Package evaluation to test ReactionNetworkImporters on Julia 1.12.6 (15346901f00) started at 2026-06-29T12:21:40.912 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 6.23s ################################################################################ # Installation # Installing ReactionNetworkImporters... Resolving package versions... Installed SciMLBase ───── v3.30.0 Installed SymbolicUtils ─ v4.37.2 Installed Krylov ──────── v0.10.8 Updating `~/.julia/environments/v1.12/Project.toml` [b4db0fb7] + ReactionNetworkImporters v1.3.1 Updating `~/.julia/environments/v1.12/Manifest.toml` [47edcb42] + ADTypes v1.22.1 [14f7f29c] + AMD v0.5.3 [6e696c72] + AbstractPlutoDingetjes v1.4.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [ec485272] + ArnoldiMethod v0.4.0 [4fba245c] + ArrayInterface v7.27.0 [4c555306] + ArrayLayouts v1.12.2 [aae01518] + BandedMatrices v1.11.0 [e2ed5e7c] + Bijections v0.2.2 [b2a6c25c] + BinaryHeaps v1.0.1 [caf10ac8] + BipartiteGraphs v0.1.8 [8e7c35d0] + BlockArrays v1.9.4 [70df07ce] + BracketingNonlinearSolve v1.12.2 [479239e8] + Catalyst v16.2.0 ⌅ [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.9 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [34da2185] + Compat v4.18.1 [b152e2b5] + CompositeTypes v0.1.4 [a33af91c] + CompositionsBase v0.1.2 [2569d6c7] + ConcreteStructs v0.2.5 [187b0558] + ConstructionBase v1.6.0 [864edb3b] + DataStructures v0.19.6 [2b5f629d] + DiffEqBase v7.6.0 [459566f4] + DiffEqCallbacks v4.18.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [a0c0ee7d] + DifferentiationInterface v0.7.18 [8d63f2c5] + DispatchDoctor v0.4.28 [ffbed154] + DocStringExtensions v0.9.5 [5b8099bc] + DomainSets v0.8.0 [7c1d4256] + DynamicPolynomials v0.6.6 [06fc5a27] + DynamicQuantities v1.13.0 [4e289a0a] + EnumX v1.0.7 [f151be2c] + EnzymeCore v0.8.20 [e2ba6199] + ExprTools v0.1.10 [55351af7] + ExproniconLite v0.10.14 [7034ab61] + FastBroadcast v1.3.3 [9aa1b823] + FastClosures v0.3.2 [a4df4552] + FastPower v1.3.3 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.31.1 [1fa38f19] + Format v1.3.7 [f6369f11] + ForwardDiff v1.4.1 [a85aefff] + FunctionMaps v0.1.2 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v1.9.3 [46192b85] + GPUArraysCore v0.2.0 [86223c79] + Graphs v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [3263718b] + ImplicitDiscreteSolve v2.1.2 [d25df0c9] + Inflate v0.1.5 [18e54dd8] + IntegerMathUtils v0.1.3 [8197267c] + IntervalSets v0.7.14 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [ae98c720] + Jieko v0.2.1 [ccbc3e58] + JumpProcesses v9.29.0 [ba0b0d4f] + Krylov v0.10.8 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.10 [87fe0de2] + LineSearch v0.1.10 [7ed4a6bd] + LinearSolve v3.87.0 [2ab3a3ac] + LogExpFunctions v1.0.1 [e6f89c97] + LoggingExtras v1.2.0 [1914dd2f] + MacroTools v0.5.16 [bb5d69b7] + MaybeInplace v0.1.5 [7771a370] + ModelingToolkitBase v1.48.1 [2e0e35c7] + Moshi v0.3.8 [46d2c3a1] + MuladdMacro v0.2.6 [102ac46a] + MultivariatePolynomials v0.5.19 [d8a4904e] + MutableArithmetics v1.8.0 [77ba4419] + NaNMath v1.1.4 [be0214bd] + NonlinearSolveBase v2.31.3 [5959db7a] + NonlinearSolveFirstOrder v2.1.2 [6fe1bfb0] + OffsetArrays v1.17.0 ⌅ [bac558e1] + OrderedCollections v1.8.2 [bbf590c4] + OrdinaryDiffEqCore v4.5.0 ⌅ [d96e819e] + Parameters v0.12.3 [e409e4f3] + PoissonRandom v0.4.10 [d236fae5] + PreallocationTools v1.2.1 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [27ebfcd6] + Primes v0.5.7 [0c0d3e7f] + PureKLU v1.0.2 [b4db0fb7] + ReactionNetworkImporters v1.3.1 [988b38a3] + ReadOnlyArrays v0.2.0 [795d4caa] + ReadOnlyDicts v1.0.1 [3cdcf5f2] + RecipesBase v1.3.4 [731186ca] + RecursiveArrayTools v4.3.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.21 [9dfe8606] + SCCNonlinearSolve v1.13.2 [0bca4576] + SciMLBase v3.30.0 [19f34311] + SciMLJacobianOperators v0.1.14 [a6db7da4] + SciMLLogging v2.0.1 [c0aeaf25] + SciMLOperators v1.22.1 [431bcebd] + SciMLPublic v1.2.1 [53ae85a6] + SciMLStructures v1.10.1 [efcf1570] + Setfield v1.1.2 [727e6d20] + SimpleNonlinearSolve v2.12.1 [699a6c99] + SimpleTraits v0.9.6 [a57abbd0] + SparseColumnPivotedQR v2.1.2 [276daf66] + SpecialFunctions v2.8.0 [0c0c59c1] + StarAlgebras v0.3.