Package evaluation to test RetentionParameterEstimator on Julia 1.14.0-DEV.1441 (812f3beb0a*) started at 2025-12-31T01:48:07.828 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 6.19s ################################################################################ # Installation # Installing RetentionParameterEstimator... Resolving package versions... Installed Libuuid_jll ───────────────────────── v2.41.2+0 Installed Qt6Base_jll ───────────────────────── v6.8.2+2 Installed CommonWorldInvalidations ──────────── v1.0.0 Installed libass_jll ────────────────────────── v0.17.4+0 Installed MultivariateStats ─────────────────── v0.10.3 Installed libaom_jll ────────────────────────── v3.13.1+0 Installed MonteCarloIntegration ─────────────── v0.2.0 Installed CMAEvolutionStrategy ──────────────── v0.2.6 Installed Bzip2_jll ─────────────────────────── v1.0.9+0 Installed InlineStrings ─────────────────────── v1.4.5 Installed Calculus ──────────────────────────── v0.5.2 Installed HarfBuzz_jll ──────────────────────── v8.5.1+0 Installed Lz4_jll ───────────────────────────── v1.10.1+0 Installed MKL_jll ───────────────────────────── v2025.2.0+0 Installed FastPower ─────────────────────────── v1.3.0 Installed Libtiff_jll ───────────────────────── v4.7.2+0 Installed Optim ─────────────────────────────── v1.13.3 Installed SymbolicUtils 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EnzymeCore ────────────────────────── v0.8.17 Installed OrdinaryDiffEqFIRK ────────────────── v1.19.0 Installed MIMEs ─────────────────────────────── v1.1.0 Installed SentinelArrays ────────────────────── v1.4.9 Installed fzf_jll ───────────────────────────── v0.61.1+0 Installed Distances ─────────────────────────── v0.10.12 Installed Widgets ───────────────────────────── v0.6.7 Installed NaNMath ───────────────────────────── v1.1.3 Installed QuadGK ────────────────────────────── v2.11.2 Installed Fontconfig_jll ────────────────────── v2.17.1+0 Installed Sobol ─────────────────────────────── v1.5.0 Installed OrdinaryDiffEqQPRK ────────────────── v1.7.0 Installed OpenSpecFun_jll ───────────────────── v0.5.6+0 Installed StaticArrayInterface ──────────────── v1.8.0 Installed FastBroadcast ─────────────────────── v0.3.5 Installed WoodburyMatrices ──────────────────── v1.0.0 Installed Tables ────────────────────────────── v1.12.1 Installed NonlinearSolveBase ────────────────── v2.2.0 Installed Einsum ────────────────────────────── v0.4.1 Installed Opus_jll ──────────────────────────── v1.5.2+0 Installed Ogg_jll ───────────────────────────── v1.3.6+0 Installed Xorg_libxcb_jll ───────────────────── v1.17.1+0 Installed EnumX ─────────────────────────────── v1.0.5 Installed LinearSolve ───────────────────────── v3.52.0 Installed Arpack ────────────────────────────── v0.5.4 Installed BracketingNonlinearSolve ──────────── v1.6.1 Installed NLSolversBase ─────────────────────── v7.10.0 Installed OrdinaryDiffEqLowOrderRK ──────────── v1.9.0 Installed ManifoldsBase ─────────────────────── v1.2.0 Installed Unzip ─────────────────────────────── v0.2.0 Installed DiffEqBase ────────────────────────── v6.194.0 Installed LZO_jll ───────────────────────────── v2.10.3+0 Installed Xorg_xcb_util_wm_jll ──────────────── v0.4.2+0 Installed Reexport ──────────────────────────── v1.2.2 Installed InverseFunctions ──────────────────── v0.1.17 Installed Jieko ─────────────────────────────── 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OrdinaryDiffEqSymplecticRK ────────── v1.10.0 Installed Wayland_jll ───────────────────────── v1.24.0+0 Installed Measures ──────────────────────────── v0.3.3 Installed Colors ────────────────────────────── v0.13.1 Installed StaticArrays ──────────────────────── v1.9.16 Installed SciMLStructures ───────────────────── v1.9.0 Installed ChemicalIdentifiers ───────────────── v0.1.10 Installed FastGaussQuadrature ───────────────── v1.1.0 Installed OrdinaryDiffEqLowStorageRK ────────── v1.10.0 Installed StaticArraysCore ──────────────────── v1.4.4 Installed AbstractPlutoDingetjes ────────────── v1.3.2 Installed TaskLocalValues ───────────────────── v0.1.3 Installed Xorg_libxkbfile_jll ───────────────── v1.1.3+0 Installed MultivariatePolynomials ───────────── v0.5.13 Installed Libglvnd_jll ──────────────────────── v1.7.1+1 Installed AbstractFFTs ──────────────────────── v1.5.0 Installed ColorTypes ────────────────────────── v0.12.1 Installed Latexify ──────────────────────────── v0.16.10 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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 27.66s ################################################################################ # Precompilation # ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:10 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/precompile.jl:6 caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull) The function `setindex!` exists, but no method is defined for this combination of argument types. Stacktrace: [1] top-level scope @ /PkgEval.jl/scripts/precompile.jl:7 [2] include(mod::Module, _path::String) @ Base ./Base.jl:309 [3] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [4] _start() @ Base ./client.jl:585 Precompilation failed after 7.35s ################################################################################ # Testing # Testing RetentionParameterEstimator Status `/tmp/jl_1hqSau/Project.toml` [dd82b6e2] GasChromatographySimulator v0.5.6 [0afdae40] RetentionParameterEstimator v0.