Package evaluation to load OpenADMIXTURE on Julia 1.14.0-DEV.29 (7d6ae45e5a*) started at 2025-11-05T11:21:34.757 ################################################################################ # Set-up # Set-up completed after 0.1s ################################################################################ # Installation # Installing OpenADMIXTURE... Resolving package versions... Installed Formatting ─────────────────────── v0.4.3 Installed Glob ───────────────────────────── v1.3.1 Installed CommonWorldInvalidations ───────── v1.0.0 Installed ManualMemory ───────────────────── v0.1.8 Installed CodecZstd ──────────────────────── v0.8.6 Installed FilePathsBase ──────────────────── v0.9.24 Installed SparseKmeansFeatureRanking ─────── v0.1.2 Installed DataStructures ─────────────────── v0.19.3 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed Adapt ──────────────────────────── v3.7.2 Installed InlineStrings ──────────────────── v1.4.5 Installed SLEEFPirates ───────────────────── v0.6.43 Installed DelimitedFiles ─────────────────── v1.9.1 Installed AliasTables ────────────────────── v1.1.3 Installed StatsBase ──────────────────────── v0.34.7 Installed VectorizationBase ──────────────── v0.21.72 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed SIMDTypes ──────────────────────── v0.1.0 Installed CodecZlib ──────────────────────── v0.7.8 Installed OrderedCollections ─────────────── v1.8.1 Installed ArrayInterface ─────────────────── v7.7.1 Installed Compat ─────────────────────────── v4.18.1 Installed TranscodingStreams ─────────────── v0.9.13 Installed StrideArraysCore ───────────────── v0.5.8 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed Suppressor ─────────────────────── v0.2.8 Installed HostCPUFeatures ────────────────── v0.1.17 Installed SIMD ───────────────────────────── v3.7.2 Installed DataAPI ────────────────────────── v1.16.0 Installed LoopVectorization ──────────────── v0.12.173 Installed InvertedIndices ────────────────── v1.3.1 Installed Statistics ─────────────────────── v1.11.1 Installed DataValueInterfaces ────────────── v1.0.0 Installed CpuId ──────────────────────────── v0.3.1 Installed StatsAPI ───────────────────────── v1.7.1 Installed PrecompileTools ────────────────── v1.3.3 Installed ProgressMeter ──────────────────── v1.11.0 Installed SentinelArrays ─────────────────── v1.4.8 Installed IrrationalConstants ────────────── v0.2.6 Installed OffsetArrays ───────────────────── v1.17.0 Installed LayoutPointers ─────────────────── v0.1.17 Installed StaticArrayInterface ───────────── v1.8.0 Installed Distances ──────────────────────── v0.10.12 Installed CodecBzip2 ─────────────────────── v0.8.5 Installed NaNMath ────────────────────────── v1.1.3 Installed CPUSummary ─────────────────────── v0.2.7 Installed StringManipulation ─────────────── v0.4.1 Installed SciMLPublic ────────────────────── v1.0.0 Installed Requires ───────────────────────── v1.3.1 Installed Tullio ─────────────────────────── v0.3.8 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Parsers ────────────────────────── v2.8.3 Installed DiffRules ──────────────────────── v1.15.1 Installed BufferedStreams ────────────────── v1.2.2 Installed LogExpFunctions ────────────────── v0.3.29 Installed IfElse ─────────────────────────── v0.1.1 Installed BioGenerics ────────────────────── v0.1.5 Installed PrettyTables ───────────────────── v3.1.0 Installed PtrArrays ──────────────────────── v1.3.0 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed Polyester ──────────────────────── v0.7.18 Installed Tables ─────────────────────────── v1.12.1 Installed CSV ────────────────────────────── v0.10.15 Installed OpenADMIXTURE ──────────────────── v0.1.0 Installed SpecialFunctions ───────────────── v2.6.1 Installed Reexport ───────────────────────── v1.2.2 Installed Missings ───────────────────────── v1.2.0 Installed Static ─────────────────────────── v1.3.1 Installed DataFrames ─────────────────────── v1.8.1 Installed Preferences ────────────────────── v1.5.0 Installed WeakRefStrings ─────────────────── v1.4.2 Installed JLLWrappers ────────────────────── v1.7.1 Installed PooledArrays ───────────────────── v1.4.3 Installed TableTraits ────────────────────── v1.0.1 Installed LaTeXStrings ───────────────────── v1.4.0 Installed XZ_jll ─────────────────────────── v5.8.1+0 Installed SortingAlgorithms ──────────────── v1.2.2 Installed BGZFStreams ────────────────────── v0.3.2 Installed Crayons ────────────────────────── v4.1.1 Installed CodecXz ────────────────────────── v0.7.4 Installed Automa ─────────────────────────── v1.1.0 Installed VariantCallFormat ──────────────── v0.5.9 Installed ThreadingUtilities ─────────────── v0.5.5 Installed PolyesterWeave ─────────────────── v0.2.2 Installed UnPack ─────────────────────────── v1.0.2 Installed WorkerUtilities ────────────────── v1.6.1 Installed DocStringExtensions ────────────── v0.9.5 Installed SnpArrays ──────────────────────── v0.3.22 Installing 3 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact XZ 1.5 MiB Updating `~/.julia/environments/v1.14/Project.toml` [425c031d] + OpenADMIXTURE v0.1.