Package evaluation of BulkLMM on Julia 1.13.0-DEV.453 (0d3c9b0bb4*) started at 2025-05-03T08:49:26.688


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.3s


################################################################################
# Installation
#

Installing BulkLMM...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [b8d15608] + BulkLMM v1.2.0
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [47edcb42] + ADTypes v1.14.0
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [4fba245c] + ArrayInterface v7.18.0
  [b8d15608] + BulkLMM v1.2.0
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] + Compat v4.16.0
  [187b0558] + ConstructionBase v1.5.8
  [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
  [8bb1440f] + DelimitedFiles v1.9.1
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [a0c0ee7d] + DifferentiationInterface v0.6.52
  [31c24e10] + Distributions v0.25.119
  [ffbed154] + DocStringExtensions v0.9.4
  [4e289a0a] + EnumX v1.0.5
  [48062228] + FilePathsBase v0.9.24
  [1a297f60] + FillArrays v1.13.0
  [6a86dc24] + FiniteDiff v2.27.0
  [f6369f11] + ForwardDiff v1.0.1
  [34004b35] + HypergeometricFunctions v0.3.28
  [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
  [d3d80556] + LineSearches v7.3.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] + Missings v1.2.0
  [d41bc354] + NLSolversBase v7.9.1
  [77ba4419] + NaNMath v1.1.3
  [429524aa] + Optim v1.12.0
  [bac558e1] + OrderedCollections v1.8.0
  [90014a1f] + PDMats v0.11.34
  [d96e819e] + Parameters v0.12.3
  [69de0a69] + Parsers v2.8.3
  [2dfb63ee] + PooledArrays v1.4.3
  [85a6dd25] + PositiveFactorizations v0.2.4
  [aea7be01] + PrecompileTools v1.3.2
  [21216c6a] + Preferences v1.4.3
  [08abe8d2] + PrettyTables v2.4.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [79098fc4] + Rmath v0.8.0
  [91c51154] + SentinelArrays v1.4.8
  [efcf1570] + Setfield v1.1.2
  [a2af1166] + SortingAlgorithms v1.2.1
  [276daf66] + SpecialFunctions v2.5.1
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.0
  [2913bbd2] + StatsBase v0.34.4
  [4c63d2b9] + StatsFuns v1.5.0
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.0
  [3bb67fe8] + TranscodingStreams v0.11.3
  [3a884ed6] + UnPack v1.0.2
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [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 v1.12.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap 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 v1.12.0
  [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
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.5+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.12.0+0

Installation completed after 4.27s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...
Precompiling packages...
   5753.4 ms  ✓ TestEnv
  1 dependency successfully precompiled in 6 seconds. 25 already precompiled.

Precompiling package dependencies...

Precompilation completed after 392.22s


################################################################################
# Testing
#

