Package evaluation to test OrdinalGWAS on Julia 1.14.0-DEV.1299 (6d6224db99*) started at 2025-11-27T21:39:42.500 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.95s ################################################################################ # Installation # Installing OrdinalGWAS... Resolving package versions... Installed Glob ───────────────────────────── v1.3.1 Installed CommonWorldInvalidations ───────── v1.0.0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed MUMPS_seq_jll ──────────────────── v500.800.100+0 Installed InlineStrings ──────────────────── v1.4.5 Installed SIMDTypes ──────────────────────── v0.1.0 Installed OrderedCollections ─────────────── v1.8.1 Installed HypothesisTests ────────────────── v0.11.6 Installed Xorg_libpciaccess_jll ──────────── v0.18.1+0 Installed CpuId ──────────────────────────── v0.3.1 Installed SentinelArrays ─────────────────── v1.4.8 Installed NaNMath ────────────────────────── v1.1.3 Installed StaticArrayInterface ───────────── v1.8.0 Installed QuadGK ─────────────────────────── v2.11.2 Installed Ipopt_jll ──────────────────────── v300.1400.1900+0 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed FileIO ─────────────────────────── v1.17.1 Installed Tables ─────────────────────────── v1.12.1 Installed Reexport ───────────────────────── v1.2.2 Installed InverseFunctions ───────────────── v0.1.17 Installed DBInterface ────────────────────── v2.6.1 Installed Missings ───────────────────────── v1.2.0 Installed TableTraits ────────────────────── v1.0.1 Installed Static ─────────────────────────── v1.3.1 Installed Preferences ────────────────────── v1.5.0 Installed TZJData ────────────────────────── v1.5.0+2025b Installed UnPack ─────────────────────────── v1.0.2 Installed LaTeXStrings ───────────────────── v1.4.0 Installed Crayons ────────────────────────── v4.1.1 Installed SortingAlgorithms ──────────────── v1.2.2 Installed DiffResults ────────────────────── v1.1.0 Installed MacroTools ─────────────────────── v0.5.16 Installed DataStructures ─────────────────── v0.19.3 Installed CodecZstd ──────────────────────── v0.8.7 Installed FillArrays ─────────────────────── v1.15.0 Installed ManualMemory ───────────────────── v0.1.8 Installed CodecZlib ──────────────────────── v0.7.8 Installed DelimitedFiles ─────────────────── v1.9.1 Installed ExprTools ──────────────────────── v0.1.10 Installed VCFTools ───────────────────────── v0.2.10 Installed VectorizationBase ──────────────── v0.21.72 Installed StatsBase ──────────────────────── v0.34.8 Installed CommonSubexpressions ───────────── v0.3.1 Installed DataValueInterfaces ────────────── v1.0.0 Installed HostCPUFeatures ────────────────── v0.1.17 Installed IrrationalConstants ────────────── v0.2.6 Installed ArrayInterface ─────────────────── v7.22.0 Installed LayoutPointers ─────────────────── v0.1.17 Installed StructUtils ────────────────────── v2.6.0 Installed TimeZones ──────────────────────── v1.22.2 Installed Hwloc_jll ──────────────────────── v2.12.2+0 Installed BufferedStreams ────────────────── v1.2.2 Installed SPRAL_jll ──────────────────────── v2025.5.20+0 Installed PooledArrays ───────────────────── v1.4.3 Installed Scratch ────────────────────────── v1.3.0 Installed Roots ──────────────────────────── v2.2.10 Installed BenchmarkTools ─────────────────── v1.6.3 Installed PDMats ─────────────────────────── v0.11.36 Installed WorkerUtilities ────────────────── v1.6.1 Installed CodecXz ────────────────────────── v0.7.4 Installed CompositionsBase ───────────────── v0.1.2 Installed CommonSolve ────────────────────── v0.2.4 Installed SQLite ─────────────────────────── v1.6.1 Installed DocStringExtensions ────────────── v0.9.5 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed StatsModels ────────────────────── v0.7.7 Installed