Package evaluation of PeriodicHiddenMarkovModels on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T14:21:41.109 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.58s ################################################################################ # Installation # Installing PeriodicHiddenMarkovModels... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [4873b48c] + PeriodicHiddenMarkovModels v0.2.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [dce04be8] + ArgCheck v2.5.0 [d360d2e6] + ChainRulesCore v1.25.2 [34da2185] + Compat v4.17.0 [b429d917] + DensityInterface v0.4.0 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 ⌅ [84ca31d5] + HiddenMarkovModels v0.5.4 [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 [4873b48c] + PeriodicHiddenMarkovModels v0.2.0 [21216c6a] + Preferences v1.4.3 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [276daf66] + SpecialFunctions v2.5.1 [82ae8749] + StatsAPI v1.7.1 [4c63d2b9] + StatsFuns v1.5.0 [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 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [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 v1.12.0 [f489334b] + StyledStrings 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 v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.29s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 74.37s ################################################################################ # Testing # Testing PeriodicHiddenMarkovModels Status `/tmp/jl_Dsa75c/Project.toml` [31c24e10] Distributions v0.25.120 ⌅ [84ca31d5] HiddenMarkovModels v0.5.4 [4873b48c] PeriodicHiddenMarkovModels v0.2.0 [860ef19b] StableRNGs v1.0.3 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_Dsa75c/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 [d360d2e6] ChainRulesCore v1.25.2 [34da2185] Compat v4.17.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [b429d917] DensityInterface v0.4.0 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.13.0 ⌅ [84ca31d5] HiddenMarkovModels v0.5.4 [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 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [4873b48c] PeriodicHiddenMarkovModels v0.2.0 [21216c6a] Preferences v1.4.3 [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 v2.5.1 [860ef19b] StableRNGs v1.0.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [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 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [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 v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [8e850b90] libblastrampoline_jll v5.13.1+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 4421.6 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 50 already precompiled. Precompiling packages... 4005.0 ms ✓ Distributions → DistributionsDensityInterfaceExt 1 dependency successfully precompiled in 5 seconds. 57 already precompiled. Precompiling packages... 4459.8 ms ✓ Distributions → DistributionsChainRulesCoreExt 1 dependency successfully precompiled in 5 seconds. 53 already precompiled. Comparing with HiddenMarkovModels.jl in trivial case T = 1 (homogeneous): Error During Test at /home/pkgeval/.julia/packages/PeriodicHiddenMarkovModels/dkyMt/test/runtests.jl:8 Got exception outside of a @test TypeError: in keyword argument seq_ends, expected AbstractVector{Int64}, got a value of type Tuple{Int64} Stacktrace: [1] baum_welch!(fb_storage::HiddenMarkovModels.ForwardBackwardStorage{Float64, Matrix{Float64}}, logL_evolution::Vector{Float64}, hmm::PeriodicHMM{Float64, Distribution{Univariate, Continuous}, 1, Vector{Float64}, SubArray{Float64, 2, Array{Float64, 3}, Tuple{Base.Slice{Base.OneTo{Int64}}, Base.Slice{Base.OneTo{Int64}}, Int64}, true}, SubArray{Distribution{Univariate, Continuous}, 1, Matrix{Distribution{Univariate, Continuous}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}}, obs_seq::Vector{Float64}, control_seq::Vector{Int64}; seq_ends::Tuple{Int64}, atol::Float64, max_iterations::Int64, loglikelihood_increasing::Bool) @ HiddenMarkovModels ~/.julia/packages/HiddenMarkovModels/TAbNC/src/inference/baum_welch.jl:33 [2] baum_welch(hmm_guess::PeriodicHMM{Float64, Distribution{Univariate, Continuous}, 1, Vector{Float64}, SubArray{Float64, 2, Array{Float64, 3}, Tuple{Base.Slice{Base.OneTo{Int64}}, Base.Slice{Base.OneTo{Int64}}, Int64}, true}, SubArray{Distribution{Univariate, Continuous}, 1, Matrix{Distribution{Univariate, Continuous}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}}, obs_seq::Vector{Float64}, control_seq::Vector{Int64}; seq_ends::Tuple{Int64}, atol::Float64, max_iterations::Int64, loglikelihood_increasing::Bool) @ HiddenMarkovModels ~/.julia/packages/HiddenMarkovModels/TAbNC/src/inference/baum_welch.jl:67 [3] baum_welch(hmm_guess::PeriodicHMM{Float64, Distribution{Univariate, Continuous}, 1, Vector{Float64}, SubArray{Float64, 2, Array{Float64, 3}, Tuple{Base.Slice{Base.OneTo{Int64}}, Base.Slice{Base.OneTo{Int64}}, Int64}, true}, SubArray{Distribution{Univariate, Continuous}, 1, Matrix{Distribution{Univariate, Continuous}}, Tuple{Base.Slice{Base.OneTo{Int64}}, Int64}, true}}, obs_seq::Vector{Float64}, control_seq::Vector{Int64}) @ HiddenMarkovModels ~/.julia/packages/HiddenMarkovModels/TAbNC/src/inference/baum_welch.jl:54 [4] top-level scope @ ~/.julia/packages/PeriodicHiddenMarkovModels/dkyMt/test/runtests.jl:9 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/.julia/packages/PeriodicHiddenMarkovModels/dkyMt/test/runtests.jl:55 [inlined] [7] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [8] top-level scope @ none:6 [9] eval(m::Module, e::Any) @ Core ./boot.jl:489 [10] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [11] _start() @ Base ./client.jl:554 Test Summary: | Error Total Time Comparing with HiddenMarkovModels.jl in trivial case T = 1 (homogeneous) | 1 1 17.0s RNG of the outermost testset: Xoshiro(0x0c48963a8afc77c4, 0x217d80fe7c45a771, 0xd7a00538900dd871, 0xf8c0f86cbd85a011, 0x7427fe49feba08c3) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PeriodicHiddenMarkovModels/dkyMt/test/runtests.jl:8 Testing failed after 49.17s ERROR: LoadError: Package PeriodicHiddenMarkovModels errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.12/Pkg/src/Operations.jl:2458 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.12/Pkg/src/API.jl:511 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 158.23s: package tests unexpectedly errored