Package evaluation to test HiddenMarkovModels on Julia 1.11.8 (e29b8e6612*) started at 2026-01-26T08:41:22.718 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.15s ################################################################################ # Installation # Installing HiddenMarkovModels... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [84ca31d5] + HiddenMarkovModels v0.7.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [dce04be8] + ArgCheck v2.5.0 [d360d2e6] + ChainRulesCore v1.26.0 [34da2185] + Compat v4.18.1 [b429d917] + DensityInterface v0.4.0 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [84ca31d5] + HiddenMarkovModels v0.7.0 [34004b35] + HypergeometricFunctions v0.3.28 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [692b3bcd] + JLLWrappers v1.7.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [21216c6a] + Preferences v1.5.1 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [276daf66] + SpecialFunctions v2.6.1 [82ae8749] + StatsAPI v1.8.0 [4c63d2b9] + StatsFuns v1.5.2 [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 [b77e0a4c] + InteractiveUtils v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [8e850b90] + libblastrampoline_jll v5.11.0+0 Installation completed after 3.41s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 1957.2 ms ✓ TestEnv 1 dependency successfully precompiled in 2 seconds. 23 already precompiled. Precompiling package dependencies... Precompiling project... 768.4 ms ✓ Calculus 541.2 ms ✓ AbstractFFTs 720.4 ms ✓ LogarithmicNumbers 422.3 ms ✓ Glob 372.8 ms ✓ ExprTools 305.8 ms ✓ IteratorInterfaceExtensions 429.2 ms ✓ StatsAPI 364.8 ms ✓ CEnum 478.5 ms ✓ ANSIColoredPrinters 979.7 ms ✓ FillArrays 408.7 ms ✓ InverseFunctions 560.2 ms ✓ Statistics 16477.7 ms ✓ JuliaSyntax 630.6 ms ✓ ArgCheck 2539.6 ms ✓ MacroTools 572.6 ms ✓ OrderedCollections 524.7 ms ✓ Requires 320.9 ms ✓ DataValueInterfaces 383.6 ms ✓ StructIO 381.6 ms ✓ RealDot 470.2 ms ✓ StableRNGs 319.6 ms ✓ Reexport 560.1 ms ✓ DocStringExtensions 539.9 ms ✓ AbstractTrees 1086.7 ms ✓ IrrationalConstants 326.1 ms ✓ PtrArrays 551.1 ms ✓ TranscodingStreams 488.5 ms ✓ NaNMath 371.4 ms ✓ LazilyInitializedFields 675.2 ms ✓ EnzymeCore 317.6 ms ✓ IfElse 488.5 ms ✓ ConstructionBase 366.2 ms ✓ CommonWorldInvalidations 440.5 ms ✓ DataAPI 452.5 ms ✓ SciMLPublic 515.9 ms ✓ StaticArraysCore 487.3 ms ✓ IOCapture 648.7 ms ✓ SuiteSparse 831.4 ms ✓ StructUtils 466.8 ms ✓ Scratch 623.6 ms ✓ Preferences 633.5 ms ✓ Compat 1118.4 ms ✓ CodeTracking 687.0 ms ✓ Measurements 1711.2 ms ✓ AbstractFFTs → AbstractFFTsTestExt 383.0 ms ✓ TableTraits 685.0 ms ✓ FillArrays → FillArraysSparseArraysExt 680.8 ms ✓ InverseFunctions → InverseFunctionsTestExt 478.0 ms ✓ InverseFunctions → InverseFunctionsDatesExt 656.2 ms ✓ Statistics → SparseArraysExt 455.3 ms ✓ FillArrays → FillArraysStatisticsExt 901.8 ms ✓ CommonSubexpressions 2487.6 ms ✓ IRTools 1862.7 ms ✓ DataStructures 480.0 ms ✓ Adapt 2652.4 ms ✓ ObjectFile 702.3 ms ✓ MarkdownAST 713.4 ms ✓ LogExpFunctions 510.8 ms ✓ AliasTables 493.5 ms ✓ CodecZlib 2419.1 ms ✓ RegistryInstances 428.1 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 496.4 ms ✓ Missings 435.1 ms ✓ DiffResults 906.5 