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1.5.0-DEV-ed177d17d6.log
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Julia Version 1.5.0-DEV.158
Commit ed177d17d6 (2020-01-27 16:45 UTC)
Platform Info:
OS: Linux (x86_64-pc-linux-gnu)
CPU: Intel(R) Xeon(R) Silver 4114 CPU @ 2.20GHz
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-8.0.1 (ORCJIT, skylake)
Environment:
JULIA_DEPOT_PATH = ::/usr/local/share/julia
JULIA_NUM_THREADS = 2
Resolving package versions...
Installed PenaltyFunctions ──────────── v0.1.2
Installed SortingAlgorithms ─────────── v0.3.1
Installed Parsers ───────────────────── v0.3.10
Installed Arpack ────────────────────── v0.4.0
Installed StatsFuns ─────────────────── v0.9.3
Installed QuadGK ────────────────────── v2.3.1
Installed Pathogen ──────────────────── v0.4.3
Installed Distributions ─────────────── v0.22.3
Installed OpenBLAS_jll ──────────────── v0.3.7+4
Installed OpenSpecFun_jll ───────────── v0.5.3+1
Installed Tables ────────────────────── v0.2.11
Installed BinaryProvider ────────────── v0.5.8
Installed Arpack_jll ────────────────── v3.5.0+2
Installed Compat ────────────────────── v3.2.0
Installed LossFunctions ─────────────── v0.5.1
Installed OrderedCollections ────────── v1.1.0
Installed IteratorInterfaceExtensions ─ v1.0.0
Installed SpecialFunctions ──────────── v0.9.0
Installed Missings ──────────────────── v0.4.3
Installed DataValueInterfaces ───────── v1.0.0
Installed JSON ──────────────────────── v0.21.0
Installed StatsBase ─────────────────── v0.32.0
Installed DataStructures ────────────── v0.17.9
Installed TableTraits ───────────────── v1.0.0
Installed PooledArrays ──────────────── v0.5.3
Installed DataAPI ───────────────────── v1.1.0
Installed ProgressMeter ─────────────── v1.2.0
Installed OnlineStats ───────────────── v1.0.2
Installed CategoricalArrays ─────────── v0.7.7
Installed RecipesBase ───────────────── v0.7.0
Installed FillArrays ────────────────── v0.8.4
Installed InvertedIndices ───────────── v1.0.0
Installed DataFrames ────────────────── v0.20.0
Installed PDMats ────────────────────── v0.9.11
Installed Rmath ─────────────────────── v0.6.0
Installed Reexport ──────────────────── v0.2.0
Installed OnlineStatsBase ───────────── v1.0.2
Installed LearnBase ─────────────────── v0.2.2
Installed SweepOperator ─────────────── v0.3.0
Updating `~/.julia/environments/v1.5/Project.toml`
[c8189ad9] + Pathogen v0.4.3
Updating `~/.julia/environments/v1.5/Manifest.toml`
[7d9fca2a] + Arpack v0.4.0
[68821587] + Arpack_jll v3.5.0+2
[b99e7846] + BinaryProvider v0.5.8
[324d7699] + CategoricalArrays v0.7.7
[34da2185] + Compat v3.2.0
[9a962f9c] + DataAPI v1.1.0
[a93c6f00] + DataFrames v0.20.0
[864edb3b] + DataStructures v0.17.9
[e2d170a0] + DataValueInterfaces v1.0.0
[31c24e10] + Distributions v0.22.3
[1a297f60] + FillArrays v0.8.4
[41ab1584] + InvertedIndices v1.0.0
[82899510] + IteratorInterfaceExtensions v1.0.0
[682c06a0] + JSON v0.21.0
[7f8f8fb0] + LearnBase v0.2.2
[30fc2ffe] + LossFunctions v0.5.1
[e1d29d7a] + Missings v0.4.3
[a15396b6] + OnlineStats v1.0.2
[925886fa] + OnlineStatsBase v1.0.2
