Package evaluation of DynamicHMCExamples on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T07:09:58.082 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.2s ################################################################################ # Installation # Installing DynamicHMCExamples... Resolving package versions... Installed GPUArraysCore ─────────────── v0.1.6 Installed ScientificTypesBase ───────── v3.0.0 Installed IrrationalConstants ───────── v0.2.4 Installed TransmuteDims ─────────────── v0.1.16 Installed Adapt ─────────────────────── v4.3.0 Installed DiffRules ─────────────────── v1.15.1 Installed Rmath ─────────────────────── v0.8.0 Installed TransformVariables ────────── v0.8.16 Installed HypergeometricFunctions ───── v0.3.28 Installed ArgCheck ──────────────────── v2.5.0 Installed MLJModelInterface ─────────── v1.11.1 Installed StatsFuns ─────────────────── v1.5.0 Installed DynamicHMC ────────────────── v3.5.0 Installed JSON ──────────────────────── v0.21.4 Installed Preferences ───────────────── v1.4.3 Installed PtrArrays ─────────────────── v1.3.0 Installed StatisticalTraits ─────────── v3.4.0 Installed TableTraits ───────────────── v1.0.1 Installed DiffResults ───────────────── v1.1.0 Installed Parsers ───────────────────── v2.8.3 Installed SpecialFunctions ──────────── v2.5.1 Installed BenchmarkTools ────────────── v1.6.0 Installed DynamicHMCExamples ────────── v0.2.2 Installed DataAPI ───────────────────── v1.16.0 Installed PDMats ────────────────────── v0.11.34 Installed Tables ────────────────────── v1.12.0 Installed TensorCast ────────────────── v0.4.8 Installed AbstractFFTs ──────────────── v1.5.0 Installed JLLWrappers ───────────────── v1.7.0 Installed StaticArrays ──────────────── v1.9.13 Installed ProgressMeter ─────────────── v1.10.4 Installed StaticArraysCore ──────────── v1.4.3 Installed TransformedLogDensities ───── v1.1.1 Installed NaNMath ───────────────────── v1.1.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataValueInterfaces ───────── v1.0.0 Installed OrderedCollections ────────── v1.8.0 Installed LazyStack ─────────────────── v0.1.3 Installed MCMCDiagnosticTools ───────── v0.3.14 Installed PrecompileTools ───────────── v1.3.2 Installed QuadGK ────────────────────── v2.11.2 Installed FillArrays ────────────────── v1.13.0 Installed ForwardDiff ───────────────── v0.10.38 Installed ChainRulesCore ────────────── v1.25.1 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed Reexport ──────────────────── v1.2.2 Installed Statistics ────────────────── v1.11.1 Installed CommonSubexpressions ──────── v0.3.1 Installed Requires ──────────────────── v1.3.1 Installed LogExpFunctions ───────────── v0.3.29 Installed DataStructures ────────────── v0.18.22 Installed StridedViews ──────────────── v0.4.1 Installed AliasTables ───────────────── v1.1.3 Installed LogDensityProblemsAD ──────── v1.13.0 Installed Strided ───────────────────── v2.3.0 Installed MacroTools ────────────────── v0.5.16 Installed PackageExtensionCompat ────── v1.0.2 Installed StatsAPI ──────────────────── v1.7.0 Installed Compat ────────────────────── v4.16.0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed UnPack ────────────────────── v1.0.2 Installed LogDensityProblems ────────── v2.1.2 Installed Parameters ────────────────── v0.12.3 Installed Missings ──────────────────── v1.2.0 Installed Distributions ─────────────── v0.25.119 Installed TupleTools ────────────────── v1.6.0 Installed SortingAlgorithms ─────────── v1.2.1 Installed StatsBase ─────────────────── v0.34.4 Installed DocStringExtensions ───────── v0.9.4 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [2771e1c8] + DynamicHMCExamples v0.2.