Package evaluation of MetidaBioeq on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T14:26:19.638 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.31s ################################################################################ # Installation # Installing MetidaBioeq... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [00e1d80e] + MetidaBioeq v0.2.9 Updating `~/.julia/environments/v1.10/Manifest.toml` [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 [4c555306] + ArrayLayouts v1.11.1 [69666777] + Arrow v2.8.0 [31f734f8] + ArrowTypes v2.3.0 [093aae92] + BSplineKit v0.18.2 [aae01518] + BandedMatrices v1.9.1 [c3b6d118] + BitIntegers v0.3.2 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 [324d7699] + CategoricalArrays v0.10.8 [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 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [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 [e2ba6199] + ExprTools v0.1.10 [442a2c76] + FastGaussQuadrature v1.0.2 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [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 [b964fa9f] + LaTeXStrings v1.4.0 [d3d80556] + LineSearches v7.3.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [a1dec852] + Metida v0.16.4 [075456b7] + MetidaBase v0.14.1 [00e1d80e] + MetidaBioeq v0.2.9 [097c2839] + MetidaNCA v0.5.17 [e1d29d7a] + Missings v1.2.0 [ff71e718] + MixedModels v4.30.1 [7e9fb7ac] + MixedModelsDatasets v0.1.2 [78c3b35d] + Mocking v0.8.1 [d41bc354] + NLSolversBase v7.8.3 [76087f3c] + NLopt v1.1.3 [77ba4419] + NaNMath v1.1.2 [429524aa] + Optim v1.11.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [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 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.0 [79098fc4] + Rmath v0.8.0 [6c6a2e73] + Scratch v1.2.1 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.1 [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 [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 [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 [3a884ed6] + UnPack v1.0.2 [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 v1.1.1 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [8ba89e20] + Distributed [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching [9fa8497b] + Future [b77e0a4c] + InteractiveUtils [4af54fe1] + LazyArtifacts [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [a63ad114] + Mmap [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.10.0 [de0858da] + Printf [3fa0cd96] + REPL [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [6462fe0b] + Sockets [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] + LibCURL_jll v8.4.0+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [14a3606d] + MozillaCACerts_jll v2023.1.10 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.52.0+1 [3f19e933] + p7zip_jll v17.4.0+2 Installation completed after 7.41s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 227.57s ################################################################################ # Testing # Testing MetidaBioeq Status `/tmp/jl_Pf7sEJ/Project.toml` [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v0.10.8 [a93c6f00] DataFrames v1.7.0 [31c24e10] Distributions v0.25.117 [38e38edf] GLM v1.9.0 [a1dec852] Metida v0.16.4 [075456b7] MetidaBase v0.14.1 [00e1d80e] MetidaBioeq v0.2.9 [097c2839] MetidaNCA v0.5.17 [ff71e718] MixedModels v4.30.1 [2913bbd2] StatsBase v0.34.4 [3eaba693] StatsModels v0.7.4 [8dfed614] Test Status `/tmp/jl_Pf7sEJ/Manifest.toml` [79e6a3ab] Adapt v4.2.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.18.0 [4c555306] ArrayLayouts v1.11.1 [69666777] Arrow v2.8.0 [31f734f8] ArrowTypes v2.3.0 [093aae92] BSplineKit v0.18.2 [aae01518] BandedMatrices v1.9.1 [c3b6d118] BitIntegers v0.3.2 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.6 [336ed68f] CSV v0.10.15 [324d7699] CategoricalArrays v0.10.8 [5ba52731] CodecLz4 v0.4.5 [944b1d66] CodecZlib v0.7.8 [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 [187b0558] ConstructionBase v1.5.8 [adafc99b] CpuId v0.3.1 [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 [e2ba6199] ExprTools v0.1.10 [442a2c76] FastGaussQuadrature v1.0.2 [48062228] FilePathsBase v0.9.23 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [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 [b964fa9f] LaTeXStrings v1.4.0 [d3d80556] LineSearches v7.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [a1dec852] Metida v0.16.4 [075456b7] MetidaBase v0.14.1 [00e1d80e] MetidaBioeq v0.2.9 [097c2839] MetidaNCA v0.5.17 [e1d29d7a] Missings v1.2.0 [ff71e718] MixedModels v4.30.1 [7e9fb7ac] MixedModelsDatasets v0.1.2 [78c3b35d] Mocking v0.8.1 [d41bc354] NLSolversBase v7.8.3 [76087f3c] NLopt v1.1.3 [77ba4419] NaNMath v1.1.2 [429524aa] Optim v1.11.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [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 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.0 [79098fc4] Rmath v0.8.0 [6c6a2e73] Scratch v1.2.1 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.1 [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 [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 [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 [3a884ed6] UnPack v1.0.