[4536629a] + OpenBLAS_jll v0.3.7+4
[efe28fd5] + OpenSpecFun_jll v0.5.3+1
[bac558e1] + OrderedCollections v1.1.0
[90014a1f] + PDMats v0.9.11
[69de0a69] + Parsers v0.3.10
[c8189ad9] + Pathogen v0.4.3
[06bb1623] + PenaltyFunctions v0.1.2
[2dfb63ee] + PooledArrays v0.5.3
[92933f4c] + ProgressMeter v1.2.0
[1fd47b50] + QuadGK v2.3.1
[3cdcf5f2] + RecipesBase v0.7.0
[189a3867] + Reexport v0.2.0
[79098fc4] + Rmath v0.6.0
[a2af1166] + SortingAlgorithms v0.3.1
[276daf66] + SpecialFunctions v0.9.0
[2913bbd2] + StatsBase v0.32.0
[4c63d2b9] + StatsFuns v0.9.3
[7522ee7d] + SweepOperator v0.3.0
[3783bdb8] + TableTraits v1.0.0
[bd369af6] + Tables v0.2.11
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[9fa8497b] + Future
[b77e0a4c] + InteractiveUtils
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[4607b0f0] + SuiteSparse
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
Building Rmath → `~/.julia/packages/Rmath/BoBag/deps/build.log`
Updating `/tmp/jl_eDi0A2/Project.toml`
[no changes]
Updating `/tmp/jl_eDi0A2/Manifest.toml`
[no changes]
Testing Pathogen
Installed Distances ─ v0.8.2
Updating `/tmp/jl_rabLZl/Project.toml`
[b4f34e82] + Distances v0.8.2
Updating `/tmp/jl_rabLZl/Manifest.toml`
[b4f34e82] + Distances v0.8.2
Running sandbox
Status `/tmp/jl_rabLZl/Project.toml`
[a93c6f00] DataFrames v0.20.0
[b4f34e82] Distances v0.8.2
[31c24e10] Distributions v0.22.3
[a15396b6] OnlineStats v1.0.2
[c8189ad9] Pathogen v0.4.3
[92933f4c] ProgressMeter v1.2.0
[3cdcf5f2] RecipesBase v0.7.0
[2913bbd2] StatsBase v0.32.0
[8ba89e20] Distributed
[37e2e46d] LinearAlgebra
[56ddb016] Logging
[9a3f8284] Random
[10745b16] Statistics
[8dfed614] Test
WARNING: Method definition _count_by_state(Pathogen.Events{T<:Pathogen.EpidemicModel}, Pathogen.DiseaseState, Float64) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/Pathogen/m8XHX/src/visualization/epidemic_curve.jl:4 overwritten at /home/pkgeval/.julia/packages/Pathogen/m8XHX/src/visualization/epidemic_curve.jl:4.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition _epidemic_curve(Pathogen.Events{T<:Pathogen.EpidemicModel}, Pathogen.DiseaseState, Float64, Float64) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/Pathogen/m8XHX/src/visualization/epidemic_curve.jl:29 overwritten at /home/pkgeval/.julia/packages/Pathogen/m8XHX/src/visualization/epidemic_curve.jl:29.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition apply_recipe(Base.Dict{Symbol, Any}, Pathogen.Events{T<:Pathogen.EpidemicModel}, Pathogen.DiseaseState, Float64, Float64) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269 overwritten at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition apply_recipe(Base.Dict{Symbol, Any}, Pathogen.Events{T<:Pathogen.EpidemicModel}, Pathogen.DiseaseState) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269 overwritten at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition apply_recipe(Base.Dict{Symbol, Any}, Pathogen.Events{T<:Pathogen.EpidemicModel}, Float64, Float64) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269 overwritten at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269.
