Package evaluation of HiddenMarkovModels on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T10:55:52.701 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.57s ################################################################################ # Installation # Installing HiddenMarkovModels... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [84ca31d5] + HiddenMarkovModels v0.6.2 Updating `~/.julia/environments/v1.11/Manifest.toml` [dce04be8] + ArgCheck v2.5.0 [d360d2e6] + ChainRulesCore v1.25.1 [34da2185] + Compat v4.16.0 [b429d917] + DensityInterface v0.4.0 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [84ca31d5] + HiddenMarkovModels v0.6.2 [34004b35] + HypergeometricFunctions v0.3.28 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [21216c6a] + Preferences v1.4.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [276daf66] + SpecialFunctions v2.5.0 [82ae8749] + StatsAPI v1.7.0 [4c63d2b9] + StatsFuns v1.4.0 [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 4.32s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 159.55s ################################################################################ # Testing # Testing HiddenMarkovModels Status `/tmp/jl_sONmzO/Project.toml` [4c88cf16] Aqua v0.8.11 [b0b7db55] ComponentArrays v0.15.26 [b429d917] DensityInterface v0.4.0 [31c24e10] Distributions v0.25.118 [e30172f5] Documenter v1.10.1 [7da242da] Enzyme v0.13.35 [f6369f11] ForwardDiff v1.0.1 [84ca31d5] HiddenMarkovModels v0.6.2 ⌅ [c3a54625] JET v0.9.19 [98e50ef6] JuliaFormatter v2.1.0 ⌃ [aa2f6b4e] LogarithmicNumbers v1.2.1 [eff96d63] Measurements v2.12.0 [860ef19b] StableRNGs v1.0.2 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [e88e6eb3] Zygote v0.7.6 [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_sONmzO/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.11 [dce04be8] ArgCheck v2.5.0 [4fba245c] ArrayInterface v7.18.0 [fa961155] CEnum v0.5.0 [49dc2e85] Calculus v0.5.2 [082447d4] ChainRules v1.72.3 [d360d2e6] ChainRulesCore v1.25.1 [da1fd8a2] CodeTracking v1.3.9 [944b1d66] CodecZlib v0.7.8 [a80b9123] CommonMark v0.9.0 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [b0b7db55] ComponentArrays v0.15.26 [187b0558] ConstructionBase v1.5.8 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b429d917] DensityInterface v0.4.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [e30172f5] Documenter v1.10.1 [7da242da] Enzyme v0.13.35 [f151be2c] EnzymeCore v0.8.8 [e2ba6199] ExprTools v0.1.10 [1a297f60] FillArrays v1.13.0 [f6369f11] ForwardDiff v1.0.1 [d9f16b24] Functors v0.5.2 [46192b85] GPUArraysCore v0.2.0 [61eb1bfa] GPUCompiler v1.3.2 [d7ba0133] Git v1.3.1 [c27321d9] Glob v1.3.1 [84ca31d5] HiddenMarkovModels v0.6.2 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [7869d1d1] IRTools v0.4.14 [615f187c] IfElse v0.1.1 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 ⌅ [c3a54625] JET v0.9.19 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [98e50ef6] JuliaFormatter v2.1.0 [aa1ae85d] JuliaInterpreter v0.9.42 ⌅ [70703baa] JuliaSyntax v0.4.10 [929cbde3] LLVM v9.2.0 [0e77f7df] LazilyInitializedFields v1.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 ⌃ [aa2f6b4e] LogarithmicNumbers v1.2.1 [6f1432cf] LoweredCodeUtils v3.1.0 [1914dd2f] MacroTools v0.5.15 [d0879d2d] MarkdownAST v0.1.2 [eff96d63] Measurements v2.12.0 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [d8793406] ObjectFile v0.4.4 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [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 v0.8.0 [6c6a2e73] Scratch v1.2.1 [a2af1166] SortingAlgorithms v1.2.1 [dc90abb0] SparseInverseSubset v0.1.2 [276daf66] SpecialFunctions v2.5.0 [860ef19b] StableRNGs v1.0.2 [aedffcd0] Static v1.2.0 [0d7ed370] StaticArrayInterface v1.8.0 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [09ab397b] StructArrays v0.7.1 [53d494c1] StructIO v0.3.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [a759f4b9] TimerOutputs v0.5.28 [3bb67fe8] TranscodingStreams v0.11.3 [e88e6eb3] Zygote v0.7.6 [700de1a5] ZygoteRules v0.2.7 [7cc45869] Enzyme_jll v0.0.173+0 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.49.0+0 [dad2f222] LLVMExtra_jll v0.0.35+0 [94ce4f54] Libiconv_jll v1.18.0+0 [458c3c95] OpenSSL_jll v3.0.16+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 [a63ad114] Mmap 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... Precompiling HiddenMarkovModels... 13417.5 ms ✓ HiddenMarkovModels 1 dependency successfully precompiled in 14 seconds. 44 already precompiled. Precompiling JuliaFormatter... 16012.7 ms ✓ CommonMark 73882.2 ms ✓ JuliaFormatter 2 dependencies successfully precompiled in 90 seconds. 