Package evaluation of CellularPotts on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T22:50:55.115 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.7s ################################################################################ # Installation # Installing CellularPotts... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [11b7dee7] + CellularPotts v0.3.6 Updating `~/.julia/environments/v1.11/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [d1d4a3ce] + BitFlags v0.1.9 [fa961155] + CEnum v0.5.0 [11b7dee7] + CellularPotts v0.3.6 [944b1d66] + CodecZlib v0.7.8 [35d6a980] + ColorSchemes v3.29.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.0 [34da2185] + Compat v4.16.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [d38c429a] + Contour v0.6.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 ⌃ [864edb3b] + DataStructures v0.17.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [ffbed154] + DocStringExtensions v0.9.4 [e30172f5] + Documenter v1.10.1 [460bff9d] + ExceptionUnwrapping v0.1.11 [c87230d0] + FFMPEG v0.4.2 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format 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[8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [efcefdf7] + PCRE2_jll v10.42.0+1 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+2 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 To see why use `status --outdated -m` Installation completed after 6.65s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/tgnBf/src/julia-1.11/activate_set.jl:63 Precompiling package dependencies... Precompilation completed after 244.76s ################################################################################ # Testing # Testing CellularPotts ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920 Status `/tmp/jl_gxq0ln/Project.toml` [6e4b80f9] BenchmarkTools v1.6.0 [11b7dee7] CellularPotts v0.3.6 [35d6a980] ColorSchemes v3.29.0 [5ae59095] Colors v0.13.0 [0c46a032] DifferentialEquations v7.16.1 [e30172f5] Documenter v1.10.1 [86223c79] Graphs v1.12.1 [98b081ad] Literate v2.20.1 [2679e427] Metis v1.5.0 [6fe1bfb0] OffsetArrays v1.16.0 [91a5bcdd] Plots v1.40.11 [08abe8d2] PrettyTables v2.4.0 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [37e2e46d] LinearAlgebra v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_gxq0ln/Manifest.toml` [47edcb42] ADTypes v1.14.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [a95523ee] AlmostBlockDiagonals v0.1.10 [ec485272] ArnoldiMethod v0.4.0 [4fba245c] ArrayInterface v7.18.0 [4c555306] ArrayLayouts v1.11.1 [aae01518] BandedMatrices v1.9.3 [6e4b80f9] BenchmarkTools v1.6.0 [d1d4a3ce] BitFlags v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [764a87c0] BoundaryValueDiffEq v5.16.0 [7227322d] BoundaryValueDiffEqAscher v1.5.0 [56b672f2] BoundaryValueDiffEqCore v1.8.0 [85d9eb09] BoundaryValueDiffEqFIRK v1.6.0 [1a22d4ce] BoundaryValueDiffEqMIRK v1.6.0 [9255f1d6] BoundaryValueDiffEqMIRKN v1.5.0 [ed55bfe0] BoundaryValueDiffEqShooting v1.6.0 [70df07ce] BracketingNonlinearSolve v1.1.3 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.6 [11b7dee7] CellularPotts v0.3.6 [d360d2e6] ChainRulesCore v1.25.1 [fb6a15b2] CloseOpenIntervals v0.1.13 [944b1d66] CodecZlib v0.7.8 [35d6a980] ColorSchemes v3.29.0 [3da002f7] 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling Documenter... 50546.0 ms ✓ Documenter 1 dependency successfully precompiled in 51 seconds. 