** incremental compilation may be fatally broken for this module **
WARNING: Method definition apply_recipe(Base.Dict{Symbol, Any}, Pathogen.Events{T<:Pathogen.EpidemicModel}) where {T<:Pathogen.EpidemicModel} in module Pathogen at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269 overwritten at /home/pkgeval/.julia/packages/RecipesBase/zBoFG/src/RecipesBase.jl:269.
** incremental compilation may be fatally broken for this module **
Initialization progress 0%|▏ | ETA: 1:59:36[KInitialization progress 32%|█████████ | ETA: 0:00:51[KInitialization progress 55%|███████████████▎ | ETA: 0:00:20[KInitialization progress 73%|████████████████████▌ | ETA: 0:00:09[KInitialization progress 89%|█████████████████████████ | ETA: 0:00:03[KInitialization progress 97%|███████████████████████████▏| ETA: 0:00:01[KInitialization progress 97%|███████████████████████████▏| ETA: 0:00:01[KInitialization progress100%|████████████████████████████| Time: 0:00:25[K
MCMC progress 0%|▏ | ETA: 1:37:55[KMCMC progress 7%|██▌ | ETA: 0:04:37[KMCMC progress 13%|████▉ | ETA: 0:02:17[KMCMC progress 21%|████████▏ | ETA: 0:01:14[KMCMC progress 24%|█████████▎ | ETA: 0:01:02[KMCMC progress 28%|██████████▊ | ETA: 0:00:51[KMCMC progress 36%|█████████████▋ | ETA: 0:00:36[KMCMC progress 44%|████████████████▉ | ETA: 0:00:26[KMCMC progress 53%|████████████████████ | ETA: 0:00:18[KMCMC progress 62%|███████████████████████▌ | ETA: 0:00:13[KMCMC progress 71%|███████████████████████████ | ETA: 0:00:08[KMCMC progress 78%|█████████████████████████████▋ | ETA: 0:00:06[KMCMC progress 85%|████████████████████████████████▎ | ETA: 0:00:04[KMCMC progress 91%|██████████████████████████████████▊ | ETA: 0:00:02[KMCMC progress 95%|████████████████████████████████████▎ | ETA: 0:00:01[KMCMC progress 96%|████████████████████████████████████▍ | ETA: 0:00:01[KMCMC progress 97%|████████████████████████████████████▉ | ETA: 0:00:01[KMCMC progress100%|██████████████████████████████████████| Time: 0:00:25[K
Test Summary: | Pass Total
SEIR Model | 224 224
Initialization progress 0%|▏ | ETA: 0:40:26[KInitialization progress 32%|█████████ | ETA: 0:00:17[KInitialization progress 62%|█████████████████▎ | ETA: 0:00:05[KInitialization progress 86%|████████████████████████ | ETA: 0:00:01[KInitialization progress 93%|██████████████████████████ | ETA: 0:00:01[KInitialization progress 97%|███████████████████████████▎| ETA: 0:00:00[KInitialization progress100%|████████████████████████████| Time: 0:00:08[K
MCMC progress 0%|▏ | ETA: 0:21:40[KMCMC progress 7%|██▋ | ETA: 0:00:59[KMCMC progress 14%|█████▌ | ETA: 0:00:27[KMCMC progress 23%|████████▋ | ETA: 0:00:16[KMCMC progress 28%|██████████▌ | ETA: 0:00:13[KMCMC progress 36%|█████████████▊ | ETA: 0:00:09[KMCMC progress 40%|███████████████▎ | ETA: 0:00:08[KMCMC progress 53%|████████████████████▎ | ETA: 0:00:04[KMCMC progress 67%|█████████████████████████▋ | ETA: 0:00:03[KMCMC progress 78%|█████████████████████████████▊ | ETA: 0:00:01[KMCMC progress 88%|█████████████████████████████████▌ | ETA: 0:00:01[KMCMC progress 89%|█████████████████████████████████▊ | ETA: 0:00:01[KMCMC progress 96%|████████████████████████████████████▌ | ETA: 0:00:00[KMCMC progress 97%|█████████████████████████████████████ | ETA: 0:00:00[KMCMC progress100%|██████████████████████████████████████| Time: 0:00:06[K