ForwardDiff ────────────────────── v1.3.0 Installed SLEEFPirates ───────────────────── v0.6.43 Installed AliasTables ────────────────────── v1.1.3 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed OrdinalGWAS ────────────────────── v0.7.2 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed SIMD ───────────────────────────── v3.7.2 Installed ShiftedArrays ──────────────────── v2.0.0 Installed Combinatorics ──────────────────── v1.0.3 Installed MathOptInterface ───────────────── v1.46.0 Installed DataAPI ────────────────────────── v1.16.0 Installed InvertedIndices ────────────────── v1.3.1 Installed SciMLPublic ────────────────────── v1.0.0 Installed StaticArraysCore ───────────────── v1.4.4 Installed StringManipulation ─────────────── v0.4.2 Installed Requires ───────────────────────── v1.3.1 Installed LogExpFunctions ────────────────── v0.3.29 Installed OpenBLAS32_jll ─────────────────── v0.3.29+0 Installed DiffRules ──────────────────────── v1.15.1 Installed PrettyTables ───────────────────── v3.1.2 Installed Parsers ────────────────────────── v2.8.3 Installed JSON ───────────────────────────── v1.3.0 Installed Rmath ──────────────────────────── v0.9.0 Installed BioGenerics ────────────────────── v0.1.5 Installed Distributions ──────────────────── v0.25.122 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed StatsFuns ──────────────────────── v1.5.2 Installed XZ_jll ─────────────────────────── v5.8.1+0 Installed WeakRefStrings ─────────────────── v1.4.2 Installed RData ──────────────────────────── v0.8.3 Installed JLLWrappers ────────────────────── v1.7.1 Installed MutableArithmetics ─────────────── v1.6.7 Installed DataFrames ─────────────────────── v1.8.1 Installed BGZFStreams ────────────────────── v0.3.2 Installed NLopt ──────────────────────────── v0.6.5 Installed StructTypes ────────────────────── v1.11.0 Installed CSV ────────────────────────────── v0.10.15 Installed VariantCallFormat ──────────────── v0.5.9 Installed CategoricalArrays ──────────────── v0.10.7 Installed ThreadingUtilities ─────────────── v0.5.5 Installed Adapt ──────────────────────────── v4.4.0 Installed FilePathsBase ──────────────────── v0.9.24 Installed ConstructionBase ───────────────── v1.6.0 Installed GLM ────────────────────────────── v1.9.0 Installed Accessors ──────────────────────── v0.1.42 Installed OrdinalMultinomialModels ───────── v0.4.5 Installed HypergeometricFunctions ────────── v0.3.28 Installed Compat ─────────────────────────── v4.18.1 Installed Statistics ─────────────────────── v1.11.1 Installed StatsAPI ───────────────────────── v1.7.1 Installed TranscodingStreams ─────────────── v0.9.13 Installed LoopVectorization ──────────────── v0.12.173 Installed PrecompileTools ────────────────── v1.3.3 Installed ProgressMeter ──────────────────── v1.11.0 Installed OffsetArrays ───────────────────── v1.17.0 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed CPUSummary ─────────────────────── v0.2.7 Installed JSON3 ──────────────────────────── v1.14.3 Installed IfElse ─────────────────────────── v0.1.1 Installed ASL_jll ────────────────────────── v0.1.3+0 Installed XML2_jll ───────────────────────── v2.13.9+0 Installed PtrArrays ──────────────────────── v1.3.0 Installed SpecialFunctions ───────────────── v2.6.1 Installed Libiconv_jll ───────────────────── v1.18.0+0 Installed RDatasets ──────────────────────── v0.7.7 Installed SQLite_jll ─────────────────────── v3.48.0+0 Installed Ipopt ──────────────────────────── v1.13.0 Installed METIS_jll ──────────────────────── v5.1.3+0 Installed Automa ─────────────────────────── v1.1.0 Installed MathProgBase ───────────────────── v0.7.8 Installed PolyesterWeave ─────────────────── v0.2.2 Installed Mocking ────────────────────────── v0.8.1 Installed NLopt_jll ──────────────────────── v2.10.0+0 