Package evaluation of BulkLMM on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T21:12:52.311


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.55s


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

Installing BulkLMM...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [b8d15608] + BulkLMM v1.2.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [47edcb42] + ADTypes v1.15.0
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [4fba245c] + ArrayInterface v7.19.0
  [b8d15608] + BulkLMM v1.2.0
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [bbf7d656] + CommonSubexpressions v0.3.1
  [34da2185] + Compat v4.17.0
  [187b0558] + ConstructionBase v1.6.0
  [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 v0.7.2
  [31c24e10] + Distributions v0.25.120
  [ffbed154] + DocStringExtensions v0.9.5
  [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 v1.4.4
  [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 v7.4.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] + Missings v1.2.0
  [d41bc354] + NLSolversBase v7.10.0
  [77ba4419] + NaNMath v1.1.3
  [429524aa] + Optim v1.13.2
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.35
  [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 v1.7.1
  [2913bbd2] + StatsBase v0.34.5
  [4c63d2b9] + StatsFuns v1.5.0
  [892a3eda] + StringManipulation v0.4.1
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [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 v7.8.3+2
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.13.1+0

Installation completed after 4.37s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 22.83s


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

     Testing BulkLMM
        Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function.
    Updating `/tmp/jl_dr6WJ2/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 ⇒ v0.25.120
  [10745b16] + Statistics v1.11.1
  [37e2e46d] ~ LinearAlgebra ⇒ v1.12.0
  [9a3f8284] ~ Random ⇒ v1.11.0
  [8dfed614] ~ Test ⇒ v1.11.0
    Updating `/tmp/jl_dr6WJ2/Manifest.toml`
  [47edcb42] + ADTypes v1.15.0
  [79e6a3ab] + Adapt v4.3.0
  [66dad0bd] + AliasTables v1.1.3
  [4fba245c] + ArrayInterface v7.19.0
  [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 ⇒ v4.17.0
  [187b0558] + ConstructionBase v1.6.0
  [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 v0.7.2
  [31c24e10] ↑ Distributions v0.25.98 ⇒ v0.25.120
  [ffbed154] ↑ DocStringExtensions v0.9.3 ⇒ v0.9.5
  [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 ⇒ v1.4.4
  [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 v7.4.0
  [2ab3a3ac] ↑ LogExpFunctions v0.3.24 ⇒ v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [e1d29d7a] ↑ Missings v1.1.0 ⇒ v1.2.0
  [d41bc354] + NLSolversBase v7.10.0
  [77ba4419] ↑ NaNMath v1.0.2 ⇒ v1.1.3
  [429524aa] + Optim v1.13.2
  [bac558e1] ↑ OrderedCollections v1.6.2 ⇒ v1.8.1
  [90014a1f] ↑ PDMats v0.11.17 ⇒ v0.11.35
  [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 ⇒ v1.7.1
  [2913bbd2] ↑ StatsBase v0.34.0 ⇒ v0.34.5
  [4c63d2b9] ↑ StatsFuns v1.3.0 ⇒ v1.5.0
  [892a3eda] ↑ StringManipulation v0.3.0 ⇒ v0.4.1
  [bd369af6] ↑ Tables v1.10.1 ⇒ v1.12.1
  [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 v7.8.3+2
  [83775a58] ↑ Zlib_jll v1.2.12+3 ⇒ v1.3.1+2
  [8e850b90] ↑ libblastrampoline_jll v5.1.1+0 ⇒ v5.13.1+0
  [8e850ede] - nghttp2_jll v1.48.0+0
  [3f19e933] - p7zip_jll v17.4.0+0
        Test Successfully re-resolved
      Status `/tmp/jl_dr6WJ2/Project.toml`
  [b8d15608] BulkLMM v1.2.0
  [336ed68f] CSV v0.10.15
  [a93c6f00] DataFrames v1.7.0
  [8bb1440f] DelimitedFiles v1.9.1
  [31c24e10] Distributions v0.25.120
  [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_dr6WJ2/Manifest.toml`
  [47edcb42] ADTypes v1.15.0
  [79e6a3ab] Adapt v4.3.0
  [66dad0bd] AliasTables v1.1.3
  [4fba245c] ArrayInterface v7.19.0
  [b8d15608] BulkLMM v1.2.0
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [bbf7d656] CommonSubexpressions v0.3.1
  [34da2185] Compat v4.17.0
  [187b0558] ConstructionBase v1.6.0
  [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 v0.7.2
  [31c24e10] Distributions v0.25.120
  [ffbed154] DocStringExtensions v0.9.5
  [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 v1.4.4
  [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 v7.4.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.16
  [e1d29d7a] Missings v1.2.0
  [d41bc354] NLSolversBase v7.10.0
  [77ba4419] NaNMath v1.1.3
  [429524aa] Optim v1.13.2
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.35
  [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 v1.7.1
  [2913bbd2] StatsBase v0.34.5
  [4c63d2b9] StatsFuns v1.5.0
  [892a3eda] StringManipulation v0.4.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [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 v7.8.3+2
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+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  4m01.5s
     Testing BulkLMM tests passed 

Testing completed after 268.4s

PkgEval succeeded after 319.79s