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [2efcf032] + SymbolicIndexingInterface v0.3.49 [19f23fe9] + SymbolicLimits v1.1.1 [d1185830] + SymbolicUtils v4.37.2 [0c5d862f] + Symbolics v7.29.0 [ed4db957] + TaskLocalValues v0.1.3 [8ea1fca8] + TermInterface v2.0.0 [1c621080] + TestItems v1.0.0 [a759f4b9] + TimerOutputs v0.5.29 [410a4b4d] + Tricks v0.1.13 [781d530d] + TruncatedStacktraces v1.4.0 [3a884ed6] + UnPack v1.0.2 [d30d5f5c] + WeakCacheSets v0.1.0 [61579ee1] + Ghostscript_jll v9.55.1+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [aacddb02] + JpegTurbo_jll v3.1.5+0 [856f044c] + MKL_jll v2025.2.0+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [1317d2d5] + oneTBB_jll v2022.3.0+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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.1 [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 v1.12.0 [f489334b] + StyledStrings v1.11.0 [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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 7.43s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 3123.4 ms ✓ Combinatorics 768.9 ms ✓ ConcreteStructs 853.1 ms ✓ Tricks 5815.9 ms ✓ ExproniconLite 852.7 ms ✓ CompositeTypes 755.2 ms ✓ WeakCacheSets 728.6 ms ✓ FastPower 1049.5 ms ✓ ReadOnlyDicts 917.2 ms ✓ AbstractPlutoDingetjes 801.6 ms ✓ TermInterface 3388.4 ms ✓ Bijections 820.2 ms ✓ BinaryHeaps 781.8 ms ✓ EnzymeCore → AdaptExt 769.6 ms ✓ ADTypes → ADTypesEnzymeCoreExt 13761.5 ms ✓ Krylov 763.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceGPUArraysCoreExt 1676.7 ms ✓ MaybeInplace 1053.2 ms ✓ FastBroadcast 1269.7 ms ✓ SciMLLogging 6353.6 ms ✓ SciMLOperators 1174.5 ms ✓ TruncatedStacktraces 5608.8 ms ✓ DispatchDoctor 14732.3 ms ✓ SparseColumnPivotedQR 16491.7 ms ✓ RecursiveArrayTools 1556.8 ms ✓ PoissonRandom 3507.7 ms ✓ SciMLStructures 1964.9 ms ✓ PreallocationTools 45127.1 ms ✓ PureKLU 1216.0 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1150.9 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 2133.9 ms ✓ SymbolicIndexingInterface → SymbolicIndexingInterfacePrettyTablesExt 7854.3 ms ✓ Latexify 10178.5 ms ✓ BipartiteGraphs 2834.1 ms ✓ ArrayLayouts → ArrayLayoutsSparseArraysExt 48344.6 ms ✓ BandedMatrices 3843.4 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 2614.4 ms ✓ BlockArrays → BlockArraysAdaptExt 2848.5 ms ✓ Jieko 2575.7 ms ✓ FunctionMaps 1056.2 ms ✓ FastPower → FastPowerForwardDiffExt 1146.3 ms ✓ MaybeInplace → MaybeInplaceSparseArraysExt 929.8 ms ✓ SciMLOperators → SciMLOperatorsStaticArraysCoreExt 1392.8 ms ✓ SciMLOperators → SciMLOperatorsSparseArraysExt 4541.2 ms ✓ FunctionWrappersWrappers 12746.4 ms ✓ DynamicQuantities 826.6 ms ✓ DispatchDoctor → DispatchDoctorEnzymeCoreExt 1262.7 ms ✓ SparseColumnPivotedQR → SparseColumnPivotedQRAMDExt 1081.8 ms ✓ RecursiveArrayTools → RecursiveArrayToolsStatisticsExt 1093.3 ms ✓ RecursiveArrayTools → RecursiveArrayToolsFastBroadcastExt 1547.2 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 1259.8 ms ✓ RecursiveArrayTools → RecursiveArrayToolsTablesExt 11049.5 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 2299.8 ms ✓ PreallocationTools → PreallocationToolsForwardDiffExt 1827.3 ms ✓ Latexify → SparseArraysExt 152024.6 ms ✓ Latexify → DataFramesExt 3196.6 ms ✓ BipartiteGraphs → BipartiteGraphsSparseArraysExt 3887.8 ms ✓ BandedMatrices → BandedMatricesSparseArraysExt 3391.3 ms ✓ ArrayInterface → ArrayInterfaceBandedMatricesExt 3369.0 ms ✓ FiniteDiff → FiniteDiffBandedMatricesExt 8023.6 ms ✓ BlockArrays → BlockArraysBandedMatricesExt 17155.6 ms ✓ Moshi 3478.8 ms ✓ DomainSets 1534.4 ms ✓ DynamicQuantities → DynamicQuantitiesLinearAlgebraExt 20770.4 ms ✓ DynamicQuantities → DynamicQuantitiesRecursiveArrayToolsExt 29679.2 