Package evaluation of StochasticGene on Julia 1.13.0-DEV.1265 (cd62cf9a08*) started at 2025-10-06T07:46:27.486 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.06s ################################################################################ # Installation # Installing StochasticGene... Resolving package versions... Installed MKL_jll ───────────────────────────── v2025.2.0+0 Installed CommonWorldInvalidations ──────────── v1.0.0 Installed InlineStrings ─────────────────────── v1.4.5 Installed SIMDTypes ─────────────────────────── v0.1.0 Installed OrderedCollections ────────────────── v1.8.1 Installed FastPower ─────────────────────────── v1.1.3 Installed MultivariateStats ─────────────────── v0.10.3 Installed OrdinaryDiffEqRosenbrock ──────────── v1.18.1 Installed EnzymeCore ────────────────────────── v0.8.14 Installed PreallocationTools ────────────────── v0.4.34 Installed CpuId ─────────────────────────────── v0.3.1 Installed Optim ─────────────────────────────── v1.13.2 Installed NonlinearSolveSpectralMethods ─────── v1.5.0 Installed Compiler ──────────────────────────── v0.1.1 Installed SentinelArrays ────────────────────── v1.4.8 Installed StaticArrayInterface ──────────────── v1.8.0 Installed OrdinaryDiffEqExponentialRK ───────── v1.8.0 Installed QuadGK ────────────────────────────── v2.11.2 Installed OrdinaryDiffEqFIRK ────────────────── v1.16.0 Installed NaNMath ───────────────────────────── v1.1.3 Installed OpenSpecFun_jll ───────────────────── v0.5.6+0 Installed FastBroadcast ─────────────────────── v0.3.5 Installed NonlinearSolveBase ────────────────── v2.0.0 Installed Revise ────────────────────────────── v3.9.0 Installed LoweredCodeUtils ──────────────────── v3.4.4 Installed Tables ────────────────────────────── v1.12.1 Installed Arpack ────────────────────────────── v0.5.4 Installed OrdinaryDiffEqQPRK ────────────────── v1.4.0 Installed EnumX ─────────────────────────────── v1.0.5 Installed NLSolversBase ─────────────────────── v7.10.0 Installed BracketingNonlinearSolve ──────────── v1.5.0 Installed DiffEqBase ────────────────────────── v6.190.2 Installed OrdinaryDiffEqLowOrderRK ──────────── v1.6.0 Installed LinearSolve ───────────────────────── v3.41.0 Installed Jieko ─────────────────────────────── v0.2.1 Installed Reexport ──────────────────────────── v1.2.2 Installed Missings ──────────────────────────── v1.2.0 Installed InverseFunctions ──────────────────── v0.1.17 Installed RegistryInstances ─────────────────── v0.1.0 Installed Preferences ───────────────────────── v1.5.0 Installed Static ────────────────────────────── v1.3.0 Installed TableTraits ───────────────────────── v1.0.1 Installed NonlinearSolve ────────────────────── v4.12.0 Installed LaTeXStrings ──────────────────────── v1.4.0 Installed Crayons ───────────────────────────── v4.1.1 Installed MaybeInplace ──────────────────────── v0.1.4 Installed RecursiveArrayTools ───────────────── v3.37.1 Installed SortingAlgorithms ─────────────────── v1.2.2 Installed OrdinaryDiffEqNordsieck ───────────── v1.4.0 Installed UnPack ────────────────────────────── v1.0.2 Installed ADTypes ───────────────────────────── v1.18.0 Installed OrdinaryDiffEqAdamsBashforthMoulton ─ v1.5.0 Installed DataStructures ────────────────────── v0.19.1 Installed OrdinaryDiffEqLinear ──────────────── v1.6.0 Installed MacroTools ────────────────────────── v0.5.16 Installed GenericSchur ──────────────────────── v0.5.6 Installed OpenSSH_jll ───────────────────────── v10.0.2+0 Installed DiffResults ───────────────────────── v1.1.0 Installed ManualMemory ──────────────────────── v0.1.8 Installed DelimitedFiles ────────────────────── v1.9.1 Installed AbstractTrees ─────────────────────── v0.4.5 Installed FillArrays ────────────────────────── v1.14.0 Installed SparseMatrixColorings ─────────────── v0.4.21 Installed oneTBB_jll ────────────────────────── v2022.0.0+0 Installed StatsBase ─────────────────────────── v0.34.6 Installed IntelOpenMP_jll ───────────────────── v2025.2.0+0 Installed SciMLJacobianOperators ────────────── v0.1.11 Installed DataValueInterfaces ───────────────── v1.0.0 Installed CodecZlib ─────────────────────────── v0.7.8 Installed ExprTools ─────────────────────────── v0.1.10 Installed CommonSubexpressions ──────────────── v0.3.1 Installed ArrayInterface ────────────────────── v7.20.0 Installed GPUArraysCore ─────────────────────── v0.2.0 Installed Expat_jll ─────────────────────────── v2.7.1+0 Installed IrrationalConstants ───────────────── v0.2.4 Installed TruncatedStacktraces ──────────────── v1.4.0 Installed LayoutPointers ────────────────────── v0.1.17 Installed ConcreteStructs ───────────────────── v0.2.3 Installed ArrayLayouts ──────────────────────── v1.11.2 Installed IOCapture ─────────────────────────── v0.2.5 Installed Setfield ──────────────────────────── v1.1.2 Installed LSODA_jll ─────────────────────────── v0.1.2+0 Installed OrdinaryDiffEqRKN ─────────────────── v1.5.0 Installed OrdinaryDiffEqStabilizedIRK ───────── v1.6.0 Installed OrdinaryDiffEqExtrapolation ───────── v1.9.0 Installed PooledArrays ──────────────────────── v1.4.3 Installed Moshi ─────────────────────────────── v0.3.7 Installed PDMats ────────────────────────────── v0.11.35 Installed WorkerUtilities ───────────────────── v1.6.1 Installed OrdinaryDiffEqPRK ─────────────────── v1.4.0 Installed NonlinearSolveQuasiNewton ─────────── v1.10.0 Installed DocStringExtensions ───────────────── v0.9.5 Installed CompositionsBase ──────────────────── v0.1.2 Installed DifferentiationInterface ──────────── v0.7.8 Installed CommonSolve ───────────────────────── v0.2.4 Installed OrdinaryDiffEqHighOrderRK ─────────── v1.5.0 Installed Rmath_jll ─────────────────────────── v0.5.1+0 Installed VersionParsing ────────────────────── v1.3.0 Installed ForwardDiff ───────────────────────── v1.2.1 Installed ZMQ ───────────────────────────────── v1.5.0 Installed OrdinaryDiffEq ────────────────────── v6.102.1 Installed SimpleUnPack ──────────────────────── v1.1.0 Installed BitTwiddlingConvenienceFunctions ──── v0.1.6 Installed AliasTables ───────────────────────── v1.1.3 Installed IteratorInterfaceExtensions ───────── v1.0.0 Installed LineSearch ────────────────────────── v0.1.4 Installed FunctionWrappersWrappers ──────────── v0.1.3 Installed RecipesBase ───────────────────────── v1.3.4 Installed DataAPI ───────────────────────────── v1.16.0 Installed SciMLOperators ────────────────────── v1.7.2 Installed OrdinaryDiffEqStabilizedRK ────────── v1.4.0 Installed Git_LFS_jll ───────────────────────── v3.7.0+0 Installed InvertedIndices ───────────────────── v1.3.1 Installed OrdinaryDiffEqBDF ─────────────────── v1.10.1 Installed Conda ─────────────────────────────── v1.10.2 Installed OrdinaryDiffEqSymplecticRK ────────── v1.7.0 Installed Krylov ────────────────────────────── v0.10.2 Installed SciMLStructures ───────────────────── v1.7.0 Installed FastGaussQuadrature ───────────────── v1.0.2 Installed StaticArraysCore ──────────────────── v1.4.3 Installed LSODA ─────────────────────────────── v0.7.5 Installed StaticArrays ──────────────────────── v1.9.15 Installed CodeTracking ──────────────────────── v2.0.1 Installed StringManipulation ────────────────── v0.4.1 Installed AbstractFFTs ──────────────────────── v1.5.0 Installed SciMLPublic ───────────────────────── v1.0.0 Installed OrdinaryDiffEqLowStorageRK ────────── v1.7.0 Installed Requires ──────────────────────────── v1.3.1 Installed Documenter ────────────────────────── v1.14.1 Installed OrdinaryDiffEqDifferentiation ─────── v1.16.1 Installed FunctionWrappers ──────────────────── v1.1.3 Installed OrdinaryDiffEqNonlinearSolve ──────── v1.14.1 Installed LogExpFunctions ───────────────────── v0.3.29 Installed DiffRules ─────────────────────────── v1.15.1 Installed OrdinaryDiffEqCore ────────────────── v1.34.0 Installed JuliaInterpreter ──────────────────── v0.10.5 Installed Git_jll ───────────────────────────── v2.51.1+0 Installed SciMLBase ─────────────────────────── v2.120.0 Installed PrettyTables ──────────────────────── v3.0.11 Installed JSON ──────────────────────────────── v0.21.4 Installed Distributions ─────────────────────── v0.25.122 Installed Rmath ─────────────────────────────── v0.8.0 Installed Parsers ───────────────────────────── v2.8.3 Installed NonlinearSolveFirstOrder ──────────── v1.9.0 Installed Arpack_jll ────────────────────────── v3.5.1+1 Installed libsodium_jll ─────────────────────── v1.0.21+0 Installed OrdinaryDiffEqExplicitRK ──────────── v1.4.0 Installed FastClosures ──────────────────────── v0.3.2 Installed FiniteDiff ────────────────────────── v2.28.1 