Package evaluation to test PGENFiles on Julia 1.14.0-DEV.3128 (f573e2bf71*) started at 2026-09-06T20:21:07.097 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 13.42s ################################################################################ # Installation # Installing PGENFiles... Resolving package versions... Installed CodecZlib ─────────────────── v0.7.9 Installed InlineStrings ─────────────── v1.4.6 Installed DataStructures ────────────── v0.19.6 Installed StatsBase ─────────────────── v0.34.13 Installed CSV ───────────────────────── v0.10.17 Installed AliasTables ───────────────── v1.1.3 Installed TranscodingStreams ────────── v0.11.3 Installed OrderedCollections ────────── v2.0.1 Installed Statistics ────────────────── v1.11.5 Installed Compat ────────────────────── v4.18.1 Installed InvertedIndices ───────────── v1.3.1 Installed DataAPI ───────────────────── v1.16.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed PrecompileTools ───────────── v1.3.4 Installed StatsAPI ──────────────────── v1.8.0 Installed SentinelArrays ────────────── v1.4.10 Installed FilePathsBase ─────────────── v0.9.24 Installed StringManipulation ────────── v0.5.0 Installed IrrationalConstants ───────── v0.2.6 Installed DataValueInterfaces ───────── v1.0.0 Installed Parsers ───────────────────── v2.8.8 Installed LogExpFunctions ───────────── v1.0.1 Installed BitIntegers ───────────────── v0.3.7 Installed GeneticVariantBase ────────── v0.1.2 Installed PGENFiles ─────────────────── v0.2.2 Installed Tables ────────────────────── v1.14.0 Installed PrettyTables ──────────────── v3.4.8 Installed PtrArrays ─────────────────── v1.4.0 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed WeakRefStrings ────────────── v1.4.3 Installed PooledArrays ──────────────── v1.4.3 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.5.2 Installed LaTeXStrings ──────────────── v1.4.1 Installed SortingAlgorithms ─────────── v1.2.3 Installed DataFrames ────────────────── v1.8.2 Installed Crayons ───────────────────── v4.2.0 Installed WorkerUtilities ───────────── v1.6.1 Installed DocStringExtensions ───────── v0.9.5 Updating `~/.julia/environments/v1.14/Project.toml` [bbb59ef6] + PGENFiles v0.2.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [c3b6d118] + BitIntegers v0.3.7 [336ed68f] + CSV v0.10.17 [944b1d66] + CodecZlib v0.7.9 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.2.0 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [2447270c] + GeneticVariantBase v0.1.2 ⌅ [842dd82b] + InlineStrings v1.4.6 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.1 [2ab3a3ac] + LogExpFunctions v1.0.1 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v2.0.1 [bbb59ef6] + PGENFiles v0.2.2 ⌅ [69de0a69] + Parsers v2.8.8 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.8 [43287f4e] + PtrArrays v1.4.0 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.10 [a2af1166] + SortingAlgorithms v1.2.3 [10745b16] + Statistics v1.11.5 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.13 ⌅ [892a3eda] + StringManipulation v0.5.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.3 [76eceee3] + WorkerUtilities v1.6.1 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [4536629a] + OpenBLAS_jll v0.3.34+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [8e850b90] + libblastrampoline_jll v5.15.0+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 3.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.6 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 1.6 s ✓ InlineStrings 0.5 s ✓ Reexport 0.8 s ✓ Statistics 0.6 s ✓ DataAPI 2.0 s ✓ IrrationalConstants 0.5 s ✓ DataValueInterfaces 0.6 s ✓ StatsAPI 0.6 s ✓ DBInterface 1.2 s ✓ OrderedCollections 0.6 s ✓ InvertedIndices 0.9 s ✓ DocStringExtensions 0.8 s ✓ WorkerUtilities 0.5 s ✓ PtrArrays 0.9 s ✓ TranscodingStreams 0.5 s ✓ IteratorInterfaceExtensions 0.6 s ✓ LaTeXStrings 1.1 s ✓ BitIntegers 2.6 s ✓ Crayons 2.0 s ✓ SentinelArrays 1.1 s ✓ Compat 1.3 s ✓ Preferences 1.5 s ✓ Statistics → SparseArraysExt 0.7 s ✓ Missings 0.8 s ✓ PooledArrays 3.6 s ✓ DataStructures 1.0 s ✓ LogExpFunctions 0.7 s ✓ AliasTables 1.5 s ✓ CodecZstd 0.7 s ✓ CodecZlib 0.5 s ✓ TableTraits 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ JLLWrappers 1.0 s ✓ PrecompileTools 0.8 s ✓ SortingAlgorithms 1.7 s ✓ Tables 2.0 s ✓ FilePathsBase 1.0 s ✓ dlfcn_win32_jll 1.7 s ✓ OpenSpecFun_jll 6.3 s ✓ StringManipulation 12.3 s ✓ SIMD 10.7 s ✓ Parsers 4.7 s ✓ StatsBase 3.1 s ✓ FilePathsBase → FilePathsBaseTestExt 0.9 s ✓ FilePathsBase → FilePathsBaseMmapExt 1.2 s ✓ SQLite_jll 5.3 s ✓ SpecialFunctions 44.0 s ✓ PrettyTables 0.9 s ✓ InlineStrings → ParsersExt 2.0 s ✓ GeneticVariantBase 81.1 s ✓ DataFrames 2.4 s ✓ WeakRefStrings 28.0 s ✓ CSV 4.5 s ✓ SQLite 9.8 s ✓ PGENFiles 3.9 s ✓ BGEN 55 dependencies successfully precompiled in 264 seconds. 