Package evaluation to test MixedModels on Julia 1.12.7-DEV.42 (6f510b6086*) started at 2026-06-20T02:43:44.063 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 8.37s ################################################################################ # Installation # Installing MixedModels... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [ff71e718] + MixedModels v5.7.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [79e6a3ab] + Adapt v4.6.1 [66dad0bd] + AliasTables v1.1.3 [4c555306] + ArrayLayouts v1.12.2 [69666777] + Arrow v2.8.1 [31f734f8] + ArrowTypes v2.3.0 [093aae92] + BSplineKit v0.19.2 [aae01518] + BandedMatrices v1.11.0 [c3b6d118] + BitIntegers v0.3.7 [fa961155] + CEnum v0.5.0 [5ba52731] + CodecLz4 v0.4.6 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [f0e56b4a] + ConcurrentUtilities v2.5.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.19.5 [e2d170a0] + DataValueInterfaces v1.0.0 [85a47980] + Dictionaries v0.4.6 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.16.0 [31c24e10] + Distributions v0.25.127 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.7 [e2ba6199] + ExprTools v0.1.10 [442a2c76] + FastGaussQuadrature v1.3.0 [1a297f60] + FillArrays v1.16.0 [f6369f11] + ForwardDiff v1.4.1 [38e38edf] + GLM v1.9.5 [34004b35] + HypergeometricFunctions v0.3.28 [615f187c] + IfElse v0.1.1 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.5 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.8.0 [0f8b85d8] + JSON3 v1.14.3 [2ab3a3ac] + LogExpFunctions v1.0.1 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [ff71e718] + MixedModels v5.7.0 [7e9fb7ac] + MixedModelsDatasets v0.1.2 [78c3b35d] + Mocking v0.8.1 [76087f3c] + NLopt v1.2.1 [77ba4419] + NaNMath v1.1.4 ⌅ [bac558e1] + OrderedCollections v1.8.2 [90014a1f] + PDMats v0.11.37 [69de0a69] + Parsers v2.8.6 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [189a3867] + Reexport v1.2.2 [545c379f] + RegressionFormulae v0.1.4 [79098fc4] + Rmath v0.9.0 [431bcebd] + SciMLPublic v1.0.1 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.10 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.8.0 [03a91e81] + SplitApplyCombine v1.3.0 [aedffcd0] + Static v1.4.0 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.12 [4c63d2b9] + StatsFuns v2.2.0 [3eaba693] + StatsModels v0.7.10 ⌅ [354b36f9] + StringViews v1.3.7 [856f2bd8] + StructTypes v1.11.0 [dc5dba14] + TZJData v1.5.0+2025b [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [f269a46b] + TimeZones v1.22.2 [3bb67fe8] + TranscodingStreams v0.11.3 [9d95f2ec] + TypedTables v1.4.6 [5ced341a] + Lz4_jll v1.10.1+0 [079eb43e] + NLopt_jll v2.11.0+0 [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 [4af54fe1] + LazyArtifacts v1.11.0 [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 [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 v3.5.6+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. To see why use `status --outdated -m` Installation completed after 6.49s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 39023.8 ms ✓ MixedModels → MixedModelsPRIMAExt 35758.9 ms ✓ MixedModels → MixedModelsFiniteDiffExt 2 dependencies successfully precompiled in 85 seconds. 179 already precompiled. 24 dependencies precompiled but different versions are currently loaded (ArgTools, Base64, Dates, Downloads, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, Logging, Markdown, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, Pkg, Printf, StyledStrings, TOML, Tar, UUIDs, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 83 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompilation completed after 102.69s ################################################################################ # Testing # Testing MixedModels Status `/tmp/jl_p2flep/Project.toml` [4c88cf16] Aqua v0.8.16 [69666777] Arrow v2.8.1 [093aae92] BSplineKit v0.19.2 [324d7699] CategoricalArrays v1.1.1 [34da2185] Compat v4.18.