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [79e6a3ab] + Adapt v3.7.2 [66dad0bd] + AliasTables v1.1.3 ⌃ [4fba245c] + ArrayInterface v7.7.1 [67c07d97] + Automa v1.1.0 [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 v0.8.6 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [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 [b552c78f] + DiffRules v1.15.1 [b4f34e82] + Distances v0.10.12 [ffbed154] + DocStringExtensions v0.9.5 [48062228] + FilePathsBase v0.9.24 [59287772] + Formatting v0.4.3 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.5 [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 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.17.0 [425c031d] + OpenADMIXTURE v0.1.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [f517fe37] + Polyester v0.7.18 [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 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [fdea26ae] + SIMD v3.7.2 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [431bcebd] + SciMLPublic v1.0.0 [91c51154] + SentinelArrays v1.4.8 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.2 [a6138be3] + SparseKmeansFeatureRanking v0.1.2 [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 v0.34.7 [7792a7ef] + StrideArraysCore v0.5.8 [892a3eda] + StringManipulation v0.4.1 [fd094767] + Suppressor v0.2.8 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [8290d209] + ThreadingUtilities v0.5.5 ⌅ [3bb67fe8] + TranscodingStreams v0.9.13 [bc48ee85] + Tullio v0.3.8 [3a884ed6] + UnPack v1.0.2 [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 [ffd25f8a] + XZ_jll v5.8.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [7b1f6079] + FileWatching 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 v1.13.0 [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 v1.0.0 [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 [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 v0.8.7+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 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 13.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 1036.5 ms ✓ Glob 1782.1 ms ✓ Crayons 1707.6 ms ✓ InlineStrings 1003.4 ms ✓ ManualMemory 857.7 ms ✓ Reexport 1095.0 ms ✓ Statistics 900.9 ms ✓ DataAPI 868.7 ms ✓ SciMLPublic 2052.7 ms ✓ IrrationalConstants 829.4 ms ✓ UnPack 839.5 ms ✓ CommonWorldInvalidations 788.9 ms ✓ DataValueInterfaces 879.6 ms ✓ StatsAPI 1185.9 ms ✓ Requires 1324.0 ms ✓ OrderedCollections 885.5 ms ✓ InvertedIndices 1521.5 ms ✓ DocStringExtensions 1276.0 ms ✓ WorkerUtilities 1214.4 ms ✓ Suppressor 1641.0 ms ✓ OffsetArrays 1042.8 ms ✓ BufferedStreams 795.5 ms ✓ IfElse 831.1 ms ✓ PtrArrays 810.0 ms ✓ SIMDTypes 810.1 ms ✓ IteratorInterfaceExtensions 896.9 ms ✓ LaTeXStrings 1290.4 ms ✓ SuiteSparse ┌ Warning: DEPRECATION NOTICE │ │ Formatting.jl has been unmaintained for a while, with some serious │ correctness bugs compromising the original purpose of the package. As a result, │ it has been deprecated - consider using an alternative, such as │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ If you are not using Formatting.jl as a direct dependency, please consider │ opening an issue on any packages you are using that do use it as a dependency. │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ package originally brings it in as a dependency. └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 1397.2 ms ✓ Formatting 1001.2 ms ✓ NaNMath 986.0 ms ✓ DelimitedFiles 1830.2 ms ✓ ProgressMeter 2578.7 ms ✓ SentinelArrays 1878.3 ms ✓ CpuId 1197.9 ms ✓ Compat 1135.9 ms ✓ Preferences 2266.3 ms ✓ TranscodingStreams 1698.6 ms ✓ ThreadingUtilities 1331.2 ms ✓ Statistics → SparseArraysExt 955.2 ms ✓ Missings 1020.7 ms ✓ PooledArrays 1450.6 ms ✓ Distances 956.2 ms ✓ Adapt 3644.9 ms ✓ DataStructures 1454.5 ms ✓ LogExpFunctions 977.1 ms ✓ AliasTables 785.9 ms ✓ TableTraits 864.3 ms ✓ Compat → CompatLinearAlgebraExt 1223.6 ms ✓ JLLWrappers 967.4 ms ✓ PrecompileTools 1641.7 ms ✓ BioGenerics 2418.4 ms ✓ CodecZstd 1639.0 ms ✓ CodecZlib 1313.1 ms ✓ Distances → DistancesSparseArraysExt 1686.4 ms ✓ ArrayInterface 850.8 ms ✓ OffsetArrays → OffsetArraysAdaptExt 1088.8 ms ✓ SortingAlgorithms 1750.3 ms ✓ Tables 2129.9 ms ✓ FilePathsBase 1445.8 ms ✓ Bzip2_jll 1503.0 ms ✓ XZ_jll 1540.8 ms ✓ OpenSpecFun_jll 3054.7 ms ✓ StringManipulation 16387.3 ms ✓ SIMD 16394.0 ms ✓ Parsers 5189.1 ms ✓ Static 1616.5 ms ✓ BGZFStreams 4276.3 ms ✓ StatsBase 2591.6 ms ✓ FilePathsBase → FilePathsBaseTestExt 965.4 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1673.8 ms ✓ CodecBzip2 1639.6 ms ✓ CodecXz 4846.8 ms ✓ SpecialFunctions 39099.7 ms ✓ PrettyTables 22355.0 ms ✓ Automa 978.5 ms ✓ InlineStrings → ParsersExt 942.7 ms ✓ BitTwiddlingConvenienceFunctions 2257.9 ms ✓ CPUSummary 11962.0 ms ✓ StaticArrayInterface 1270.5 ms ✓ DiffRules 81855.2 ms ✓ DataFrames [ Info: Compiling VCF parser... 