Package evaluation of HMMBase on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T12:33:14.102 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.57s ################################################################################ # Installation # Installing HMMBase... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [b2b3ca75] + HMMBase v1.0.7 Updating `~/.julia/environments/v1.11/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 ⌅ [aaaa29a8] + Clustering v0.14.4 [34da2185] + Compat v4.16.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [b2b3ca75] + HMMBase v1.0.7 ⌅ [e91730f6] + Hungarian v0.6.0 [34004b35] + HypergeometricFunctions v0.3.28 [92d709cd] + IrrationalConstants v0.2.4 [692b3bcd] + JLLWrappers v1.7.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [b8a86587] + NearestNeighbors v0.4.21 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 ⌅ [aea7be01] + PrecompileTools v1.2.1 [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 v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [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 [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 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [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 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 4.52s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 37.29s ################################################################################ # Testing # Testing HMMBase Status `/tmp/jl_RedgHg/Project.toml` [dce04be8] ArgCheck v2.5.0 ⌅ [aaaa29a8] Clustering v0.14.4 [31c24e10] Distributions v0.25.118 [b2b3ca75] HMMBase v1.0.7 ⌅ [e91730f6] Hungarian v0.6.0 [682c06a0] JSON v0.21.4 [37e2e46d] LinearAlgebra v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_RedgHg/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 ⌅ [aaaa29a8] Clustering v0.14.4 [34da2185] Compat v4.16.0 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [1a297f60] FillArrays v1.13.0 [b2b3ca75] HMMBase v1.0.7 ⌅ [e91730f6] Hungarian v0.6.0 [34004b35] HypergeometricFunctions v0.3.28 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.21 [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 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [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 [a63ad114] Mmap 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 [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 v1.1.1+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 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling DistributionsTestExt... 3653.3 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 5 seconds. 48 already precompiled. ┌ Warning: `MvNormal(μ::AbstractVector{<:Real}, σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(μ, LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 Test Summary: | Pass Total Time Base | 4 4 8.4s Test Summary: | Pass Total Time Base (2) | 5 5 1.7s Test Summary: | Pass Total Time Base (3) | 4 4 0.9s Test Summary: | Pass Total Time Base (4) | 10 10 5.0s Test Summary: | Pass Total Time Base (5) | 1 1 2.1s Test Summary: | Pass Total Time Constructors | 6 6 2.0s Test Summary: | Pass Total Time Stationnary Distributions | 6 6 18.4s Test Summary: | Pass Total Time Messages (1) | 4 4 3.9s Test Summary: | Pass Broken Total Time Messages (3) | 4 2 6 2.3s Test Summary: | Pass Total Time Viterbi | 1 1 0.0s Test Summary: | Pass Total Time MLE | 4 4 25.5s Test Summary: | Pass Total Time Utilities (1) | 8 8 0.0s Test Summary: | Pass Total Time Utilities (2) | 2 2 8.4s Test Summary: | Pass Total Time Reproducibility | 4 4 1.6s Test Summary: | Pass Broken Total Time Experimental | 3 1 4 11.1s Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 9 9 0.1s Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 9 9 0.1s Iteration 0: logtot = -1511.0412838786463 Iteration 1: logtot = -1509.4380712270909 EM has not converged after 1 iterations, logtot = -1509.4380712270909 ┌ Warning: `colwise!(r::AbstractArray, dist::PreMetric, a, b)` is deprecated, use `colwise!(dist, r, a, b)` instead. │ caller = initseeds!(iseeds::Vector{Int64}, alg::Clustering.KmppAlg, X::Matrix{Float64}, metric::Distances.SqEuclidean; rng::TaskLocalRNG) at seeding.jl:184 └ @ Clustering ~/.julia/packages/Clustering/lI5MF/src/seeding.jl:184 ┌ Warning: `pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix, b::AbstractMatrix; dims::Union{Nothing, Integer} = nothing)` is deprecated, use `pairwise!(dist, r, a, b; dims = dims)` instead. │ caller = _kmeans!(X::Matrix{Float64}, weights::Nothing, centers::Matrix{Float64}, maxiter::Int64, tol::Float64, displevel::Int64, distance::Distances.SqEuclidean, rng::TaskLocalRNG) at kmeans.jl:172 └ @ Clustering ~/.julia/packages/Clustering/lI5MF/src/kmeans.jl:172 ┌ Warning: `pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix, b::AbstractMatrix; dims::Union{Nothing, Integer} = nothing)` is deprecated, use `pairwise!(dist, r, a, b; dims = dims)` instead. │ caller = _kmeans!(X::Matrix{Float64}, weights::Nothing, centers::Matrix{Float64}, maxiter::Int64, tol::Float64, displevel::Int64, distance::Distances.SqEuclidean, rng::TaskLocalRNG) at kmeans.jl:176 └ @ Clustering ~/.julia/packages/Clustering/lI5MF/src/kmeans.jl:176 Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 15 15 1.1s Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 9 9 0.0s Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 9 9 0.1s Iteration 0: logtot = -954.953220074617 Iteration 1: logtot = -953.6309944421664 EM has not converged after 1 iterations, logtot = -953.6309944421664 Test Summary: | Pass Total Time Integration HMM{Univariate, Float64} | 15 15 6.0s Test Summary: | Pass Total Time Integration HMM{Multivariate, Float64} | 9 9 1.0s Test Summary: | Pass Total Time Integration HMM{Multivariate, Float64} | 9 9 0.8s Iteration 0: logtot = -3113.578587406826 Iteration 1: logtot = -3107.0941769233973 EM has not converged after 1 iterations, logtot = -3107.0941769233973 Test Summary: | Pass Total Time Integration HMM{Multivariate, Float64} | 15 15 5.0s ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `likelihoods(...)` is deprecated, use `loglikelihoods(...)` or `exp.(loglikelihoods(...))` instead. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:68 ┌ Warning: `likelihoods(...)` is deprecated, use `loglikelihoods(...)` or `exp.(loglikelihoods(...))` instead. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:68 Test Summary: | Pass Total Time < v1.1 | 6 6 1.4s ┌ Warning: `n_parameters(hmm)` is deprecated, use `nparams(hmm)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `log_likelihoods(hmm, observations)` is deprecated, use `loglikelihoods(hmm, observations)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `forward_backward(hmm, observations)` is deprecated, use `posteriors(hmm, observations, logl = true)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `messages_forwards(hmm, observations)` is deprecated, use `forward(hmm, observations, logl = true)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `messages_backwards(hmm, observations)` is deprecated, use `backward(hmm, observations, logl = true)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `logl` keyword argument is deprecated. └ @ HMMBase ~/.julia/packages/HMMBase/ZYC4P/src/HMMBase.jl:73 ┌ Warning: `compute_transition_matrix(seq)` is deprecated, use `gettransmat(seq, relabel = true)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 ┌ Warning: `rand_transition_matrix(K, α = 1.0)` is deprecated, use `randtransmat(K, α)` instead. │ caller = macro expansion at Test.jl:676 [inlined] └ @ Core /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 Test Summary: | Pass Total Time < v1.0 | 7 7 1.0s Testing HMMBase tests passed Testing completed after 130.57s PkgEval succeeded after 190.02s