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [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 v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [4af54fe1] LazyArtifacts [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 [8f399da3] Libdl [37e2e46d] LinearAlgebra [56ddb016] Logging [d6f4376e] Markdown [a63ad114] Mmap [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg v1.10.0 [de0858da] Printf [3fa0cd96] REPL [9a3f8284] Random [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization [6462fe0b] Sockets [2f01184e] SparseArrays v1.10.0 [10745b16] Statistics v1.10.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test [cf7118a7] UUIDs [4ec0a83e] Unicode [e66e0078] CompilerSupportLibraries_jll v1.1.1+0 [deac9b47] LibCURL_jll v8.4.0+0 [e37daf67] LibGit2_jll v1.6.4+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.2+1 [14a3606d] MozillaCACerts_jll v2023.1.10 [4536629a] OpenBLAS_jll v0.3.23+4 [05823500] OpenLibm_jll v0.8.1+4 [bea87d4a] SuiteSparse_jll v7.2.1+1 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.52.0+1 [3f19e933] p7zip_jll v17.4.0+2 Testing Running tests... [ Info: autoseq is `true`, but sequence defined - sequence column used [ Info: Dropuot(s) found in dataframe! [ Info: Sequences looks correct... [ Info: Trying to find out the design... [ Info: Seems design type is: 2X2X4 Minimizing 2 Time: 0:00:00 ( 0.14 s/it) objective: 539.6041230960641   Minimizing 17 Time: 0:00:00 (26.27 ms/it) ┌ Warning: `confint(obj::LinearModel, level::Real)` is deprecated, use `confint(obj, level = level)` instead. │ caller = #confint#87 at statsmodel.jl:28 [inlined] └ @ Core ~/.julia/packages/StatsModels/mPD8T/src/statsmodel.jl:28 ┌ Warning: Method B used, estimator changed to MixedModels.jl! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:500 ┌ Warning: Method C used, estimator changed to Metida.jl! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:503 ┌ Warning: Method C used, estimator changed to Metida.jl! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:506 ┌ Warning: Method P or unknown, method changed to "B"! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:495 ┌ Warning: Method P or unknown, method changed to "B"! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:495 [ Info: Reference formulation not specified. First used: "R". [ Info: autoseq is `true`, but sequence defined - sequence column used [ Info: No dropuot(s) found in dataframe! [ Info: Sequences looks correct... [ Info: Trying to find out the design... [ Info: Seems design type is: 2X2X2 [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. ┌ Warning: Method not P (parallel), for parallel simple GLM model will be used! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:426 ┌ Warning: Design is parallel, but estimator not GLM, GLM will be used! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:425 ┌ Warning: Design is parallel, but estimator not GLM, GLM will be used! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:425 [ Info: Reference formulation not specified. First used: "R". [ Info: autoseq is `true`, but sequence defined - sequence column used [ Info: No dropuot(s) found in dataframe! [ Info: Sequences looks correct... [ Info: Design type seems fine... ┌ Warning: Method C can't be used with 2X2 design! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:444 ┌ Warning: Method B will be used! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:450 ┌ Warning: Method for parallel design can't be used with 2X2 design! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:445 ┌ Warning: Method A will be used! └ @ MetidaBioeq ~/.julia/packages/MetidaBioeq/iXqnI/src/bioequivalence.jl:447 [ Info: No dropuot(s) found in dataframe! [ Info: Sequences looks correct... [ Info: Trying to find out the design... [ Info: Seems design type is: 2X2X2 [ Info: autoseq is `true`, but sequence defined - sequence column used [ Info: Dropuot(s) found in dataframe! [ Info: Sequences looks correct... [ Info: Trying to find out the design... [ Info: Seems design type is: 2X2X2 [ Info: autoseq is `true`, but sequence defined - sequence column used [ Info: Dropuot(s) found in dataframe! [ Info: Dropuot(s) removed! [ Info: Sequences looks correct... [ Info: Trying to find out the design... [ Info: Seems design type is: 2X2X2 Test Summary: | Pass Total Time Basic test | 62 62 4m12.4s Test Summary: | Pass Total Time Validation 2x2 | 48 48 10.0s [ Info: DF for Metida method B = 197.55566268106588, reference value SAS = 192, reference value SPSS = 197.44. CI check passed. [ Info: DF for Metida method B = 178.33549031310002, reference value SAS = 164, reference value SPSS = 177.92. CI check passed. Test Summary: | Pass Total Time Validation replicate (model B) | 300 300 33.3s [ Info: RDS23 LCI for Metida method C = 95.7581653935994, reference value SPSS = 95.53. [ Info: RDS23 UCI for Metida method C = 130.00970885535884, reference value SPSS = 130.33. Test Summary: | Pass Total Time Validation replicate (model C) | 29 29 5.1s [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. [ Info: Reference formulation not specified. First used: "R". [ Info: Parallel desigh used. Test Summary: | Pass Total Time Validation parallel, no welch correction | 44 44 3.3s Test Summary: | Pass Total Time NCA parallel design | 10 10 16.9s Testing MetidaBioeq tests passed Testing completed after 418.07s PkgEval succeeded after 663.21s