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 [6e4b80f9] + BenchmarkTools v1.6.0 [d360d2e6] + ChainRulesCore v1.25.1 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions 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To see why use `status --outdated -m` Installation completed after 8.55s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5372.4 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 372.18s ################################################################################ # Testing # Testing DynamicHMCExamples Status `/tmp/jl_OpCoX1/Project.toml` [6e4b80f9] BenchmarkTools v1.6.0 [31c24e10] Distributions v0.25.119 [e30172f5] Documenter v1.10.2 [bbc10e6e] DynamicHMC v3.5.0 [2771e1c8] DynamicHMCExamples v0.2.2 ⌅ [f6369f11] ForwardDiff v0.10.38 [98b081ad] Literate v2.20.1 [6fdf6af0] LogDensityProblems v2.1.2 [996a588d] LogDensityProblemsAD v1.13.0 [2ab3a3ac] LogExpFunctions v0.3.29 [be115224] MCMCDiagnosticTools v0.3.14 [d96e819e] Parameters v0.12.3 [10745b16] Statistics v1.11.1 [4c63d2b9] StatsFuns v1.5.0 [84d833dd] TransformVariables v0.8.16 [f9bc47f6] TransformedLogDensities v1.1.1 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_OpCoX1/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] 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compatibility constraints restrict them from upgrading. Testing Running tests... independent bernoulli: Error During Test at /home/pkgeval/.julia/packages/DynamicHMCExamples/IH95Y/test/runtests.jl:9 Got exception outside of a @test LoadError: MethodError: no method matching mapreduce_impl(::Statistics.var"#centralizedabs2fun##0#centralizedabs2fun##1"{Float64}, ::typeof(+), ::Matrix{Float64}, ::Int64, ::Int64) The function `mapreduce_impl` exists, but no method is defined for this combination of argument types. Closest candidates are: mapreduce_impl(::Any, ::Any, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer, !Matched::Int64) @ Base reduce.jl:263 mapreduce_impl(::Any, ::Any, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer) @ Base reduce.jl:286 mapreduce_impl(::Any, !Matched::Union{typeof(max), typeof(min)}, ::Union{Base.AbstractBroadcasted, AbstractArray}, ::Any, ::Integer, !Matched::Integer) @ Base reduce.jl:649 ... Stacktrace: [1] centralize_sumabs2(A::Matrix{Float64}, m::Float64, ifirst::Int64, ilast::Int64) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:257 [2] centralize_sumabs2!(R::Matrix{Float64}, A::Matrix{Float64}, means::Matrix{Float64}) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:275 [3] varm!(R::Matrix{Float64}, A::Matrix{Float64}, m::Matrix{Float64}; corrected::Bool) @ Statistics ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:309 [4] varm! @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:304 [inlined] [5] _varm @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:341 [inlined] [6] varm @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:339 [inlined] [7] _var @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:386 [inlined] [8] var @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:380 [inlined] [9] sample_M⁻¹ @ ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:204 [inlined] [10] warmup(sampling_logdensity::DynamicHMC.SamplingLogDensity{TaskLocalRNG, LogDensityProblemsADForwardDiffExt.ForwardDiffLogDensity{TransformedLogDensity{TransformVariables.TransformTuple{@NamedTuple{α::TransformVariables.ScaledShiftedLogistic{Int64}}}, BernoulliProblem}, ForwardDiff.Chunk{1}, Nothing, Nothing}, NUTS{Val{:generalized}}, NoProgressReport}, tuning::TuningNUTS{Diagonal, DualAveraging{Float64}}, warmup_state::DynamicHMC.WarmupState{DynamicHMC.EvaluatedLogDensity{Vector{Float64}, Float64}, GaussianKineticEnergy{Diagonal{Float64, FillArrays.Fill{Float64, 1, Tuple{Base.OneTo{Int64}}}}, Diagonal{Float64, FillArrays.Fill{Float64, 1, Tuple{Base.OneTo{Int64}}}}}, Float64}) @ DynamicHMC ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:263 [11] #_warmup##0 @ ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:430 [inlined] [12] BottomRF @ ./reduce.jl:78 [inlined] [13] afoldl(::Base.BottomRF{DynamicHMC.var"#_warmup##0#_warmup##1"{DynamicHMC.SamplingLogDensity{TaskLocalRNG, LogDensityProblemsADForwardDiffExt.ForwardDiffLogDensity{TransformedLogDensity{TransformVariables.TransformTuple{@NamedTuple{α::TransformVariables.ScaledShiftedLogistic{Int64}}}, BernoulliProblem}, ForwardDiff.Chunk{1}, Nothing, Nothing}, NUTS{Val{:generalized}}, NoProgressReport}}}, ::Tuple{Tuple{}, DynamicHMC.WarmupState{DynamicHMC.EvaluatedLogDensity{Vector{Float64}, Float64}, GaussianKineticEnergy{Diagonal{Float64, FillArrays.Fill{Float64, 