Package evaluation of ReactionNetworkEvolution on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-07T01:59:46.819 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.08s ################################################################################ # Installation # Installing ReactionNetworkEvolution... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [61220d1e] + ReactionNetworkEvolution v0.1.5 Updating `~/.julia/environments/v1.10/Manifest.toml` ⌅ [79e6a3ab] + Adapt v3.7.2 [66dad0bd] + AliasTables v1.1.3 [c7e460c6] + ArgParse v1.2.0 [ec485272] + ArnoldiMethod v0.4.0 ⌅ [4fba245c] + ArrayInterface v6.0.25 [30b0a656] + ArrayInterfaceCore v0.1.29 [6ba088a2] + ArrayInterfaceGPUArrays v0.2.2 [015c0d05] + ArrayInterfaceOffsetArrays v0.1.7 [b0d46f97] + ArrayInterfaceStaticArrays v0.1.5 [dd5226c6] + ArrayInterfaceStaticArraysCore v0.1.4 ⌃ [4c555306] + ArrayLayouts v0.8.19 ⌅ [aae01518] + BandedMatrices v0.17.18 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 ⌅ [764a87c0] + BoundaryValueDiffEq v2.11.0 ⌅ [fa961155] + CEnum v0.4.2 ⌅ [2a0fbf3d] + CPUSummary v0.1.30 [336ed68f] + CSV v0.10.15 [d360d2e6] + ChainRulesCore v1.25.1 ⌃ [fb6a15b2] + CloseOpenIntervals v0.1.11 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + 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⌅ [f6369f11] + ForwardDiff v0.10.38 [069b7b12] + FunctionWrappers v1.1.3 [77dc65aa] + FunctionWrappersWrappers v0.1.3 ⌅ [46192b85] + GPUArraysCore v0.1.5 [c145ed77] + GenericSchur v0.5.5 [86223c79] + Graphs v1.13.0 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 ⌅ [b5f81e59] + IOCapture v0.1.1 [615f187c] + IfElse v0.1.1 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [42fd0dbc] + IterativeSolvers v0.9.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 ⌃ [ccbc3e58] + JumpProcesses v9.5.1 ⌅ [ef3ab10e] + KLU v0.4.1 ⌅ [ba0b0d4f] + Krylov v0.9.10 ⌅ [0b1a1467] + KrylovKit v0.6.1 [b964fa9f] + LaTeXStrings v1.4.0 ⌃ [10f19ff3] + LayoutPointers v0.1.13 [2d8b4e74] + LevyArea v1.0.0 [d3d80556] + LineSearches v7.3.0 ⌅ [7ed4a6bd] + LinearSolve v1.34.1 [2ab3a3ac] + LogExpFunctions v0.3.29 ⌃ [bdcacae8] + LoopVectorization 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RecursiveArrayTools v2.32.3 ⌃ [f2c3362d] + RecursiveFactorization v0.2.22 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [ae5879a3] + ResettableStacks v1.1.1 [79098fc4] + Rmath v0.8.0 [e916ade1] + RoadRunner v2.7.1 [7e49a35a] + RuntimeGeneratedFunctions v0.5.15 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 ⌅ [0bca4576] + SciMLBase v1.81.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 ⌅ [727e6d20] + SimpleNonlinearSolve v0.1.5 [699a6c99] + SimpleTraits v0.9.4 [ce78b400] + SimpleUnPack v1.1.0 [66db9d55] + SnoopPrecompile v1.0.3 [a2af1166] + SortingAlgorithms v1.2.1 ⌅ [47a9eef4] + SparseDiffTools v1.30.0 [e56a9233] + Sparspak v0.3.11 [276daf66] + SpecialFunctions v2.5.1 ⌅ [aedffcd0] + Static v0.8.10 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [9672c7b4] + SteadyStateDiffEq v1.12.0 ⌃ [789caeaf] + StochasticDiffEq v6.58.0 ⌅ [7792a7ef] + StrideArraysCore v0.4.7 [892a3eda] + StringManipulation v0.4.1 ⌃ [c3572dad] + Sundials v4.15.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [b718987f] + TextWrap v1.0.2 [8290d209] + ThreadingUtilities v0.5.4 [3bb67fe8] + TranscodingStreams v0.11.3 [a2a6695c] + TreeViews v0.3.0 ⌅ [d5829a12] + TriangularSolve v0.1.21 [410a4b4d] + Tricks v0.1.10 [3a884ed6] + UnPack v1.0.2 ⌃ [3d5dd08c] + VectorizationBase v0.21.58 [19fa3120] + VertexSafeGraphs v0.2.0 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [700de1a5] + ZygoteRules v0.2.7 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [fb77eaff] + Sundials_jll v5.2.2+0 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [1a1011a3] + SharedArrays [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 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 