Package evaluation of Pathogen on Julia 1.13.0-DEV.888 (0e1aa6c7eb*) started at 2025-07-22T18:27:43.098 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.91s ################################################################################ # Installation # Installing Pathogen... Resolving package versions... 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 v4.17.0 [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 v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.4 [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 v1.8.1 [90014a1f] + PDMats v0.11.35 [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 v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [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 v1.13.0 [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 v1.13.0 [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 v5.13.1+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 4.61s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 110.29s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_lNZJeZ/Project.toml` [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [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 v1.13.0 [56ddb016] Logging v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_lNZJeZ/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.17.0 [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 v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.4 [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 v1.8.1 [90014a1f] PDMats v0.11.35 [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 v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [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 v1.13.0 [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 v1.13.0 [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 v5.13.1+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 9515.0 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 11 seconds. 49 already precompiled. ┌ 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: 2:46:06 Initialization progress 37%|██████████▌ | ETA: 0:01:53 Initialization progress 73%|████████████████████▌ | ETA: 0:00:25 Initialization progress 100%|████████████████████████████| Time: 0:01:07 MCMC progress 1%|▎ | ETA: 2:04:07 MCMC progress 9%|███▎ | ETA: 0:08:48 MCMC progress 17%|██████▋ | ETA: 0:03:59 MCMC progress 25%|█████████▋ | ETA: 0:02:28 MCMC progress 34%|████████████▊ | ETA: 0:01:39 MCMC progress 42%|████████████████▏ | ETA: 0:01:09 MCMC progress 51%|███████████████████▎ | ETA: 0:00:49 MCMC progress 58%|██████████████████████▏ | ETA: 0:00:36 MCMC progress 66%|█████████████████████████▎ | ETA: 0:00:26 MCMC progress 75%|████████████████████████████▌ | ETA: 0:00:17 MCMC progress 84%|███████████████████████████████▊ | ETA: 0:00:10 MCMC progress 92%|███████████████████████████████████▏ | ETA: 0:00:05 MCMC progress 100%|██████████████████████████████████████| Time: 0:01:03 Initialization progress 2%|▌ | ETA: 0:00:43 Initialization progress 100%|████████████████████████████| Time: 0:00:00 MCMC progress 2%|▊ | ETA: 0:02:38 MCMC progress 36%|█████████████▋ | ETA: 0:00:06 MCMC progress 73%|███████████████████████████▊ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:03 Test Summary: | Pass Total Time SEIR Model | 92 92 3m26.2s Initialization progress 1%|▏ | ETA: 1:15:17 Initialization progress 31%|████████▋ | ETA: 0:01:08 Initialization progress 62%|█████████████████▍ | ETA: 0:00:19 Initialization progress 93%|██████████████████████████ | ETA: 0:00:02 Initialization progress 100%|████████████████████████████| Time: 0:00:31 MCMC progress 1%|▎ | ETA: 0:54:25 MCMC progress 11%|████▏ | ETA: 0:02:58 MCMC progress 22%|████████▌ | ETA: 0:01:17 MCMC progress 34%|████████████▊ | ETA: 0:00:44 MCMC progress 45%|█████████████████ | ETA: 0:00:28 MCMC progress 55%|█████████████████████ | ETA: 0:00:18 MCMC progress 66%|█████████████████████████▎ | ETA: 0:00:11 MCMC progress 77%|█████████████████████████████▏ | ETA: 0:00:07 MCMC progress 87%|█████████████████████████████████▏ | ETA: 0:00:03 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:24 MCMC progress 9%|███▍ | ETA: 0:00:01 MCMC progress 66%|█████████████████████████▏ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SEI Model | 166 166 1m19.1s Initialization progress 1%|▏ | ETA: 1:20:14 Initialization progress 32%|█████████ | ETA: 0:01:09 Initialization progress 63%|█████████████████▌ | ETA: 0:00:19 Initialization progress 92%|█████████████████████████▉ | ETA: 0:00:03 Initialization progress 100%|████████████████████████████| Time: 0:00:33 MCMC progress 1%|▎ | ETA: 0:54:12 MCMC progress 10%|███▊ | ETA: 0:03:17 MCMC progress 19%|███████▍ | ETA: 0:01:32 MCMC progress 28%|██████████▋ | ETA: 0:00:57 MCMC progress 37%|██████████████ | ETA: 0:00:38 MCMC progress 47%|█████████████████▉ | ETA: 0:00:25 MCMC progress 56%|█████████████████████▍ | ETA: 0:00:17 MCMC progress 66%|█████████████████████████▎ | ETA: 0:00:11 MCMC progress 76%|████████████████████████████▉ | ETA: 0:00:07 MCMC progress 87%|████████████████████████████████▉ | ETA: 0:00:04 MCMC progress 97%|████████████████████████████████████▉ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:23 MCMC progress 9%|███▍ | ETA: 0:00:01 MCMC progress 59%|██████████████████████▍ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SIR Model | 173 173 1m21.5s Initialization progress 1%|▏ | ETA: 1:16:08 Initialization progress 25%|██████▉ | ETA: 0:01:34 Initialization progress 53%|██████████████▉ | ETA: 0:00:27 Initialization progress 82%|███████████████████████ | ETA: 0:00:07 Initialization progress 100%|████████████████████████████| Time: 0:00:31 MCMC progress 1%|▎ | ETA: 0:52:58 MCMC progress 11%|████▎ | ETA: 0:02:48 MCMC progress 22%|████████▌ | ETA: 0:01:15 MCMC progress 34%|████████████▊ | ETA: 0:00:43 MCMC progress 45%|█████████████████ | ETA: 0:00:27 MCMC progress 55%|█████████████████████ | ETA: 0:00:18 MCMC progress 66%|█████████████████████████▎ | ETA: 0:00:11 MCMC progress 77%|█████████████████████████████▏ | ETA: 0:00:07 MCMC progress 87%|█████████████████████████████████ | ETA: 0:00:03 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:23 MCMC progress 2%|▊ | ETA: 0:00:09┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 MCMC progress 12%|████▌ | ETA: 0:00:17┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 ┌ Error: All transmission rates = 0.0, No transmission generated │ external_or_internal = │ 2-element StatsBase.Weights{Float64, Float64, Vector{Float64}}: │ 0.0 │ 0.0 └ @ Pathogen ~/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:28 MCMC progress 33%|████████████▌ | ETA: 0:00:05 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:02 Test Summary: | Pass Total Time SI Model | 109 109 1m20.3s Testing Pathogen tests passed Testing completed after 454.08s PkgEval succeeded after 721.51s