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [31c24e10] Distributions v0.25.127 [7d51a73a] ExplicitImports v1.15.0 [6a86dc24] FiniteDiff v2.31.0 [f6369f11] ForwardDiff v1.4.1 [38e38edf] GLM v1.9.5 [92d709cd] IrrationalConstants v0.2.6 [0f8b85d8] JSON3 v1.14.3 [ff71e718] MixedModels v5.7.0 [7e9fb7ac] MixedModelsDatasets v0.1.2 [76087f3c] NLopt v1.2.1 [0a7d04aa] PRIMA v0.2.4 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [92933f4c] ProgressMeter v1.11.0 [545c379f] RegressionFormulae v0.1.4 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.18 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [3eaba693] StatsModels v0.7.10 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [bd369af6] Tables v1.12.1 [9d95f2ec] TypedTables v1.4.6 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_p2flep/Manifest.toml` [79e6a3ab] Adapt v4.6.1 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.16 [4fba245c] ArrayInterface v7.25.0 [4c555306] ArrayLayouts v1.12.2 [69666777] Arrow v2.8.1 [31f734f8] ArrowTypes v2.3.0 [093aae92] BSplineKit v0.19.2 [aae01518] BandedMatrices v1.11.0 [c3b6d118] BitIntegers v0.3.7 [fa961155] CEnum v0.5.0 [324d7699] CategoricalArrays v1.1.1 [5ba52731] CodecLz4 v0.4.6 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.1.0 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.1 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.5 [e2d170a0] DataValueInterfaces v1.0.0 [85a47980] Dictionaries v0.4.6 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.16.0 [31c24e10] Distributions v0.25.127 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.7 [7d51a73a] ExplicitImports v1.15.0 [e2ba6199] ExprTools v0.1.10 [442a2c76] FastGaussQuadrature v1.3.0 [1a297f60] FillArrays v1.16.0 [6a86dc24] FiniteDiff v2.31.0 [f6369f11] ForwardDiff v1.4.1 [38e38edf] GLM v1.9.5 [34004b35] HypergeometricFunctions v0.3.28 [615f187c] IfElse v0.1.1 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v1.0.1 [1914dd2f] MacroTools v0.5.16 [e1d29d7a] Missings v1.2.0 [ff71e718] MixedModels v5.7.0 [7e9fb7ac] MixedModelsDatasets v0.1.2 [78c3b35d] Mocking v0.8.1 [76087f3c] NLopt v1.2.1 [77ba4419] NaNMath v1.1.4 ⌅ [bac558e1] OrderedCollections v1.8.2 [90014a1f] PDMats v0.11.37 [0a7d04aa] PRIMA v0.2.4 [69de0a69] Parsers v2.8.6 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.3.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [189a3867] Reexport v1.2.2 [545c379f] RegressionFormulae v0.1.4 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [431bcebd] SciMLPublic v1.0.1 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.10 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.8.0 [03a91e81] SplitApplyCombine v1.3.0 [860ef19b] StableRNGs v1.0.4 [aedffcd0] Static v1.4.0 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.12 [4c63d2b9] StatsFuns v2.2.0 [3eaba693] StatsModels v0.7.10 [892a3eda] StringManipulation v0.4.4 ⌅ [354b36f9] StringViews v1.3.7 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [dc5dba14] TZJData v1.5.0+2025b [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [f269a46b] TimeZones v1.22.2 [3bb67fe8] TranscodingStreams v0.11.3 ⌅ [c3b1956e] TypeUtils v1.14.0 [9d95f2ec] TypedTables v1.4.6 [5ced341a] Lz4_jll v1.10.1+0 [079eb43e] NLopt_jll v2.11.