21 already precompiled. Precompilation completed after 281.87s ################################################################################ # Testing # Testing PGENFiles Status `/tmp/jl_Ae57C5/Project.toml` [6db4b851] BGEN v0.2.2 [2447270c] GeneticVariantBase v0.1.2 [bbb59ef6] PGENFiles v0.2.2 [8dfed614] Test v1.11.0 Status `/tmp/jl_Ae57C5/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [6db4b851] BGEN v0.2.2 [c3b6d118] BitIntegers v0.3.7 [336ed68f] CSV v0.10.17 [944b1d66] CodecZlib v0.7.9 [6b39b394] CodecZstd v0.8.7 [34da2185] Compat v4.18.1 [a8cc5b0e] Crayons v4.2.0 [a10d1c49] DBInterface v2.7.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [864edb3b] DataStructures v0.19.6 [e2d170a0] DataValueInterfaces v1.0.0 [ffbed154] DocStringExtensions v0.9.5 [48062228] FilePathsBase v0.9.24 [2447270c] GeneticVariantBase v0.1.2 ⌅ [842dd82b] InlineStrings v1.4.6 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.8.0 [b964fa9f] LaTeXStrings v1.4.1 [2ab3a3ac] LogExpFunctions v1.0.1 [e1d29d7a] Missings v1.2.0 [bac558e1] OrderedCollections v2.0.1 [bbb59ef6] PGENFiles v0.2.2 ⌅ [69de0a69] Parsers v2.8.8 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [43287f4e] PtrArrays v1.4.0 [189a3867] Reexport v1.2.2 [fdea26ae] SIMD v3.7.2 [0aa819cd] SQLite v1.8.2 [91c51154] SentinelArrays v1.4.10 [a2af1166] SortingAlgorithms v1.2.3 [276daf66] SpecialFunctions v2.9.0 [10745b16] Statistics v1.11.5 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.13 ⌅ [892a3eda] StringManipulation v0.5.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.14.0 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.3 [76eceee3] WorkerUtilities v1.6.1 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [76ed43ae] SQLite_jll v3.53.2+0 [c4b69c83] dlfcn_win32_jll v1.4.2+0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.5.7+0 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.8+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Difflist: Error During Test at /home/pkgeval/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:27 Got exception outside of a @test ArgumentError: cannot reinterpret an `UInt8` array to `PGENFiles.UInt24` whose first dimension has size `6`. The resulting array would have a non-integral first dimension. Stacktrace: [1] (::Base.var"#thrownonint#reinterpret##0")(S::Core.TypeEgal{UInt8}, T::Core.TypeEgal{PGENFiles.UInt24}, dim::Int64) @ Base reinterpretarray.jl:76 [2] reinterpret(::Core.TypeEgal{PGENFiles.UInt24}, a::SubArray{UInt8, 1, Vector{UInt8}, Tuple{UnitRange{Int64}}, true}) @ Base reinterpretarray.jl:96 [3] parse_difflist(data::Vector{UInt8}, offset::UInt64, bytes_per_sample_id::Int64, has_genotype::Bool) @ PGENFiles ~/.julia/packages/PGENFiles/N7YcR/src/difflist.jl:20 [4] top-level scope @ ~/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:7 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [6] macro expansion @ ~/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:30 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [8] macro expansion @ ~/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:55 [inlined] Test Summary: | Pass Error Total Time PGENFiles.jl | 1609 1 1610 1m15.7s Header | 15 15 48.3s Difflist | 1 1 5.7s dosage | 1592 1592 21.4s Custom collect for PgenVariantIterator | 2 2 0.3s RNG of the outermost testset: Random.Xoshiro(0x264f0d2bd9953d32, 0xd8ed5d4626502f09, 0x294dfb5e90d36007, 0x006aec70e4f86930, 0x828984ed63718ac0) ERROR: LoadError: Some tests did not pass: 1609 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PGENFiles/N7YcR/test/runtests.jl:5 Testing failed after 102.23s ERROR: LoadError: Package PGENFiles 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:3298 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 458.44s: package tests unexpectedly errored