50 already precompiled. Test Summary: | Pass Total Time Spaces or graphs, who's to say? | 3 3 4.4s Test Summary: | Pass Total Time Periodic grids | 8 8 0.2s Test Summary: | Pass Total Time Neighborhoods | 2 2 0.0s Test Summary: | Pass Total Time Lonely cells | 2 2 7.8s Test Summary: | Pass Total Time Testing positions keyword | 2 2 2.2s Test Summary: | Pass Total Time Adding Cell Properties | 6 6 0.0s Test Summary: | Pass Total Time Add/Delete Cells | 2 2 0.6s Test Summary: | Pass Total Time Penalty tests | 1 1 0.5s Test Summary: | Pass Total Time General Fragment Test | 1 1 3.5s Test Summary: | Pass Total Time Euler Characteristic | 2 2 3.0s Test Summary: | Pass Total Time Show me the CPM | 1 1 0.7s Test Summary: | Pass Total Time Hello World | 1 1 3.0s Test Summary: | Pass Total Time Going 3D | 1 1 4.7s Test Summary: | Pass Total Time Lets Get Moving | 1 1 5.4s Test Summary: | Pass Total Time OnPatrol | 1 1 16.2s Test Summary: | Pass Total Time Over Here | 1 1 3.4s Precompiling DifferentialEquations... 4427.5 ms ✓ RecursiveArrayTools 1913.2 ms ✓ LevyArea 3203.9 ms ✓ SparseConnectivityTracer → SparseConnectivityTracerSpecialFunctionsExt 16442.6 ms ✓ FastAlmostBandedMatrices 1737.6 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 9652.0 ms ✓ Distributions 1851.0 ms ✓ FastPower → FastPowerForwardDiffExt 1940.7 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 2052.2 ms ✓ PreallocationTools 8945.0 ms ✓ SparseDiffTools 2358.5 ms ✓ RecursiveArrayTools → RecursiveArrayToolsFastBroadcastExt 2036.9 ms ✓ RecursiveArrayTools → RecursiveArrayToolsSparseArraysExt 2274.5 ms ✓ RecursiveArrayTools → RecursiveArrayToolsForwardDiffExt 31256.8 ms ✓ SciMLBase 5797.2 ms ✓ Distributions → DistributionsChainRulesCoreExt 2498.6 ms ✓ NLSolversBase 2476.2 ms ✓ PreallocationTools → PreallocationToolsSparseConnectivityTracerExt 5318.2 ms ✓ SparseDiffTools → SparseDiffToolsPolyesterExt 2938.4 ms ✓ SciMLBase → SciMLBaseChainRulesCoreExt 7754.2 ms ✓ SciMLJacobianOperators 10207.7 ms ✓ DiffEqBase 5221.4 ms ✓ LineSearches 29482.6 ms ✓ LinearSolve 51992.7 ms ✓ LineSearch 18625.1 ms ✓ NonlinearSolveBase 20797.0 ms ✓ DiffEqBase → DiffEqBaseChainRulesCoreExt 5078.1 ms ✓ DiffEqBase → DiffEqBaseForwardDiffExt 7528.8 ms ✓ DiffEqBase → DiffEqBaseDistributionsExt 3925.6 ms ✓ DiffEqBase → DiffEqBaseSparseArraysExt 10602.2 ms ✓ DiffEqCallbacks 11966.9 ms ✓ OrdinaryDiffEqCore 3610.4 ms ✓ NLsolve 7075.6 ms ✓ Optim 74017.3 ms ✓ LinearSolve → LinearSolveFastAlmostBandedMatricesExt 4341.7 ms ✓ LinearSolve → LinearSolveEnzymeExt 5226.0 ms ✓ LinearSolve → LinearSolveBandedMatricesExt 8953.0 ms ✓ LinearSolve → LinearSolveSparseArraysExt 22199.8 ms ✓ LineSearch → LineSearchLineSearchesExt 23146.6 ms ✓ NonlinearSolveBase → NonlinearSolveBaseBandedMatricesExt 3313.5 ms ✓ NonlinearSolveBase → NonlinearSolveBaseSparseMatrixColoringsExt 4195.1 ms ✓ NonlinearSolveBase → NonlinearSolveBaseForwardDiffExt 3268.6 ms ✓ NonlinearSolveBase → NonlinearSolveBaseSparseArraysExt 2950.1 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLineSearchExt 4574.5 ms ✓ NonlinearSolveBase → NonlinearSolveBaseLinearSolveExt 23774.9 ms ✓ NonlinearSolveBase → NonlinearSolveBaseDiffEqBaseExt 9450.4 ms ✓ BracketingNonlinearSolve 30276.3 ms ✓ Sundials 9402.1 ms ✓ JumpProcesses 18296.7 ms ✓ OrdinaryDiffEqCore → OrdinaryDiffEqCoreEnzymeCoreExt 26375.9 ms ✓ DiffEqNoiseProcess 34378.6 ms ✓ NonlinearSolveQuasiNewton 17611.4 ms ✓ NonlinearSolveSpectralMethods 52634.7 ms ✓ NonlinearSolveFirstOrder 19475.4 ms ✓ SteadyStateDiffEq 3811.2 ms ✓ BracketingNonlinearSolve → BracketingNonlinearSolveForwardDiffExt 6983.8 ms ✓ OrdinaryDiffEqExplicitRK 8030.8 ms ✓ OrdinaryDiffEqHighOrderRK 7840.9 ms ✓ OrdinaryDiffEqStabilizedRK 6906.0 ms ✓ OrdinaryDiffEqSymplecticRK 9852.4 ms ✓ OrdinaryDiffEqSSPRK 10397.2 ms ✓ OrdinaryDiffEqLowOrderRK 4948.1 ms ✓ OrdinaryDiffEqFunctionMap 16976.5 ms ✓ OrdinaryDiffEqTsit5 73928.7 ms ✓ OrdinaryDiffEqVerner 6842.7 ms ✓ OrdinaryDiffEqPRK 7680.5 ms ✓ OrdinaryDiffEqRKN 7449.2 ms ✓ OrdinaryDiffEqFeagin 6778.9 ms ✓ OrdinaryDiffEqQPRK 11291.1 ms ✓ OrdinaryDiffEqLowStorageRK 15349.4 ms ✓ OrdinaryDiffEqDifferentiation 6661.8 ms ✓ NonlinearSolveQuasiNewton → NonlinearSolveQuasiNewtonForwardDiffExt 4518.8 ms ✓ NonlinearSolveSpectralMethods → NonlinearSolveSpectralMethodsForwardDiffExt 24386.7 ms ✓ BoundaryValueDiffEqCore 24853.1 ms ✓ SimpleNonlinearSolve 9240.2 ms ✓ OrdinaryDiffEqAdamsBashforthMoulton 5743.4 ms ✓ OrdinaryDiffEqNordsieck 6570.7 ms ✓ OrdinaryDiffEqLinear 14499.6 ms ✓ OrdinaryDiffEqExtrapolation 52470.6 ms ✓ OrdinaryDiffEqRosenbrock 270624.6 ms ✓ BoundaryValueDiffEqFIRK 16001.5 ms ✓ BoundaryValueDiffEqShooting 16177.3 ms ✓ BoundaryValueDiffEqMIRKN 155375.4 ms ✓ BoundaryValueDiffEqMIRK 14159.0 ms ✓ BoundaryValueDiffEqAscher 6471.5 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveDiffEqBaseExt 4819.0 ms ✓ SimpleNonlinearSolve → SimpleNonlinearSolveChainRulesCoreExt 40598.3 ms ✓ BoundaryValueDiffEq 33712.3 ms ✓ NonlinearSolve 13170.4 ms ✓ NonlinearSolve → NonlinearSolveNLsolveExt 10050.4 ms ✓ NonlinearSolve → NonlinearSolveSundialsExt 14869.2 ms ✓ OrdinaryDiffEqNonlinearSolve 13449.0 ms ✓ OrdinaryDiffEqStabilizedIRK 17816.4 ms ✓ OrdinaryDiffEqSDIRK 12847.1 ms ✓ OrdinaryDiffEqIMEXMultistep 14917.9 ms ✓ OrdinaryDiffEqPDIRK 54333.3 ms ✓ OrdinaryDiffEqFIRK 40305.9 ms ✓ StochasticDiffEq 12597.0 ms ✓ OrdinaryDiffEqExponentialRK 40387.2 ms ✓ OrdinaryDiffEqBDF 72938.1 ms ✓ OrdinaryDiffEqDefault 16208.3 ms ✓ OrdinaryDiffEq 17543.5 ms ✓ DelayDiffEq 62773.9 ms ✓ DifferentialEquations 103 dependencies successfully precompiled in 2039 seconds. 209 already precompiled. Precompiling DistributionsTestExt... 5618.2 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 9 seconds. 48 already precompiled. Precompiling SparseMatrixColoringsColorsExt... 1965.6 ms ✓ SparseMatrixColorings → SparseMatrixColoringsColorsExt 1 dependency successfully precompiled in 2 seconds. 12 already precompiled. 168 Test Summary: | Pass Total Time Bringing ODEs To Life | 1 1 36m27.4s WARNING: Method definition cpmUpdate!(Any, Any) in module Main at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/BringingODEsToLife/BringingODEsToLife.jl:42 overwritten at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionInsideCells/DiffusionInsideCells.jl:36. Test Summary: | Pass Total Time Diffusion Inside Cells | 1 1 1m09.1s WARNING: redefinition of constant Main.N. This may fail, cause incorrect answers, or produce other errors. ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 27 running 1 of 1 signal (10): User defined signal 1 _ZN4llvm14DomTreeBuilder11SemiNCAInfoINS_17DominatorTreeBaseINS_10BasicBlockELb0EEEE10runSemiNCAERS4_j at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm14DomTreeBuilder11SemiNCAInfoINS_17DominatorTreeBaseINS_10BasicBlockELb0EEEE20CalculateFromScratchERS4_PNS5_15BatchUpdateInfoE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN12_GLOBAL__N_115LoopConstrainer3runEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN12_GLOBAL__N_130InductiveRangeCheckElimination3runEPN4llvm4LoopENS1_12function_refIFvS3_bEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm8IRCEPass3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 run at /source/usr/include/llvm/IR/PassManager.h:517 [inlined] run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:89 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) run at /source/src/pipeline.cpp:777 operator() at /source/src/jitlayers.cpp:1298 withModuleDo<(anonymous namespace)::OptimizerT::operator()(llvm::orc::ThreadSafeModule, llvm::orc::MaterializationResponsibility&) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1259 [inlined] CallImpl<(anonymous namespace)::OptimizerT<4> > at /source/usr/include/llvm/ADT/FunctionExtras.h:221 _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16IRTransformLayer4emitESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EENS0_16ThreadSafeModuleE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc31BasicIRLayerMaterializationUnit11materializeESt10unique_ptrINS0_29MaterializationResponsibilityESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc19MaterializationTask3runEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm6detail18UniqueFunctionBaseIvJSt10unique_ptrINS_3orc4TaskESt14default_deleteIS4_EEEE8CallImplIPFvS7_EEEvPvRS7_ at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession22dispatchOutstandingMUsEv at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession17OL_completeLookupESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EESt10shared_ptrINS0_23AsynchronousSymbolQueryEESt8functionIFvRKNS_8DenseMapIPNS0_8JITDylibENS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISF_vEEEENSG_ISD_vEENS_6detail12DenseMapPairISD_SI_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc25InProgressFullLookupState8completeESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession19OL_applyQueryPhase1ESt10unique_ptrINS0_21InProgressLookupStateESt14default_deleteIS3_EENS_5ErrorE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession6lookupENS0_10LookupKindERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS8_EENS0_15SymbolLookupSetENS0_11SymbolStateENS_15unique_functionIFvNS_8ExpectedINS_8DenseMapINS0_15SymbolStringPtrENS_18JITEvaluatedSymbolENS_12DenseMapInfoISI_vEENS_6detail12DenseMapPairISI_SJ_EEEEEEEEESt8functionIFvRKNSH_IS6_NS_8DenseSetISI_SL_EENSK_IS6_vEENSN_IS6_SV_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) _ZN4llvm3orc16ExecutionSession6lookupERKSt6vectorISt4pairIPNS0_8JITDylibENS0_19JITDylibLookupFlagsEESaIS7_EENS0_15SymbolLookupSetENS0_10LookupKindENS0_11SymbolStateESt8functionIFvRKNS_8DenseMapIS5_NS_8DenseSetINS0_15SymbolStringPtrENS_12DenseMapInfoISI_vEEEENSJ_IS5_vEENS_6detail12DenseMapPairIS5_SL_EEEEEE at /opt/julia/bin/../lib/julia/libLLVM-16jl.so (unknown line) addModule at /source/src/jitlayers.cpp:1875 jl_add_to_ee at /source/src/jitlayers.cpp:2306 _jl_compile_codeinst at /source/src/jitlayers.cpp:277 jl_generate_fptr_impl at /source/src/jitlayers.cpp:536 jl_compile_method_internal at /source/src/gf.c:2536 [inlined] jl_compile_method_internal at /source/src/gf.c:2423 _jl_invoke at /source/src/gf.c:2940 [inlined] ijl_apply_generic at /source/src/gf.c:3125 sparse at /source/usr/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:1093 sparse at /source/usr/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:1328 [inlined] _spdiagm at /source/usr/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:4262 [inlined] spdiagm at /source/usr/share/julia/stdlib/v1.11/SparseArrays/src/sparsematrix.jl:4224 unknown function (ip: 0x79345db78d72) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 #laplacian_matrix#4 at /home/pkgeval/.julia/packages/Graphs/OIRln/src/linalg/spectral.jl:94 laplacian_matrix at /home/pkgeval/.julia/packages/Graphs/OIRln/src/linalg/spectral.jl:86 [inlined] laplacian_matrix at /home/pkgeval/.julia/packages/Graphs/OIRln/src/linalg/spectral.jl:86 unknown function (ip: 0x79345db727ca) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./sysimg.jl:35 unknown function (ip: 0x79345e778a26) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 eval_body at /source/src/interpreter.c:539 eval_body at /source/src/interpreter.c:539 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x79347a100082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] exec_options at ./client.jl:296 _start at ./client.jl:531 jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x79347b3f4249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) ============================================================== Profile collected. A report will print at the next yield point ============================================================== WARNING: Method definition cpmUpdate!