Installed SnpArrays ──────────────────────── v0.3.22 Installed BGEN ───────────────────────────── v0.1.17 Installing 17 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact NLopt 322.7 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Xorg_libpciaccess 24.8 KiB Installed artifact Ipopt 1.3 MiB Installed artifact tzjdata 112.5 KiB Installed artifact Hwloc 3.5 MiB Installed artifact XML2 2.5 MiB Installed artifact ASL 276.3 KiB Installed artifact XZ 1.5 MiB Installed artifact METIS 1.1 MiB Installed artifact SPRAL 691.8 KiB Installed artifact Bzip2 503.5 KiB Installed artifact MUMPS_seq 8.6 MiB Installed artifact SQLite 5.0 MiB Installed artifact OpenBLAS32 10.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [00428148] + OrdinalGWAS v0.7.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [6e4b80f9] + BenchmarkTools v1.6.3 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.15 ⌅ [324d7699] + CategoricalArrays v0.10.7 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.0.3 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 [864edb3b] + DataStructures v0.19.3 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [e2ba6199] + ExprTools v0.1.10 [5789e2e9] + FileIO v1.17.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [f6369f11] + ForwardDiff v1.3.0 [38e38edf] + GLM v1.9.0 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 [09f84164] + HypothesisTests v0.11.6 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [3587e190] + InverseFunctions v0.1.17 [41ab1584] + InvertedIndices v1.3.1 [b6b21f68] + Ipopt v1.13.0 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.3.0 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.173 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [b8f27783] + MathOptInterface v1.46.0 [fdba3010] + MathProgBase v0.7.8 [e1d29d7a] + Missings v1.2.0 [78c3b35d] + Mocking v0.8.1 [d8a4904e] + MutableArithmetics v1.6.7 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [00428148] + OrdinalGWAS v0.7.2 [b51826c6] + OrdinalMultinomialModels v0.4.5 [90014a1f] + PDMats v0.11.36 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.2 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 ⌅ [df47a6cb] + RData v0.8.3 [ce6b1742] + RDatasets v0.7.7 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [0aa819cd] + SQLite v1.6.1 [431bcebd] + SciMLPublic v1.0.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 [3eaba693] + StatsModels v0.7.7 [892a3eda] + StringManipulation v0.4.2 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.6.0 [dc5dba14] + TZJData v1.5.0+2025b [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 [f269a46b] + TimeZones v1.22.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.9 [3d5dd08c] + VectorizationBase v0.21.72 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [ae81ac8f] + ASL_jll v0.1.3+0 [6e34b625] + Bzip2_jll v1.0.9+0 [e33a78d0] + Hwloc_jll v2.12.2+0 [9cc047cb] + Ipopt_jll v300.1400.1900+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [d00139f3] + METIS_jll v5.1.3+0 [d7ed1dd3] + MUMPS_seq_jll v500.800.100+0 [079eb43e] + NLopt_jll v2.10.0+0 [656ef2d0] + OpenBLAS32_jll v0.3.29+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 ⌅ [319450e9] + SPRAL_jll v2025.5.20+0 [76ed43ae] + SQLite_jll v3.48.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [ffd25f8a] + XZ_jll v5.8.1+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.18.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9abbd945] + Profile 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 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.17.