.3.2
  [442a2c76] + FastGaussQuadrature v1.0.2
  [a4df4552] + FastPower v1.1.2
  [48062228] + FilePathsBase v0.9.24
  [1a297f60] + FillArrays v1.13.0
  [6a86dc24] + FiniteDiff v2.27.0
⌅ [f6369f11] + ForwardDiff v0.10.38
  [069b7b12] + FunctionWrappers v1.1.3
  [77dc65aa] + FunctionWrappersWrappers v0.1.3
  [46192b85] + GPUArraysCore v0.2.0
  [c145ed77] + GenericSchur v0.5.5
  [34004b35] + HypergeometricFunctions v0.3.28
  [7073ff75] + IJulia v1.27.0
  [615f187c] + IfElse v0.1.1
  [842dd82b] + InlineStrings v1.4.3
  [3587e190] + InverseFunctions v0.1.17
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.4
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [682c06a0] + JSON v0.21.4
  [ae98c720] + Jieko v0.2.1
  [aa1ae85d] + JuliaInterpreter v0.10.1
  [ba0b0d4f] + Krylov v0.10.0
  [7f56f5a3] + LSODA v0.7.5
  [b964fa9f] + LaTeXStrings v1.4.0
  [10f19ff3] + LayoutPointers v0.1.17
  [5078a376] + LazyArrays v2.6.1
  [87fe0de2] + LineSearch v0.1.4
  [d3d80556] + LineSearches v7.3.0
  [7ed4a6bd] + LinearSolve v3.9.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [6f1432cf] + LoweredCodeUtils v3.3.0
  [1914dd2f] + MacroTools v0.5.16
  [d125e4d3] + ManualMemory v0.1.8
  [bb5d69b7] + MaybeInplace v0.1.4
  [739be429] + MbedTLS v1.1.9
  [e1d29d7a] + Missings v1.2.0
  [2e0e35c7] + Moshi v0.3.5
  [46d2c3a1] + MuladdMacro v0.2.4
  [6f286f6a] + MultivariateStats v0.10.3
  [d41bc354] + NLSolversBase v7.9.1
  [77ba4419] + NaNMath v1.1.3
  [8913a72c] + NonlinearSolve v4.8.0
  [be0214bd] + NonlinearSolveBase v1.6.0
  [5959db7a] + NonlinearSolveFirstOrder v1.4.0
  [9a2c21bd] + NonlinearSolveQuasiNewton v1.3.0
  [26075421] + NonlinearSolveSpectralMethods v1.2.0
  [429524aa] + Optim v1.12.0
  [bac558e1] + OrderedCollections v1.8.0
  [1dea7af3] + OrdinaryDiffEq v6.95.1
  [89bda076] + OrdinaryDiffEqAdamsBashforthMoulton v1.2.0
  [6ad6398a] + OrdinaryDiffEqBDF v1.5.0
  [bbf590c4] + OrdinaryDiffEqCore v1.23.0
  [50262376] + OrdinaryDiffEqDefault v1.3.0
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  [e0540318] + OrdinaryDiffEqExponentialRK v1.4.0
  [becaefa8] + OrdinaryDiffEqExtrapolation v1.5.0
  [5960d6e9] + OrdinaryDiffEqFIRK v1.10.0
  [101fe9f7] + OrdinaryDiffEqFeagin v1.1.0
  [d3585ca7] + OrdinaryDiffEqFunctionMap v1.1.1
  [d28bc4f8] + OrdinaryDiffEqHighOrderRK v1.1.0
  [9f002381] + OrdinaryDiffEqIMEXMultistep v1.3.0
  [521117fe] + OrdinaryDiffEqLinear v1.1.0
  [1344f307] + OrdinaryDiffEqLowOrderRK v1.2.0
  [b0944070] + OrdinaryDiffEqLowStorageRK v1.3.0
  [127b3ac7] + OrdinaryDiffEqNonlinearSolve v1.6.1
  [c9986a66] + OrdinaryDiffEqNordsieck v1.1.0
  [5dd0a6cf] + OrdinaryDiffEqPDIRK v1.3.0
  [5b33eab2] + OrdinaryDiffEqPRK v1.1.0
  [04162be5] + OrdinaryDiffEqQPRK v1.1.0
  [af6ede74] + OrdinaryDiffEqRKN v1.1.0
  [43230ef6] + OrdinaryDiffEqRosenbrock v1.9.0
  [2d112036] + OrdinaryDiffEqSDIRK v1.3.0
  [669c94d9] + OrdinaryDiffEqSSPRK v1.3.0
  [e3e12d00] + OrdinaryDiffEqStabilizedIRK v1.3.0
  [358294b1] + OrdinaryDiffEqStabilizedRK v1.1.0
  [fa646aed] + OrdinaryDiffEqSymplecticRK v1.3.0
  [b1df2697] + OrdinaryDiffEqTsit5 v1.1.0
  [79d7bb75] + OrdinaryDiffEqVerner v1.2.0
  [90014a1f] + PDMats v0.11.34
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.3
  [f517fe37] + Polyester v0.7.16
  [1d0040c9] + PolyesterWeave v0.2.2
  [2dfb63ee] + PooledArrays v1.4.3
  [85a6dd25] + PositiveFactorizations v0.2.4
  [d236fae5] + PreallocationTools v0.4.26
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [3cdcf5f2] + RecipesBase v1.3.4
  [731186ca] + RecursiveArrayTools v3.33.0
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [295af30f] + Revise v3.7.6
  [79098fc4] + Rmath v0.8.0
  [7e49a35a] + RuntimeGeneratedFunctions v0.5.14
  [94e857df] + SIMDTypes v0.1.0
  [0bca4576] + SciMLBase v2.86.2
  [19f34311] + SciMLJacobianOperators v0.1.3
  [c0aeaf25] + SciMLOperators v0.3.13
  [53ae85a6] + SciMLStructures v1.7.0
  [91c51154] + SentinelArrays v1.4.8
  [efcf1570] + Setfield v1.1.2
  [727e6d20] + SimpleNonlinearSolve v2.3.0
  [ce78b400] + SimpleUnPack v1.1.0
  [b85f4697] + SoftGlobalScope v1.1.0
  [a2af1166] + SortingAlgorithms v1.2.1
  [0a514795] + SparseMatrixColorings v0.4.19
  [276daf66] + SpecialFunctions v2.5.1
  [aedffcd0] + Static v1.2.0
  [0d7ed370] + StaticArrayInterface v1.8.0
  [90137ffa] + StaticArrays v1.9.13
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.0
  [2913bbd2] + StatsBase v0.34.4
  [4c63d2b9] + StatsFuns v1.5.0
  [a2598c62] + StochasticGene v1.4.0
  [7792a7ef] + StrideArraysCore v0.5.7
  [892a3eda] + StringManipulation v0.4.1
  [2efcf032] + SymbolicIndexingInterface v0.3.40
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [8290d209] + ThreadingUtilities v0.5.3
  [a759f4b9] + TimerOutputs v0.5.28
  [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 v1.4.0
⌅ [68821587] + Arpack_jll v3.5.1+1
  [f5851436] + FFTW_jll v3.3.11+0
  [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0
  [aae0fff6] + LSODA_jll v0.1.2+0
  [856f044c] + MKL_jll v2025.0.1+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+2
  [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+0
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [f43a241f] + Downloads v1.7.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
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  [f489334b] + StyledStrings v1.11.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [deac9b47] + LibCURL_jll v8.12.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2024.12.31
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.5+0
  [458c3c95] + OpenSSL_jll v3.0.16+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.12.0+0
  [8e850ede] + nghttp2_jll v1.65.0+0
  [3f19e933] + p7zip_jll v17.5.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`
    Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log`
    Building IJulia → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/be30be76e25b0aff2c9a85930ed3ac34c5f10c83/build.log`

