Package evaluation of Pathogen on Julia 1.13.0-DEV.140 (fac1ce7906*) started at 2025-03-02T12:31:02.953 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.91s ################################################################################ # 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 v4.16.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [1a297f60] + FillArrays v1.13.0 [34004b35] + HypergeometricFunctions v0.3.27 [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 v0.11.32 [c8189ad9] + Pathogen v0.4.13 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.2 [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 v2.5.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.3.2 [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 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [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 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [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 3.04s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 94.8s ################################################################################ # Testing # Testing Pathogen Status `/tmp/jl_1fW8UO/Project.toml` [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.117 [a15396b6] OnlineStats v1.7.1 [c8189ad9] Pathogen v0.4.13 [92933f4c] ProgressMeter v1.10.2 [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_1fW8UO/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 v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 [1a297f60] FillArrays v1.13.0 [34004b35] HypergeometricFunctions v0.3.27 [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 v0.11.32 [c8189ad9] Pathogen v0.4.13 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [92933f4c] ProgressMeter v1.10.2 [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 v2.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.3.2 [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 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.3.0 [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 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [bea87d4a] SuiteSparse_jll v7.8.3+2 [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... Precompiling packages... 14967.9 ms ✓ OnlineStatsBase 30969.6 ms ✓ OnlineStats Info Given Pathogen was explicitly requested, output will be shown live  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. 69677.0 ms ✓ Pathogen 3 dependencies successfully precompiled in 118 seconds. 73 already precompiled. 1 dependency had output during precompilation: ┌ Pathogen │ [Output was shown above] └ Precompiling packages... 7732.0 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 9 seconds. 55 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: 2:50:56 Initialization progress 34%|█████████▌ | ETA: 0:02:14 Initialization progress 64%|█████████████████▉ | ETA: 0:00:39 Initialization progress 90%|█████████████████████████▏ | ETA: 0:00:08 Initialization progress 100%|████████████████████████████| Time: 0:01:10 MCMC progress 1%|▎ | ETA: 2:16:54 MCMC progress 9%|███▍ | ETA: 0:09:18 MCMC progress 17%|██████▌ | ETA: 0:04:30 MCMC progress 25%|█████████▌ | ETA: 0:02:46 MCMC progress 33%|████████████▋ | ETA: 0:01:51 MCMC progress 41%|███████████████▋ | ETA: 0:01:20 MCMC progress 49%|██████████████████▌ | ETA: 0:00:59 MCMC progress 56%|█████████████████████▍ | ETA: 0:00:43 MCMC progress 64%|████████████████████████▎ | ETA: 0:00:32 MCMC progress 71%|███████████████████████████▏ | ETA: 0:00:23 MCMC progress 79%|██████████████████████████████ | ETA: 0:00:15 MCMC progress 86%|████████████████████████████████▊ | ETA: 0:00:09 MCMC progress 93%|███████████████████████████████████▌ | ETA: 0:00:05 MCMC progress 100%|██████████████████████████████████████| Time: 0:01:09 Initialization progress 2%|▌ | ETA: 0:00:47 Initialization progress 100%|████████████████████████████| Time: 0:00:00 MCMC progress 2%|▊ | ETA: 0:02:32 MCMC progress 34%|████████████▉ | ETA: 0:00:06 MCMC progress 74%|████████████████████████████▏ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:03 Test Summary: | Pass Total Time SEIR Model | 92 92 3m39.7s Initialization progress 1%|▏ | ETA: 1:19:44 Initialization progress 32%|█████████ | ETA: 0:01:08 Initialization progress 64%|█████████████████▉ | ETA: 0:00:18 Initialization progress 95%|██████████████████████████▊ | ETA: 0:00:02 Initialization progress 100%|████████████████████████████| Time: 0:00:32 MCMC progress 1%|▎ | ETA: 0:59:12 MCMC progress 10%|███▉ | ETA: 0:03:28 MCMC progress 20%|███████▊ | ETA: 0:01:34 MCMC progress 30%|███████████▌ | ETA: 0:00:55 MCMC progress 40%|███████████████▍ | ETA: 0:00:36 MCMC progress 50%|███████████████████▏ | ETA: 0:00:24 MCMC progress 61%|███████████████████████▏ | ETA: 0:00:16 MCMC progress 72%|███████████████████████████▎ | ETA: 0:00:10 MCMC progress 82%|███████████████████████████████▏ | ETA: 0:00:05 MCMC progress 92%|███████████████████████████████████ | ETA: 0:00:02 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:25 MCMC progress 2%|▊ | ETA: 0:00:05 MCMC progress 45%|█████████████████▏ | ETA: 0:00:00 MCMC progress 97%|████████████████████████████████████▉ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SEI Model | 173 173 1m26.4s Initialization progress 1%|▏ | ETA: 1:22:49 Initialization progress 42%|███████████▉ | ETA: 0:00:46 Initialization progress 84%|███████████████████████▌ | ETA: 0:00:06 Initialization progress 100%|████████████████████████████| Time: 0:00:33 MCMC progress 1%|▎ | ETA: 0:59:32 MCMC progress 12%|████▌ | ETA: 0:02:57 MCMC progress 22%|████████▎ | ETA: 0:01:27 MCMC progress 31%|███████████▊ | ETA: 0:00:54 MCMC progress 40%|███████████████▍ | ETA: 0:00:36 MCMC progress 50%|███████████████████ | ETA: 0:00:25 MCMC progress 59%|██████████████████████▌ | ETA: 0:00:17 MCMC progress 68%|██████████████████████████ | ETA: 0:00:11 MCMC progress 78%|█████████████████████████████▌ | ETA: 0:00:07 MCMC progress 86%|████████████████████████████████▊ | ETA: 0:00:04 MCMC progress 95%|████████████████████████████████████▎ | ETA: 0:00:01 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:25 MCMC progress 2%|▊ | ETA: 0:00:05 MCMC progress 46%|█████████████████▌ | ETA: 0:00:00 MCMC progress 94%|███████████████████████████████████▊ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SIR Model | 166 166 1m27.2s Initialization progress 1%|▏ | ETA: 1:13:13 Initialization progress 37%|██████████▍ | ETA: 0:00:50 Initialization progress 73%|████████████████████▌ | ETA: 0:00:11 Initialization progress 100%|████████████████████████████| Time: 0:00:30 MCMC progress 1%|▎ | ETA: 0:54:30 MCMC progress 11%|████▏ | ETA: 0:02:58 MCMC progress 23%|████████▋ | ETA: 0:01:16 MCMC progress 35%|█████████████▏ | ETA: 0:00:42 MCMC progress 46%|█████████████████▋ | ETA: 0:00:26 MCMC progress 58%|██████████████████████▏ | ETA: 0:00:16 MCMC progress 70%|██████████████████████████▊ | ETA: 0:00:10 MCMC progress 82%|███████████████████████████████▎ | ETA: 0:00:05 MCMC progress 90%|██████████████████████████████████▎ | ETA: 0:00:03 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:23 MCMC progress 2%|▊ | ETA: 0:00:10 MCMC progress 66%|█████████████████████████▏ | ETA: 0:00:00 MCMC progress 100%|██████████████████████████████████████| Time: 0:00:00 Test Summary: | Pass Total Time SI Model | 102 102 1m19.2s Testing Pathogen tests passed Testing completed after 581.47s PkgEval succeeded after 839.44s