Package evaluation of TumorGrowth on Julia 1.13.0-DEV.880 (5ebc5b463e*) started at 2025-07-21T08:18:20.892 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.6s ################################################################################ # Installation # Installing TumorGrowth... Resolving package versions... Installed CommonWorldInvalidations ──────────── v1.0.0 Installed MKL_jll ───────────────────────────── v2025.2.0+0 Installed InlineStrings ─────────────────────── v1.4.4 Installed FastPower ─────────────────────────── v1.1.3 Installed AlmostBlockDiagonals ──────────────── v0.1.10 Installed GPUCompiler ───────────────────────── v1.6.1 Installed SIMDTypes ─────────────────────────── v0.1.0 Installed OrdinaryDiffEqRosenbrock ──────────── v1.11.0 Installed Functors ──────────────────────────── v0.5.2 Installed OrderedCollections ────────────────── v1.8.1 Installed WeightInitializers ────────────────── v1.1.3 Installed LeastSquaresOptim ─────────────────── v0.8.7 Installed Sundials ──────────────────────────── v4.28.0 Installed PreallocationTools ────────────────── v0.4.29 Installed Optim ─────────────────────────────── v1.13.2 Installed OrdinaryDiffEqExponentialRK ───────── v1.4.0 Installed NonlinearSolveSpectralMethods ─────── v1.2.0 Installed EnzymeCore ────────────────────────── v0.8.12 Installed ArgCheck ──────────────────────────── v2.5.0 Installed OrdinaryDiffEqFIRK ────────────────── v1.12.0 Installed CpuId ─────────────────────────────── v0.3.1 Installed BoundaryValueDiffEqShooting ───────── v1.9.0 Installed SentinelArrays ────────────────────── v1.4.8 Installed Distances ─────────────────────────── v0.10.12 Installed StaticArrayInterface ──────────────── v1.8.0 Installed DispatchDoctor ────────────────────── v0.4.26 Installed QuadGK ────────────────────────────── v2.11.2 Installed BoundaryValueDiffEqFIRK ───────────── v1.9.0 Installed DiffEqCallbacks ───────────────────── v4.8.0 Installed NaNMath ───────────────────────────── v1.1.3 Installed OrdinaryDiffEqQPRK ────────────────── v1.1.0 Installed OpenSpecFun_jll ───────────────────── v0.5.6+0 Installed NonlinearSolveBase ────────────────── v1.13.0 Installed StructIO ──────────────────────────── v0.3.1 Installed FastBroadcast ─────────────────────── v0.3.5 Installed ScopedValues ──────────────────────── v1.4.0 Installed Tables ────────────────────────────── v1.12.1 Installed ChainRules ────────────────────────── v1.72.5 Installed BoundaryValueDiffEqMIRKN ──────────── v1.8.0 Installed LinearSolve ───────────────────────── v3.20.0 Installed OrdinaryDiffEqLowOrderRK ──────────── v1.2.0 Installed EnumX ─────────────────────────────── v1.0.5 Installed NLSolversBase ─────────────────────── v7.10.0 Installed JumpProcesses ─────────────────────── v9.16.1 Installed BracketingNonlinearSolve ──────────── v1.3.0 Installed DiffEqBase ────────────────────────── v6.177.2 Installed BandedMatrices ────────────────────── v1.9.4 Installed InverseFunctions ──────────────────── v0.1.17 Installed Reexport ──────────────────────────── v1.2.2 Installed Jieko ─────────────────────────────── v0.2.1 Installed Preferences ───────────────────────── v1.4.3 Installed NonlinearSolve ────────────────────── v4.10.0 Installed Missings ──────────────────────────── v1.2.0 Installed Static ────────────────────────────── v1.2.0 Installed OrdinaryDiffEqNordsieck ───────────── v1.1.0 Installed LaTeXStrings ──────────────────────── v1.4.0 Installed MaybeInplace ──────────────────────── v0.1.4 Installed TableTraits ───────────────────────── v1.0.1 Installed OrdinaryDiffEqAdamsBashforthMoulton ─ v1.2.0 Installed Crayons ───────────────────────────── v4.1.1 Installed SortingAlgorithms ─────────────────── v1.2.1 Installed RecursiveArrayTools ───────────────── v3.34.1 Installed OrdinaryDiffEqLinear ──────────────── v1.3.0 Installed ADTypes ───────────────────────────── v1.15.0 Installed UnPack ────────────────────────────── v1.0.2 Installed Inflate ───────────────────────────── v0.1.5 Installed MacroTools ────────────────────────── v0.5.16 Installed DataStructures ────────────────────── v0.18.22 Installed DiffResults ───────────────────────── v1.1.0 Installed ManualMemory ──────────────────────── v0.1.8 Installed SparseMatrixColorings ─────────────── v0.4.21 Installed FillArrays ────────────────────────── v1.13.0 Installed oneTBB_jll ────────────────────────── v2022.0.0+0 Installed ArnoldiMethod ─────────────────────── v0.4.0 Installed GenericSchur ──────────────────────── v0.5.5 Installed LevyArea ──────────────────────────── v1.0.0 Installed StatsBase ─────────────────────────── v0.34.5 Installed CodecZlib ─────────────────────────── v0.7.8 Installed ExprTools ─────────────────────────── v0.1.10 Installed SciMLJacobianOperators ────────────── v0.1.7 Installed ArrayInterface ────────────────────── v7.19.0 Installed Zygote ────────────────────────────── v0.7.10 Installed IntelOpenMP_jll ───────────────────── v2025.2.0+0 Installed RandomNumbers ─────────────────────── v1.6.0 Installed DataValueInterfaces ───────────────── v1.0.0 Installed CEnum ─────────────────────────────── v0.5.0 Installed CommonSubexpressions ──────────────── v0.3.1 Installed LayoutPointers ────────────────────── v0.1.17 Installed RealDot ───────────────────────────── v0.1.0 Installed ConcreteStructs ───────────────────── v0.2.3 Installed IrrationalConstants ───────────────── v0.2.4 Installed TruncatedStacktraces ──────────────── v1.4.0 Installed Optimisers ────────────────────────── v0.4.6 Installed ObjectFile ────────────────────────── v0.4.4 Installed GPUArraysCore ─────────────────────── v0.2.0 Installed BoundaryValueDiffEq ───────────────── v5.18.0 Installed SimpleTraits ──────────────────────── v0.9.4 Installed ArrayLayouts ──────────────────────── v1.11.1 Installed SparseConnectivityTracer ──────────── v1.0.0 Installed OrdinaryDiffEqRKN ─────────────────── v1.1.0 Installed OrdinaryDiffEqStabilizedIRK ───────── v1.3.0 Installed OrdinaryDiffEqExtrapolation ───────── v1.5.0 Installed PooledArrays ──────────────────────── v1.4.3 Installed OrdinaryDiffEqPRK ─────────────────── v1.1.0 Installed Scratch ───────────────────────────── v1.3.0 Installed Setfield ──────────────────────────── v1.1.2 Installed PDMats ────────────────────────────── v0.11.35 Installed NonlinearSolveQuasiNewton ─────────── v1.6.0 Installed WorkerUtilities ───────────────────── v1.6.1 Installed SteadyStateDiffEq ─────────────────── v2.5.0 Installed DocStringExtensions ───────────────── v0.9.5 Installed Moshi ─────────────────────────────── v0.3.7 Installed DifferentiationInterface ──────────── v0.7.3 Installed OrdinaryDiffEq ────────────────────── v6.99.0 Installed OrdinaryDiffEqHighOrderRK ─────────── v1.1.0 Installed ResettableStacks ──────────────────── v1.1.1 Installed CompositionsBase ──────────────────── v0.1.2 Installed CommonSolve ───────────────────────── v0.2.4 Installed ForwardDiff ───────────────────────── v1.0.1 Installed Rmath_jll ─────────────────────────── v0.5.1+0 Installed SimpleUnPack ──────────────────────── v1.1.0 Installed OrdinaryDiffEqStabilizedRK ────────── v1.1.2 Installed Sundials_jll ──────────────────────── v5.2.3+0 Installed MLDataDevices ─────────────────────── v1.11.0 Installed AliasTables ───────────────────────── v1.1.3 Installed BitTwiddlingConvenienceFunctions ──── v0.1.6 Installed LibTracyClient_jll ────────────────── v0.9.1+6 Installed ComponentArrays ───────────────────── v0.15.28 Installed Krylov ────────────────────────────── v0.10.1 Installed LineSearch ────────────────────────── v0.1.4 Installed SparseInverseSubset ───────────────── v0.1.2 Installed IteratorInterfaceExtensions ───────── v1.0.0 Installed BoundaryValueDiffEqMIRK ───────────── v1.9.0 Installed SciMLSensitivity ──────────────────── v7.88.0 Installed HashArrayMappedTries ──────────────── v0.2.0 