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [eead6e0c] PRIMA_jll v0.7.1+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 [4af54fe1] LazyArtifacts v1.11.0 [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 v3.5.6+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... 2691.1 ms ✓ NLopt_jll 2171.3 ms ✓ CodecLz4 1284.6 ms ✓ JSON3 → JSON3ArrowExt 27861.7 ms ✓ BSplineKit 4541.1 ms ✓ RegressionFormulae 2294.2 ms ✓ NLopt 18753.4 ms ✓ Arrow 9445.9 ms ✓ MixedModelsDatasets 165736.1 ms ✓ MixedModels 33746.2 ms ✓ MixedModels → MixedModelsForwardDiffExt 10 dependencies successfully precompiled in 273 seconds. 131 already precompiled. 73 dependencies precompiled but different versions are currently loaded (AliasTables, ArgTools, Base64, CompilerSupportLibraries_jll, DataAPI, DataStructures, DataValueInterfaces, Dates, Distributions, DocStringExtensions, Downloads, FillArrays, FillArrays → FillArraysPDMatsExt, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStatisticsExt, GLM, HypergeometricFunctions, InteractiveUtils, IrrationalConstants, IteratorInterfaceExtensions, JLLWrappers, JuliaSyntaxHighlighting, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, Markdown, Missings, MozillaCACerts_jll, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, PDMats, PDMats → StatsBaseExt, Pkg, Pkg → REPLExt, PrecompileTools, Preferences, Printf, PtrArrays, QuadGK, REPL, Reexport, Rmath, Rmath_jll, Serialization, ShiftedArrays, SortingAlgorithms, SparseArrays, SpecialFunctions, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StatsFuns, StatsModels, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, TableTraits, Tables, Tar, UUIDs, Unicode, Zlib_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 48 dependents of these packages may trigger further precompilation to work with the unexpected versions. ┌ Info: Julia Version 1.12.7-DEV.42 │ Commit 6f510b6086* (2026-06-17 00:39 UTC) │ Platform Info: │ OS: Linux (x86_64-linux-gnu) │ CPU: 128 × AMD EPYC 7502 32-Core Processor │ WORD_SIZE: 64 │ LLVM: libLLVM-18.1.7 (ORCJIT, znver2) │ GC: Built with stock GC │ Threads: 1 default, 0 interactive, 1 GC (on 1 virtual cores) │ Environment: │ JULIA_CPU_THREADS = 1 │ JULIA_NUM_PRECOMPILE_TASKS = 1 │ JULIA_PKG_PRECOMPILE_AUTO = 0 │ JULIA_PKGEVAL = true │ JULIA_DEPOT_PATH = /home/pkgeval/.julia:/usr/local/share/julia: │ JULIA_NUM_THREADS = 1 └ JULIA_LOAD_PATH = @:/tmp/jl_p2flep [ Info: LBTConfig([ILP64] libopenblas64_.so) Test Summary: | Pass Total Time Aqua | 9 9 2m15.0s Test Summary: | Pass Total Time ExplicitImports | 2 2 1m16.8s Test Summary: | Pass Total Time average | 1 1 0.2s Test Summary: | Pass Total Time densify | 3 3 2.3s Test Summary: | Pass Total Time isconstant | 13 13 2.9s Test Summary: | Pass Total Time PCA | 3 3 55.5s Test Summary: | Pass Total Time formula | 2 2 36.7s Test Summary: | Pass Total Time formula misspecification | 8 8 21.2s Test Summary: | Pass Total Time non-unicode function aliases for exports | 2 2 0.0s Test Summary: | Pass Total Time fullranknumeric | 1 1 1.5s Test Summary: | Pass Total Time fullrankcategorical | 2 2 6.9s Test Summary: | Pass Total Time dependentcolumn | 4 4 1.4s Test Summary: | Pass Total Time qr missing cells | 2 2 0.1s Test Summary: | Pass Total Time zero columns in X | 2 2 0.0s Test Summary: | Pass Total Time UBlk | 24 24 20.1s Test Summary: | Pass Total Time mul! | 36 36 2.1s ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = fit(::Type{LinearMixedModel}, f::FormulaTerm{Term, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::@NamedTuple{Y::Vector{Float64}, A::PooledVector{String, UInt32, Vector{UInt32}}, G::PooledVector{String, UInt32, Vector{UInt32}}, H::PooledVector{String, UInt32, Vector{UInt32}}}; weights::Vector{Any}, wts::Vector{Float64}, contrasts::Dict{Symbol, Any}, σ::Nothing, amalgamate::Bool, kwargs::Base.Pairs{Symbol, Bool, Nothing, @NamedTuple{progress::Bool}}) at linearmixedmodel.jl:234 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/linearmixedmodel.jl:234 Test Summary: | Pass Total Time reweight! | 2 2 14.4s Test Summary: | Pass Total Time rankupdate! | 2 2 3.1s Test Summary: | Pass Total Time lmulλ! | 1 1 13.2s Test Summary: | Pass Total Time Xymat | 15 15 2.1s Test Summary: | Pass Broken Total Time XymatSparse | 12 1 13 1m09.0s Precompiling packages... 