Package evaluation to test Pathogen on Julia 1.14.0-DEV.24 (d5fb6bbb43*) started at 2025-11-02T18:43:45.171 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.23s ################################################################################ # Installation # Installing Pathogen... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [c8189ad9] + Pathogen v0.4.13 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [66dad0bd] + AliasTables v1.1.3 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.14.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [a15396b6] + OnlineStats v1.7.2 [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 v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [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 [7b1f6079] + FileWatching 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 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [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 v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 5.04s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 9514.8 ms ✓ StatsBase 4349.7 ms ✓ OnlineStatsBase 15101.9 ms ✓ Distributions 9091.7 ms ✓ OnlineStats 15437.2 ms ✓ Pathogen 5 dependencies successfully precompiled in 58 seconds. 66 already precompiled. 2 dependencies had output during precompilation: ┌ OnlineStats │ WARNING: Constructor for type "Extrema" was extended in `OnlineStats` without explicit qualification or import. │ NOTE: Assumed "Extrema" refers to `OnlineStatsBase.Extrema`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Extrema end`. │ Hint: To silence the warning, qualify `Extrema` as `OnlineStatsBase.Extrema` in the method signature or explicitly `import OnlineStatsBase: Extrema`. └ ┌ Pathogen │ WARNING: Constructor for type "UInt8" was extended in `Pathogen` without explicit qualification or import. │ NOTE: Assumed "UInt8" refers to `Base.UInt8`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function UInt8 end`. │ Hint: To silence the warning, qualify `UInt8` as `Base.UInt8` in the method signature or explicitly `import Base: UInt8`. │ WARNING: method definition for generate at /home/pkgeval/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:1 declares type variable T but does not use it. │ WARNING: method definition for generate at /home/pkgeval/.julia/packages/Pathogen/0VMLl/src/inference/generate.jl:20 declares type variable T but does not use it. │ WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. │ WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. │ WARNING: method definition for apply_recipe at /home/pkgeval/.julia/packages/RecipesBase/BRe07/src/RecipesBase.jl:296 declares type variable T but does not use it. └ Precompilation completed after 66.96s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_u80oac/Project.toml` [a93c6f00] DataFrames v1.8.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [a15396b6] OnlineStats v1.7.2 [c8189ad9] Pathogen v0.4.13 [92933f4c] ProgressMeter v1.11.0 [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_u80oac/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.14.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [a15396b6] OnlineStats v1.7.2 [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 v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [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 [7b1f6079] FileWatching 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 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [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 v0.8.7+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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: 2:53:12 Initialization progress 100%|████████████████████████████| Time: 0:01:10 MCMC progress 1%|▎ | ETA: 2:13:05 MCMC progress 9%|███▎ | ETA: 0:09:26 MCMC progress 17%|██████▋ | ETA: 0:04:17 MCMC progress 26%|█████████▉ | ETA: 0:02:33 MCMC progress 34%|████████████▉ | ETA: 0:01:45 MCMC progress 42%|███████████████▉ | ETA: 0:01:16 MCMC progress 50%|███████████████████ | ETA: 0:00:54 MCMC progress 59%|██████████████████████▎ | ETA: 0:00:38 MCMC progress 67%|█████████████████████████▍ | ETA: 0:00:27 MCMC progress 75%|████████████████████████████▌ | ETA: 0:00:18 MCMC progress 83%|███████████████████████████████▋ | ETA: 0:00:11 MCMC progress 91%|██████████████████████████████████▌ | ETA: 0:00:06 MCMC progress 94%|███████████████████████████████████▊ | ETA: 0:00:04 MCMC progress 100%|██████████████████████████████████████| Time: 0:01:08 Initialization progress 2%|▌ | ETA: 0:00:43 Initialization progress 100%|████████████████████████████| Time: 0:00:00 MCMC progress 2%|▊ | ETA: 0:03:00 MCMC progress 50%|███████████████████ | ETA: 0:00:04 MCMC progress 94%|███████████████████████████████████▊ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:04 Test Summary: | Pass Total Time SEIR Model | 92 92 3m40.9s Initialization progress 1%|▏ | ETA: 1:22:44 Initialization progress 27%|███████▌ | ETA: 0:01:32 Initialization progress 56%|███████████████▋ | ETA: 0:00:27 Initialization progress 85%|███████████████████████▊ | ETA: 0:00:06 Initialization progress 100%|████████████████████████████| Time: 0:00:34 MCMC progress 1%|▎ | ETA: 1:05:54 MCMC progress 11%|████ | ETA: 0:03:43 MCMC progress 22%|████████▎ | ETA: 0:01:37 MCMC progress 33%|████████████▍ | ETA: 0:00:55 MCMC progress 43%|████████████████▌ | ETA: 0:00:35 MCMC progress 54%|████████████████████▌ | ETA: 0:00:23 MCMC progress 64%|████████████████████████▍ | ETA: 0:00:15 MCMC progress 74%|████████████████████████████▏ | ETA: 0:00:10 MCMC progress 83%|███████████████████████████████▋ | ETA: 0:00:05 MCMC progress 93%|███████████████████████████████████▎ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:28 MCMC progress 2%|▊ | ETA: 0:00:05 MCMC progress 64%|████████████████████████▍ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SEI Model | 170 170 1m29.8s Initialization progress 1%|▏ | ETA: 1:26:16 Initialization progress 16%|████▍ | ETA: 0:03:08 Initialization progress 44%|████████████▍ | ETA: 0:00:44 Initialization progress 74%|████████████████████▋ | ETA: 0:00:13 Initialization progress 100%|████████████████████████████| Time: 0:00:35 MCMC progress 1%|▎ | ETA: 0:48:01 MCMC progress 11%|████▎ | ETA: 0:02:32 MCMC progress 22%|████████▍ | ETA: 0:01:09 MCMC progress 32%|████████████▏ | ETA: 0:00:42 MCMC progress 42%|████████████████ | ETA: 0:00:27 MCMC progress 52%|███████████████████▉ | ETA: 0:00:18 MCMC progress 63%|███████████████████████▉ | ETA: 0:00:12 MCMC progress 73%|███████████████████████████▋ | ETA: 0:00:08 MCMC progress 83%|███████████████████████████████▍ | ETA: 0:00:04 MCMC progress 91%|██████████████████████████████████▊ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:21 MCMC progress 2%|▊ | ETA: 0:00:05 MCMC progress 50%|███████████████████ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SIR Model | 173 173 1m21.4s Initialization progress 1%|▏ | ETA: 1:16:42 Initialization progress 31%|████████▋ | ETA: 0:01:09 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: 0:53:18 MCMC progress 15%|█████▋ | ETA: 0:02:05 MCMC progress 28%|██████████▋ | ETA: 0:00:56 MCMC progress 41%|███████████████▊ | ETA: 0:00:31 MCMC progress 54%|████████████████████▋ | ETA: 0:00:18 MCMC progress 67%|█████████████████████████▌ | ETA: 0:00:11 MCMC progress 80%|██████████████████████████████▍ | ETA: 0:00:06 MCMC progress 93%|███████████████████████████████████▍ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:22 MCMC progress 2%|▊ | ETA: 0:00:10 MCMC progress 86%|████████████████████████████████▋ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SI Model | 107 107 1m19.6s Testing Pathogen tests passed Testing completed after 479.27s PkgEval succeeded after 711.79s