Installed FunctionWrappersWrappers ──────────── v0.1.3 Installed NNlib ─────────────────────────────── v0.9.30 Installed RecipesBase ───────────────────────── v1.3.4 Installed DataAPI ───────────────────────────── v1.16.0 Installed SciMLOperators ────────────────────── v1.3.1 Installed OrdinaryDiffEqBDF ─────────────────── v1.6.0 Installed OrdinaryDiffEqSymplecticRK ────────── v1.3.0 Installed EarlyStopping ─────────────────────── v0.3.0 Installed SciMLStructures ───────────────────── v1.7.0 Installed OrdinaryDiffEqLowStorageRK ────────── v1.3.0 Installed StaticArraysCore ──────────────────── v1.4.3 Installed StaticArrays ──────────────────────── v1.9.14 Installed FastGaussQuadrature ───────────────── v1.0.2 Installed Lux ───────────────────────────────── v1.16.0 Installed Requires ──────────────────────────── v1.3.1 Installed AbstractFFTs ──────────────────────── v1.5.0 Installed StringManipulation ────────────────── v0.4.1 Installed OrdinaryDiffEqDifferentiation ─────── v1.10.1 Installed OrdinaryDiffEqNonlinearSolve ──────── v1.11.0 Installed LogExpFunctions ───────────────────── v0.3.29 Installed Enzyme_jll ────────────────────────── v0.0.186+0 Installed ReverseDiff ───────────────────────── v1.16.1 Installed LLVM ──────────────────────────────── v9.4.2 Installed PrettyTables ──────────────────────── v2.4.0 Installed DifferentialEquations ─────────────── v7.16.1 Installed CSV ───────────────────────────────── v0.10.15 Installed FunctionWrappers ──────────────────── v1.1.3 Installed DiffRules ─────────────────────────── v1.15.1 Installed OrdinaryDiffEqCore ────────────────── v1.26.2 Installed Parsers ───────────────────────────── v2.8.3 Installed SciMLBase ─────────────────────────── v2.104.0 Installed Distributions ─────────────────────── v0.25.120 Installed NonlinearSolveFirstOrder ──────────── v1.5.0 Installed Rmath ─────────────────────────────── v0.8.0 Installed OrdinaryDiffEqExplicitRK ──────────── v1.1.0 Installed FiniteDiff ────────────────────────── v2.27.0 Installed FastClosures ──────────────────────── v0.3.2 Installed CloseOpenIntervals ────────────────── v0.1.13 Installed UnsafeAtomics ─────────────────────── v0.3.0 Installed OrdinaryDiffEqFeagin ──────────────── v1.1.0 Installed OrdinaryDiffEqIMEXMultistep ───────── v1.3.0 Installed Polyester ─────────────────────────── v0.7.18 Installed StatsFuns ─────────────────────────── v1.5.0 Installed LuxLib ────────────────────────────── v1.10.0 Installed BoundaryValueDiffEqCore ───────────── v1.11.1 Installed IRTools ───────────────────────────── v0.4.15 Installed WeakRefStrings ────────────────────── v1.4.2 Installed ZygoteRules ───────────────────────── v0.2.7 Installed JLLWrappers ───────────────────────── v1.7.0 Installed OrdinaryDiffEqPDIRK ───────────────── v1.3.1 Installed OrdinaryDiffEqSSPRK ───────────────── v1.3.0 Installed BoundaryValueDiffEqAscher ─────────── v1.8.0 Installed IterationControl ──────────────────── v0.5.4 Installed OrdinaryDiffEqSDIRK ───────────────── v1.3.0 Installed ThreadingUtilities ────────────────── v0.5.5 Installed Accessors ─────────────────────────── v0.1.42 Installed OrdinaryDiffEqDefault ─────────────── v1.5.0 Installed LLVMExtra_jll ─────────────────────── v0.0.37+2 Installed FilePathsBase ─────────────────────── v0.9.24 Installed ExponentialUtilities ──────────────── v1.27.0 Installed OrdinaryDiffEqVerner ──────────────── v1.2.0 Installed Adapt ─────────────────────────────── v4.3.0 Installed Graphs ────────────────────────────── v1.13.0 Installed RuntimeGeneratedFunctions ─────────── v0.5.15 Installed ConstructionBase ──────────────────── v1.6.0 Installed HypergeometricFunctions ───────────── v0.3.28 Installed PoissonRandom ─────────────────────── v0.4.5 Installed SymbolicIndexingInterface ─────────── v0.3.42 Installed Random123 ─────────────────────────── v1.7.1 Installed StochasticDiffEq ──────────────────── v6.80.0 