9.32s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 834.87s ################################################################################ # Testing # Testing ReactionNetworkEvolution Status `/tmp/jl_ljnJvq/Project.toml` [c7e460c6] ArgParse v1.2.0 [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.0.3 [a93c6f00] DataFrames v1.7.0 ⌃ [0c46a032] DifferentialEquations v7.6.0 [31c24e10] Distributions v0.25.120 [682c06a0] JSON v0.21.4 [61220d1e] ReactionNetworkEvolution v0.1.5 [e916ade1] RoadRunner v2.7.1 ⌃ [c3572dad] Sundials v4.15.1 [ade2ca70] Dates [9a3f8284] Random [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_ljnJvq/Manifest.toml` ⌅ [79e6a3ab] Adapt v3.7.2 [66dad0bd] AliasTables v1.1.3 [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 ⌅ [4fba245c] ArrayInterface v6.0.25 [30b0a656] ArrayInterfaceCore v0.1.29 [6ba088a2] ArrayInterfaceGPUArrays v0.2.2 [015c0d05] ArrayInterfaceOffsetArrays v0.1.7 [b0d46f97] ArrayInterfaceStaticArrays v0.1.5 [dd5226c6] ArrayInterfaceStaticArraysCore 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... WARNING: Method definition boundscheck() in module StrideArraysCore at /home/pkgeval/.julia/packages/StrideArraysCore/lUhTe/src/ptr_array.jl:886 overwritten at /home/pkgeval/.julia/packages/StrideArraysCore/lUhTe/src/StrideArraysCore.jl:72. WARNING: Method definition (::Type{RoadRunner.RRVector})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:1 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRStringArray})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:4 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRDoubleMatrix})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:7 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRComplex})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:10 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRComplexVector})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:13 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRComplexMatrix})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:16 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRCData})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:19 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRList})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:22 overwritten on the same line (check for duplicate calls to `include`). WARNING: Method definition (::Type{RoadRunner.RRListItem})() in module RoadRunner at /home/pkgeval/.julia/packages/RoadRunner/SJjp6/src/rrc_types.jl:25 overwritten on the same line (check for duplicate calls to `include`). Using default settings Test Summary: | Pass Total Time basic functions | 6 6 14.2s Using default settings Test Summary: | Pass Total Time solver | 3 3 7.5s Using default settings Test Summary: | Pass Total Time network mutations | 4 4 0.9s output processing: Test Failed at /home/pkgeval/.julia/packages/ReactionNetworkEvolution/GQEYD/test/output_processing_test.jl:72 Expression: !(ReactionNetworkEvolution.is_oscillator(broken_astr)) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] top-level scope @ ~/.julia/packages/ReactionNetworkEvolution/GQEYD/test/output_processing_test.jl:508 [3] include(fname::String) @ Base.MainInclude ./client.jl:494 [4] macro expansion @ ~/.julia/packages/ReactionNetworkEvolution/GQEYD/test/runtests.jl:17 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [6] top-level scope @ ~/.julia/packages/ReactionNetworkEvolution/GQEYD/test/runtests.jl:17 Test Summary: | Pass Fail Total Time output processing | 3 1 4 6.8s ERROR: LoadError: Some tests did not pass: 3 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ReactionNetworkEvolution/GQEYD/test/runtests.jl:16 Testing failed after 84.04s ERROR: LoadError: Package ReactionNetworkEvolution errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 952.16s: package has test failures