Package evaluation of MixedModels on Julia 1.13.0-DEV.111 (ce76dbf07d*) started at 2025-02-28T04:50:14.154 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.15s ################################################################################ # Installation # Installing MixedModels... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [ff71e718] + MixedModels v4.31.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4c555306] + ArrayLayouts v1.11.1 [69666777] + Arrow v2.8.0 [31f734f8] + ArrowTypes v2.3.0 [093aae92] + BSplineKit v0.18.2 [aae01518] + BandedMatrices v1.9.2 [c3b6d118] + BitIntegers v0.3.2 [fa961155] + CEnum v0.5.0 [5ba52731] + CodecLz4 v0.4.5 [6b39b394] + CodecZstd v0.8.6 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [f0e56b4a] + ConcurrentUtilities v2.5.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [85a47980] + Dictionaries v0.4.4 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [4e289a0a] + EnumX v1.0.4 [e2ba6199] + ExprTools v0.1.10 [442a2c76] + FastGaussQuadrature v1.0.2 [1a297f60] + FillArrays v1.13.0 [f6369f11] + ForwardDiff v0.10.38 [38e38edf] + GLM v1.9.0 [34004b35] + HypergeometricFunctions v0.3.27 [615f187c] + IfElse v0.1.1 [313cdc1a] + Indexing v1.1.1 [842dd82b] + InlineStrings v1.4.3 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [0f8b85d8] + JSON3 v1.14.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [e1d29d7a] + Missings v1.2.0 [ff71e718] + MixedModels v4.31.0 [7e9fb7ac] + MixedModelsDatasets v0.1.2 [78c3b35d] + Mocking v0.8.1 [76087f3c] + NLopt v1.1.3 [77ba4419] + NaNMath v1.1.2 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.2 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [6c6a2e73] + Scratch v1.2.1 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [03a91e81] + SplitApplyCombine v1.2.3 [aedffcd0] + Static v1.1.1 [90137ffa] + StaticArrays v1.9.12 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 [3eaba693] + StatsModels v0.7.4 [354b36f9] + StringViews v1.3.4 [856f2bd8] + StructTypes v1.11.0 [dc5dba14] + TZJData v1.4.0+2025a [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [f269a46b] + TimeZones v1.21.2 [3bb67fe8] + TranscodingStreams v0.11.3 [9d95f2ec] + TypedTables v1.4.6 [5ced341a] + Lz4_jll v1.10.1+0 [079eb43e] + NLopt_jll v2.10.0+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 v1.12.0 [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 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 3.18s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 69.18s ################################################################################ # Testing # Testing MixedModels Status `/tmp/jl_loWLA7/Project.toml` [4c88cf16] Aqua v0.8.11 [69666777] Arrow v2.8.0 [093aae92] BSplineKit v0.18.2 [34da2185] Compat v4.16.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [31c24e10] Distributions v0.25.117 [7d51a73a] ExplicitImports v1.11.1 [38e38edf] GLM v1.9.0 [0f8b85d8] JSON3 v1.14.1 [ff71e718] MixedModels v4.31.0 [7e9fb7ac] MixedModelsDatasets v0.1.2 [76087f3c] NLopt v1.1.3 [0a7d04aa] PRIMA v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [92933f4c] ProgressMeter v1.10.2 [860ef19b] StableRNGs v1.0.2 [90137ffa] StaticArrays v1.9.12 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.3.2 [3eaba693] StatsModels v0.7.4 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [bd369af6] Tables v1.12.0 [9d95f2ec] TypedTables v1.4.6 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [d6f4376e] Markdown v1.11.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_loWLA7/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.2.