93347.4 ms ✓ DataFrames 1 dependency successfully precompiled in 95 seconds. 35 already precompiled. 30 dependencies precompiled but different versions are currently loaded (Base64, Compat, Compat → CompatLinearAlgebraExt, DataAPI, DataStructures, DataValueInterfaces, Dates, Future, InlineStrings, InteractiveUtils, IteratorInterfaceExtensions, JuliaSyntaxHighlighting, Markdown, Missings, OrderedCollections, PooledArrays, PrecompileTools, Preferences, Printf, REPL, Reexport, SentinelArrays, SortingAlgorithms, Statistics, StyledStrings, TOML, TableTraits, Tables, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 3 dependents of these packages may trigger further precompilation to work with the unexpected versions. Test Summary: | Pass Total Time scalarReMat | 39 39 27.7s Test Summary: | Pass Total Time RandomEffectsTerm | 18 18 23.8s Test Summary: | Pass Total Time random effects term syntax | 24 24 39.2s Precompiling packages... 1052.3 ms ✓ CategoricalArrays → CategoricalArraysStructTypesExt 1 dependency successfully precompiled in 1 seconds. 14 already precompiled. 13 dependencies precompiled but different versions are currently loaded (CategoricalArrays, Compat, Compat → CompatLinearAlgebraExt, DataAPI, Dates, Future, Missings, Printf, Statistics, StructTypes, TOML, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 1110.9 ms ✓ CategoricalArrays → CategoricalArraysSentinelArraysExt 1 dependency successfully precompiled in 1 seconds. 14 already precompiled. 13 dependencies precompiled but different versions are currently loaded (CategoricalArrays, Compat, Compat → CompatLinearAlgebraExt, DataAPI, Dates, Future, Missings, Printf, SentinelArrays, Statistics, TOML, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 6576.9 ms ✓ CategoricalArrays → CategoricalArraysArrowExt 1 dependency successfully precompiled in 7 seconds. 55 already precompiled. 54 dependencies precompiled but different versions are currently loaded (ArgTools, Arrow, ArrowTypes, BitIntegers, CategoricalArrays, CategoricalArrays → CategoricalArraysSentinelArraysExt, CodecLz4, CodecZstd, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, ConcurrentUtilities, DataAPI, DataValueInterfaces, Dates, Downloads, EnumX, ExprTools, Future, InlineStrings, InlineStrings → ArrowTypesExt, IteratorInterfaceExtensions, JLLWrappers, LibCURL, LibCURL_jll, LibSSH2_jll, Lz4_jll, Missings, Mmap, Mocking, MozillaCACerts_jll, NetworkOptions, OpenSSL_jll, OrderedCollections, PooledArrays, Preferences, Printf, Scratch, SentinelArrays, Serialization, Statistics, StringViews, TOML, TZJData, TableTraits, Tables, TimeZones, TranscodingStreams, UUIDs, Unicode, Zlib_jll, Zstd_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Test Summary: | Pass Total Time Grouping | 1 1 0.5s Test Summary: | Pass Total Time Grouping pseudo-contrasts | 10 10 18.0s Test Summary: | Pass Broken Total Time Auto application of Grouping() | 36 3 39 19.1s Test Summary: | Pass Total Time LMM from MixedModel | 3 3 7.9s Test Summary: | Pass Total Time offset | 2 2 2.2s Test Summary: | Pass Total Time Dyestuff | 83 83 1m20.5s ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 ┌ Warning: NLopt was roundoff limited └ @ MixedModels.MixedModelsNLoptExt ~/.julia/packages/MixedModels/QWl8z/src/MixedModelsNLoptExt.jl:132 Test Summary: | Pass Total Time Dyestuff2 | 11 11 7.7s Test Summary: | Pass Total Time penicillin | 26 26 7.2s Test Summary: | Pass Total Time pastes | 22 22 9.3s Test Summary: | Pass Total Time InstEval | 26 26 4.2s ┌ Warning: optsum was saved with an older version of MixedModels.jl: consider resaving. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/serialization.jl:135 ┌ Warning: optsum was saved with an older version of MixedModels.jl: consider resaving. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/serialization.jl:135 ┌ Warning: optsum was saved with an older version of MixedModels.jl: consider resaving. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/serialization.jl:135 ┌ Warning: optsum was saved with an older version of MixedModels.jl: consider resaving. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/serialization.jl:135 Test Summary: | Pass Total Time sleep | 139 139 1m33.2s Test Summary: | Pass Total Time d3 | 6 6 27.8s Test Summary: | Pass Total Time kb07 | 6 6 23.9s Test Summary: | Pass Total Time oxide | 1 1 14.6s Test Summary: | Pass Total Time Rank deficient | 7 7 5.8s Test Summary: | Pass Total Time coeftable | 1 1 0.0s ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = fit(::Type{LinearMixedModel}, f::FormulaTerm{Term, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::@NamedTuple{a::Vector{Float64}, b::Vector{Float64}, c::PooledVector{String, UInt32, Vector{UInt32}}, w1::Vector{Int64}, w2::Vector{Float64}}; weights::Vector{Any}, wts::Vector{Int64}, contrasts::Dict{Symbol, Any}, σ::Nothing, amalgamate::Bool, kwargs::Base.Pairs{Symbol, Bool, Nothing, @NamedTuple{progress::Bool}}) at linearmixedmodel.jl:234 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/linearmixedmodel.jl:234 Test Summary: | Pass Total Time wts | 3 3 3.9s Test Summary: | Pass Total Time unifying ReMat eltypes | 3 3 4.5s Test Summary: | Pass Total Time recovery from misscaling | 2 2 10.6s Test Summary: | Pass Total Time methods we don't define | 4 4 0.8s Test Summary: | Pass Total Time GLMM from MixedModel | 2 2 13.7s Test Summary: | Pass Total Time Type for instance | 9 9 0.3s Test Summary: | Pass Total Time contra | 41 41 22.9s ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = fit(::Type{GeneralizedLinearMixedModel}, f::FormulaTerm{FunctionTerm{typeof(/), Vector{Term}}, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::@NamedTuple{herd::Arrow.DictEncoded{String, Int8, Arrow.List{String, Int32, Vector{UInt8}}}, period::Arrow.DictEncoded{String, Int8, Arrow.List{String, Int32, Vector{UInt8}}}, incid::Arrow.Primitive{Int8, Vector{Int8}}, hsz::Arrow.Primitive{Int8, Vector{Int8}}}, d::Binomial{Float64}, l::LogitLink; weights::Vector{Any}, wts::Vector{Float64}, contrasts::Dict{Symbol, Any}, offset::Vector{Any}, amalgamate::Bool, kwargs::Base.Pairs{Symbol, Any, Nothing, @NamedTuple{progress::Bool, init_from_lmm::Vector{Symbol}}}) at generalizedlinearmixedmodel.jl:187 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/generalizedlinearmixedmodel.jl:187 ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = GeneralizedLinearMixedModel(f::FormulaTerm{FunctionTerm{typeof(/), Vector{Term}}, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::DataFrame, d::Binomial{Float64}, l::LogitLink; kwargs::Base.Pairs{Symbol, Vector{Float64}, Nothing, @NamedTuple{wts::Vector{Float64}}}) at generalizedlinearmixedmodel.jl:352 