Installed CSV ───────────────────────────────── v0.10.15 Installed CloseOpenIntervals ────────────────── v0.1.13 Installed StatsFuns ─────────────────────────── v1.5.0 Installed Polyester ─────────────────────────── v0.7.18 Installed IJulia ────────────────────────────── v1.30.5 Installed ZeroMQ_jll ────────────────────────── v4.3.6+0 Installed WeakRefStrings ────────────────────── v1.4.2 Installed JLLWrappers ───────────────────────── v1.7.1 Installed OrdinaryDiffEqFeagin ──────────────── v1.4.0 Installed OrdinaryDiffEqIMEXMultistep ───────── v1.7.0 Installed OrdinaryDiffEqSSPRK ───────────────── v1.7.0 Installed DataFrames ────────────────────────── v1.8.0 Installed OrdinaryDiffEqSDIRK ───────────────── v1.7.0 Installed ThreadingUtilities ────────────────── v0.5.5 Installed FilePathsBase ─────────────────────── v0.9.24 Installed Accessors ─────────────────────────── v0.1.42 Installed ExponentialUtilities ──────────────── v1.27.0 Installed OrdinaryDiffEqPDIRK ───────────────── v1.6.0 Installed OrdinaryDiffEqDefault ─────────────── v1.8.0 Installed OrdinaryDiffEqVerner ──────────────── v1.6.0 Installed Adapt ─────────────────────────────── v4.4.0 Installed RuntimeGeneratedFunctions ─────────── v0.5.15 Installed ConstructionBase ──────────────────── v1.6.0 Installed HypergeometricFunctions ───────────── v0.3.28 Installed SymbolicIndexingInterface ─────────── v0.3.45 Installed TranscodingStreams ────────────────── v0.11.3 Installed Compat ────────────────────────────── v4.18.1 Installed StrideArraysCore ──────────────────── v0.5.8 Installed Statistics ────────────────────────── v1.11.1 Installed PositiveFactorizations ────────────── v0.2.4 Installed LazyArrays ────────────────────────── v2.7.0 Installed StatsAPI ──────────────────────────── v1.7.1 Installed PrecompileTools ───────────────────── v1.3.3 Installed TimerOutputs ──────────────────────── v0.5.29 Installed ExproniconLite ────────────────────── v0.10.14 Installed MarkdownAST ───────────────────────── v0.1.2 Installed ChainRulesCore ────────────────────── v1.26.0 Installed CPUSummary ────────────────────────── v0.2.7 Installed IfElse ────────────────────────────── v0.1.1 Installed PtrArrays ─────────────────────────── v1.3.0 Installed Parameters ────────────────────────── v0.12.3 Installed MuladdMacro ───────────────────────── v0.2.4 Installed SpecialFunctions ──────────────────── v2.6.1 Installed StochasticGene ────────────────────── v1.5.10 Installed Git ───────────────────────────────── v1.5.0 Installed FFTW_jll ──────────────────────────── v3.3.11+0 Installed Libiconv_jll ──────────────────────── v1.18.0+0 Installed SimpleNonlinearSolve ──────────────── v2.9.0 Installed FFTW ──────────────────────────────── v1.10.0 Installed OrdinaryDiffEqTsit5 ───────────────── v1.5.0 Installed PolyesterWeave ────────────────────── v0.2.2 Installed LineSearches ──────────────────────── v7.4.0 Installed ANSIColoredPrinters ───────────────── v0.0.1 Installed LazilyInitializedFields ───────────── v1.3.0 Installed OrdinaryDiffEqFunctionMap ─────────── v1.5.0 Installing 13 artifacts Installed artifact Rmath 121.9 KiB Installed artifact Arpack 147.2 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact ZeroMQ 316.1 KiB Installed artifact LSODA 24.9 KiB Installed artifact oneTBB 435.6 KiB Installed artifact Expat 274.7 KiB Installed artifact libsodium 1.6 MiB Installed artifact FFTW 2.2 MiB Installed artifact Libiconv 1.9 MiB Installed artifact OpenSSH 4.2 MiB Installed artifact Git_LFS 9.6 MiB Installed artifact Git 48.9 MiB Updating `~/.julia/environments/v1.13/Project.toml` [a2598c62] + StochasticGene v1.5.10 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [a4c015fc] + ANSIColoredPrinters v0.0.1 [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.20.0 [4c555306] + ArrayLayouts v1.11.2 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [70df07ce] + BracketingNonlinearSolve v1.5.0 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.26.0 [fb6a15b2] + CloseOpenIntervals v0.1.13 [da1fd8a2] + CodeTracking v2.0.1 [944b1d66] + CodecZlib v0.7.8 [38540f10] + CommonSolve v0.2.4 [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 v1.10.