ms ✓ PDMats 600.5 ms ✓ SparseInverseSubset 534.1 ms ✓ JLLWrappers 470.0 ms ✓ PrecompileTools 441.5 ms ✓ Compat → CompatLinearAlgebraExt 8106.1 ms ✓ JuliaInterpreter 473.9 ms ✓ StructUtils → StructUtilsMeasurementsExt 866.7 ms ✓ Tables 708.3 ms ✓ DensityInterface 525.2 ms ✓ SortingAlgorithms 1182.7 ms ✓ QuadGK 597.9 ms ✓ Adapt → AdaptSparseArraysExt 568.2 ms ✓ ArrayInterface 516.4 ms ✓ GPUArraysCore 423.7 ms ✓ EnzymeCore → AdaptExt 429.9 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 655.3 ms ✓ FillArrays → FillArraysPDMatsExt 700.7 ms ✓ OpenSSL_jll 684.9 ms ✓ Rmath_jll 692.6 ms ✓ LibTracyClient_jll 1987.0 ms ✓ Enzyme_jll 2134.9 ms ✓ LLVMExtra_jll 720.8 ms ✓ Expat_jll 735.1 ms ✓ Libiconv_jll 701.3 ms ✓ Git_LFS_jll 704.1 ms ✓ OpenSpecFun_jll 9266.8 ms ✓ CommonMark 11511.1 ms ✓ Parsers 962.0 ms ✓ Static 1311.3 ms ✓ ChainRulesCore 3314.8 ms ✓ Aqua 726.6 ms ✓ Functors 14793.3 ms ✓ LoweredCodeUtils 863.8 ms ✓ StructArrays 478.7 ms ✓ StructUtils → StructUtilsTablesExt 2410.5 ms ✓ StatsBase 609.0 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 403.3 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 425.0 ms ✓ ArrayInterface → ArrayInterfaceGPUArraysCoreExt 824.3 ms ✓ OpenSSH_jll 921.5 ms ✓ Rmath 1541.8 ms ✓ Tracy 8202.2 ms ✓ LLVM 811.6 ms ✓ Git_jll 3099.8 ms ✓ SpecialFunctions 48160.1 ms ✓ JuliaFormatter 4373.0 ms ✓ JSON 1538.1 ms ✓ StaticArrayInterface 672.4 ms ✓ ChainRulesCore → ChainRulesCoreSparseArraysExt 1494.9 ms ✓ ZygoteRules 496.1 ms ✓ AbstractFFTs → AbstractFFTsChainRulesCoreExt 739.1 ms ✓ EnzymeCore → EnzymeCoreChainRulesCoreExt 1790.6 ms ✓ LogExpFunctions → LogExpFunctionsChainRulesCoreExt 439.6 ms ✓ ArrayInterface → ArrayInterfaceChainRulesCoreExt 7159.0 ms ✓ JET 448.8 ms ✓ StructArrays → StructArraysAdaptExt 655.7 ms ✓ StructArrays → StructArraysSparseArraysExt 479.5 ms ✓ StructArrays → StructArraysLinearAlgebraExt 719.1 ms ✓ PDMats → StatsBaseExt 19101.9 ms ✓ GPUCompiler 569.2 ms ✓ Git 2427.4 ms ✓ SpecialFunctions → SpecialFunctionsChainRulesCoreExt 1267.2 ms ✓ HypergeometricFunctions 646.1 ms ✓ Measurements → MeasurementsSpecialFunctionsExt 708.3 ms ✓ DiffRules 1062.2 ms ✓ ComponentArrays 6809.0 ms ✓ ChainRules 61459.0 ms ✓ Enzyme 33676.4 ms ✓ Documenter 1834.3 ms ✓ StatsFuns 4392.1 ms ✓ ForwardDiff 814.6 ms ✓ ArrayInterface → ArrayInterfaceChainRulesExt 31775.3 ms ✓ Enzyme → EnzymeSpecialFunctionsExt 33051.0 ms ✓ Enzyme → EnzymeChainRulesCoreExt 31064.0 ms ✓ Enzyme → EnzymeLogExpFunctionsExt 32377.1 ms ✓ Enzyme → EnzymeGPUArraysCoreExt 28515.7 ms ✓ QuadGK → QuadGKEnzymeExt 728.0 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 2130.7 ms ✓ StatsFuns → StatsFunsChainRulesCoreExt 5244.0 ms ✓ Distributions 683.6 ms ✓ LogarithmicNumbers → LogarithmicNumbersForwardDiffExt 35583.7 ms ✓ Zygote 2086.7 ms ✓ HiddenMarkovModels 1369.9 ms ✓ Distributions → DistributionsDensityInterfaceExt 1483.6 ms ✓ Distributions → DistributionsTestExt 1580.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 1900.7 ms ✓ ComponentArrays → ComponentArraysZygoteExt 1431.7 ms ✓ HiddenMarkovModels → HiddenMarkovModelsDistributionsExt 152 dependencies successfully precompiled in 566 seconds. 