Installed TranscodingStreams ────────────────── v0.11.3 Installed Compat ────────────────────────────── v4.17.0 Installed StrideArraysCore ──────────────────── v0.5.7 Installed PositiveFactorizations ────────────── v0.2.4 Installed Suppressor ────────────────────────── v0.2.8 Installed Statistics ────────────────────────── v1.11.1 Installed PrecompileTools ───────────────────── v1.3.2 Installed FastAlmostBandedMatrices ──────────── v0.1.5 Installed StatsAPI ──────────────────────────── v1.7.1 Installed LazyArrays ────────────────────────── v2.6.1 Installed Cassette ──────────────────────────── v0.3.14 Installed TimerOutputs ──────────────────────── v0.5.29 Installed Atomix ────────────────────────────── v1.1.1 Installed ExproniconLite ────────────────────── v0.10.14 Installed CPUSummary ────────────────────────── v0.2.6 Installed Tracy ─────────────────────────────── v0.1.5 Installed NLsolve ───────────────────────────── v4.5.1 Installed StructArrays ──────────────────────── v0.7.1 Installed ChainRulesCore ────────────────────── v1.25.2 Installed Enzyme ────────────────────────────── v0.13.61 Installed IfElse ────────────────────────────── v0.1.1 Installed Parameters ────────────────────────── v0.12.3 Installed KernelAbstractions ────────────────── v0.9.37 Installed Tracker ───────────────────────────── v0.2.38 Installed DelayDiffEq ───────────────────────── v5.54.0 Installed LuxCore ───────────────────────────── v1.2.6 Installed DiffEqNoiseProcess ────────────────── v5.24.1 Installed MuladdMacro ───────────────────────── v0.2.4 Installed PtrArrays ─────────────────────────── v1.3.0 Installed OrdinaryDiffEqTsit5 ───────────────── v1.1.0 Installed SimpleNonlinearSolve ──────────────── v2.6.0 Installed LineSearches ──────────────────────── v7.4.0 Installed SpecialFunctions ──────────────────── v2.5.1 Installed MatrixFactorizations ──────────────── v3.0.1 Installed FunctionProperties ────────────────── v0.1.2 Installed PolyesterWeave ────────────────────── v0.2.2 Installed OrdinaryDiffEqFunctionMap ─────────── v1.1.1 Installed TumorGrowth ───────────────────────── v0.3.2 Installing 6 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact oneTBB 435.6 KiB Installed artifact LibTracyClient 436.3 KiB Installed artifact LLVMExtra 3.2 MiB Installed artifact Sundials 2.1 MiB Updating `~/.julia/environments/v1.13/Project.toml` [f6b3d34e] + TumorGrowth v0.3.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [621f4979] + AbstractFFTs v1.5.0 [7d9f7c33] + 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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 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+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` Installation completed after 17.29s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 3796.0 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 26 already precompiled. Precompiling package dependencies... ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 274 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:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000733cde5f41f0 Total snapshots: 675. Utilization: 0% ╎675 @Base/task.jl:1129 wait_forever() 674╎ 675 @Base/task.jl:1192 wait() ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000078671d603580 Total snapshots: 674. Utilization: 0% ╎674 @Base/task.jl:1129 wait_forever() 673╎ 674 @Base/task.jl:1192 wait() [274] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/precompile.jl:37 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:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_43063.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3807 [inlined] ijl_apply_generic at /source/src/gf.c:4004 jl_apply at /source/src/julia.h:2345 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 17936761 (Pool: 17934975; Big: 1786); GC: 47 PkgEval terminated after 2730.68s: test duration exceeded the time limit