Package evaluation of Pathogen on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T03:32:53.432 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.97s ################################################################################ # Installation # Installing Pathogen... Resolving package versions... Installed IrrationalConstants ───────── v0.2.4 Installed Rmath ─────────────────────── v0.8.0 Installed Crayons ───────────────────── v4.1.1 Installed OnlineStatsBase ───────────── v1.7.1 Installed StatsFuns ─────────────────── v1.5.0 Installed HypergeometricFunctions ───── v0.3.28 Installed Preferences ───────────────── v1.4.3 Installed PtrArrays ─────────────────── v1.3.0 Installed SentinelArrays ────────────── v1.4.8 Installed TableTraits ───────────────── v1.0.1 Installed Tables ────────────────────── v1.12.0 Installed SpecialFunctions ──────────── v2.5.1 Installed PDMats ────────────────────── v0.11.34 Installed DataAPI ───────────────────── v1.16.0 Installed PrettyTables ──────────────── v2.4.0 Installed RecipesBase ───────────────── v1.3.4 Installed PooledArrays ──────────────── v1.4.3 Installed InlineStrings ─────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.0 Installed ProgressMeter ─────────────── v1.10.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataValueInterfaces ───────── v1.0.0 Installed LaTeXStrings ──────────────── v1.4.0 Installed InvertedIndices ───────────── v1.3.1 Installed OrderedCollections ────────── v1.8.0 Installed AbstractTrees ─────────────── v0.4.5 Installed PrecompileTools ───────────── v1.3.2 Installed QuadGK ────────────────────── v2.11.2 Installed FillArrays ────────────────── v1.13.0 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed Reexport ──────────────────── v1.2.2 Installed Statistics ────────────────── v1.11.1 Installed DataStructures ────────────── v0.18.22 Installed LogExpFunctions ───────────── v0.3.29 Installed DataFrames ────────────────── v1.7.0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed StatsAPI ──────────────────── v1.7.0 Installed Compat ────────────────────── v4.16.0 Installed AliasTables ───────────────── v1.1.3 Installed StringManipulation ────────── v0.4.1 Installed SortingAlgorithms ─────────── v1.2.1 Installed Missings ──────────────────── v1.2.0 Installed StatsBase ─────────────────── v0.33.21 Installed DocStringExtensions ───────── v0.9.4 Installed OnlineStats ───────────────── v1.7.1 Installed Distributions ─────────────── v0.25.119 Installed Pathogen ──────────────────── v0.4.13 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.13/Project.toml` [c8189ad9] + Pathogen v0.4.13 Updating `~/.julia/environments/v1.13/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.119 [ffbed154] + DocStringExtensions v0.9.4 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [a15396b6] + OnlineStats v1.7.1 [925886fa] + OnlineStatsBase v1.7.1 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.34 [c8189ad9] + Pathogen v0.4.13 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [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 [8ba89e20] + Distributed v1.11.0 [9fa8497b] + Future 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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [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 v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.12.0+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 8.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5782.9 ms ✓ TestEnv 1 dependency successfully precompiled in 6 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 287.14s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_8JSA9r/Project.toml` [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.119 [a15396b6] OnlineStats v1.7.1 [c8189ad9] Pathogen v0.4.13 [92933f4c] ProgressMeter v1.10.4 [3cdcf5f2] RecipesBase v1.3.4 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_8JSA9r/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.16.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.119 [ffbed154] DocStringExtensions v0.9.4 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [a15396b6] OnlineStats v1.7.1 [925886fa] OnlineStatsBase v1.7.1 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.34 [c8189ad9] Pathogen v0.4.13 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [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 [8ba89e20] Distributed v1.11.0 [9fa8497b] Future 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 [6462fe0b] Sockets 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 v7.10.1+0 [8e850b90] libblastrampoline_jll v5.12.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: `Progress(n::Integer, desc::AbstractString, offset::Integer = 0; kwargs...)` is deprecated, use `Progress(n; desc = desc, offset = offset, kwargs...)` instead. │ caller = ip:0x0 └ @ Core :-1 Initialization progress 1%|▏ | ETA: 2:57:14 Initialization progress 38%|██████████▊ | ETA: 0:01:55 Initialization progress 74%|████████████████████▉ | ETA: 0:00:25 Initialization progress 100%|████████████████████████████| Time: 0:01:12 MCMC progress 1%|▎ | ETA: 2:14:25 MCMC progress 10%|███▉ | ETA: 0:07:51 MCMC progress 19%|███████▍ | ETA: 0:03:47 MCMC progress 27%|██████████▍ | ETA: 0:02:25 MCMC progress 35%|█████████████▍ | ETA: 0:01:40 MCMC progress 44%|████████████████▋ | ETA: 0:01:11 MCMC progress 51%|███████████████████▌ | ETA: 0:00:52 MCMC progress 59%|██████████████████████▍ | ETA: 0:00:38 MCMC progress 67%|█████████████████████████▌ | ETA: 0:00:27 MCMC progress 75%|████████████████████████████▍ | ETA: 0:00:19 MCMC progress 82%|███████████████████████████████▎ | ETA: 0:00:12 MCMC progress 90%|██████████████████████████████████▍ | ETA: 0:00:06 MCMC progress 94%|███████████████████████████████████▋ | ETA: 0:00:04 MCMC progress 100%|██████████████████████████████████████| Time: 0:01:08 Initialization progress 2%|▌ | ETA: 0:00:48 Initialization progress 100%|████████████████████████████| Time: 0:00:01 MCMC progress 2%|▊ | ETA: 0:02:49 MCMC progress 45%|█████████████████▏ | ETA: 0:00:04 MCMC progress 88%|█████████████████████████████████▌ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:03 SEIR Model: Error During Test at /home/pkgeval/.julia/packages/Pathogen/0VMLl/test/runtests.jl:95 Test threw exception Expression: typeof(summary(mcmc, burnin = 50, thin = 2)) == DataFrame 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#11 @ ~/.julia/packages/Statistics/gbcbG/src/Statistics.jl:380 [inlined] [9] summary(mcmc::MCMC{SEIR}; burnin::Int64, thin::Int64, bychain::Bool, credibleinterval::Float64) @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/summary.jl:42 [10] top-level scope @ ~/.julia/packages/Pathogen/0VMLl/test/runtests.jl:26 [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1835 [inlined] [12] macro expansion @ ~/.julia/packages/Pathogen/0VMLl/test/runtests.jl:95 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:728 [inlined] Test Summary: | Pass Error Total Time SEIR Model | 90 1 91 3m46.0s RNG of the outermost testset: Xoshiro(0x535d54a65a58bfbb, 0x57bde37aaa4004c8, 0x9010ac282f089ad8, 0x17e061cc56457d10, 0xd20d0875a02a3fbb) ERROR: LoadError: Some tests did not pass: 90 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Pathogen/0VMLl/test/runtests.jl:23 Testing failed after 279.98s ERROR: LoadError: Package Pathogen 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 678.95s: package tests unexpectedly errored