Package evaluation to test MendelIHT on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-12T00:55:23.353 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.47s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Installed CommonSolve ────────────────────── v0.2.4 Installed Glob ───────────────────────────── v1.3.1 Installed CommonWorldInvalidations ───────── v1.0.0 Installed CompositionsBase ───────────────── v0.1.2 Installed MacroTools ─────────────────────── v0.5.16 Installed CodecZstd ──────────────────────── v0.8.7 Installed FilePathsBase ──────────────────── v0.9.24 Installed DataStructures ─────────────────── v0.19.3 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed ManualMemory ───────────────────── v0.1.8 Installed GLM ────────────────────────────── v1.9.0 Installed InlineStrings ──────────────────── v1.4.5 Installed FillArrays ─────────────────────── v1.15.0 Installed VectorizationBase ──────────────── v0.21.72 Installed VCFTools ───────────────────────── v0.2.10 Installed Adapt ──────────────────────────── v4.4.0 Installed StatsModels ────────────────────── v0.7.7 Installed ConstructionBase ───────────────── v1.6.0 Installed HypergeometricFunctions ────────── v0.3.28 Installed SLEEFPirates ───────────────────── v0.6.43 Installed DelimitedFiles ─────────────────── v1.9.1 Installed AliasTables ────────────────────── v1.1.3 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed CodecZlib ──────────────────────── v0.7.8 Installed SIMDTypes ──────────────────────── v0.1.0 Installed StatsBase ──────────────────────── v0.34.8 Installed ShiftedArrays ──────────────────── v2.0.0 Installed ArrayInterface ─────────────────── v7.22.0 Installed TranscodingStreams ─────────────── v0.9.13 Installed Compat ─────────────────────────── v4.18.1 Installed OrderedCollections ─────────────── v1.8.1 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed HypothesisTests ────────────────── v0.11.6 Installed HostCPUFeatures ────────────────── v0.1.17 Installed Combinatorics ──────────────────── v1.0.3 Installed LoopVectorization ──────────────── v0.12.173 Installed DataAPI ────────────────────────── v1.16.0 Installed SIMD ───────────────────────────── v3.7.2 Installed Statistics ─────────────────────── v1.11.1 Installed InvertedIndices ────────────────── v1.3.1 Installed DataValueInterfaces ────────────── v1.0.0 Installed StatsAPI ───────────────────────── v1.7.1 Installed CpuId ──────────────────────────── v0.3.1 Installed PrecompileTools ────────────────── v1.3.3 Installed ProgressMeter ──────────────────── v1.11.0 Installed SentinelArrays ─────────────────── v1.4.8 Installed OffsetArrays ───────────────────── v1.17.0 Installed IrrationalConstants ────────────── v0.2.6 Installed LayoutPointers ─────────────────── v0.1.17 Installed Distances ──────────────────────── v0.10.12 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed StaticArrayInterface ───────────── v1.8.0 Installed QuadGK ─────────────────────────── v2.11.2 Installed StringManipulation ─────────────── v0.4.1 Installed SciMLPublic ────────────────────── v1.0.0 Installed CPUSummary ─────────────────────── v0.2.7 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Requires ───────────────────────── v1.3.1 Installed CSV ────────────────────────────── v0.10.15 Installed BufferedStreams ────────────────── v1.2.2 Installed LogExpFunctions ────────────────── v0.3.29 Installed Parsers ────────────────────────── v2.8.3 Installed Rmath ──────────────────────────── v0.9.0 Installed Roots ──────────────────────────── v2.2.10 Installed IfElse ─────────────────────────── v0.1.1 Installed BioGenerics ────────────────────── v0.1.5 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed Tables ─────────────────────────── v1.12.1 Installed StatsFuns ──────────────────────── v1.5.2 Installed Distributions ──────────────────── v0.25.122 Installed PrettyTables ───────────────────── v3.1.0 Installed PtrArrays ──────────────────────── v1.3.0 Installed SpecialFunctions ───────────────── v2.6.1 Installed InverseFunctions ───────────────── v0.1.17 Installed Reexport ───────────────────────── v1.2.2 Installed DataFrames ─────────────────────── v1.8.1 Installed Missings ───────────────────────── v1.2.0 Installed Static ─────────────────────────── v1.3.1 Installed Preferences ────────────────────── v1.5.0 Installed DBInterface ────────────────────── v2.6.1 Installed PooledArrays ───────────────────── v1.4.3 Installed WeakRefStrings ─────────────────── v1.4.2 Installed JLLWrappers ────────────────────── v1.7.1 Installed TableTraits ────────────────────── v1.0.1 