Package evaluation of MendelIHT on Julia 1.13.0-DEV.140 (fac1ce7906*) started at 2025-03-02T16:01:24.315 ################################################################################ # Set-up # Set-up completed after 0.25s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.13/Manifest.toml` [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 ⌅ [67c07d97] + Automa v0.8.4 ⌅ [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 v0.2.6 [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 v0.8.6 [861a8166] + Combinatorics v1.0.2 [38540f10] + CommonSolve v0.2.4 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.16.0 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.5.8 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 [48062228] + FilePathsBase v0.9.23 [1a297f60] + FillArrays v1.13.0 [38e38edf] + GLM v1.9.0 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.27 [09f84164] + HypothesisTests v0.11.3 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.3 [3587e190] + InverseFunctions v0.1.17 [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 [10f19ff3] + LayoutPointers v0.1.17 [2ab3a3ac] + LogExpFunctions v0.3.29 [bdcacae8] + LoopVectorization v0.12.171 [1914dd2f] + MacroTools v0.5.15 [d125e4d3] + ManualMemory v0.1.8 [921c7187] + MendelIHT v1.4.11 [e1d29d7a] + Missings v1.2.0 [6fe1bfb0] + OffsetArrays v1.15.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [69de0a69] + Parsers v2.8.1 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [92933f4c] + ProgressMeter v1.10.2 [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 [f2b01f46] + Roots v2.2.6 [fdea26ae] + SIMD v3.7.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [0aa819cd] + SQLite v1.6.1 [91c51154] + SentinelArrays v1.4.8 [1277b4bf] + ShiftedArrays v2.0.0 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [aedffcd0] + Static v1.1.1 [0d7ed370] + StaticArrayInterface v1.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.3.2 [3eaba693] + StatsModels v0.7.4 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [8290d209] + ThreadingUtilities v0.5.2 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [3a884ed6] + UnPack v1.0.2 [a620830f] + VCFTools v0.2.10 [28eba6e3] + VariantCallFormat v0.5.6 [3d5dd08c] + VectorizationBase v0.21.71 [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 v5.6.4+1 [3161d3a3] + Zstd_jll v1.5.7+1 [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 v0.6.4 [76f85450] + LibGit2 v1.11.0 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL 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 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.5.0+2 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 6.46s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 9010.9 ms ✓ BGEN 21458.3 ms ✓ VCFTools 165239.6 ms ✓ SnpArrays 168251.7 ms ✓ MendelIHT 4 dependencies successfully precompiled in 370 seconds. 162 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 378.18s ################################################################################ # Loading # Loading MendelIHT... ERROR: InitError: TaskFailedException nested task error: BoundsError: attempt to access 1-element Vector{MendelIHT.IHTVariable{Float64, SnpArrays.SnpLinAlg{Float64}}} at index [2] Stacktrace: [1] throw_boundserror(A::Vector{MendelIHT.IHTVariable{Float64, SnpArrays.SnpLinAlg{Float64}}}, I::Tuple{Int64}) @ Base ./essentials.jl:15 [2] getindex @ ./essentials.jl:950 [inlined] [3] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/src/cross_validation.jl:105 [inlined] [4] (::MendelIHT.var"#75#76"{MendelIHT.var"#77#78"{Float64, Vector{Int64}, Bool, Bool, Int64, Int64, Bool, Vector{Float64}, Vector{Tuple{Int64, Int64}}, Nothing, Vector{MendelIHT.IHTVariable{Float64, SnpArrays.SnpLinAlg{Float64}}}, Vector{BitVector}, Vector{BitVector}, Base.OneTo{Int64}}})(tid::Int64; onethread::Bool) @ MendelIHT ./threadingconstructs.jl:276 [5] #75 @ ./threadingconstructs.jl:243 [inlined] [6] (::Base.Threads.var"#threading_run##0#threading_run##1"{MendelIHT.var"#75#76"{MendelIHT.var"#77#78"{Float64, Vector{Int64}, Bool, Bool, Int64, Int64, Bool, Vector{Float64}, Vector{Tuple{Int64, Int64}}, Nothing, Vector{MendelIHT.IHTVariable{Float64, SnpArrays.SnpLinAlg{Float64}}}, Vector{BitVector}, Vector{BitVector}, Base.OneTo{Int64}}}, Int64})() @ Base.Threads ./threadingconstructs.jl:177 Stacktrace: [1] threading_run(fun::MendelIHT.var"#75#76"{MendelIHT.var"#77#78"{Float64, Vector{Int64}, Bool, Bool, Int64, Int64, Bool, Vector{Float64}, Vector{Tuple{Int64, Int64}}, Nothing, Vector{MendelIHT.IHTVariable{Float64, SnpArrays.SnpLinAlg{Float64}}}, Vector{BitVector}, Vector{BitVector}, Base.OneTo{Int64}}}, static::Bool) @ Base.Threads ./threadingconstructs.jl:196 [2] macro expansion @ ./threadingconstructs.jl:217 [inlined] [3] cv_iht(y::Vector{Float64}, x::SnpArrays.SnpLinAlg{Float64}, z::Vector{Float64}; d::Distributions.Normal{Float64}, l::GLM.IdentityLink, path::UnitRange{Int64}, q::Int64, est_r::Symbol, group::Vector{Int64}, weight::Vector{Float64}, zkeep::BitVector, folds::Vector{Int64}, debias::Bool, verbose::Bool, max_iter::Int64, min_iter::Int64, init_beta::Bool, memory_efficient::Bool) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/cross_validation.jl:100 [4] cross_validate(filename::String, d::UnionAll; path::UnitRange{Int64}, phenotypes::Int64, covariates::String, cv_summaryfile::String, q::Int64, exclude_std_idx::Vector{Int64}, dosage::Bool, kwargs::@Kwargs{verbose::Bool}) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:337 [5] __init__() @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/MendelIHT.jl:56 [6] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1424 [7] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1412 [8] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}, ignore_native::Nothing; register::Bool) @ Base ./loading.jl:1300 [9] _include_from_serialized (repeats 2 times) @ ./loading.jl:1246 [inlined] [10] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String}) @ Base ./loading.jl:2126 [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2630 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2493 [13] macro expansion @ ./loading.jl:2421 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2386 [16] #invoke_in_world#2 @ ./essentials.jl:1125 [inlined] [17] invoke_in_world @ ./essentials.jl:1121 [inlined] [18] require(into::Module, mod::Symbol) @ Base ./loading.jl:2366 [19] eval(m::Module, e::Any) @ Core ./boot.jl:488 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:294 [21] _start() @ Base ./client.jl:560 during initialization of module MendelIHT Loading failed after 208.77s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using MendelIHT'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:598 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:513 [3] run(::Cmd) @ Base ./process.jl:510 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:306 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [7] _start() @ Base ./client.jl:560 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 616.47s: there were unidentified errors