18068.1 ms ✓ VariantCallFormat 2672.3 ms ✓ WeakRefStrings 1552.5 ms ✓ HostCPUFeatures 1736.3 ms ✓ PolyesterWeave 1814.3 ms ✓ StaticArrayInterface → StaticArrayInterfaceOffsetArraysExt 1641.0 ms ✓ CloseOpenIntervals 1856.7 ms ✓ LayoutPointers ERROR: LoadError: UndefVarError: `_shrink` not defined in `Base` Suggestion: check for spelling errors or missing imports. Stacktrace:  [1] getproperty  @ ./Base_compiler.jl:50 [inlined]  [2] _precompile_()  @ Tullio._Precompile_Base ~/.julia/packages/Tullio/2zyFP/src/precompile/precompile_Base.jl:77  [3] top-level scope  @ ~/.julia/packages/Tullio/2zyFP/src/precompile.jl:14  [4] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [5] top-level scope  @ ~/.julia/packages/Tullio/2zyFP/src/Tullio.jl:27  [6] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [7] 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:3148  [8] top-level scope  @ stdin:5  [9] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [11] include_string  @ ./loading.jl:3004 [inlined]  [12] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [13] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Tullio/2zyFP/src/precompile.jl:13 in expression starting at /home/pkgeval/.julia/packages/Tullio/2zyFP/src/Tullio.jl:1 in expression starting at stdin:5 2 dependencies had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ ┌ Formatting │ ┌ Warning: DEPRECATION NOTICE │ │ │ │ Formatting.jl has been unmaintained for a while, with some serious │ │ correctness bugs compromising the original purpose of the package. As a result, │ │ it has been deprecated - consider using an alternative, such as │ │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ │ │ If you are not using Formatting.jl as a direct dependency, please consider │ │ opening an issue on any packages you are using that do use it as a dependency. │ │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ │ package originally brings it in as a dependency. │ └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 └ Precompilation completed after 344.71s ################################################################################ # Loading # Loading OpenADMIXTURE... ERROR: LoadError: UndefVarError: `_shrink` not defined in `Base` Suggestion: check for spelling errors or missing imports. Stacktrace:  [1] getproperty  @ ./Base_compiler.jl:50 [inlined]  [2] _precompile_()  @ Tullio._Precompile_Base ~/.julia/packages/Tullio/2zyFP/src/precompile/precompile_Base.jl:77  [3] top-level scope  @ ~/.julia/packages/Tullio/2zyFP/src/precompile.jl:14  [4] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [5] top-level scope  @ ~/.julia/packages/Tullio/2zyFP/src/Tullio.jl:27  [6] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [7] 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:3148  [8] top-level scope  @ stdin:5  [9] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2994  [11] include_string  @ ./loading.jl:3004 [inlined]  [12] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [13] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/Tullio/2zyFP/src/precompile.jl:13 in expression starting at /home/pkgeval/.julia/packages/Tullio/2zyFP/src/Tullio.jl:1 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:3148  [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:2994  [7] include_string  @ ./loading.jl:3004 [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_X8o3dj" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/OpenADMIXTURE/SRfRR/src/OpenADMIXTURE.jl:1 Loading failed after 117.54s 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 OpenADMIXTURE'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:611 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:526 [3] run(::Cmd) @ Base ./process.jl:523 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:309 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [7] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 546.98s: package fails to precompile