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.11 [4c555306] ArrayLayouts v1.11.1 [69666777] Arrow v2.8.0 [31f734f8] ArrowTypes v2.3.0 [093aae92] BSplineKit v0.18.2 [aae01518] BandedMatrices v1.9.2 [c3b6d118] BitIntegers v0.3.2 [fa961155] CEnum v0.5.0 [5ba52731] CodecLz4 v0.4.5 [6b39b394] CodecZstd v0.8.6 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [f0e56b4a] ConcurrentUtilities v2.5.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [85a47980] Dictionaries v0.4.4 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 [4e289a0a] EnumX v1.0.4 [7d51a73a] ExplicitImports v1.11.1 [e2ba6199] ExprTools v0.1.10 [442a2c76] FastGaussQuadrature v1.0.2 [1a297f60] FillArrays v1.13.0 [f6369f11] ForwardDiff v0.10.38 [38e38edf] GLM v1.9.0 [34004b35] HypergeometricFunctions v0.3.27 [615f187c] IfElse v0.1.1 [313cdc1a] Indexing v1.1.1 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [0f8b85d8] JSON3 v1.14.1 [70703baa] JuliaSyntax v0.4.10 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [e1d29d7a] Missings v1.2.0 [ff71e718] MixedModels v4.31.0 [7e9fb7ac] MixedModelsDatasets v0.1.2 [78c3b35d] Mocking v0.8.1 [76087f3c] NLopt v1.1.3 [77ba4419] NaNMath v1.1.2 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [0a7d04aa] PRIMA v0.2.2 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [6c6a2e73] Scratch v1.2.1 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [03a91e81] SplitApplyCombine v1.2.3 [860ef19b] StableRNGs v1.0.2 [aedffcd0] Static v1.1.1 [90137ffa] StaticArrays v1.9.12 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.3.2 [3eaba693] StatsModels v0.7.4 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [dc5dba14] TZJData v1.4.0+2025a [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [f269a46b] TimeZones v1.21.2 [3bb67fe8] TranscodingStreams v0.11.3 [c3b1956e] TypeUtils v1.4.2 [9d95f2ec] TypedTables v1.4.6 [5ced341a] Lz4_jll v1.10.1+0 [079eb43e] NLopt_jll v2.10.0+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 v1.12.0 [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 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [3f19e933] p7zip_jll v17.5.0+2 Testing Running tests... ┌ Info: Julia Version 1.13.0-DEV.111 │ Commit ce76dbf07d* (2025-02-24 19:42 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, 1 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_loWLA7 [ Info: LBTConfig([ILP64] libopenblas64_.so) Test Summary: | Pass Total Time Aqua | 9 9 2m50.6s Test Summary: | Pass Total Time ExplicitImports | 2 2 1m00.1s Test Summary: | Pass Total Time average | 1 1 0.2s Test Summary: | Pass Total Time densify | 3 3 2.4s Test Summary: | Pass Total Time isconstant | 13 13 2.7s Test Summary: | Pass Total Time replicate | 2 2 3.4s Test Summary: | Pass Total Time datasets | 6 6 0.6s Test Summary: | Pass Total Time PCA | 3 3 55.6s Test Summary: | Pass Total Time formula | 2 2 40.7s Test Summary: | Pass Total Time formula misspecification | 8 8 23.0s Test Summary: | Pass Total Time non-unicode function aliases for exports | 2 2 0.0s WARNING: Method definition rank(LinearAlgebra.QRPivoted{T, S, C, P} where P<:(AbstractArray{var"#s4740", 1} where var"#s4740"<:Integer) where C<:AbstractArray{T, 1} where S<:AbstractArray{T, 2} where T) in module LinearAlgebra at /source/usr/share/julia/stdlib/v1.13/LinearAlgebra/src/qr.jl:538 overwritten in module Main at /home/pkgeval/.julia/packages/MixedModels/UklDx/test/pivot.jl:6. WARNING: Method definition kwcall(NamedTuple{names, T} where T<:Tuple where names, typeof(LinearAlgebra.rank), LinearAlgebra.QRPivoted{T, S, C, P} where P<:(AbstractArray{var"#s4740", 1} where var"#s4740"<:Integer) where C<:AbstractArray{T, 1} where S<:AbstractArray{T, 2} where T) in module LinearAlgebra at /source/usr/share/julia/stdlib/v1.13/LinearAlgebra/src/qr.jl:538 overwritten in module Main at /home/pkgeval/.julia/packages/MixedModels/UklDx/test/pivot.jl:6. Test Summary: | Pass Total Time fullranknumeric | 1 1 1.5s Test Summary: | Pass Total Time fullrankcategorical | 2 2 5.6s Test Summary: | Pass Total Time dependentcolumn | 4 4 1.2s 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 18.7s Test Summary: | Pass Total Time mul! | 36 36 2.2s Test Summary: | Pass Total Time reweight! | 2 2 13.3s Test Summary: | Pass Total Time rankupdate! | 2 2 3.8s Test Summary: | Pass Total Time lmulλ! | 1 1 14.1s Test Summary: | Pass Total Time Xymat | 10 10 1.2s Test Summary: | Pass Broken Total Time XymatSparse | 12 1 13 39.1s Test Summary: | Pass Total Time scalarReMat | 40 40 29.9s Test Summary: | Pass Total Time RandomEffectsTerm | 18 18 33.8s Test Summary: | Pass Total Time random effects term syntax | 26 26 44.3s Test Summary: | Pass Total Time Grouping | 1 1 0.0s Test Summary: | Pass Total Time Grouping pseudo-contrasts | 6 6 5.6s Test Summary: | Pass Broken Total Time Auto application of Grouping() | 24 3 27 17.1s Test Summary: | Pass Total Time LMM from MixedModel | 3 3 0.8s Test Summary: | Pass Total Time offset | 2 2 0.2s Test Summary: | Pass Total Time Dyestuff | 84 84 1m18.5s Test Summary: | Pass Total Time Dyestuff2 | 12 12 6.1s Test Summary: | Pass Total Time penicillin | 26 26 7.6s Test Summary: | Pass Total Time pastes | 24 24 4.5s Test Summary: | Pass Total Time InstEval | 22 22 2.9s Test Summary: | Pass Total Time sleep | 137 137 1m42.5s Test Summary: | Pass Total Time d3 | 6 6 32.5s Test Summary: | Pass Total Time kb07 | 6 6 28.3s Test Summary: | Pass Total Time oxide | 4 4 23.3s Test Summary: | Pass Total Time Rank deficient | 7 7 6.9s Test Summary: | Pass Total Time coeftable | 1 1 0.0s Test Summary: | Pass Total Time wts | 3 3 4.1s Test Summary: | Pass Total Time unifying ReMat eltypes | 3 3 4.7s 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 13.6s Test Summary: | Pass Total Time Type for instance | 9 9 0.4s Test Summary: | Pass Total Time contra | 43 43 14.7s Test Summary: | Pass Total Time cbpp | 20 20 25.2s Test Summary: | Pass Total Time verbagg | 5 5 12.6s Test Summary: | Pass Total Time grouseticks | 8 8 1m52.2s Test Summary: | Pass Total Time goldstein | 8 8 4.8s Test Summary: | Pass Total Time dispersion | 3 3 14.8s Test Summary: | Pass Total Time mmec | 4 4 4.4s Test Summary: | Pass Total Time GLMM saveoptsum | 6 6 3.3s Test Summary: | Pass Total Time Bad initial value | 2 2 20.0s Test Summary: | Pass Total Time GHnorm | 5 5 0.6s Test Summary: | Pass Total Time linear | 1 1 0.8s Test Summary: | Pass Total Time generalized | 1 1 7.5s Test Summary: | Pass Total Time Normal-IdentityLink | 2 2 0.2s Test Summary: | Pass Total Time Normal Distribution GLMM | 1 1 2.6s Test Summary: | Pass Total Time Missing Omit | 2 2 4.9s Test Summary: | Pass Total Time isnested | 5 5 13.6s Test Summary: | Pass Total Time likelihoodratio test | 41 41 31.4s Test Summary: | Pass Total Time simulate!(::MixedModel) | 9 9 23.5s ┌ Warning: NLopt was roundoff limited └ @ MixedModels ~/.julia/packages/MixedModels/UklDx/src/nlopt.jl:114 ┌ Warning: Fixed-effects matrix is rank deficient └ @ MixedModels ~/.julia/packages/MixedModels/UklDx/src/Xymat.jl:41 Test Summary: | Pass Total Time bootstrap | 54 54 3m05.6s Test Summary: | Pass Total Time show and summary | 8 8 19.0s 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 1.9s Test Summary: | Pass Total Time simulate[!](::AbstractVector) | 11 11 27.4s Test Summary: | Pass Total Time predict | 48 48 1m32.3s Test Summary: | Pass Total Time fixed sigma | 8 8 4.9s Test Summary: | Pass Total Time PRIMA | 19 19 57.7s Testing MixedModels tests passed Testing completed after 1837.82s PkgEval succeeded after 1938.54s