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+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 17.75s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4098.8 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4009.6 ms ✓ MacroTools 1531.0 ms ✓ InlineStrings 767.1 ms ✓ Reexport 1051.1 ms ✓ ConstructionBase 2021.7 ms ✓ IrrationalConstants 774.8 ms ✓ DataValueInterfaces 832.6 ms ✓ StatsAPI 2026.6 ms ✓ Combinatorics 776.6 ms ✓ CommonSolve 876.5 ms ✓ LaTeXStrings 885.8 ms ✓ Glob 1100.4 ms ✓ Statistics 947.4 ms ✓ StaticArraysCore 795.0 ms ✓ IfElse 777.0 ms ✓ PtrArrays 910.6 ms ✓ ManualMemory 850.9 ms ✓ DataAPI 846.9 ms ✓ SciMLPublic 782.9 ms ✓ CommonWorldInvalidations 863.3 ms ✓ InvertedIndices 930.9 ms ✓ InverseFunctions 814.5 ms ✓ CompositionsBase 865.7 ms ✓ ShiftedArrays 1136.9 ms ✓ WorkerUtilities 894.9 ms ✓ TZJData 2042.1 ms ✓ FillArrays 894.2 ms ✓ ExprTools 769.5 ms ✓ UnPack 857.1 ms ✓ DBInterface 1234.7 ms ✓ OrderedCollections 1092.3 ms ✓ DocStringExtensions 1579.7 ms ✓ OffsetArrays 1020.6 ms ✓ BufferedStreams 815.8 ms ✓ SIMDTypes 785.0 ms ✓ IteratorInterfaceExtensions 1758.0 ms ✓ Crayons 995.4 ms ✓ DelimitedFiles 943.6 ms ✓ NaNMath 1085.8 ms ✓ Requires 1174.6 ms ✓ SuiteSparse 1696.6 ms ✓ CpuId 2104.9 ms ✓ MathProgBase 926.6 ms ✓ Scratch 2732.2 ms ✓ SentinelArrays 1665.2 ms ✓ StructTypes 1373.9 ms ✓ StructUtils 1712.2 ms ✓ ProgressMeter 1180.0 ms ✓ Compat 1321.9 ms ✓ Preferences 1982.2 ms ✓ TranscodingStreams 10639.3 ms ✓ MutableArithmetics 1787.8 ms ✓ CommonSubexpressions 843.1 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1356.8 ms ✓ Statistics → SparseArraysExt 864.6 ms ✓ DiffResults 964.7 ms ✓ AliasTables 1757.3 ms ✓ ThreadingUtilities 981.9 ms ✓ Missings 1612.8 ms ✓ PooledArrays 856.0 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1605.5 ms ✓ InverseFunctions → InverseFunctionsTestExt 824.5 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1567.3 ms ✓ FillArrays → FillArraysSparseArraysExt 961.7 ms ✓ FillArrays → FillArraysStatisticsExt 3247.8 ms ✓ DataStructures 1284.2 ms ✓ LogExpFunctions 738.2 ms ✓ TableTraits 940.9 ms ✓ Adapt 7988.7 ms ✓ FileIO 1673.2 ms ✓ PDMats 851.1 ms ✓ Compat → CompatLinearAlgebraExt 890.5 ms ✓ PrecompileTools 1126.4 ms ✓ JLLWrappers 1513.3 ms ✓ BioGenerics 2264.4 ms ✓ CodecZstd 1599.2 ms ✓ CodecZlib 6749.4 ms ✓ CategoricalArrays 4862.5 ms ✓ Accessors 1090.2 ms ✓ SortingAlgorithms 2285.0 ms ✓ QuadGK 824.5 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1865.6 ms ✓ Tables 1158.2 ms ✓ ArrayInterface 1265.2 ms ✓ Adapt → AdaptSparseArraysExt 829.1 ms ✓ OffsetArrays → OffsetArraysAdaptExt 1420.1 ms ✓ FillArrays → FillArraysPDMatsExt 1960.5 ms ✓ FilePathsBase 1179.1 ms ✓ Mocking 3107.1 ms ✓ StringManipulation 16423.2 ms ✓ SIMD 16352.3 ms ✓ Parsers 5275.4 ms ✓ Static 1436.7 ms ✓ OpenBLAS32_jll 1415.5 ms ✓ Bzip2_jll 1473.0 ms ✓ XZ_jll 1425.3 ms ✓ NLopt_jll 1394.8 ms ✓ Rmath_jll 1446.5 ms ✓ OpenSpecFun_jll 1434.8 ms ✓ ASL_jll 1464.1 ms ✓ SQLite_jll 1667.7 ms ✓ METIS_jll 1509.5 ms ✓ Xorg_libpciaccess_jll 1546.4 ms ✓ Libiconv_jll 1750.8 ms ✓ BGZFStreams 1748.9 ms ✓ Accessors → TestExt 2414.9 ms ✓ Accessors → LinearAlgebraExt 4440.3 ms ✓ StatsBase 878.2 ms ✓ StructUtils → StructUtilsTablesExt 823.0 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1283.8 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 2675.2 ms ✓ FilePathsBase → FilePathsBaseTestExt 981.2 ms ✓ FilePathsBase → FilePathsBaseMmapExt 5664.6 ms ✓ TimeZones 39181.0 ms ✓ PrettyTables 22435.1 ms ✓ Automa 14158.8 ms ✓ JSON3 7416.1 ms ✓ JSON 960.5 ms ✓ InlineStrings → ParsersExt 967.1 ms ✓ BitTwiddlingConvenienceFunctions 2389.3 ms ✓ CPUSummary 4012.9 ms ✓ StaticArrayInterface 1997.6 ms ✓ CodecBzip2 2275.1 ms ✓ CodecXz 1775.6 ms ✓ Rmath 4951.8 ms ✓ SpecialFunctions 1498.3 ms ✓ MUMPS_seq_jll 1492.8 ms ✓ XML2_jll 6818.0 ms ✓ Roots 1579.0 ms ✓ PDMats → StatsBaseExt 89360.9 ms ✓ DataFrames [ Info: Compiling VCF parser... 