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/generalizedlinearmixedmodel.jl:352 Test Summary: | Pass Total Time cbpp | 19 19 24.7s Test Summary: | Pass Total Time verbagg | 4 4 20.9s Test Summary: | Pass Total Time grouseticks | 8 8 3m19.3s Test Summary: | Pass Total Time dispersion | 3 3 15.9s Test Summary: | Pass Total Time mmec | 4 4 4.7s ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = GeneralizedLinearMixedModel(f::FormulaTerm{FunctionTerm{typeof(/), Vector{Term}}, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::Arrow.Table, d::Binomial{Float64}, l::LogitLink; kwargs::Base.Pairs{Symbol, Arrow.Primitive{Int8, Vector{Int8}}, Nothing, @NamedTuple{wts::Arrow.Primitive{Int8, Vector{Int8}}}}) at generalizedlinearmixedmodel.jl:352 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/generalizedlinearmixedmodel.jl:352 Test Summary: | Pass Total Time GLMM saveoptsum | 6 6 3.2s Test Summary: | Pass Total Time Bad initial value | 2 2 17.3s Test Summary: | Pass Total Time GHnorm | 5 5 0.5s Test Summary: | Pass Total Time linear, and lmm wrapper | 8 8 0.8s Test Summary: | Pass Total Time generalized | 1 1 15.0s Test Summary: | Pass Total Time Normal-IdentityLink | 2 2 0.2s Test Summary: | Pass Total Time Normal Distribution GLMM | 1 1 2.8s Test Summary: | Pass Total Time Missing Omit | 2 2 4.7s ┌ Error: Random effects are not nested. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/likelihoodratiotest.jl:253 ┌ Error: Fixed effects are not nested. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/likelihoodratiotest.jl:231 ┌ Error: Inner models have grouping variables not present in outer models. └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/likelihoodratiotest.jl:240 Test Summary: | Pass Total Time isnested | 10 10 11.7s Test Summary: | Pass Total Time likelihoodratio test | 22 22 35.3s ┌ Warning: `wts` keyword argument is deprecated, use `weights` instead │ caller = fit(::Type{GeneralizedLinearMixedModel}, f::FormulaTerm{FunctionTerm{typeof(/), Vector{Term}}, Tuple{ConstantTerm{Int64}, Term, FunctionTerm{typeof(|), Vector{AbstractTerm}}}}, tbl::@NamedTuple{herd::Arrow.DictEncoded{String, Int8, Arrow.List{String, Int32, Vector{UInt8}}}, period::Arrow.DictEncoded{String, Int8, Arrow.List{String, Int32, Vector{UInt8}}}, incid::Arrow.Primitive{Int8, Vector{Int8}}, hsz::Arrow.Primitive{Int8, Vector{Int8}}}, d::Binomial{Float64}, l::LogitLink; weights::Vector{Any}, wts::Vector{Float64}, contrasts::Dict{Symbol, Any}, offset::Vector{Any}, amalgamate::Bool, kwargs::Base.Pairs{Symbol, Bool, Nothing, @NamedTuple{progress::Bool}}) at generalizedlinearmixedmodel.jl:187 └ @ Core ~/.julia/packages/MixedModels/QWl8z/src/generalizedlinearmixedmodel.jl:187 Test Summary: | Pass Total Time simulate!(::MixedModel) | 9 9 25.7s ┌ Warning: Fixed-effects matrix is rank deficient └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/Xymat.jl:67 Test Summary: | Pass Total Time bootstrap | 52 52 3m06.6s Test Summary: | Pass Total Time show and summary | 7 7 16.0s Test Summary: | Pass Total Time markdown | 10 10 12.1s Test Summary: | Pass Total Time html | 3 3 0.4s Test Summary: | Pass Total Time latex | 7 7 0.4s Test Summary: | Pass Total Time opt limits | 6 6 1.3s Test Summary: | Pass Total Time simulate[!](::AbstractVector) | 11 11 30.4s ┌ Warning: Fixed-effects matrix is rank deficient └ @ MixedModels ~/.julia/packages/MixedModels/QWl8z/src/Xymat.jl:67 Test Summary: | Pass Total Time predict | 55 55 2m08.6s Test Summary: | Pass Total Time fixed sigma | 14 14 4.2s Precompiling packages... 1551.8 ms ✓ PRIMA_jll 2149.5 ms ✓ PRIMA 2 dependencies successfully precompiled in 4 seconds. 