Package evaluation to test Mice on Julia 1.12.4 (0f21d93eaa*) started at 2026-01-26T23:47:58.945 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.03s ################################################################################ # Installation # Installing Mice... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [d4678d24] + Mice v0.3.8 Updating `~/.julia/environments/v1.12/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [39de3d68] + AxisArrays v0.4.8 ⌅ [324d7699] + CategoricalArrays v0.10.9 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [34004b35] + HypergeometricFunctions v0.3.28 [8197267c] + IntervalSets v0.7.13 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [d4678d24] + Mice v0.3.8 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.8 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization 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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 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 5.08s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 80166.8 ms ✓ Mice 221079.1 ms ✓ BetaML ✗ Mice → MiceDataFramesExt 171268.7 ms ✓ Mice → MiceBetaMLExt 3 dependencies successfully precompiled in 616 seconds. 204 already precompiled. 1 dependency had output during precompilation: ┌ BetaML │ [ Info: Beginning BetaML PrecompileTool workflow.... │ [ Info: ...done BetaML PrecompileTool workflow. └ ERROR: LoadError: The following 1 direct dependency failed to precompile: Mice → MiceDataFramesExt Failed to precompile MiceDataFramesExt [3df86665-4806-5a29-9709-e60aaa713d84] to "/home/pkgeval/.julia/compiled/v1.12/MiceDataFramesExt/jl_XiZ48G". ERROR: LoadError: PosDefException: matrix is not positive definite; Factorization failed. Stacktrace: [1] checkpositivedefinite @ /opt/julia/share/julia/stdlib/v1.12/LinearAlgebra/src/factorization.jl:68 [inlined] [2] #cholesky!#163 @ /opt/julia/share/julia/stdlib/v1.12/LinearAlgebra/src/cholesky.jl:418 [inlined] [3] cholesky! (repeats 2 times) @ /opt/julia/share/julia/stdlib/v1.12/LinearAlgebra/src/cholesky.jl:416 [inlined] [4] _cholesky @ /opt/julia/share/julia/stdlib/v1.12/LinearAlgebra/src/cholesky.jl:552 [inlined] [5] cholesky (repeats 2 times) @ /opt/julia/share/julia/stdlib/v1.12/LinearAlgebra/src/cholesky.jl:542 [inlined] [6] blrDraw!(yₒ::Vector{Float64}, Xₒ::Matrix{Float64}, κ::Float64, yVar::String, iterCounter::Int64, j::Int64, loggedEvents::Vector{String}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/normImpute.jl:44 [7] pmmImpute!(yₒ::Vector{Int64}, X::Matrix{Float64}, whereY::Vector{Bool}, whereCount::Int64, yVar::String, iterCounter::Int64, j::Int64, loggedEvents::Vector{String}; donors::Int64, ridge::Float64, unusedKwargs::@Kwargs{}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/pmmImpute.jl:31 [8] pmmImpute!(yₒ::Vector{Int64}, X::Matrix{Float64}, whereY::Vector{Bool}, whereCount::Int64, yVar::String, iterCounter::Int64, j::Int64, loggedEvents::Vector{String}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/pmmImpute.jl:2 [9] sampler!(workingData::AxisArrays.AxisVector{Vector, Vector{Vector}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, workingDataPacified::AxisArrays.AxisVector{Vector{Matrix{Float64}}, Vector{Vector{Matrix{Float64}}}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, workingDataLevels::AxisArrays.AxisVector{Vector, Vector{Vector}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, meanTraces::Vector{Matrix{Float64}}, varTraces::Vector{Matrix{Float64}}, imputeWhere::AxisArrays.AxisVector{Vector{Bool}, Vector{Vector{Bool}}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, m::Int64, visitSequence::Vector{String}, methods::AxisArrays.AxisVector{String, Vector{String}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, predictorMatrix::AxisArrays.AxisMatrix{Int64, Matrix{Int64}, Tuple{AxisArrays.Axis{:row, Vector{String}}, AxisArrays.Axis{:col, Vector{String}}}}, iter::Int64, iterCounter::Int64, i::Int64, progressReports::Bool, loggedEvents::Vector{String}; kwargs::@Kwargs{}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/sampler.jl:89 [10] sampler!(workingData::AxisArrays.AxisVector{Vector, Vector{Vector}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, workingDataPacified::AxisArrays.AxisVector{Vector{Matrix{Float64}}, Vector{Vector{Matrix{Float64}}}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, workingDataLevels::AxisArrays.AxisVector{Vector, Vector{Vector}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, meanTraces::Vector{Matrix{Float64}}, varTraces::Vector{Matrix{Float64}}, imputeWhere::AxisArrays.AxisVector{Vector{Bool}, Vector{Vector{Bool}}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, m::Int64, visitSequence::Vector{String}, methods::AxisArrays.AxisVector{String, Vector{String}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, predictorMatrix::AxisArrays.AxisMatrix{Int64, Matrix{Int64}, Tuple{AxisArrays.Axis{:row, Vector{String}}, AxisArrays.Axis{:col, Vector{String}}}}, iter::Int64, iterCounter::Int64, i::Int64, progressReports::Bool, loggedEvents::Vector{String}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/sampler.jl:2 [11] mice(data::DataFrames.DataFrame; m::Int64, imputeWhere::AxisArrays.AxisVector{Vector{Bool}, Vector{Vector{Bool}}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, visitSequence::Vector{String}, methods::AxisArrays.AxisVector{String, Vector{String}, Tuple{AxisArrays.Axis{:row, Vector{String}}}}, predictorMatrix::AxisArrays.AxisMatrix{Int64, Matrix{Int64}, Tuple{AxisArrays.Axis{:row, Vector{String}}, AxisArrays.Axis{:col, Vector{String}}}}, iter::Int64, progressReports::Bool, kwargs::@Kwargs{}) @ Mice ~/.julia/packages/Mice/FRsUZ/src/Mice.jl:153 [12] macro expansion @ ~/.julia/packages/Mice/FRsUZ/ext/MiceDataFramesExt.jl:24 [inlined] [13] macro expansion @ ~/.julia/packages/PrecompileTools/gn08A/src/workloads.jl:73 [inlined] [14] top-level scope @ ~/.julia/packages/Mice/FRsUZ/ext/MiceDataFramesExt.jl:8 [15] include(mod::Module, _path::String) @ Base ./Base.jl:306 [16] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:3024 [17] top-level scope @ stdin:5 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2870 [20] include_string @ ./loading.jl:2880 [inlined] [21] exec_options(opts::Base.JLOptions) @ Base ./client.jl:315 [22] _start() @ Base ./client.jl:550 in expression starting at /home/pkgeval/.julia/packages/Mice/FRsUZ/ext/MiceDataFramesExt.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:34 Precompilation failed after 635.16s ################################################################################ # Testing # Testing Mice Status `/tmp/jl_zagRWc/Project.toml` [024491cd] BetaML v0.12.6 [336ed68f] CSV v0.10.15 ⌅ [324d7699] CategoricalArrays v0.10.9 [a93c6f00] DataFrames v1.8.1 [38e38edf] GLM v1.9.2 [d4678d24] Mice v0.3.8 [bd369af6] Tables v1.12.1 [9d95f2ec] TypedTables v1.4.6 [8dfed614] Test v1.11.0 Status `/tmp/jl_zagRWc/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [39de3d68] AxisArrays v0.4.8 [024491cd] BetaML v0.12.6 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.15 ⌅ [324d7699] CategoricalArrays v0.10.9 [082447d4] ChainRules v1.72.6 [d360d2e6] ChainRulesCore v1.26.0 [0b6fb165] ChunkCodecCore v1.0.1 [4c0bbee4] ChunkCodecLibZlib v1.0.0 [55437552] ChunkCodecLibZstd v1.0.0 [fb6a15b2] CloseOpenIntervals v0.1.13 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [85a47980] Dictionaries v0.4.6 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [9dda63f9] ForceImport v0.0.3 [f6369f11] ForwardDiff v1.3.1 [38e38edf] GLM v1.9.2 [46192b85] GPUArraysCore v0.2.0 [076d061b] HashArrayMappedTries v0.2.0 [3e5b6fbb] HostCPUFeatures v0.1.18 [34004b35] HypergeometricFunctions v0.3.28 [7869d1d1] IRTools v0.4.15 [615f187c] IfElse v0.1.1 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.6.3 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [e80e1ace] MLJModelInterface v1.12.1 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [d4678d24] Mice v0.3.8 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [b3c3ace0] RangeArrays v0.3.2 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [431bcebd] SciMLPublic v1.0.1 [30f210dd] ScientificTypesBase v3.0.0 [7e506255] ScopedValues v1.5.0 [91c51154] SentinelArrays v1.4.9 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [dc90abb0] SparseInverseSubset v0.1.2 [276daf66] SpecialFunctions v2.6.1 [03a91e81] SplitApplyCombine v1.2.3 [860ef19b] StableRNGs v1.0.4 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [64bff920] StatisticalTraits v3.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.8 [892a3eda] StringManipulation v0.4.2 [09ab397b] StructArrays v0.7.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 [3bb67fe8] TranscodingStreams v0.11.3 [9d95f2ec] TypedTables v1.4.6 [3a884ed6] UnPack v1.0.2 [3d5dd08c] VectorizationBase v0.21.72 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [e88e6eb3] Zygote v0.7.10 [700de1a5] ZygoteRules v0.2.7 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [3161d3a3] Zstd_jll v1.5.7+1 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [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 v1.12.1 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization 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 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+0 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 5814.7 ms ✓ WeakRefStrings 29119.0 ms ✓ CSV 2 dependencies successfully precompiled in 36 seconds. 28 already precompiled. Precompiling packages... 1126.1 ms ✓ CategoricalArrays → CategoricalArraysSentinelArraysExt 1 dependency successfully precompiled in 1 seconds. 11 already precompiled. Precompiling packages... 46646.9 ms ✓ PrettyTables 99621.7 ms ✓ DataFrames 2 dependencies successfully precompiled in 147 seconds. 34 already precompiled. Precompiling packages... 6344.8 ms ✓ GLM 1 dependency successfully precompiled in 8 seconds. 53 already precompiled. Precompiling packages... 62687.4 ms ✓ Mice → MiceDataFramesExt 1 dependency successfully precompiled in 64 seconds. 80 already precompiled. Precompiling packages... 4344.4 ms ✓ TypedTables 1 dependency successfully precompiled in 4 seconds. 14 already precompiled. Test Summary: | Pass Total Time Mice (PMM, DF) | 8 8 4m01.1s Test Summary: | Pass Total Time Mice (PMM, TT) | 4 4 13.6s Test Summary: | Pass Total Time Mice (norm, DF) | 4 4 9.7s Test Summary: | Pass Total Time Mice (sample, DF) | 4 4 1.9s Test Summary: | Pass Total Time Mice (mean, DF) | 4 4 0.2s Test Summary: | Pass Total Time Mice (RF, DF) | 4 4 1m57.9s Testing Mice tests passed Testing completed after 703.94s PkgEval succeeded after 1371.83s