Package evaluation of EpithelialDynamics1D on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T21:37:49.473


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.99s


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# Installation
#

Installing EpithelialDynamics1D...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [ace8a2d7] + EpithelialDynamics1D v1.8.3
    Updating `~/.julia/environments/v1.12/Manifest.toml`
⌅ [47edcb42] + ADTypes v0.2.7
  [7d9f7c33] + Accessors v0.1.42
⌅ [79e6a3ab] + Adapt v3.7.2
  [66dad0bd] + AliasTables v1.1.3
⌃ [4fba245c] + ArrayInterface v7.7.1
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] + CPUSummary v0.2.6
  [d360d2e6] + ChainRulesCore v1.25.1
  [fb6a15b2] + CloseOpenIntervals v0.1.13
  [38540f10] + CommonSolve v0.2.4
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] + Compat v4.16.0
  [a33af91c] + CompositionsBase v0.1.2
  [187b0558] + ConstructionBase v1.5.8
  [adafc99b] + CpuId v0.3.1
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
⌅ [82cc6244] + DataInterpolations v4.8.0
  [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
⌃ [2b5f629d] + DiffEqBase v6.130.0
⌅ [459566f4] + DiffEqCallbacks v2.36.1
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [b4f34e82] + Distances v0.10.12
  [ffbed154] + DocStringExtensions v0.9.3
  [4e289a0a] + EnumX v1.0.4
  [ace8a2d7] + EpithelialDynamics1D v1.8.3
  [e2ba6199] + ExprTools v0.1.10
⌅ [7034ab61] + FastBroadcast v0.2.8
  [1a297f60] + FillArrays v1.13.0
  [64ca27bc] + FindFirstFunctions v1.4.1
  [6a86dc24] + FiniteDiff v2.27.0
⌃ [cfdabe9e] + FiniteVolumeMethod1D v1.1.3
  [f6369f11] + ForwardDiff v0.10.38
  [069b7b12] + FunctionWrappers v1.1.3
  [77dc65aa] + FunctionWrappersWrappers v0.1.3
⌅ [d9f16b24] + Functors v0.4.12
⌅ [46192b85] + GPUArraysCore v0.1.5
  [615f187c] + IfElse v0.1.1
  [3587e190] + InverseFunctions v0.1.17
  [92d709cd] + IrrationalConstants v0.2.4
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [10f19ff3] + LayoutPointers v0.1.17
  [d3d80556] + LineSearches v7.3.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.15
  [d125e4d3] + ManualMemory v0.1.8
  [e1d29d7a] + Missings v1.2.0
  [a903a81a] + MovingBoundaryProblems1D v1.0.3
  [46d2c3a1] + MuladdMacro v0.2.4
⌃ [d41bc354] + NLSolversBase v7.8.3
  [2774e3e8] + NLsolve v4.5.1
  [77ba4419] + NaNMath v1.1.2
  [bac558e1] + OrderedCollections v1.8.0
  [d96e819e] + Parameters v0.12.3
  [f517fe37] + Polyester v0.7.16
  [1d0040c9] + PolyesterWeave v0.2.2
⌃ [d236fae5] + PreallocationTools v0.4.24
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [43287f4e] + PtrArrays v1.3.0
  [3cdcf5f2] + RecipesBase v1.3.4
⌅ [731186ca] + RecursiveArrayTools v2.38.10
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [7e49a35a] + RuntimeGeneratedFunctions v0.5.13
  [94e857df] + SIMDTypes v0.1.0
⌅ [0bca4576] + SciMLBase v1.98.1
  [c0aeaf25] + SciMLOperators v0.3.13
  [efcf1570] + Setfield v1.1.2
  [a2af1166] + SortingAlgorithms v1.2.1
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⌅ [aedffcd0] + Static v0.8.10
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⌅ [2efcf032] + SymbolicIndexingInterface v0.2.2
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  [c8ffd9c3] + MbedTLS_jll v2.28.6+1
  [4536629a] + OpenBLAS_jll v0.3.28+3
  [05823500] + OpenLibm_jll v0.8.1+3
  [bea87d4a] + SuiteSparse_jll v7.8.0+1
  [8e850b90] + libblastrampoline_jll v5.11.2+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 6.55s


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# 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 1078.06s