Test Summary: | Pass Total
SEI Model | 152 152
Initialization progress 0%|▏ | ETA: 0:42:40[KInitialization progress 24%|██████▊ | ETA: 0:00:27[KInitialization progress 50%|██████████████▏ | ETA: 0:00:09[KInitialization progress 74%|████████████████████▋ | ETA: 0:00:03[KInitialization progress 89%|████████████████████████▉ | ETA: 0:00:01[KInitialization progress 97%|███████████████████████████▏| ETA: 0:00:00[KInitialization progress100%|████████████████████████████| Time: 0:00:09[K
MCMC progress 0%|▏ | ETA: 0:22:06[KMCMC progress 11%|████▏ | ETA: 0:00:37[KMCMC progress 22%|████████▎ | ETA: 0:00:17[KMCMC progress 30%|███████████▌ | ETA: 0:00:11[KMCMC progress 39%|██████████████▉ | ETA: 0:00:08[KMCMC progress 49%|██████████████████▋ | ETA: 0:00:05[KMCMC progress 57%|█████████████████████▌ | ETA: 0:00:04[KMCMC progress 66%|█████████████████████████▏ | ETA: 0:00:03[KMCMC progress 75%|████████████████████████████▋ | ETA: 0:00:02[KMCMC progress 83%|███████████████████████████████▋ | ETA: 0:00:01[KMCMC progress 89%|█████████████████████████████████▊ | ETA: 0:00:01[KMCMC progress 94%|███████████████████████████████████▊ | ETA: 0:00:00[KMCMC progress 96%|████████████████████████████████████▌ | ETA: 0:00:00[KMCMC progress 97%|█████████████████████████████████████ | ETA: 0:00:00[KMCMC progress100%|██████████████████████████████████████| Time: 0:00:05[K
Test Summary: | Pass Total
SIR Model | 152 152
Initialization progress 0%|▏ | ETA: 0:44:26[KInitialization progress 17%|████▉ | ETA: 0:00:43[KInitialization progress 49%|█████████████▉ | ETA: 0:00:09[KInitialization progress 73%|████████████████████▌ | ETA: 0:00:03[KInitialization progress 89%|████████████████████████▉ | ETA: 0:00:01[KInitialization progress 97%|███████████████████████████▏| ETA: 0:00:00[KInitialization progress100%|████████████████████████████| Time: 0:00:09[K
MCMC progress 0%|▏ | ETA: 0:23:14[KMCMC progress 10%|███▋ | ETA: 0:00:45[KMCMC progress 15%|█████▉ | ETA: 0:00:27[KMCMC progress 24%|█████████▏ | ETA: 0:00:16[KMCMC progress 34%|█████████████ | ETA: 0:00:10[KMCMC progress 44%|████████████████▋ | ETA: 0:00:07[KMCMC progress 51%|███████████████████▌ | ETA: 0:00:05[KMCMC progress 60%|██████████████████████▊ | ETA: 0:00:04[KMCMC progress 64%|████████████████████████▌ | ETA: 0:00:03[KMCMC progress 69%|██████████████████████████▍ | ETA: 0:00:02[KMCMC progress 79%|██████████████████████████████ | ETA: 0:00:02[KMCMC progress 87%|████████████████████████████████▉ | ETA: 0:00:01[KMCMC progress 93%|███████████████████████████████████▎ | ETA: 0:00:00[KMCMC progress 97%|████████████████████████████████████▊ | ETA: 0:00:00[KMCMC progress 97%|████████████████████████████████████▉ | ETA: 0:00:00[KMCMC progress100%|██████████████████████████████████████| Time: 0:00:06[K
Test Summary: | Pass Total
SI Model | 80 80
Testing Pathogen tests passed