     Testing BulkLMM
        Test Could not use exact versions of packages in manifest. Re-resolving dependencies
    Updating `/tmp/jl_CrEAPM/Project.toml`
  [b8d15608] + BulkLMM v1.2.0
  [336ed68f] ↑ CSV v0.10.11 ⇒ v0.10.15
  [a93c6f00] ↑ DataFrames v1.6.1 ⇒ v1.7.0
  [8bb1440f] + DelimitedFiles v1.9.1
  [31c24e10] ↑ Distributions v0.25.98 ⇒ v0.25.119
  [10745b16] + Statistics v1.11.1
  [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0
  [9a3f8284] ~ Random ⇒ v1.11.0
  [8dfed614] ~ Test ⇒ v1.11.0
    Updating `/tmp/jl_CrEAPM/Manifest.toml`
  [47edcb42] + ADTypes v1.14.0
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [4fba245c] + ArrayInterface v7.18.0
  [b8d15608] + BulkLMM v1.2.0
  [336ed68f] ↑ CSV v0.10.11 ⇒ v0.10.15
  [49dc2e85] - Calculus v0.5.1
  [d360d2e6] - ChainRulesCore v1.16.0
  [9e997f8a] - ChangesOfVariables v0.1.8
  [944b1d66] ↑ CodecZlib v0.7.2 ⇒ v0.7.8
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] ↑ Compat v4.7.0 ⇒ v4.16.0
  [187b0558] + ConstructionBase v1.5.8
  [9a962f9c] ↑ DataAPI v1.15.0 ⇒ v1.16.0
  [a93c6f00] ↑ DataFrames v1.6.1 ⇒ v1.7.0
  [864edb3b] ↑ DataStructures v0.18.14 ⇒ v0.18.22
  [8bb1440f] + DelimitedFiles v1.9.1
  [b429d917] - DensityInterface v0.4.0
  [163ba53b] + DiffResults v1.1.0
  [b552c78f] + DiffRules v1.15.1
  [a0c0ee7d] + DifferentiationInterface v0.6.52
  [31c24e10] ↑ Distributions v0.25.98 ⇒ v0.25.119
  [ffbed154] ↑ DocStringExtensions v0.9.3 ⇒ v0.9.4
  [fa6b7ba4] - DualNumbers v0.6.8
  [4e289a0a] + EnumX v1.0.5
  [48062228] ↑ FilePathsBase v0.9.20 ⇒ v0.9.24
  [1a297f60] ↑ FillArrays v1.4.2 ⇒ v1.13.0
  [6a86dc24] + FiniteDiff v2.27.0
  [59287772] - Formatting v0.4.2
  [f6369f11] + ForwardDiff v1.0.1
  [34004b35] ↑ HypergeometricFunctions v0.3.21 ⇒ v0.3.28
  [842dd82b] ↑ InlineStrings v1.4.0 ⇒ v1.4.3
  [3587e190] - InverseFunctions v0.1.11
  [41ab1584] ↑ InvertedIndices v1.3.0 ⇒ v1.3.1
  [92d709cd] ↑ IrrationalConstants v0.2.2 ⇒ v0.2.4
  [692b3bcd] ↑ JLLWrappers v1.4.1 ⇒ v1.7.0
  [b964fa9f] ↑ LaTeXStrings v1.3.0 ⇒ v1.4.0
  [d3d80556] + LineSearches v7.3.0
  [2ab3a3ac] ↑ LogExpFunctions v0.3.24 ⇒ v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] ↑ Missings v1.1.0 ⇒ v1.2.0
  [d41bc354] + NLSolversBase v7.9.1
  [77ba4419] ↑ NaNMath v1.0.2 ⇒ v1.1.3
  [429524aa] + Optim v1.12.0
  [bac558e1] ↑ OrderedCollections v1.6.2 ⇒ v1.8.0
  [90014a1f] ↑ PDMats v0.11.17 ⇒ v0.11.34
  [d96e819e] + Parameters v0.12.3
  [69de0a69] ↑ Parsers v2.7.1 ⇒ v2.8.3
  [2dfb63ee] ↑ PooledArrays v1.4.2 ⇒ v1.4.3
  [85a6dd25] + PositiveFactorizations v0.2.4
  [aea7be01] ↑ PrecompileTools v1.1.2 ⇒ v1.3.2
  [21216c6a] ↑ Preferences v1.4.0 ⇒ v1.4.3
  [08abe8d2] ↑ PrettyTables v2.2.6 ⇒ v2.4.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] ↑ QuadGK v2.8.2 ⇒ v2.11.2
  [ae029012] + Requires v1.3.1
  [79098fc4] ↑ Rmath v0.7.1 ⇒ v0.8.0
  [91c51154] ↑ SentinelArrays v1.4.0 ⇒ v1.4.8
  [efcf1570] + Setfield v1.1.2
  [a2af1166] ↑ SortingAlgorithms v1.1.1 ⇒ v1.2.1
  [276daf66] ↑ SpecialFunctions v2.3.0 ⇒ v2.5.1
  [1e83bf80] + StaticArraysCore v1.4.3
  [10745b16] + Statistics v1.11.1
  [82ae8749] ↑ StatsAPI v1.6.0 ⇒ v1.7.0
  [2913bbd2] ↑ StatsBase v0.34.0 ⇒ v0.34.4
  [4c63d2b9] ↑ StatsFuns v1.3.0 ⇒ v1.5.0
  [892a3eda] ↑ StringManipulation v0.3.0 ⇒ v0.4.1
  [bd369af6] ↑ Tables v1.10.1 ⇒ v1.12.0
  [3bb67fe8] ↑ TranscodingStreams v0.9.13 ⇒ v0.11.3
  [3a884ed6] + UnPack v1.0.2
  [c8ffd9c3] - MbedTLS_jll v2.28.0+0
  [efe28fd5] ↑ OpenSpecFun_jll v0.5.5+0 ⇒ v0.5.6+0
  [f50d1b31] ↑ Rmath_jll v0.4.0+0 ⇒ v0.5.1+0
  [0dad84c5] - ArgTools v1.1.1
  [56f22d72] ~ Artifacts ⇒ v1.11.0
  [2a0f44e3] ~ Base64 ⇒ v1.11.0
  [ade2ca70] ~ Dates ⇒ v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [f43a241f] - Downloads v1.6.0
  [7b1f6079] - FileWatching
  [9fa8497b] ~ Future ⇒ v1.11.0
  [b77e0a4c] ~ InteractiveUtils ⇒ v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [b27032c2] - LibCURL v0.6.3
  [76f85450] - LibGit2
  [8f399da3] ~ Libdl ⇒ v1.11.0
  [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0
  [56ddb016] ~ Logging ⇒ v1.11.0
  [d6f4376e] ~ Markdown ⇒ v1.11.0
  [a63ad114] ~ Mmap ⇒ v1.11.0
  [ca575930] - NetworkOptions v1.2.0
  [44cfe95a] - Pkg v1.8.0
  [de0858da] ~ Printf ⇒ v1.11.0
  [3fa0cd96] - REPL
  [9a3f8284] ~ Random ⇒ v1.11.0
  [9e88b42a] ~ Serialization ⇒ v1.11.0
  [6462fe0b] ~ Sockets ⇒ v1.11.0