Installation completed after 14.66s


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# Precompilation
#

Precompiling PkgEval dependencies...
No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml`
No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml`

Precompiling package dependencies...
Precompiling packages...
           ✗ ZMQ
           ✗ IJulia
  72720.1 ms  ? StochasticGene
  0 dependencies successfully precompiled in 98 seconds. 307 already precompiled.
  1 dependencies failed but may be precompilable after restarting julia
  1 dependency had output during precompilation:
┌ StochasticGene
│  WARNING: Method definition setindex(GPUArraysCore.AbstractGPUArray{T, N} where N where T, Any, Int64) in module ArrayInterfaceGPUArraysCoreExt at /home/pkgeval/.julia/packages/ArrayInterface/9wQIY/ext/ArrayInterfaceGPUArraysCoreExt.jl:12 overwritten in module ArrayInterfaceGPUArraysCoreExt on the same line (check for duplicate calls to `include`).
│  ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
└  

Precompilation completed after 103.16s


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# Loading
#

Loading StochasticGene...
Precompiling packages...
           ✗ ZMQ
           ✗ IJulia
Info Given StochasticGene was explicitly requested, output will be shown live 
WARNING: Detected access to binding `SimpleNonlinearSolve.SimpleNewtonRaphson` in a world prior to its definition world.
  Julia 1.12 has introduced more strict world age semantics for global bindings.
  !!! This code may malfunction under Revise.
  !!! This code will error in future versions of Julia.
Hint: Add an appropriate `invokelatest` around the access to this binding.
WARNING: Detected access to binding `NonlinearSolveFirstOrder.GeneralizedFirstOrderAlgorithm` in a world prior to its definition world.
  Julia 1.12 has introduced more strict world age semantics for global bindings.
  !!! This code may malfunction under Revise.
  !!! This code will error in future versions of Julia.
Hint: Add an appropriate `invokelatest` around the access to this binding.
1.2430183e6 ms  ✓ StochasticGene
  1 dependency successfully precompiled in 1267 seconds. 307 already precompiled.
  1 dependency had output during precompilation:
┌ StochasticGene
│  [Output was shown above]
└  

Loading completed after 1304.07s

PkgEval succeeded after 1461.25s