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.0 [864edb3b] + DataStructures v0.19.1 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [2b5f629d] + DiffEqBase v6.190.2 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.8 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [e30172f5] + Documenter v1.14.1 [4e289a0a] + EnumX v1.0.5 [f151be2c] + EnzymeCore v0.8.14 [d4d017d3] + ExponentialUtilities v1.27.0 [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 v1.0.2 [a4df4552] + FastPower v1.1.3 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.14.0 [6a86dc24] + FiniteDiff v2.28.1 [f6369f11] + ForwardDiff v1.2.1 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 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v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.46.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+0 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/a961561e3b73c70715ea3442190ba80e7be80af8/build.log` Installation completed after 81.17s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4862.5 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompilation completed after 1761.67s ################################################################################ # Testing # Testing StochasticGene Status `/tmp/jl_KGGXks/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 [e30172f5] Documenter v1.14.1 [7a1cc6ca] FFTW v1.10.0 [7073ff75] IJulia v1.30.5 ⌅ [682c06a0] JSON v0.21.4 [7f56f5a3] LSODA v0.7.5 [6f286f6a] MultivariateStats v0.10.3 [429524aa] Optim v1.13.2 [1dea7af3] OrdinaryDiffEq v6.102.1 [295af30f] Revise v3.9.0 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.6 [a2598c62] StochasticGene v1.5.10 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [37e2e46d] LinearAlgebra v1.13.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_KGGXks/Manifest.toml` [47edcb42] ADTypes v1.18.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 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[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 v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.46.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Sampling StochasticGene: Test Failed at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/test/runtests.jl:20 Expression: isapprox(h1, h2, rtol = 0.05) Evaluated: isapprox([0.413267243145626, 0.2672936785320047, 2.6437897130705386, 1.0], [0.33, 0.19, 2.5, 1.0]; rtol = 0.05) Stacktrace: [1] top-level scope @ ~/.julia/packages/StochasticGene/iWmSF/test/runtests.jl:13 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1952 [inlined] [3] macro expansion @ ~/.julia/packages/StochasticGene/iWmSF/test/runtests.jl:20 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:751 [inlined] Histogram count: 6774.0 Sampling Sampling 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 1464 running 1 of 1 signal (10): User defined signal 1 checkbounds at ./abstractarray.jl:702 [inlined] getindex at ./subarray.jl:340 [inlined] searchsortedfirst at ./sort.jl:192 [inlined] searchsortedfirst at ./sort.jl:308 [inlined] #searchsortedfirst#5 at ./sort.jl:310 [inlined] searchsortedfirst at ./sort.jl:310 [inlined] getindex at /source/usr/share/julia/stdlib/v1.13/SparseArrays/src/sparsevector.jl:712 normalized_nullspace at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/chemical_master.jl:290 steady_state at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/chemical_master.jl:25 [inlined] steady_state at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/chemical_master.jl:22 unknown function (ip: 0x775e9a58c53a) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 predictedarray at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/likelihoods.jl:773 unknown function (ip: 0x775e4c3b2304) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 predictedarray at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/likelihoods.jl:635 predictedfn at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/likelihoods.jl:548 loglikelihood at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/likelihoods.jl:449 mhstep at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:552 unknown function (ip: 0x775e4c3bd596) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 sample at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:459 sample at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:450 unknown function (ip: 0x775e4c3bb616) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 