  [2f01184e] ~ SparseArrays ⇒ v1.12.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] ↑ TOML v1.0.0 ⇒ v1.0.3
  [a4e569a6] - Tar v1.10.1
  [8dfed614] ~ Test ⇒ v1.11.0
  [cf7118a7] ~ UUIDs ⇒ v1.11.0
  [4ec0a83e] ~ Unicode ⇒ v1.11.0
  [e66e0078] ↑ CompilerSupportLibraries_jll v0.5.2+0 ⇒ v1.3.0+1
  [deac9b47] - LibCURL_jll v7.84.0+0
  [29816b5a] - LibSSH2_jll v1.10.2+0
  [14a3606d] - MozillaCACerts_jll v2022.2.1
  [4536629a] ↑ OpenBLAS_jll v0.3.20+0 ⇒ v0.3.29+0
  [05823500] ↑ OpenLibm_jll v0.8.1+0 ⇒ v0.8.5+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] ↑ Zlib_jll v1.2.12+3 ⇒ v1.3.1+2
  [8e850b90] ↑ libblastrampoline_jll v5.1.1+0 ⇒ v5.12.0+0
  [8e850ede] - nghttp2_jll v1.48.0+0
  [3f19e933] - p7zip_jll v17.4.0+0
        Test Successfully re-resolved
      Status `/tmp/jl_CrEAPM/Project.toml`
  [b8d15608] BulkLMM v1.2.0
  [336ed68f] CSV v0.10.15
  [a93c6f00] DataFrames v1.7.0
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.119
  [3f79f04f] Helium v0.2.1
  [10745b16] Statistics v1.11.1
  [37e2e46d] LinearAlgebra v1.12.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_CrEAPM/Manifest.toml`
  [47edcb42] ADTypes v1.14.0
  [79e6a3ab] Adapt v4.3.0
  [66dad0bd] AliasTables v1.1.3
  [4fba245c] ArrayInterface v7.18.0
  [b8d15608] BulkLMM v1.2.0
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.16.0
  [187b0558] ConstructionBase v1.5.8
  [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
  [8bb1440f] DelimitedFiles v1.9.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [a0c0ee7d] DifferentiationInterface v0.6.52
  [31c24e10] Distributions v0.25.119
  [ffbed154] DocStringExtensions v0.9.4
  [4e289a0a] EnumX v1.0.5
  [48062228] FilePathsBase v0.9.24
  [1a297f60] FillArrays v1.13.0
  [6a86dc24] FiniteDiff v2.27.0
  [f6369f11] ForwardDiff v1.0.1
  [3f79f04f] Helium v0.2.1
  [34004b35] HypergeometricFunctions v0.3.28
  [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
  [d3d80556] LineSearches v7.3.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.16
  [e1d29d7a] Missings v1.2.0
  [d41bc354] NLSolversBase v7.9.1
  [77ba4419] NaNMath v1.1.3
  [429524aa] Optim v1.12.0
  [bac558e1] OrderedCollections v1.8.0
  [90014a1f] PDMats v0.11.34
  [d96e819e] Parameters v0.12.3
  [69de0a69] Parsers v2.8.3
  [2dfb63ee] PooledArrays v1.4.3
  [85a6dd25] PositiveFactorizations v0.2.4
  [aea7be01] PrecompileTools v1.3.2
  [21216c6a] Preferences v1.4.3
  [08abe8d2] PrettyTables v2.4.0
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [79098fc4] Rmath v0.8.0
  [91c51154] SentinelArrays v1.4.8
  [efcf1570] Setfield v1.1.2
  [a2af1166] SortingAlgorithms v1.2.1
  [276daf66] SpecialFunctions v2.5.1
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.4
  [4c63d2b9] StatsFuns v1.5.0
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [3a884ed6] UnPack v1.0.2
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [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 v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap 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 v1.12.0
  [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
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.5+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.12.0+0
     Testing Running tests...
Utility functions test: 
WLS functions test: 
WARNING: Method definition biasSquared(AbstractArray{Float64, 2}, AbstractArray{Float64, 2}) in module Main at /home/pkgeval/.julia/packages/BulkLMM/bdDFk/test/wls_basic_test.jl:21 overwritten at /home/pkgeval/.julia/packages/BulkLMM/bdDFk/test/wls_results_test.jl:100.
WLS functions test: 
Kinship test: Test Passed
Permutation LODs test: Test Passed
Permutation thresholds test: Test Passed
LMM functions test: 
Transform helper functions test: 
Scan functions test: 
Weighted residual variance functions test: 
Scan with covariates functions test: Test Passed
Scan with covariates functions test (SVD): Test Passed
Scan with covariates functions test (SVD2): Test Passed
Scan with covariates functions test (p-vals output): Test Passed
Bulkscan with covariates functions test (p-vals output): Test Passed
Scan with covariates functions test (vector trait input): Test Passed
Bulkscan functions test: 
Profile likelihood functions test: 
Test Summary: | Pass  Total     Time
BulkLMM       |  222    222  4m00.3s
     Testing BulkLMM tests passed 

Testing completed after 266.41s

PkgEval succeeded after 692.18s