Package evaluation to test Pathogen on Julia 1.14.0-DEV.1893 (b4aba01002*) started at 2026-03-15T19:36:08.079 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 12.75s ################################################################################ # 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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 [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 v1.7.3 [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 v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.4 [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 v1.13.0 [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 v1.13.0 [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 v0.3.30+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 5.55s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 3357.6 ms ✓ OnlineStatsBase 6980.4 ms ✓ OnlineStats 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. 12940.6 ms ✓ Pathogen 3 dependencies successfully precompiled in 24 seconds. 72 already precompiled. 9 dependencies precompiled but different versions are currently loaded (Base64, Dates, JuliaSyntaxHighlighting, Logging, Markdown, Printf, StyledStrings, TOML and UUIDs). Restart julia to access the new versions. Otherwise, 29 dependents of these packages may trigger further precompilation to work with the unexpected versions. 1 dependency had output during precompilation: ┌ 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 47.51s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_kPOJmW/Project.toml` [a93c6f00] DataFrames v1.8.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [a15396b6] OnlineStats v1.7.3 [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_kPOJmW/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 v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [1a297f60] FillArrays v1.16.0 [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 v1.7.3 [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 v1.5.2 [08abe8d2] PrettyTables v3.2.3 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.2 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.7.1 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.4 [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 v1.13.0 [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 v1.13.0 [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 v0.3.30+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: 2:22:43 Initialization progress 100%|████████████████████████████| Time: 0:00:58 MCMC progress 1%|▎ | ETA: 1:57:37 MCMC progress 9%|███▌ | ETA: 0:07:41 MCMC progress 18%|███████ | ETA: 0:03:32 MCMC progress 27%|██████████▍ | ETA: 0:02:07 MCMC progress 36%|█████████████▋ | ETA: 0:01:25 MCMC progress 45%|█████████████████ | ETA: 0:00:59 MCMC progress 54%|████████████████████▌ | ETA: 0:00:41 MCMC progress 63%|████████████████████████ | ETA: 0:00:28 MCMC progress 72%|███████████████████████████▍ | ETA: 0:00:19 MCMC progress 81%|██████████████████████████████▊ | ETA: 0:00:11 MCMC progress 90%|██████████████████████████████████▏ | ETA: 0:00:06 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:57 Initialization progress 2%|▌ | ETA: 0:00:45 Initialization progress 100%|████████████████████████████| Time: 0:00:00 MCMC progress 2%|▊ | ETA: 0:02:54 MCMC progress 47%|█████████████████▉ | ETA: 0:00:04 MCMC progress 92%|███████████████████████████████████ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:03 Test Summary: | Pass Total Time SEIR Model | 94 94 3m02.7s Initialization progress 1%|▏ | ETA: 1:28:50 Initialization progress 30%|████████▍ | ETA: 0:01:24 Initialization progress 59%|████████████████▍ | ETA: 0:00:25 Initialization progress 88%|████████████████████████▋ | ETA: 0:00:05 Initialization progress 100%|████████████████████████████| Time: 0:00:36 MCMC progress 1%|▎ | ETA: 1:08:12 MCMC progress 11%|████▎ | ETA: 0:03:36 MCMC progress 22%|████████▎ | ETA: 0:01:40 MCMC progress 32%|████████████▏ | ETA: 0:00:59 MCMC progress 43%|████████████████▎ | ETA: 0:00:37 MCMC progress 53%|████████████████████▎ | ETA: 0:00:25 MCMC progress 63%|████████████████████████▏ | ETA: 0:00:16 MCMC progress 74%|████████████████████████████▏ | ETA: 0:00:10 MCMC progress 85%|████████████████████████████████▍ | ETA: 0:00:05 MCMC progress 96%|████████████████████████████████████▌ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:29 MCMC progress 7%|██▋ | ETA: 0:00:01 MCMC progress 62%|███████████████████████▌ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SEI Model | 173 173 1m34.0s Initialization progress 1%|▏ | ETA: 1:34:15 Initialization progress 28%|███████▉ | ETA: 0:01:36 Initialization progress 57%|████████████████ | ETA: 0:00:29 Initialization progress 86%|████████████████████████▏ | ETA: 0:00:06 Initialization progress 100%|████████████████████████████| Time: 0:00:38 MCMC progress 1%|▎ | ETA: 1:11:01 MCMC progress 10%|███▊ | ETA: 0:04:18 MCMC progress 20%|███████▌ | ETA: 0:01:58 MCMC progress 29%|███████████▏ | ETA: 0:01:10 MCMC progress 38%|██████████████▋ | ETA: 0:00:47 MCMC progress 48%|██████████████████▎ | ETA: 0:00:32 MCMC progress 58%|█████████████████████▉ | ETA: 0:00:21 MCMC progress 66%|█████████████████████████ | ETA: 0:00:15 MCMC progress 75%|████████████████████████████▋ | ETA: 0:00:10 MCMC progress 85%|████████████████████████████████▎ | ETA: 0:00:05 MCMC progress 95%|████████████████████████████████████▏ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:30 MCMC progress 6%|██▎ | ETA: 0:00:02 MCMC progress 58%|██████████████████████ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SIR Model | 175 175 1m39.4s Initialization progress 1%|▏ | ETA: 1:29:51 Initialization progress 29%|████████▎ | ETA: 0:01:27 Initialization progress 59%|████████████████▋ | ETA: 0:00:25 Initialization progress 90%|█████████████████████████▎ | ETA: 0:00:04 Initialization progress 100%|████████████████████████████| Time: 0:00:36 MCMC progress 1%|▎ | ETA: 0:58:52 MCMC progress 12%|████▍ | ETA: 0:03:00 MCMC progress 23%|████████▊ | ETA: 0:01:20 MCMC progress 35%|█████████████▏ | ETA: 0:00:45 MCMC progress 46%|█████████████████▍ | ETA: 0:00:29 MCMC progress 57%|█████████████████████▋ | ETA: 0:00:18 MCMC progress 69%|██████████████████████████▏ | ETA: 0:00:11 MCMC progress 81%|██████████████████████████████▋ | ETA: 0:00:06 MCMC progress 92%|███████████████████████████████████ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:25 MCMC progress 2%|▊ | ETA: 0:00:09 MCMC progress 71%|███████████████████████████ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SI Model | 111 111 1m29.4s Testing Pathogen tests passed Testing completed after 445.34s PkgEval succeeded after 648.41s