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_1hqSau/Manifest.toml` [47edcb42] ADTypes v1.21.0 [621f4979] AbstractFFTs v1.5.0 [6e696c72] AbstractPlutoDingetjes v1.3.2 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.22.0 [4c555306] ArrayLayouts v1.12.2 [69666777] Arrow v2.8.0 [31f734f8] ArrowTypes v2.3.0 [13072b0f] AxisAlgorithms 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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...  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB WARNING: Constructor for type "Type" was extended in `Flatbuf` without explicit qualification or import.  NOTE: Assumed "Type" refers to `Base.Type`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Type end`.  Hint: To silence the warning, qualify `Type` as `Base.Type` in the method signature or explicitly `import Base: Type`. WARNING: Constructor for type "PowerManifold" was extended in `Manifolds` without explicit qualification or import.  NOTE: Assumed "PowerManifold" refers to `ManifoldsBase.PowerManifold`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function PowerManifold end`.  Hint: To silence the warning, qualify `PowerManifold` as `ManifoldsBase.PowerManifold` in the method signature or explicitly `import ManifoldsBase: PowerManifold`. WARNING: Constructor for type "Matrix" was extended in `Manifolds` without explicit qualification or import.  NOTE: Assumed "Matrix" refers to `Base.Matrix`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Matrix end`.  Hint: To silence the warning, qualify `Matrix` as `Base.Matrix` in the method signature or explicitly `import Base: Matrix`. [ Info: :short database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/chemical%20identifiers%20pubchem%20small.tsv [ Info: :short database file downloaded. [ Info: :short arrow file not generated, processing... [ Info: :inorganic database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/Inorganic%20db.tsv [ Info: :inorganic database file downloaded. [ Info: :inorganic arrow file not generated, processing... [ Info: :long database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/chemical%20identifiers%20pubchem%20large.tsv [ Info: :long database file downloaded. [ Info: :long arrow file not generated, processing... 4 dependencies had output during precompilation: ┌ Arrow │ WARNING: Constructor for type "Type" was extended in `Flatbuf` without explicit qualification or import. │ NOTE: Assumed "Type" refers to `Base.Type`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Type end`. │ Hint: To silence the warning, qualify `Type` as `Base.Type` in the method signature or explicitly `import Base: Type`. └ ┌ Manifolds │ WARNING: Constructor for type "PowerManifold" was extended in `Manifolds` without explicit qualification or import. │ NOTE: Assumed "PowerManifold" refers to `ManifoldsBase.PowerManifold`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function PowerManifold end`. │ Hint: To silence the warning, qualify `PowerManifold` as `ManifoldsBase.PowerManifold` in the method signature or explicitly `import ManifoldsBase: PowerManifold`. │ WARNING: Constructor for type "Matrix" was extended in `Manifolds` without explicit qualification or import. │ NOTE: Assumed "Matrix" refers to `Base.Matrix`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Matrix end`. │ Hint: To silence the warning, qualify `Matrix` as `Base.Matrix` in the method signature or explicitly `import Base: Matrix`. └ ┌ GasChromatographySimulator │ [ Info: :short database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/chemical%20identifiers%20pubchem%20small.tsv │ [ Info: :short database file downloaded. │ [ Info: :short arrow file not generated, processing... │ [ Info: :inorganic database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/Inorganic%20db.tsv │ [ Info: :inorganic database file downloaded. │ [ Info: :inorganic arrow file not generated, processing... │ [ Info: :long database file not found, downloading from https://raw.githubusercontent.com/CalebBell/chemicals/refs/heads/master/chemicals/Identifiers/chemical%20identifiers%20pubchem%20large.tsv │ [ Info: :long database file downloaded. │ [ Info: :long arrow file not generated, processing... └ ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ [ Info: :custom database file not found, downloading from https://raw.githubusercontent.com/JanLeppert/RetentionData/main/data/add_CI_db.tsv [ Info: :custom database file downloaded. [ Info: :custom arrow file not generated, processing... Test Summary: | Pass Total Time Simulation Test | 2 2 1m23.3s Test Summary: | Pass Total Time Loading Data | 9 9 12.6s ┌ Warning: Using arrays or dicts to store parameters of different types can hurt performance. │ Consider using tuples instead. └ @ SciMLBase ~/.julia/packages/SciMLBase/YE7xF/src/performance_warnings.jl:33 Test Summary: | Pass Total Time Optimization | 6 6 1m37.2s Test Summary: | Pass Total Time Optimization with Missing Values | 4 4 15.9s Testing RetentionParameterEstimator tests passed Testing completed after 1833.74s PkgEval succeeded after 1904.59s