Package evaluation of ControlledHiddenMarkovModels on Julia 1.10.8 (92f03a4775*) started at 2025-02-25T07:59:03.342 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 5.05s ################################################################################ # Installation # Installing ControlledHiddenMarkovModels... Resolving package versions... Updating `~/.julia/environments/v1.10/Project.toml` [7732c362] + ControlledHiddenMarkovModels v0.1.0 Updating `~/.julia/environments/v1.10/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.16.0 [7732c362] + ControlledHiddenMarkovModels v0.1.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.20 [b429d917] + DensityInterface v0.4.0 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.27 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [21216c6a] + Preferences v1.4.3 [33c8b6b6] + ProgressLogging v0.1.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts [2a0f44e3] + Base64 [ade2ca70] + Dates [b77e0a4c] + InteractiveUtils [76f85450] + LibGit2 [8f399da3] + Libdl [37e2e46d] + LinearAlgebra [56ddb016] + Logging [d6f4376e] + Markdown [ca575930] + NetworkOptions v1.2.0 [de0858da] + Printf [9a3f8284] + Random [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization [2f01184e] + SparseArrays v1.10.0 [10745b16] + Statistics v1.10.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [8dfed614] + Test [cf7118a7] + UUIDs [4ec0a83e] + Unicode [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [e37daf67] + LibGit2_jll v1.6.4+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [c8ffd9c3] + MbedTLS_jll v2.28.2+1 [4536629a] + OpenBLAS_jll v0.3.23+4 [05823500] + OpenLibm_jll v0.8.1+4 [bea87d4a] + SuiteSparse_jll v7.2.1+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 Installation completed after 6.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 21.86s ################################################################################ # Testing # Testing ControlledHiddenMarkovModels Status `/tmp/jl_jJyeN8/Project.toml` [4c88cf16] Aqua v0.8.11 [b0b7db55] ComponentArrays v0.15.24 [7732c362] ControlledHiddenMarkovModels v0.1.0 [31c24e10] Distributions v0.25.117 [e30172f5] Documenter v1.8.1 [f6369f11] ForwardDiff v0.10.38 [98e50ef6] JuliaFormatter v1.0.62 [aa2f6b4e] LogarithmicNumbers v1.4.0 [7f7a1694] Optimization v4.1.1 [36348300] OptimizationOptimJL v0.4.1 [af0b7596] PointProcesses v0.5.0 [37e2e46d] LinearAlgebra [9a3f8284] Random [10745b16] Statistics v1.10.0 [8dfed614] Test Status `/tmp/jl_jJyeN8/Manifest.toml` [47edcb42] ADTypes v1.13.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.41 [79e6a3ab] Adapt v4.2.0 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.11 [4fba245c] ArrayInterface v7.18.0 [00ebfdb7] CSTParser v3.4.3 [d360d2e6] ChainRulesCore v1.25.1 [944b1d66] CodecZlib v0.7.8 [a80b9123] CommonMark v0.8.15 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.16.0 [b0b7db55] ComponentArrays v0.15.24 [a33af91c] CompositionsBase v0.1.2 [88cd18e8] ConsoleProgressMonitor v0.1.2 [187b0558] ConstructionBase v1.5.8 [7732c362] ControlledHiddenMarkovModels v0.1.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [b429d917] DensityInterface v0.4.0 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.6.42 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 [e30172f5] Documenter v1.8.1 [4e289a0a] EnumX v1.0.4 [e2ba6199] ExprTools v0.1.10 [55351af7] ExproniconLite v0.10.14 [9aa1b823] FastClosures v0.3.2 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [f6369f11] ForwardDiff v0.10.38 [069b7b12] FunctionWrappers v1.1.3 [77dc65aa] FunctionWrappersWrappers v0.1.3 [d9f16b24] Functors v0.5.2 [46192b85] GPUArraysCore v0.2.0 [d7ba0133] Git v1.3.1 [c27321d9] Glob v1.3.1 [34004b35] HypergeometricFunctions v0.3.27 [b5f81e59] IOCapture v0.2.5 [615f187c] IfElse v0.1.1 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [ae98c720] Jieko v0.2.1 [98e50ef6] JuliaFormatter v1.0.62 [5be7bae1] LBFGSB v0.4.1 [0e77f7df] LazilyInitializedFields v1.3.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [d3d80556] LineSearches v7.