19433.3 ms ✓ VariantCallFormat 3569.3 ms ✓ BenchmarkTools 2562.5 ms ✓ WeakRefStrings 1514.6 ms ✓ HostCPUFeatures 1652.5 ms ✓ PolyesterWeave 1100.4 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1080.5 ms ✓ CloseOpenIntervals 1444.1 ms ✓ LayoutPointers 2517.0 ms ✓ HypergeometricFunctions 1322.2 ms ✓ DiffRules 1462.4 ms ✓ Hwloc_jll 22124.8 ms ✓ RData 29892.5 ms ✓ CSV 4033.5 ms ✓ SQLite 15126.9 ms ✓ VectorizationBase 2372.5 ms ✓ StatsFuns 5955.7 ms ✓ ForwardDiff 1481.4 ms ✓ SPRAL_jll 21667.7 ms ✓ RDatasets 8271.5 ms ✓ BGEN 4291.1 ms ✓ SLEEFPirates 1003.7 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 4992.8 ms ✓ StatsModels 9023.0 ms ✓ Distributions 1350.8 ms ✓ Roots → RootsForwardDiffExt 75456.0 ms ✓ MathOptInterface 1617.8 ms ✓ Ipopt_jll 38621.1 ms ✓ LoopVectorization 4657.4 ms ✓ GLM 3726.7 ms ✓ Distributions → DistributionsTestExt 4328.1 ms ✓ HypothesisTests 7626.2 ms ✓ NLopt 1365.0 ms ✓ Ipopt 3245.0 ms ✓ LoopVectorization → SpecialFunctionsExt 7633.2 ms ✓ VCFTools 44247.6 ms ✓ Ipopt → IpoptMathOptInterfaceExt ERROR: LoadError: invalid assignment to constant SnpArrays.AbstractSnpArray. This redefinition may be permitted using the `const` keyword. Stacktrace:  [1] top-level scope  @ ~/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:48  [2] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3157  [4] top-level scope  @ stdin:5  [5] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3003  [7] include_string  @ ./loading.jl:3013 [inlined]  [8] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [9] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 819.99s ################################################################################ # Testing # Testing OrdinalGWAS Status `/tmp/jl_s41chh/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [31c24e10] Distributions v0.25.122 [b8f27783] MathOptInterface v1.46.0 [00428148] OrdinalGWAS v0.7.2 [b51826c6] OrdinalMultinomialModels v0.4.5 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [3eaba693] StatsModels v0.7.7 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [37e2e46d] LinearAlgebra v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_s41chh/Manifest.toml` [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 ⌅ [6db4b851] BGEN v0.1.17 [28d598bf] BGZFStreams v0.3.2 [6e4b80f9] BenchmarkTools v1.6.3 [47718e42] BioGenerics v0.1.5 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] BufferedStreams v1.2.2 [2a0fbf3d] CPUSummary v0.2.7 [336ed68f] CSV v0.10.15 ⌅ [324d7699] CategoricalArrays v0.10.7 [fb6a15b2] CloseOpenIntervals v0.1.13 [523fee87] CodecBzip2 v0.8.5 [ba30903b] CodecXz v0.7.4 [944b1d66] CodecZlib v0.7.8 [6b39b394] CodecZstd v0.8.7 [861a8166] Combinatorics v1.0.3 [38540f10] CommonSolve v0.2.4 [bbf7d656] CommonSubexpressions v0.3.1 [f70d9fcc] CommonWorldInvalidations v1.0.0 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [187b0558] ConstructionBase v1.6.0 [adafc99b] CpuId v0.3.1 [a8cc5b0e] Crayons v4.1.1 [a10d1c49] DBInterface v2.6.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 [864edb3b] DataStructures v0.19.3 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [e2ba6199] ExprTools v0.1.10 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [f6369f11] ForwardDiff v1.3.0 [38e38edf] GLM v1.9.0 [c27321d9] Glob v1.3.1 [3e5b6fbb] HostCPUFeatures v0.1.17 [34004b35] HypergeometricFunctions v0.3.28 [09f84164] HypothesisTests v0.11.6 [615f187c] IfElse v0.1.1 [842dd82b] InlineStrings v1.4.5 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [b6b21f68] Ipopt v1.13.0 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.3.0 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [10f19ff3] LayoutPointers v0.1.17 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [b8f27783] MathOptInterface v1.46.0 [fdba3010] MathProgBase v0.7.8 [e1d29d7a] Missings v1.2.0 [78c3b35d] Mocking v0.8.1 [d8a4904e] MutableArithmetics v1.6.7 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.3 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [00428148] OrdinalGWAS v0.7.2 [b51826c6] OrdinalMultinomialModels v0.4.5 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [1d0040c9] PolyesterWeave v0.2.2 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.2 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 ⌅ [df47a6cb] RData v0.8.3 [ce6b1742] RDatasets v0.7.7 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v2.2.10 [fdea26ae] SIMD v3.7.2 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [0aa819cd] SQLite v1.6.1 [431bcebd] SciMLPublic v1.0.