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# Testing
#

     Testing EpithelialDynamics1D
        Test Could not use exact versions of packages in manifest. Re-resolving dependencies
    Updating `/tmp/jl_1ozZSV/Project.toml`
  [13f3f980] + CairoMakie v0.13.2
⌅ [459566f4] ↓ DiffEqCallbacks v2.36.1 ⇒ v2.35.0
  [ace8a2d7] + EpithelialDynamics1D v1.8.3
⌅ [7ed4a6bd] + LinearSolve v2.16.2
⌃ [1dea7af3] + OrdinaryDiffEq v6.58.2
  [324d217c] + ReferenceTests v0.10.5
  [1bc83da4] + SafeTestsets v0.1.0
  [860ef19b] + StableRNGs v1.0.2
⌃ [9672c7b4] + SteadyStateDiffEq v1.16.1
  [8dfed614] ~ Test ⇒ v1.11.0
    Updating `/tmp/jl_1ozZSV/Manifest.toml`
  [621f4979] + AbstractFFTs v1.5.0
  [1520ce14] + AbstractTrees v0.4.5
  [35492f91] + AdaptivePredicates v1.2.0
  [27a7e980] + Animations v0.4.2
  [ec485272] + ArnoldiMethod v0.4.0
  [67c07d97] + Automa v1.1.0
  [13072b0f] + AxisAlgorithms v1.1.0
  [39de3d68] + AxisArrays v0.4.7
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  [13f3f980] + CairoMakie v0.13.2
  [a2cac450] + ColorBrewer v0.4.1
  [35d6a980] + ColorSchemes v3.29.0
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  [ab62b9b5] + DeepDiffs v1.2.0
  [927a84f5] + DelaunayTriangulation v1.6.4
⌅ [459566f4] ↓ DiffEqCallbacks v2.36.1 ⇒ v2.35.0
  [31c24e10] + Distributions v0.25.118
⌅ [f151be2c] + EnzymeCore v0.6.6
  [ace8a2d7] + EpithelialDynamics1D v1.8.3
  [429591f6] + ExactPredicates v2.2.8
  [d4d017d3] + ExponentialUtilities v1.27.0
  [411431e0] + Extents v0.1.5
  [7a1cc6ca] + FFTW v1.8.1
  [9aa1b823] + FastClosures v0.3.2
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⌅ [8fc22ac5] + FilePaths v0.8.3
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⌃ [9672c7b4] + SteadyStateDiffEq v1.16.1
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  [8dfed614] ~ Test ⇒ v1.11.0
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        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`
        Test Successfully re-resolved
      Status `/tmp/jl_1ozZSV/Project.toml`
  [13f3f980] CairoMakie v0.13.2
  [38540f10] CommonSolve v0.2.4
⌅ [82cc6244] DataInterpolations v4.8.0
⌅ [459566f4] DiffEqCallbacks v2.35.0
  [ace8a2d7] EpithelialDynamics1D v1.8.3
⌃ [cfdabe9e] FiniteVolumeMethod1D v1.1.3
  [f6369f11] ForwardDiff v0.10.38
⌅ [7ed4a6bd] LinearSolve v2.16.2
  [a903a81a] MovingBoundaryProblems1D v1.0.3
⌃ [1dea7af3] OrdinaryDiffEq v6.58.2
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⌅ [0bca4576] SciMLBase v1.98.1
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⌃ [9672c7b4] SteadyStateDiffEq v1.16.1
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      Status `/tmp/jl_1ozZSV/Manifest.toml`
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⌃ [4fba245c] ArrayInterface v7.7.1
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⌅ [82cc6244] DataInterpolations v4.8.0
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⌃ [2b5f629d] DiffEqBase v6.130.0
⌅ [459566f4] DiffEqCallbacks v2.35.0
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⌅ [f151be2c] EnzymeCore v0.6.6
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⌅ [7034ab61] FastBroadcast v0.2.8
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⌅ [8fc22ac5] FilePaths v0.8.3
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⌃ [cfdabe9e] FiniteVolumeMethod1D v1.1.3
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⌅ [731186ca] RecursiveArrayTools v2.38.10
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⌅ [0bca4576] SciMLBase v1.98.1
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⌅ [727e6d20] SimpleNonlinearSolve v0.1.23
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⌃ [47a9eef4] SparseDiffTools v2.18.0
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⌅ [aedffcd0] Static v0.8.10
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⌃ [9672c7b4] SteadyStateDiffEq v1.16.1
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⌅ [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
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⌅ [e9f186c6] Libffi_jll v3.2.2+2
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⌅ [856f044c] MKL_jll v2024.2.0+0
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        Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading.
     Testing Running tests...
Precompiling packages...
   6752.2 ms  ? SciMLBase
   8231.1 ms  ? MovingBoundaryProblems1D
   8058.1 ms  ? FiniteVolumeMethod1D
  13267.6 ms  ? DiffEqBase
  13630.4 ms  ? DiffEqCallbacks
Info Given EpithelialDynamics1D was explicitly requested, output will be shown live 
WARNING: Method definition islinear(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:311 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:7.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