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [aa2f6b4e] LogarithmicNumbers v1.4.0 [e6f89c97] LoggingExtras v1.1.0 [1914dd2f] MacroTools v0.5.15 [d0879d2d] MarkdownAST v0.1.2 [e1d29d7a] Missings v1.2.0 [2e0e35c7] Moshi v0.3.5 [d41bc354] NLSolversBase v7.8.3 [77ba4419] NaNMath v1.1.2 [429524aa] Optim v1.11.0 [7f7a1694] Optimization v4.1.1 [bca83a33] OptimizationBase v2.4.0 [36348300] OptimizationOptimJL v0.4.1 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [af0b7596] PointProcesses v0.5.0 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [33c8b6b6] ProgressLogging v0.1.4 [92933f4c] ProgressMeter v1.10.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [731186ca] RecursiveArrayTools v3.30.0 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [ae029012] Requires v1.3.0 [79098fc4] Rmath v0.8.0 [7e49a35a] RuntimeGeneratedFunctions v0.5.13 [0bca4576] SciMLBase v2.75.0 [c0aeaf25] SciMLOperators v0.3.12 [53ae85a6] SciMLStructures v1.6.1 [efcf1570] Setfield v1.1.1 [a2af1166] SortingAlgorithms v1.2.1 [9f842d2f] SparseConnectivityTracer v0.6.13 [0a514795] SparseMatrixColorings v0.4.13 [276daf66] SpecialFunctions v2.5.0 [aedffcd0] Static v1.1.1 [0d7ed370] StaticArrayInterface v1.8.0 [1e83bf80] StaticArraysCore v1.4.3 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.3.2 [2efcf032] SymbolicIndexingInterface v0.3.38 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [5d786b92] TerminalLoggers v0.1.7 [0796e94c] Tokenize v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 [3a884ed6] UnPack v1.0.2 [2e619515] Expat_jll v2.6.5+0 [f8c6e375] Git_jll v2.47.1+0 [81d17ec3] L_BFGS_B_jll v3.0.1+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 v1.1.1 [56f22d72] Artifacts [2a0f44e3] Base64 [ade2ca70] Dates [8ba89e20] Distributed [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching [9fa8497b] Future [b77e0a4c] InteractiveUtils [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 [efcefdf7] PCRE2_jll v10.42.0+1 [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... ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] does not declare a compat entry for the following deps: 2-element Vector{Base.PkgId}: LinearAlgebra [37e2e46d-f89d-539d-b4ee-838fcccc9c8e] Random [9a3f8284-a2c9-5f02-9a11-845980a1fd5c] ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] deps: Test Failed at /home/pkgeval/.julia/packages/Aqua/epbUr/src/deps_compat.jl:60 Expression: isempty(result) Evaluated: isempty(Base.PkgId[LinearAlgebra [37e2e46d-f89d-539d-b4ee-838fcccc9c8e], Random [9a3f8284-a2c9-5f02-9a11-845980a1fd5c]]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] test_deps_compat(pkg::Base.PkgId, deps_type::String; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:60 [3] test_deps_compat @ ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:55 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:41 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [6] test_deps_compat(pkg::Base.PkgId; check_julia::Bool, check_extras::Bool, check_weakdeps::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:41 ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] does not declare a compat entry for the following extras: 1-element Vector{Base.PkgId}: Test [8dfed614-e22c-5e08-85e1-65c5234f0b40] ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] extras: Test Failed at /home/pkgeval/.julia/packages/Aqua/epbUr/src/deps_compat.jl:60 Expression: isempty(result) Evaluated: isempty(Base.PkgId[Test [8dfed614-e22c-5e08-85e1-65c5234f0b40]]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:672 [inlined] [2] test_deps_compat(pkg::Base.PkgId, deps_type::String; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:60 [3] test_deps_compat @ ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:55 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:45 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [6] test_deps_compat(pkg::Base.PkgId; check_julia::Bool, check_extras::Bool, check_weakdeps::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/epbUr/src/deps_compat.jl:45 ┌ 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/iwb7N/src/utilities/utilities.jl:651 [ 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). Vanilla HMM: Error During Test at /home/pkgeval/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/runtests.jl:27 Got exception outside of a @test LoadError: UndefVarError: `add_suffstats` not defined Stacktrace: [1] fit_from_multiple_sequences(D::Type{MultivariatePoissonProcess{Float64}}, xs::Base.Generator{UnitRange{Int64}, ControlledHiddenMarkovModels.var"#47#52"{Vector{Vector{History{Int64, Float64}}}}}, ws::Base.Generator{UnitRange{Int64}, ControlledHiddenMarkovModels.var"#48#53"{Vector{Matrix{Float64}}, Int64}}) @ Main ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/hmm.jl:88 [2] macro expansion @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/src/free/concrete/baum_welch.jl:43 [inlined] [3] macro expansion @ ~/.julia/packages/ProgressLogging/6KXlp/src/ProgressLogging.jl:470 [inlined] [4] baum_welch_multiple_sequences!(obs_densities::Vector{Matrix{Float64}}, fb_storage::ControlledHiddenMarkovModels.ForwardBackwardStorage{Float64}, obs_sequences::Vector{Vector{History{Int64, Float64}}}, hmm_init::HiddenMarkovModel{LogFloat32, LogFloat32, MultivariatePoissonProcess{Float64}}, par::Nothing; max_iterations::Int64, tol::Float64) @ ControlledHiddenMarkovModels ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/src/free/concrete/baum_welch.jl:21 [5] baum_welch_multiple_sequences! @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/src/free/concrete/baum_welch.jl:1 [inlined] [6] #baum_welch_multiple_sequences#54 @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/src/free/concrete/baum_welch.jl:70 [inlined] [7] baum_welch_multiple_sequences @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/src/free/concrete/baum_welch.jl:64 [inlined] [8] top-level scope @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/hmm.jl:111 [9] include(fname::String) @ Base.MainInclude ./client.jl:494 [10] macro expansion @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/runtests.jl:28 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [12] macro expansion @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/runtests.jl:28 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined] [14] top-level scope @ ~/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/runtests.jl:18 [15] include(fname::String) @ Base.MainInclude ./client.jl:494 [16] top-level scope @ none:6 [17] eval @ ./boot.jl:385 [inlined] [18] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [19] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/hmm.jl:111 Test Summary: | Pass Fail Error Total Time ControlledHiddenMarkovModels.jl | 16 2 1 19 4m33.5s Code quality (Aqua.jl) | 8 2 10 29.0s Unbound type parameters | 1 1 0.3s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.2s Stale dependencies | 1 1 3.7s Compat bounds | 2 2 4 4.8s julia | 1 1 0.0s ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] deps | 1 1 4.8s ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] extras | 1 1 0.0s ControlledHiddenMarkovModels [7732c362-7152-4a8d-b9b6-d99facdeb807] weakdeps | 1 1 0.0s Piracy | 1 1 0.2s Persistent tasks | 1 1 10.1s Formatting | 1 1 35.0s Doctests | 1 1 25.4s Doctests: ControlledHiddenMarkovModels | 1 1 24.8s Vanilla HMM | 4 1 5 2m18.0s Controlled HMM | 2 2 46.0s ERROR: LoadError: Some tests did not pass: 16 passed, 2 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/ControlledHiddenMarkovModels/wxm2M/test/runtests.jl:17 Testing failed after 343.32s ERROR: LoadError: Package ControlledHiddenMarkovModels errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70 [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/v1.10/Pkg/src/Operations.jl:2034 [3] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [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::Base.PipeEndpoint}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.10/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 389.83s: package tests unexpectedly errored