9 already precompiled. Resolving package versions... Updating `/tmp/jl_sONmzO/Project.toml` [619c5ee3] + HMMTest v0.1.0 `~/.julia/packages/HiddenMarkovModels/7asbg/libs/HMMTest` Updating `/tmp/jl_sONmzO/Manifest.toml` [6e4b80f9] + BenchmarkTools v1.6.0 [619c5ee3] + HMMTest v0.1.0 `~/.julia/packages/HiddenMarkovModels/7asbg/libs/HMMTest` [9abbd945] + Profile v1.11.0 Code formatting: Test Failed at /home/pkgeval/.julia/packages/HiddenMarkovModels/7asbg/test/runtests.jl:20 Expression: JuliaFormatter.format(HiddenMarkovModels; verbose = false, overwrite = false) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/HiddenMarkovModels/7asbg/test/runtests.jl:20 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [4] macro expansion @ ~/.julia/packages/HiddenMarkovModels/7asbg/test/runtests.jl:20 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [6] top-level scope @ ~/.julia/packages/HiddenMarkovModels/7asbg/test/runtests.jl:18 Precompiling Distributions... 10802.8 ms ✓ Distributions 1 dependency successfully precompiled in 14 seconds. 45 already precompiled. Precompiling HiddenMarkovModelsDistributionsExt... 3108.5 ms ✓ HiddenMarkovModels → HiddenMarkovModelsDistributionsExt 3008.8 ms ✓ Distributions → DistributionsDensityInterfaceExt 3370.8 ms ✓ Distributions → DistributionsTestExt 3640.4 ms ✓ Distributions → DistributionsChainRulesCoreExt 4 dependencies successfully precompiled in 14 seconds. 61 already precompiled. Precompiling Zygote... 75275.3 ms ✓ Zygote 1 dependency successfully precompiled in 76 seconds. 64 already precompiled. Precompiling ComponentArrays... 1976.4 ms ✓ ComponentArrays 1 dependency successfully precompiled in 2 seconds. 23 already precompiled. Precompiling ArrayInterfaceChainRulesExt... 1760.9 ms ✓ ArrayInterface → ArrayInterfaceChainRulesExt 1 dependency successfully precompiled in 3 seconds. 40 already precompiled. Precompiling ComponentArraysZygoteExt... 3998.4 ms ✓ ComponentArrays → ComponentArraysZygoteExt 1 dependency successfully precompiled in 5 seconds. 77 already precompiled. Precompiling Enzyme... 364332.6 ms ✓ Enzyme 1 dependency successfully precompiled in 365 seconds. 43 already precompiled. Precompiling QuadGKEnzymeExt... 16550.8 ms ✓ QuadGK → QuadGKEnzymeExt 1 dependency successfully precompiled in 17 seconds. 49 already precompiled. Precompiling EnzymeLogExpFunctionsExt... 16664.5 ms ✓ Enzyme → EnzymeLogExpFunctionsExt 1 dependency successfully precompiled in 17 seconds. 47 already precompiled. Precompiling EnzymeChainRulesCoreExt... 62906.2 ms ✓ Enzyme → EnzymeChainRulesCoreExt 1 dependency successfully precompiled in 63 seconds. 48 already precompiled. Precompiling EnzymeSpecialFunctionsExt... 20934.6 ms ✓ Enzyme → EnzymeSpecialFunctionsExt 1 dependency successfully precompiled in 21 seconds. 52 already precompiled. Precompiling EnzymeGPUArraysCoreExt... 20224.6 ms ✓ Enzyme → EnzymeGPUArraysCoreExt 1 dependency successfully precompiled in 21 seconds. 49 already precompiled. Precompiling HMMTest... 3295.6 ms ✓ BenchmarkTools 8295.8 ms ✓ HMMTest 2 dependencies successfully precompiled in 12 seconds. 74 already precompiled. Precompiling MeasurementsSpecialFunctionsExt... 1134.0 ms ✓ Measurements → MeasurementsSpecialFunctionsExt 1 dependency successfully precompiled in 1 seconds. 15 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/tbj1p/src/utilities/utilities.jl:660 [ 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 Fail Broken Total Time HiddenMarkovModels.jl | 574 1 5 580 34m46.4s Code formatting | 1 1 1m35.6s Code quality | 9 9 39.0s Code linting | 1 1 4m05.7s Distributions | 100 100 18.6s Example - autodiff.jl | 26 3 29 19m24.3s Example - basics.jl | 40 40 1m09.4s Example - controlled.jl | 38 38 34.0s Example - interfaces.jl | 33 33 1m02.4s Example - temporal.jl | 37 37 54.5s Example - types.jl | 42 1 43 1m07.9s Doctests | 1 1 52.9s Correctness - Standard | 246 1 247 3m01.7s Normal | 40 40 40.8s Coherence | 22 22 8.5s Type stability | 14 14 0.8s Allocations | 4 4 23.1s DiagNormal | 36 36 15.9s Coherence | 22 22 7.1s Type stability | 14 14 0.7s LightCategorical | 40 40 31.9s Coherence | 22 22 7.0s Type stability | 14 14 0.8s Allocations | 4 4 17.7s LightDiagNormal | 40 40 29.7s Coherence | 22 22 5.2s Type stability | 14 14 0.7s Allocations | 4 4 17.0s Normal (sparse) | 32 1 33 4.5s Coherence | 18 18 2.2s Type stability | 14 14 0.0s Normal transposed | 40 40 41.3s Coherence | 22 22 9.6s Type stability | 14 14 1.3s Allocations | 4 4 23.2s Normal and Exponential | 18 18 16.2s Coherence | 18 18 13.1s Miscellaneous | 1 1 0.1s Allow NaN density | 1 1 0.1s ERROR: LoadError: Some tests did not pass: 574 passed, 1 failed, 0 errored, 5 broken. in expression starting at /home/pkgeval/.julia/packages/HiddenMarkovModels/7asbg/test/runtests.jl:17 Testing failed after 2226.92s ERROR: LoadError: Package HiddenMarkovModels errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2439.44s: package has test failures