(Any, Any) in module Main at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionInsideCells/DiffusionInsideCells.jl:36 overwritten at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionOutsideCells/DiffusionOutsideCells.jl:30. WARNING: Method definition f(Any, Any, Any, Any) in module Main at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/BringingODEsToLife/BringingODEsToLife.jl:55 overwritten at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionOutsideCells/DiffusionOutsideCells.jl:50. ====================================================================================== 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:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 #wait#731 at ./condition.jl:130 wait at ./condition.jl:125 [inlined] wait at ./process.jl:694 wait at ./process.jl:687 unknown function (ip: 0x738cea53c032) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 subprocess_handler at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2142 #131 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2082 withenv at ./env.jl:265 #118 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1931 with_temp_env at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1789 #116 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1898 #mktempdir#28 at ./file.jl:819 unknown function (ip: 0x738cea5290dd) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 mktempdir at ./file.jl:815 mktempdir at ./file.jl:815 [inlined] #sandbox#115 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1845 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1837 unknown function (ip: 0x738cea51d69a) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 #test#128 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2063 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] #test#146 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:460 unknown function (ip: 0x738cea51d39d) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 #test#77 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 unknown function (ip: 0x738cea51cd8d) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:148 #test#75 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] #test#74 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 unknown function (ip: 0x738cea519236) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 eval_body at /source/src/interpreter.c:539 eval_body at /source/src/interpreter.c:539 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./Base.jl:557 jfptr_include_46977.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 exec_options at ./client.jl:323 _start at ./client.jl:531 jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x738ceb789249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) ============================================================== 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/v1.11/Profile/src/Profile.jl:1240 Overhead ╎ [+additional indent] Count File:Line; Function ========================================================= Thread 1 Task 0x0000738cde200010 Total snapshots: 24. Utilization: 0% ╎24 @Base/client.jl:531; _start() ╎ 24 @Base/client.jl:323; exec_options(opts::Base.JLOptions) ╎ 24 @Base/Base.jl:557; include(mod::Module, _path::String) ╎ 24 @Base/loading.jl:2794; _include(mapexpr::Function, mod::Module, _path:… ╎ 24 @Base/loading.jl:2734; include_string(mapexpr::typeof(identity), mod:… ╎ 24 @Base/boot.jl:430; eval ╎ ╎ 24 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typeo… ╎ ╎ 24 @Pkg/src/API.jl:146; #test#74 ╎ ╎ 24 @Pkg/src/API.jl:147; test ╎ ╎ 24 @Pkg/src/API.jl:147; #test#75 ╎ ╎ 24 