36 already precompiled. Precompilation completed after 594.96s ################################################################################ # Testing # Testing HiddenMarkovModels Status `/tmp/jl_1NJlTq/Project.toml` [4c88cf16] Aqua v0.8.14 [b0b7db55] ComponentArrays v0.15.31 [b429d917] DensityInterface v0.4.0 [31c24e10] Distributions v0.25.123 [e30172f5] Documenter v1.16.1 [7da242da] Enzyme v0.13.119 [f6369f11] ForwardDiff v1.3.1 [84ca31d5] HiddenMarkovModels v0.7.0 ⌅ [c3a54625] JET v0.9.20 [98e50ef6] JuliaFormatter v2.2.0 [aa2f6b4e] LogarithmicNumbers v1.4.1 [eff96d63] Measurements v2.14.1 [860ef19b] StableRNGs v1.0.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [e88e6eb3] Zygote v0.7.10 [37e2e46d] LinearAlgebra v1.11.0 [44cfe95a] Pkg v1.11.0 [9a3f8284] Random v1.11.0 [2f01184e] SparseArrays v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_1NJlTq/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [dce04be8] ArgCheck v2.5.0 [4fba245c] ArrayInterface v7.22.0 [fa961155] CEnum v0.5.0 [49dc2e85] Calculus v0.5.2 [082447d4] ChainRules v1.72.6 [d360d2e6] ChainRulesCore v1.26.0 ⌅ [da1fd8a2] CodeTracking v1.3.9 [944b1d66] CodecZlib v0.7.8 ⌅ [a80b9123] CommonMark v0.9.1 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [b0b7db55] ComponentArrays v0.15.31 [187b0558] ConstructionBase v1.6.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [b429d917] DensityInterface v0.4.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.16.1 [7da242da] Enzyme v0.13.119 [f151be2c] EnzymeCore v0.8.18 [e2ba6199] ExprTools v0.1.10 [1a297f60] FillArrays v1.16.0 [f6369f11] ForwardDiff v1.3.1 [d9f16b24] Functors v0.5.2 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v1.8.1 [d7ba0133] Git v1.5.0 [c27321d9] Glob v1.4.0 [84ca31d5] HiddenMarkovModels v0.7.0 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v1.0.0 [7869d1d1] IRTools v0.4.15 [615f187c] IfElse v0.1.1 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [c3a54625] JET v0.9.20 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.4.0 [98e50ef6] JuliaFormatter v2.2.0 ⌅ [aa1ae85d] JuliaInterpreter v0.9.46 ⌅ [70703baa] JuliaSyntax v0.4.10 [929cbde3] LLVM v9.4.4 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [aa2f6b4e] LogarithmicNumbers v1.4.1 ⌃ [6f1432cf] LoweredCodeUtils v3.2.2 [1914dd2f] MacroTools v0.5.16 [d0879d2d] MarkdownAST v0.1.2 [eff96d63] Measurements v2.14.1 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [d8793406] ObjectFile v0.5.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [69de0a69] Parsers v2.8.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.5.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [c1ae055f] RealDot v0.1.0 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [431bcebd] SciMLPublic v1.0.1 [6c6a2e73] Scratch v1.3.0 [a2af1166] SortingAlgorithms v1.2.2 [dc90abb0] SparseInverseSubset v0.1.2 [276daf66] SpecialFunctions v2.6.1 [860ef19b] StableRNGs v1.0.4 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [09ab397b] StructArrays v0.7.2 [53d494c1] StructIO v0.3.1 [ec057cc2] StructUtils v2.6.2 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [e689c965] Tracy v0.1.6 [3bb67fe8] TranscodingStreams v0.11.3 [e88e6eb3] Zygote v0.7.10 [700de1a5] ZygoteRules v0.2.7 [7cc45869] Enzyme_jll v0.0.240+0 [2e619515] Expat_jll v2.7.3+0 [020c3dae] Git_LFS_jll v3.7.0+0 [f8c6e375] Git_jll v2.52.0+0 [dad2f222] LLVMExtra_jll v0.0.38+0 [ad6e5548] LibTracyClient_jll v0.13.