ms ✓ SciMLBase 181908.1 ms ✓ SymbolicUtils 1280.4 ms ✓ DomainSets → DomainSetsRandomExt 2359.5 ms ✓ SciMLBase → SciMLBaseStaticArraysExt 1984.3 ms ✓ SciMLBase → SciMLBaseDifferentiationInterfaceExt 21100.9 ms ✓ SciMLBase → SciMLBaseForwardDiffExt 2235.0 ms ✓ SCCNonlinearSolve 20492.4 ms ✓ LinearSolve 2218.3 ms ✓ DynamicQuantities → DynamicQuantitiesSciMLBaseExt 153945.0 ms ✓ SymbolicLimits 9781.2 ms ✓ SciMLJacobianOperators 6360.3 ms ✓ LinearSolve → LinearSolveForwardDiffExt 69109.5 ms ✓ LinearSolve → LinearSolveBandedMatricesExt 76299.1 ms ✓ LinearSolve → LinearSolveSparseArraysExt 317624.6 ms ✓ Symbolics 46427.1 ms ✓ LineSearch 20490.9 ms ✓ NonlinearSolveBase 37920.5 ms ✓ LinearSolve → LinearSolveEnzymeExt 20272.5 ms ✓ Symbolics → SymbolicsHypergeometricFunctionsExt 185002.4 ms ? Symbolics → SymbolicsForwardDiffExt 158835.2 ms ✓ Symbolics → SymbolicsLatexifyExt 8735.3 ms ✓ DifferentiationInterface → DifferentiationInterfaceSymbolicsExt 88220.3 ms ✓ NonlinearSolveBase → NonlinearSolveBaseBandedMatricesExt 86843.4 ms ✓ NonlinearSolveBase → NonlinearSolveBaseForwardDiffExt 2931.8 ms ✓ NonlinearSolveBase → NonlinearSolveBaseSparseArraysExt 14254.7 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLineSearchExt 24574.7 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLinearSolveExt 5772.0 ms ✓ BracketingNonlinearSolve 224362.2 ms ✓ Symbolics → SymbolicsPreallocationToolsExt 95920.7 ms ✓ NonlinearSolveFirstOrder 1865.7 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveForwardDiffExt 6120.8 ms ✓ DiffEqBase 10761.8 ms ✓ SimpleNonlinearSolve 5014.8 ms ✓ DiffEqBase → DiffEqBaseForwardDiffExt 14995.7 ms ✓ DiffEqBase → DiffEqBaseDynamicQuantitiesExt 1775.9 ms ✓ DiffEqBase → DiffEqBaseSparseArraysExt 7854.8 ms ✓ DiffEqCallbacks 6929.2 ms ✓ OrdinaryDiffEqCore 9719.7 ms ✓ JumpProcesses 2142.0 ms ✓ OrdinaryDiffEqCore → OrdinaryDiffEqCoreSparseArraysExt 7758.9 ms ✓ OrdinaryDiffEqTsit5 2935.9 ms ✓ JumpProcesses → JumpProcessesOrdinaryDiffEqCoreExt 4512.8 ms ✓ ImplicitDiscreteSolve 104543.9 ms ? ModelingToolkitBase ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 13 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #634 at ./asyncevent.jl:359 jfptr_YY.634_15147.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1252 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000765be5948b50 Total snapshots: 607. Utilization: 0% ╎607 @Base/asyncevent.jl:359 (::Base.var"#634#635"{FileWatching.Pidfile.var… ╎ 607 @Base/asyncevent.jl:185 _trywait(t::Timer) ╎ 607 @Base/condition.jl:136 wait ╎ 607 @Base/condition.jl:141 wait(c::Base.GenericCondition{Base.Threads.S… ╎ 607 @Base/task.jl:1228 wait() 606╎ 607 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronize… ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 task_done_hook at ./task.jl:868 jfptr_task_done_hook_59905.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] jl_finish_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:341 start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1263 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007eed04320e20 Total snapshots: 598. Utilization: 0% ╎598 @Base/task.jl:868 task_done_hook(t::Task) ╎ 598 @Base/task.jl:1228 wait() 597╎ 598 @Base/task.jl:1216 poptask(W::Base.IntrusiveLinkedListSynchronized{T… [13] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:34 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 /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./condition.jl:136 [inlined] _trywait at ./asyncevent.jl:185 #634 at ./asyncevent.jl:359 jfptr_YY.634_15147.1 at /opt/julia/lib/julia/sys.so (unknown line) jl_apply at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/julia.h:2391 [inlined] start_task at /cache/build/builder-amdci5-4/julialang/julia-release-1-dot-12/src/task.c:1252 unknown function (ip: (nil)) at (unknown file) Allocations: 12177869 (Pool: 12177014; Big: 855); GC: 12 PkgEval terminated after 2743.15s: test duration exceeded the time limit