Installed LaTeXStrings ───────────────────── v1.4.0 Installed XZ_jll ─────────────────────────── v5.8.1+0 Installed Crayons ────────────────────────── v4.1.1 Installed PDMats ─────────────────────────── v0.11.36 Installed Automa ─────────────────────────── v1.1.0 Installed SortingAlgorithms ──────────────── v1.2.2 Installed BGZFStreams ────────────────────── v0.3.2 Installed SQLite_jll ─────────────────────── v3.48.0+0 Installed VariantCallFormat ──────────────── v0.5.9 Installed CodecXz ────────────────────────── v0.7.4 Installed SQLite ─────────────────────────── v1.6.1 Installed PolyesterWeave ─────────────────── v0.2.2 Installed ThreadingUtilities ─────────────── v0.5.5 Installed UnPack ─────────────────────────── v1.0.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed DocStringExtensions ────────────── v0.9.5 Installed SnpArrays ──────────────────────── v0.3.22 Installed Accessors ──────────────────────── v0.1.42 Installed BGEN ───────────────────────────── v0.1.17 Installed MendelIHT ──────────────────────── v1.4.11 Installing 5 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact XZ 1.5 MiB Installed artifact SQLite 5.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 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 [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 [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 [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 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [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 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [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 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [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 v3.1.0 [92933f4c] + ProgressMeter v1.11.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [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 [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 [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 v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [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 [6e34b625] + Bzip2_jll v1.0.9+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [76ed43ae] + SQLite_jll v3.48.0+0 [ffd25f8a] + XZ_jll v5.8.1+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 [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 v1.11.0 [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 v8.16.0+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 16.2s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4753.7 ms ✓ TestEnv 1 dependency successfully precompiled in 5 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/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/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... 4612.0 ms ✓ MacroTools 1767.0 ms ✓ InlineStrings 814.9 ms ✓ Reexport 1118.2 ms ✓ ConstructionBase 2250.6 ms ✓ IrrationalConstants 823.9 ms ✓ DataValueInterfaces 869.6 ms ✓ StatsAPI 2124.9 ms ✓ Combinatorics 800.3 ms ✓ CommonSolve 830.7 ms ✓ LaTeXStrings 876.7 ms ✓ Glob 1143.5 ms ✓ Statistics 801.2 ms ✓ IfElse 837.4 ms ✓ PtrArrays 974.4 ms ✓ ManualMemory 1219.7 ms ✓ DataAPI 1222.2 ms ✓ SciMLPublic 842.1 ms ✓ CommonWorldInvalidations 1076.4 ms ✓ InvertedIndices 1095.9 ms ✓ InverseFunctions 839.2 ms ✓ CompositionsBase 901.0 ms ✓ ShiftedArrays 1025.8 ms ✓ WorkerUtilities 2403.5 ms ✓ FillArrays 819.0 ms ✓ UnPack 866.7 ms ✓ DBInterface 1274.1 ms ✓ OrderedCollections 1180.1 ms ✓ DocStringExtensions 1725.8 ms ✓ OffsetArrays 1049.0 ms ✓ BufferedStreams 775.0 ms ✓ SIMDTypes 772.9 ms ✓ IteratorInterfaceExtensions 2260.1 ms ✓ Crayons 1066.4 ms ✓ DelimitedFiles 1229.1 ms ✓ Requires 1254.5 ms ✓ SuiteSparse 1865.9 ms ✓ CpuId 3239.0 ms ✓ SentinelArrays 1714.5 ms ✓ ProgressMeter 1156.5 ms ✓ Compat 1126.3 ms ✓ Preferences 2478.8 ms ✓ TranscodingStreams 1579.6 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1611.7 ms ✓ Statistics → SparseArraysExt 1639.7 ms ✓ Distances 1334.1 ms ✓ AliasTables 1840.9 ms ✓ ThreadingUtilities 1082.1 ms ✓ Missings 1106.3 ms ✓ PooledArrays 879.4 ms ✓ InverseFunctions → InverseFunctionsDatesExt 1487.9 ms ✓ InverseFunctions → InverseFunctionsTestExt 761.6 ms ✓ CompositionsBase → CompositionsBaseInverseFunctionsExt 1582.9 ms ✓ FillArrays → FillArraysSparseArraysExt 986.0 ms ✓ FillArrays → FillArraysStatisticsExt 3706.4 ms ✓ DataStructures 1837.4 ms ✓ LogExpFunctions 803.4 ms ✓ TableTraits 989.0 ms ✓ Adapt 1780.8 ms ✓ PDMats 873.3 ms ✓ Compat → CompatLinearAlgebraExt 902.5 ms ✓ PrecompileTools 1187.1 ms ✓ JLLWrappers 1640.3 ms ✓ BioGenerics 2882.0 ms ✓ CodecZstd 1632.7 ms ✓ CodecZlib 1330.7 ms ✓ Distances → DistancesSparseArraysExt 5419.4 ms ✓ Accessors 1115.0 ms ✓ SortingAlgorithms 2439.6 ms ✓ QuadGK 837.0 ms ✓ LogExpFunctions → LogExpFunctionsInverseFunctionsExt 1984.5 ms ✓ Tables 1194.9 ms ✓ ArrayInterface 1384.2 ms ✓ Adapt → AdaptSparseArraysExt 847.3 ms ✓ OffsetArrays → OffsetArraysAdaptExt 1492.0 ms ✓ FillArrays → FillArraysPDMatsExt 2238.6 ms ✓ FilePathsBase 3492.5 ms ✓ StringManipulation 19445.5 ms ✓ SIMD 18764.4 ms ✓ Parsers 6289.6 ms ✓ Static 1632.5 ms ✓ Bzip2_jll 1559.5 ms ✓ XZ_jll 1481.7 ms ✓ Rmath_jll 1512.7 ms ✓ OpenSpecFun_jll 1507.0 ms ✓ SQLite_jll 1935.6 ms ✓ BGZFStreams 1850.4 ms ✓ Accessors → TestExt 2737.3 ms ✓ Accessors → LinearAlgebraExt 4724.6 ms ✓ StatsBase 1337.8 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 2713.2 ms ✓ FilePathsBase → FilePathsBaseTestExt 996.2 ms ✓ FilePathsBase → FilePathsBaseMmapExt 43375.9 ms ✓ PrettyTables 25462.8 ms ✓ Automa 1117.4 ms ✓ InlineStrings → ParsersExt 954.3 ms ✓ BitTwiddlingConvenienceFunctions 2712.2 ms ✓ CPUSummary 17153.3 ms ✓ StaticArrayInterface 1673.6 ms ✓ CodecBzip2 1636.1 ms ✓ CodecXz 1507.5 ms ✓ Rmath 5460.8 ms ✓ SpecialFunctions 7470.0 ms ✓ Roots 1466.0 ms ✓ PDMats → StatsBaseExt 101811.2 ms ✓ DataFrames [ Info: Compiling VCF parser... 21286.9 ms ✓ VariantCallFormat 2706.2 ms ✓ WeakRefStrings 1585.2 ms ✓ HostCPUFeatures 1734.2 ms ✓ PolyesterWeave 1103.8 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1116.8 ms ✓ CloseOpenIntervals 1307.2 ms ✓ LayoutPointers 2413.1 ms ✓ HypergeometricFunctions 34859.1 ms ✓ CSV 4842.6 ms ✓ SQLite 17086.8 ms ✓ VectorizationBase 2561.9 ms ✓ StatsFuns 7615.4 ms ✓ BGEN 4345.8 ms ✓ SLEEFPirates 1067.4 ms ✓ StatsFuns → StatsFunsInverseFunctionsExt 5391.4 ms ✓ StatsModels 9618.5 ms ✓ Distributions 43549.7 ms ✓ LoopVectorization 4556.1 ms ✓ GLM 2875.0 ms ✓ Distributions → DistributionsTestExt 3460.0 ms ✓ HypothesisTests 3139.4 ms ✓ LoopVectorization → SpecialFunctionsExt 7955.0 ms ✓ VCFTools 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:3151  [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:2997  [7] include_string  @ ./loading.jl:3007 [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 621.44s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_G77ZZH/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.6.3 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [38e38edf] GLM v1.9.0 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.22 [276daf66] SpecialFunctions v2.6.1 [2913bbd2] StatsBase v0.34.8 [a620830f] VCFTools v0.2.10 [37e2e46d] LinearAlgebra v1.13.0 [44cfe95a] Pkg v1.13.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_G77ZZH/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 [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 [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 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [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 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.2.1 [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 [921c7187] MendelIHT v1.4.11 [e1d29d7a] Missings v1.2.0 [6fe1bfb0] OffsetArrays v1.17.0 [bac558e1] OrderedCollections v1.8.1 [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 v3.1.0 [92933f4c] ProgressMeter v1.11.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [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 [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 [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 v0.4.1 [ec057cc2] StructUtils v2.6.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [8290d209] ThreadingUtilities v0.5.5 ⌅ [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 [6e34b625] Bzip2_jll v1.0.9+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 [76ed43ae] SQLite_jll v3.48.0+0 [ffd25f8a] XZ_jll v5.8.1+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 v1.11.0 [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 v8.16.0+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:3151  [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:2997  [7] include_string  @ ./loading.jl:3007 [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:3151  [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:2997  [7] include_string  @ ./loading.jl:3007 [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_CJh0hI" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:3 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:1 Testing failed after 98.48s ERROR: LoadError: Package MendelIHT 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 787.85s: package fails to precompile