12 already precompiled. 8 dependencies precompiled but different versions are currently loaded (CompilerSupportLibraries_jll, Dates, JLLWrappers, Preferences, Printf, TOML, UUIDs and Unicode). Restart julia to access the new versions. Otherwise, 5 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 6449.1 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 1 dependency successfully precompiled in 7 seconds. 21 already precompiled. 21 dependencies precompiled but different versions are currently loaded (CompilerSupportLibraries_jll, Dates, DocStringExtensions, HypergeometricFunctions, InverseFunctions, InverseFunctions → InverseFunctionsDatesExt, IrrationalConstants, JLLWrappers, LogExpFunctions, LogExpFunctions → LogExpFunctionsInverseFunctionsExt, OpenLibm_jll, OpenSpecFun_jll, Preferences, Printf, Reexport, Rmath, Rmath_jll, SpecialFunctions, StatsFuns, TOML and Unicode). Restart julia to access the new versions. Otherwise, 1 dependent of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 35522.7 ms ✓ MixedModels → MixedModelsPRIMAExt 1 dependency successfully precompiled in 40 seconds. 149 already precompiled. 148 dependencies precompiled but different versions are currently loaded (Adapt, Adapt → AdaptSparseArraysExt, Adapt → AdaptStaticArraysExt, AliasTables, ArgTools, ArrayLayouts, ArrayLayouts → ArrayLayoutsSparseArraysExt, Arrow, ArrowTypes, BSplineKit, BandedMatrices, BandedMatrices → BandedMatricesSparseArraysExt, Base64, BitIntegers, CEnum, CodecLz4, CodecZstd, Combinatorics, CommonSubexpressions, CommonWorldInvalidations, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, ConcurrentUtilities, DataAPI, DataStructures, DataValueInterfaces, Dates, Dictionaries, DiffResults, DiffRules, Distributed, Distributions, DocStringExtensions, Downloads, EnumX, ExprTools, FastGaussQuadrature, FillArrays, FillArrays → FillArraysPDMatsExt, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStaticArraysExt, FillArrays → FillArraysStatisticsExt, ForwardDiff, ForwardDiff → ForwardDiffStaticArraysExt, Future, GLM, HypergeometricFunctions, IfElse, Indexing, InlineStrings, InlineStrings → ArrowTypesExt, InlineStrings → ParsersExt, InteractiveUtils, InverseFunctions, InverseFunctions → InverseFunctionsDatesExt, IrrationalConstants, IteratorInterfaceExtensions, JLLWrappers, JSON3, JSON3 → JSON3ArrowExt, JuliaSyntaxHighlighting, LazyArtifacts, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, LogExpFunctions → LogExpFunctionsInverseFunctionsExt, Logging, Lz4_jll, MacroTools, Markdown, Missings, MixedModels, MixedModels → MixedModelsForwardDiffExt, MixedModelsDatasets, Mmap, Mocking, MozillaCACerts_jll, NLopt, NLopt_jll, NaNMath, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, PDMats, PDMats → StatsBaseExt, PRIMA, PRIMA_jll, Parsers, Pkg, Pkg → REPLExt, PooledArrays, PrecompileTools, Preferences, Printf, ProgressMeter, PtrArrays, QuadGK, REPL, Reexport, RegressionFormulae, Rmath, Rmath_jll, SciMLPublic, Scratch, SentinelArrays, Serialization, ShiftedArrays, SortingAlgorithms, SparseArrays, SpecialFunctions, SplitApplyCombine, Static, StaticArrays, StaticArrays → StaticArraysStatisticsExt, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StatsFuns, StatsFuns → StatsFunsInverseFunctionsExt, StatsModels, StringViews, StructTypes, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, TZJData, TableTraits, Tables, Tar, TimeZones, TranscodingStreams, TypeUtils, TypedTables, UUIDs, Unicode, Zlib_jll, Zstd_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Test Summary: | Pass Total Time PRIMA | 25 25 1m55.0s Test Summary: | Pass Total Time ForwardDiff | 6 6 1m26.6s Precompiling packages... 