   8194.7 ms  ? EpithelialDynamics1D
WARNING: Method definition islinear(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:311 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:7.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
Precompiling packages...
Info Given SciMLBase was explicitly requested, output will be shown live 
WARNING: Method definition islinear(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:311 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:7.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
   6720.1 ms  ? SciMLBase
WARNING: Method definition islinear(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:311 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:7.
ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation.
WARNING: Method definition islinear(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:311 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:7.
WARNING: Method definition isconstant(Any) in module SciMLOperators at /home/pkgeval/.julia/packages/SciMLOperators/2UPBq/src/interface.jl:254 overwritten in module SciMLBase at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/operators/operators.jl:8.
ERROR: LoadError: ConcurrencyViolationError("deadlock detected in loading SciMLBase -> SciMLBase && EpithelialDynamics1D")
Stacktrace:
  [1] canstart_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2209
  [2] start_loading(modkey::Base.PkgId, build_id::UInt128, stalecheck::Bool)
    @ Base ./loading.jl:2217
  [3] _require_prelocked(uuidkey::Base.PkgId, env::Nothing)
    @ Base ./loading.jl:2479
  [4] macro expansion
    @ ./loading.jl:2412 [inlined]
  [5] macro expansion
    @ ./lock.jl:294 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2369
  [7] #invoke_in_world#2
    @ ./essentials.jl:1091 [inlined]
  [8] invoke_in_world
    @ ./essentials.jl:1087 [inlined]
  [9] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2361
 [10] top-level scope
    @ ~/.julia/packages/SciMLBase/szsYq/src/ensemble/ensemble_analysis.jl:3
 [11] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:301
 [12] top-level scope
    @ ~/.julia/packages/SciMLBase/szsYq/src/SciMLBase.jl:713
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:300
 [14] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2712
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2484
 [16] macro expansion
    @ ./loading.jl:2412 [inlined]
 [17] macro expansion
    @ ./lock.jl:294 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2369
 [19] #invoke_in_world#2
    @ ./essentials.jl:1091 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1087 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2361
 [22] top-level scope
    @ ~/.julia/packages/EpithelialDynamics1D/L1Pzd/src/EpithelialDynamics1D.jl:4
 [23] include(mod::Module, _path::String)
    @ Base ./Base.jl:300
 [24] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2712
 [25] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2484
 [26] macro expansion
    @ ./loading.jl:2412 [inlined]
 [27] macro expansion
    @ ./lock.jl:294 [inlined]
 [28] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2369
 [29] #invoke_in_world#2
    @ ./essentials.jl:1091 [inlined]
 [30] invoke_in_world
    @ ./essentials.jl:1087 [inlined]
 [31] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2361
 [32] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:301
 [33] top-level scope
    @ none:6
 [34] eval(m::Module, e::Any)
    @ Core ./boot.jl:485
 [35] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:295
 [36] _start()
    @ Base ./client.jl:558
in expression starting at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/ensemble/ensemble_analysis.jl:1
in expression starting at /home/pkgeval/.julia/packages/SciMLBase/szsYq/src/SciMLBase.jl:1
in expression starting at /home/pkgeval/.julia/packages/EpithelialDynamics1D/L1Pzd/src/EpithelialDynamics1D.jl:1
in expression starting at /home/pkgeval/.julia/packages/EpithelialDynamics1D/L1Pzd/test/runtests.jl:1

Testing failed after 130.61s

ERROR: LoadError: Package EpithelialDynamics1D errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68
  [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/v1.12/Pkg/src/Operations.jl:2359
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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::IOContext{IO}})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:481
  [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:159
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:300
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:329
 [12] _start()
    @ Base ./client.jl:558
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 1262.59s: illegal method overwrites during precompilation