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [4e780e97] SnpArrays v0.3.22 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [aedffcd0] Static v1.3.1 [0d7ed370] StaticArrayInterface v1.8.0 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.8 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.2 [856f2bd8] StructTypes v1.11.0 [ec057cc2] StructUtils v2.6.0 [dc5dba14] TZJData v1.5.0+2025b [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 [f269a46b] TimeZones v1.22.2 ⌅ [3bb67fe8] TranscodingStreams v0.9.13 [3a884ed6] UnPack v1.0.2 [a620830f] VCFTools v0.2.10 [28eba6e3] VariantCallFormat v0.5.9 [3d5dd08c] VectorizationBase v0.21.72 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [ae81ac8f] ASL_jll v0.1.3+0 [6e34b625] Bzip2_jll v1.0.9+0 [e33a78d0] Hwloc_jll v2.12.2+0 [9cc047cb] Ipopt_jll v300.1400.1900+0 [94ce4f54] Libiconv_jll v1.18.0+0 [d00139f3] METIS_jll v5.1.3+0 [d7ed1dd3] MUMPS_seq_jll v500.800.100+0 [079eb43e] NLopt_jll v2.10.0+0 [656ef2d0] OpenBLAS32_jll v0.3.29+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 ⌅ [319450e9] SPRAL_jll v2025.5.20+0 [76ed43ae] SQLite_jll v3.48.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.9+0 [ffd25f8a] XZ_jll v5.8.1+0 [a65dc6b1] Xorg_libpciaccess_jll v0.18.1+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9abbd945] Profile 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 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ERROR: LoadError: invalid assignment to constant SnpArrays.AbstractSnpArray. This redefinition may be permitted using the `const` keyword. Stacktrace:  [1] top-level scope  @ ~/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:48  [2] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3157  [4] top-level scope  @ stdin:5  [5] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3003  [7] include_string  @ ./loading.jl:3013 [inlined]  [8] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [9] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 ERROR: LoadError: invalid assignment to constant SnpArrays.AbstractSnpArray. This redefinition may be permitted using the `const` keyword. Stacktrace:  [1] top-level scope  @ ~/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:48  [2] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [3] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3157  [4] top-level scope  @ stdin:5  [5] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [6] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:3003  [7] include_string  @ ./loading.jl:3013 [inlined]  [8] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [9] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 1 dependency had output during precompilation: ┌ SnpArrays │ [Output was shown above] └ ERROR: LoadError: The following 1 package failed to precompile: SnpArrays Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.14/SnpArrays/jl_mQozug" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/OrdinalGWAS/r0sGl/src/OrdinalGWAS.jl:3 in expression starting at /home/pkgeval/.julia/packages/OrdinalGWAS/r0sGl/test/runtests.jl:1 Testing failed after 101.02s ERROR: LoadError: Package OrdinalGWAS errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 990.77s: package fails to precompile