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [9bd350c2] OpenSSH_jll v10.2.1+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [44cfe95a] Pkg 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 v1.11.0 [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 v1.1.1+0 [deac9b47] LibCURL_jll v8.6.0+0 [e37daf67] LibGit2_jll v1.7.2+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+0 [14a3606d] MozillaCACerts_jll v2023.12.12 [4536629a] OpenBLAS_jll v0.3.27+1 [05823500] OpenLibm_jll v0.8.5+0 [efcefdf7] PCRE2_jll v10.42.0+1 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+1 [8e850b90] libblastrampoline_jll v5.11.0+0 [8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+2 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... Resolving package versions... Updating `/tmp/jl_1NJlTq/Project.toml` [619c5ee3] + HMMTest v0.1.0 `~/.julia/packages/HiddenMarkovModels/Kmgf4/libs/HMMTest` Updating `/tmp/jl_1NJlTq/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.6.3 [619c5ee3] + HMMTest v0.1.0 `~/.julia/packages/HiddenMarkovModels/Kmgf4/libs/HMMTest` [9abbd945] + Profile v1.11.0 Precompiling HMMTest... 1766.7 ms ✓ BenchmarkTools 4522.5 ms ✓ HMMTest 2 dependencies successfully precompiled in 7 seconds. 74 already precompiled. ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ @ Documenter ~/.julia/packages/Documenter/xvqbW/src/utilities/utilities.jl:680 [ Info: SetupBuildDirectory: setting up build directory. [ Info: Doctest: running doctests. [ Info: Skipped ExpandTemplates step (doctest only). [ Info: Skipped CrossReferences step (doctest only). [ Info: Skipped CheckDocument step (doctest only). [ Info: Skipped Populate step (doctest only). [ Info: Skipped RenderDocument step (doctest only). Test Summary: | Pass Broken Total Time HiddenMarkovModels.jl | 669 6 675 13m16.7s Code formatting | 1 1 47.4s Code quality | 9 9 22.1s Code linting | 1 1 1m14.2s Distributions | 99 1 100 10.4s Example - autodiff.jl | 26 3 29 5m28.0s Example - basics.jl | 48 48 36.4s Example - controlled.jl | 46 46 19.7s Example - interfaces.jl | 37 37 32.9s Example - temporal.jl | 50 50 34.3s Example - types.jl | 52 1 53 35.8s Doctests | 1 1 29.7s Correctness - Standard | 298 1 299 2m05.7s Normal | 48 48 22.4s Coherence | 30 30 4.2s Type stability | 14 14 0.4s Allocations | 4 4 12.3s DiagNormal | 44 44 10.9s Coherence | 30 30 4.0s Type stability | 14 14 0.6s LightCategorical | 48 48 24.3s Coherence | 30 30 5.1s Type stability | 14 14 0.5s Allocations | 4 4 12.4s LightDiagNormal | 48 48 24.1s Coherence | 30 30 4.1s Type stability | 14 14 0.6s Allocations | 4 4 12.5s Normal (sparse) | 38 1 39 5.3s Coherence | 24 24 1.8s Type stability | 14 14 0.0s Normal transposed | 48 48 27.6s Coherence | 30 30 7.3s Type stability | 14 14 0.7s Allocations | 4 4 12.8s Normal and Exponential | 24 24 10.2s Coherence | 24 24 6.8s Miscellaneous | 1 1 0.1s Allow NaN density | 1 1 0.1s Testing HiddenMarkovModels tests passed Testing completed after 817.0s PkgEval succeeded after 1426.71s