4324.3 ms ✓ ArrayInterface → ArrayInterfaceBandedMatricesExt 1 dependency successfully precompiled in 5 seconds. 16 already precompiled. 15 dependencies precompiled but different versions are currently loaded (Adapt, Adapt → AdaptStaticArraysExt, ArrayInterface, ArrayLayouts, BandedMatrices, Dates, FillArrays, FillArrays → FillArraysStaticArraysExt, PrecompileTools, Preferences, Printf, StaticArrays, StaticArraysCore, TOML and Unicode). Restart julia to access the new versions. Otherwise, 2 dependents of these packages may trigger further precompilation to work with the unexpected versions. Precompiling packages... 4464.3 ms ✓ FiniteDiff → FiniteDiffBandedMatricesExt 37507.1 ms ✓ MixedModels → MixedModelsFiniteDiffExt 2 dependencies successfully precompiled in 46 seconds. 152 already precompiled. 146 dependencies precompiled but different versions are currently loaded (Adapt, Adapt → AdaptSparseArraysExt, Adapt → AdaptStaticArraysExt, AliasTables, ArgTools, ArrayInterface, ArrayInterface → ArrayInterfaceBandedMatricesExt, ArrayInterface → ArrayInterfaceSparseArraysExt, ArrayInterface → ArrayInterfaceStaticArraysCoreExt, ArrayLayouts, ArrayLayouts → ArrayLayoutsSparseArraysExt, Arrow, ArrowTypes, BSplineKit, BandedMatrices, BandedMatrices → BandedMatricesSparseArraysExt, Base64, BitIntegers, CEnum, CodecLz4, CodecZstd, Combinatorics, CommonSubexpressions, CommonWorldInvalidations, Compat, Compat → CompatLinearAlgebraExt, CompilerSupportLibraries_jll, ConcurrentUtilities, DataAPI, DataStructures, DataValueInterfaces, Dates, Dictionaries, DiffResults, DiffRules, Distributed, Distributions, DocStringExtensions, Downloads, EnumX, ExprTools, FastGaussQuadrature, FillArrays, FillArrays → FillArraysPDMatsExt, FillArrays → FillArraysSparseArraysExt, FillArrays → FillArraysStaticArraysExt, FillArrays → FillArraysStatisticsExt, FiniteDiff, ForwardDiff, ForwardDiff → ForwardDiffStaticArraysExt, Future, GLM, HypergeometricFunctions, IfElse, Indexing, InlineStrings, InlineStrings → ArrowTypesExt, InlineStrings → ParsersExt, InteractiveUtils, IrrationalConstants, IteratorInterfaceExtensions, JLLWrappers, JSON3, JSON3 → JSON3ArrowExt, JuliaSyntaxHighlighting, LazyArtifacts, LibCURL, LibCURL_jll, LibGit2, LibGit2_jll, LibSSH2_jll, LogExpFunctions, Logging, Lz4_jll, MacroTools, Markdown, Missings, MixedModels, MixedModels → MixedModelsForwardDiffExt, MixedModelsDatasets, Mmap, Mocking, MozillaCACerts_jll, NLopt, NLopt_jll, NaNMath, NetworkOptions, OpenLibm_jll, OpenSSL_jll, OpenSpecFun_jll, OrderedCollections, PDMats, PDMats → StatsBaseExt, Parsers, Pkg, Pkg → REPLExt, PooledArrays, PrecompileTools, Preferences, Printf, ProgressMeter, PtrArrays, QuadGK, REPL, Reexport, RegressionFormulae, Rmath, Rmath_jll, SciMLPublic, Scratch, SentinelArrays, Serialization, ShiftedArrays, SortingAlgorithms, SparseArrays, SpecialFunctions, SplitApplyCombine, Static, StaticArrays, StaticArrays → StaticArraysStatisticsExt, StaticArraysCore, Statistics, Statistics → SparseArraysExt, StatsAPI, StatsBase, StatsFuns, StatsModels, StringViews, StructTypes, StyledStrings, SuiteSparse, SuiteSparse_jll, TOML, TZJData, TableTraits, Tables, Tar, TimeZones, TranscodingStreams, TypedTables, UUIDs, Unicode, Zlib_jll, Zstd_jll, nghttp2_jll and p7zip_jll). Restart julia to access the new versions. Otherwise, 6 dependents of these packages may trigger further precompilation to work with the unexpected versions. Test Summary: | Pass Total Time FiniteDiff | 5 5 53.4s Testing MixedModels tests passed Testing completed after 2552.72s PkgEval terminated after 2701.22s: test duration exceeded the time limit