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, ::t… ╎ ╎ ╎ 24 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec};… ╎ ╎ ╎ 24 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, io… ╎ ╎ ╎ 24 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Vect… ╎ ╎ ╎ 24 …src/Operations.jl:2007; test ╎ ╎ ╎ 24 …src/Operations.jl:2063; test(ctx::Pkg.Types.Context, pkgs… ╎ ╎ ╎ ╎ 24 …rc/Operations.jl:1837; kwcall(::@NamedTuple{preferences:… ╎ ╎ ╎ ╎ 24 …rc/Operations.jl:1845; #sandbox#115 ╎ ╎ ╎ ╎ 24 @Base/file.jl:815; mktempdir ╎ ╎ ╎ ╎ 24 @Base/file.jl:815; mktempdir(fn::Function, parent::Str… ╎ ╎ ╎ ╎ 24 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var"#… ╎ ╎ ╎ ╎ ╎ 24 …/Operations.jl:1898; (::Pkg.Operations.var"#116#121… ╎ ╎ ╎ ╎ ╎ 24 …/Operations.jl:1789; with_temp_env(fn::Pkg.Operati… ╎ ╎ ╎ ╎ ╎ 24 …Operations.jl:1931; (::Pkg.Operations.var"#118#12… ╎ ╎ ╎ ╎ ╎ 24 @Base/env.jl:265; withenv(::Pkg.Operations.var"#1… ╎ ╎ ╎ ╎ ╎ 24 …Operations.jl:2082; (::Pkg.Operations.var"#131#… ╎ ╎ ╎ ╎ ╎ ╎ 24 …perations.jl:2142; subprocess_handler(cmd::Cmd… ╎ ╎ ╎ ╎ ╎ ╎ 24 …e/process.jl:687; wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 24 …e/process.jl:694; wait(x::Base.Process, sync… ╎ ╎ ╎ ╎ ╎ ╎ 24 …ondition.jl:125; wait ╎ ╎ ╎ ╎ ╎ ╎ 24 …ondition.jl:130; wait(c::Base.GenericCondi… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 …ase/task.jl:1021; wait() 23╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 …ase/task.jl:1012; poptask(W::Base.Intrus… [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 [27] signal 15: Terminated uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 in expression starting at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionOutsideCells/DiffusionOutsideCells.jl:65 getindex at ./essentials.jl:917 [inlined] ijl_task_get_next at /source/src/scheduler.c:522 _broadcast_getindex at ./broadcast.jl:644 [inlined] _getindex at ./broadcast.jl:675 [inlined] _getindex at ./broadcast.jl:674 [inlined] _broadcast_getindex at ./broadcast.jl:650 [inlined] getindex at ./broadcast.jl:610 [inlined] macro expansion at ./broadcast.jl:973 [inlined] macro expansion at ./simdloop.jl:77 [inlined] copyto! at ./broadcast.jl:972 [inlined] copyto! at ./broadcast.jl:925 [inlined] copy at ./broadcast.jl:897 [inlined] materialize at ./broadcast.jl:872 [inlined] broadcast_preserving_zero_d at ./broadcast.jl:861 [inlined] - at ./arraymath.jl:8 f at /home/pkgeval/.julia/packages/CellularPotts/EuGHg/docs/src/ExampleGallery/DiffusionOutsideCells/DiffusionOutsideCells.jl:52 Void at /home/pkgeval/.julia/packages/SciMLBase/LGLmH/src/utils.jl:486 [inlined] CallWrapper at /home/pkgeval/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:65 unknown function (ip: 0x79345db9e8a2) macro expansion at /home/pkgeval/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:137 [inlined] do_ccall at /home/pkgeval/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:125 [inlined] FunctionWrapper at /home/pkgeval/.julia/packages/FunctionWrappers/Q5cBx/src/FunctionWrappers.jl:144 [inlined] _call at /home/pkgeval/.julia/packages/FunctionWrappersWrappers/9XR0m/src/FunctionWrappersWrappers.jl:12 [inlined] FunctionWrappersWrapper at /home/pkgeval/.julia/packages/FunctionWrappersWrappers/9XR0m/src/FunctionWrappersWrappers.jl:10 [inlined] ODEFunction at /home/pkgeval/.julia/packages/SciMLBase/LGLmH/src/scimlfunctions.jl:2470 [inlined] reset_fsal! at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/integrators/integrator_utils.jl:486 [inlined] apply_step! at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/integrators/integrator_utils.jl:410 loopheader! at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/integrators/integrator_utils.jl:14 solve! at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/solve.jl:616 #__solve#62 at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/solve.jl:7 [inlined] __solve at /home/pkgeval/.julia/packages/OrdinaryDiffEqCore/bMOsj/src/solve.jl:1 [inlined] #solve_call#35 at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:635 [inlined] solve_call at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:592 [inlined] #solve_up#44 at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:1142 [inlined] solve_up at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:1120 [inlined] #solve#42 at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:1057 [inlined] solve at /home/pkgeval/.julia/packages/DiffEqBase/zYZst/src/solve.jl:1047 unknown function (ip: 0x79345db99dd9) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 poptask at ./task.jl:1012 jl_toplevel_eval_flex at /source/src/toplevel.c:886 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _include at ./loading.jl:2794 include at ./sysimg.jl:35 unknown function (ip: 0x79345e778a26) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 eval_body at /source/src/interpreter.c:539 eval_body at /source/src/interpreter.c:539 wait at ./task.jl:1021 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 #wait#731 at ./condition.jl:130 eval at ./boot.jl:430 [inlined] include_string at ./loading.jl:2734 _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 wait at ./condition.jl:125 [inlined] _trywait at ./asyncevent.jl:145 _include at ./loading.jl:2794 include at ./sysimg.jl:38 unknown function (ip: 0x79347a100082) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] do_call at /source/src/interpreter.c:126 eval_value at /source/src/interpreter.c:223 eval_stmt_value at /source/src/interpreter.c:174 [inlined] eval_body at /source/src/interpreter.c:670 jl_interpret_toplevel_thunk at /source/src/interpreter.c:824 profile_printing_listener at ./Base.jl:577 jl_toplevel_eval_flex at /source/src/toplevel.c:943 jl_toplevel_eval_flex at /source/src/toplevel.c:886 ijl_toplevel_eval_in at /source/src/toplevel.c:994 #1190 at ./Base.jl:617 eval at ./boot.jl:430 [inlined] exec_options at ./client.jl:296 jfptr_YY.1190_76096.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] _start at ./client.jl:531 start_task at /source/src/task.c:1202 unknown function (ip: (nil)) Allocations: 29864089 (Pool: 29862937; Big: 1152); GC: 27 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") jfptr__start_73523.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] true_main at /source/src/jlapi.c:900 jl_repl_entrypoint at /source/src/jlapi.c:1059 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x79347b3f4249) __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) unknown function (ip: (nil)) Allocations: 116660195 (Pool: 116657120; Big: 3075); GC: 127 error at ./error.jl:35 #schedule#761 at ./task.jl:884 schedule at ./task.jl:876 [inlined] uv_writecb_task at ./stream.jl:1200 jfptr_uv_writecb_task_67080.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jlcapi_uv_writecb_task_67543.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420 ijl_task_get_next at /source/src/scheduler.c:522 poptask at ./task.jl:1012 wait at ./task.jl:1021 uv_write at ./stream.jl:1081 unsafe_write at ./stream.jl:1154 write at ./strings/io.jl:248 [inlined] print at ./strings/io.jl:250 jfptr_print_48429.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 showerror at ./errorshow.jl:152 unknown function (ip: 0x738cea53e6a6) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _atexit at ./initdefs.jl:462 jfptr__atexit_69596.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] ijl_atexit_hook at /source/src/init.c:271 jl_exit_thread0_cb at /source/src/signals-unix.c:517 PkgEval terminated after 2724.65s: test duration exceeded the time limit