1, Tuple{Base.OneTo{Int64}}}}, Diagonal{Float64, FillArrays.Fill{Float64, 1, Tuple{Base.OneTo{Int64}}}}}, Nothing}}, ::InitialStepsizeSearch, ::TuningNUTS{Nothing, DualAveraging{Float64}}, ::TuningNUTS{Diagonal, DualAveraging{Float64}}, ::TuningNUTS{Diagonal, DualAveraging{Float64}}, ::TuningNUTS{Diagonal, DualAveraging{Float64}}, ::TuningNUTS{Diagonal, DualAveraging{Float64}}, ::TuningNUTS{Diagonal, DualAveraging{Float64}}, ::TuningNUTS{Nothing, DualAveraging{Float64}}) @ Base ./operators.jl:602 [14] _foldl_impl @ ./reduce.jl:60 [inlined] [15] foldl_impl @ ./reduce.jl:40 [inlined] [16] mapfoldl_impl @ ./reduce.jl:36 [inlined] [17] mapfoldl @ ./reduce.jl:167 [inlined] [18] foldl @ ./reduce.jl:190 [inlined] [19] _warmup @ ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:428 [inlined] [20] mcmc_keep_warmup(rng::TaskLocalRNG, ℓ::LogDensityProblemsADForwardDiffExt.ForwardDiffLogDensity{TransformedLogDensity{TransformVariables.TransformTuple{@NamedTuple{α::TransformVariables.ScaledShiftedLogistic{Int64}}}, BernoulliProblem}, ForwardDiff.Chunk{1}, Nothing, Nothing}, N::Int64; initialization::Tuple{}, warmup_stages::Tuple{InitialStepsizeSearch, TuningNUTS{Nothing, DualAveraging{Float64}}, TuningNUTS{Diagonal, DualAveraging{Float64}}, TuningNUTS{Diagonal, DualAveraging{Float64}}, TuningNUTS{Diagonal, DualAveraging{Float64}}, TuningNUTS{Diagonal, DualAveraging{Float64}}, TuningNUTS{Diagonal, DualAveraging{Float64}}, TuningNUTS{Nothing, DualAveraging{Float64}}}, algorithm::NUTS{Val{:generalized}}, reporter::NoProgressReport) @ DynamicHMC ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:505 [21] mcmc_keep_warmup @ ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:498 [inlined] [22] #mcmc_with_warmup#30 @ ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:555 [inlined] [23] mcmc_with_warmup(rng::TaskLocalRNG, ℓ::LogDensityProblemsADForwardDiffExt.ForwardDiffLogDensity{TransformedLogDensity{TransformVariables.TransformTuple{@NamedTuple{α::TransformVariables.ScaledShiftedLogistic{Int64}}}, BernoulliProblem}, ForwardDiff.Chunk{1}, Nothing, Nothing}, N::Int64) @ DynamicHMC ~/.julia/packages/DynamicHMC/wYkyM/src/mcmc.jl:552 [24] (::var"#2#3")(::Int64) @ Main ./none:-1 [25] iterate @ ./generator.jl:48 [inlined] [26] collect(itr::Base.Generator{UnitRange{Int64}, var"#2#3"}) @ Base ./array.jl:790 [27] top-level scope @ ~/.julia/packages/DynamicHMCExamples/IH95Y/src/example_independent_bernoulli.jl:72 [28] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [29] top-level scope @ ~/.julia/packages/DynamicHMCExamples/IH95Y/test/runtests.jl:10 [30] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1835 [inlined] [31] macro expansion @ ~/.julia/packages/DynamicHMCExamples/IH95Y/test/runtests.jl:10 [inlined] [32] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [33] top-level scope @ none:6 [34] eval(m::Module, e::Any) @ Core ./boot.jl:489 [35] exec_options(opts::Base.JLOptions) @ Base ./client.jl:297 [36] _start() @ Base ./client.jl:563 in expression starting at /home/pkgeval/.julia/packages/DynamicHMCExamples/IH95Y/src/example_independent_bernoulli.jl:72 Test Summary: | Error Total Time independent bernoulli | 1 1 36.3s RNG of the outermost testset: Xoshiro(0xb850045b2cef93f0, 0x13ae0d9ccc498d7e, 0xf885a58336a644c7, 0x71a09cea733b9e9e, 0xe95ab32ac9acea9f) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/DynamicHMCExamples/IH95Y/test/runtests.jl:9 Testing failed after 49.71s ERROR: LoadError: Package DynamicHMCExamples errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2414 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2269 [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/v1.13/Pkg/src/API.jl:486 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/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:303 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:331 [12] _start() @ Base ./client.jl:563 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 464.27s: package tests unexpectedly errored