metropolis_hastings at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:313 run_mh at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:128 [inlined] run_mh at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/metropolis_hastings.jl:151 #test_fit_rnadwelltime#190 at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/test.jl:243 test_fit_rnadwelltime at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/src/test.jl:237 unknown function (ip: 0x775e4c3a280f) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 include_string at ./loading.jl:2954 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:3014 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_56488.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:679 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884 jl_toplevel_eval_flex at /source/src/toplevel.c:742 jl_eval_toplevel_stmts at /source/src/toplevel.c:585 jl_toplevel_eval_flex at /source/src/toplevel.c:683 ijl_toplevel_eval at /source/src/toplevel.c:754 ijl_toplevel_eval_in at /source/src/toplevel.c:799 eval at ./boot.jl:489 exec_options at ./client.jl:310 _start at ./client.jl:577 jfptr__start_42565.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x775e9beca249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ====================================================================================== 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:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_63711.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000702e5f4931c0 Total snapshots: 422. Utilization: 0% ╎422 @Base/task.jl:1139 wait_forever() 421╎ 422 @Base/task.jl:1217 wait() StochasticGene [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1217 wait_forever at ./task.jl:1139 jfptr_wait_forever_63711.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) Allocations: 40285963 (Pool: 40284975; Big: 988); GC: 49 [1464] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/StochasticGene/iWmSF/test/runtests.jl:11 unknown function (ip: 0x775e9bf3a60d) at /lib/x86_64-linux-gnu/libc.so.6 malloc at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) _ZN4llvm15SmallVectorBaseIjE13mallocForGrowEPvmmRm at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm23SmallVectorTemplateBaseINS_14DomTreeBuilder11SemiNCAInfoINS_17DominatorTreeBaseINS_10BasicBlockELb0EEEE7InfoRecELb0EE4growEm at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm14DomTreeBuilder11SemiNCAInfoINS_17DominatorTreeBaseINS_10BasicBlockELb0EEEE11getNodeInfoEPS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm14DomTreeBuilder11SemiNCAInfoINS_17DominatorTreeBaseINS_10BasicBlockELb0EEEE20CalculateFromScratchERS4_PNS5_15BatchUpdateInfoE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm21DominatorTreeAnalysis3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm6detail17AnalysisPassModelINS_8FunctionENS_21DominatorTreeAnalysisENS_15AnalysisManagerIS2_JEE11InvalidatorEJEE3runERS2_RS5_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15AnalysisManagerINS_8FunctionEJEE13getResultImplEPNS_11AnalysisKeyERS1_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15InstCombinePass3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_8FunctionENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/src/pipeline.cpp:791 operator() at /source/src/jitlayers.cpp:1513 withModuleDo<(anonymous namespace)::sizedOptimizerT::operator()(llvm::orc::ThreadSafeModule) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1474 [inlined] operator() at /source/src/jitlayers.cpp:1649 [inlined] addModule at /source/src/jitlayers.cpp:2106 jl_compile_codeinst_now at /source/src/jitlayers.cpp:682 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:876 jl_compile_method_internal at /source/src/gf.c:3648 _jl_invoke at /source/src/gf.c:4108 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] jl_f_invokelatest at /source/src/builtins.c:889 profile_printing_listener at ./Base.jl:337 #start_profile_listener##0 at ./Base.jl:355 jfptr_YY.start_profile_listenerYY.YY.0_11016.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 unknown function (ip: (nil)) at (unknown file) Allocations: 3255244012 (Pool: 3255243070; Big: 942); GC: 5548 PkgEval terminated after 2730.26s: test duration exceeded the time limit