Package evaluation of SparseKmeansFeatureRanking on Julia 1.13.0-DEV.791 (d5209bd37d*) started at 2025-07-04T16:45:13.508 ################################################################################ # Set-up # Set-up completed after 0.2s ################################################################################ # Installation # Installing SparseKmeansFeatureRanking... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [a6138be3] + SparseKmeansFeatureRanking v0.1.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.19.0 ⌅ [67c07d97] + Automa v0.8.4 [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 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.17.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [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 [c27321d9] + Glob v1.3.1 [3e5b6fbb] + HostCPUFeatures v0.1.17 [615f187c] + IfElse v0.1.1 [842dd82b] + InlineStrings v1.4.4 [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 v0.12.172 [d125e4d3] + ManualMemory v0.1.8 [e1d29d7a] + Missings v1.2.0 [77ba4419] + NaNMath v1.1.3 [6fe1bfb0] + OffsetArrays v1.17.0 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [1d0040c9] + PolyesterWeave v0.2.2 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [91c51154] + SentinelArrays v1.4.8 [4e780e97] + SnpArrays v0.3.22 [a2af1166] + SortingAlgorithms v1.2.1 [a6138be3] + SparseKmeansFeatureRanking v0.1.2 [276daf66] + SpecialFunctions v2.5.1 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [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 [bc48ee85] + Tullio v0.3.8 [3a884ed6] + UnPack v1.0.2 [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 [ffd25f8a] + XZ_jll v5.8.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates 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 v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+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 v5.13.1+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 6.32s ################################################################################ # 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... ✗ SnpArrays ✗ SparseKmeansFeatureRanking 0 dependencies successfully precompiled in 76 seconds. 109 already precompiled. ERROR: LoadError: The following 1 direct dependency failed to precompile: SparseKmeansFeatureRanking Failed to precompile SparseKmeansFeatureRanking [a6138be3-5d3e-4f3e-9009-7e37efc59f36] to "/home/pkgeval/.julia/compiled/v1.13/SparseKmeansFeatureRanking/jl_rzV2pZ" (ProcessExited(1)). 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::String) @ Base ./loading.jl:3000 [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:2846 [7] include_string @ ./loading.jl:2856 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:322 [9] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.13/SnpArrays/jl_KWHskb" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3287 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2652 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [7] #invokelatest_gr#232 @ ./reflection.jl:1282 [inlined] [8] invokelatest_gr @ ./reflection.jl:1274 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3858 [10] maybe_cachefile_lock @ ./loading.jl:3855 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2638 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2466 [13] macro expansion @ ./loading.jl:2394 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2359 [16] require @ ./loading.jl:2335 [inlined] [17] eval_import_path @ ./module.jl:36 [inlined] [18] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [19] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [20] top-level scope @ ~/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:5 [21] include(mod::Module, _path::String) @ Base ./Base.jl:309 [22] 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:3000 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2846 [26] include_string @ ./loading.jl:2856 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:322 [28] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:1 in expression starting at stdin: in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 86.7s ################################################################################ # Loading # Loading SparseKmeansFeatureRanking... Precompiling packages... ✗ SnpArrays Info Given SparseKmeansFeatureRanking was explicitly requested, output will be shown live  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::String)  @ Base ./loading.jl:3000  [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:2846  [7] include_string  @ ./loading.jl:2856 [inlined]  [8] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:322  [9] _start()  @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.13/SnpArrays/jl_JA0Szj" (ProcessExited(1)). Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)  @ Base ./loading.jl:3287  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()  @ Base ./loading.jl:2652  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94  [5] #mkpidlock#7  @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined]  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115  [7] #invokelatest_gr#232  @ ./reflection.jl:1282 [inlined]  [8] invokelatest_gr  @ ./reflection.jl:1274 [inlined]  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)  @ Base ./loading.jl:3858  [10] maybe_cachefile_lock  @ ./loading.jl:3855 [inlined]  [11] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2638  [12] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2466  [13] macro expansion  @ ./loading.jl:2394 [inlined]  [14] macro expansion  @ ./lock.jl:376 [inlined]  [15] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2359  [16] require  @ ./loading.jl:2335 [inlined]  [17] eval_import_path  @ ./module.jl:36 [inlined]  [18] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base ./module.jl:60  [19] _eval_using(to::Module, path::Expr)  @ Base ./module.jl:137  [20] top-level scope  @ ~/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:5  [21] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [22] 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:3000  [23] top-level scope  @ stdin:5  [24] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2846  [26] include_string  @ ./loading.jl:2856 [inlined]  [27] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:322  [28] _start()  @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:1 in expression starting at stdin:5 ✗ SparseKmeansFeatureRanking 0 dependencies successfully precompiled in 69 seconds. 109 already precompiled. ERROR: The following 1 direct dependency failed to precompile: SparseKmeansFeatureRanking Failed to precompile SparseKmeansFeatureRanking [a6138be3-5d3e-4f3e-9009-7e37efc59f36] to "/home/pkgeval/.julia/compiled/v1.13/SparseKmeansFeatureRanking/jl_aGd6Lp" (ProcessExited(1)). 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::String) @ Base ./loading.jl:3000 [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:2846 [7] include_string @ ./loading.jl:2856 [inlined] [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:322 [9] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SnpArrays/CSYLc/src/SnpArrays.jl:3 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile SnpArrays [4e780e97-f5bf-4111-9dc4-b70aaf691b06] to "/home/pkgeval/.julia/compiled/v1.13/SnpArrays/jl_JA0Szj" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3287 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2652 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [7] #invokelatest_gr#232 @ ./reflection.jl:1282 [inlined] [8] invokelatest_gr @ ./reflection.jl:1274 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3858 [10] maybe_cachefile_lock @ ./loading.jl:3855 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2638 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2466 [13] macro expansion @ ./loading.jl:2394 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2359 [16] require @ ./loading.jl:2335 [inlined] [17] eval_import_path @ ./module.jl:36 [inlined] [18] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [19] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [20] top-level scope @ ~/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:5 [21] include(mod::Module, _path::String) @ Base ./Base.jl:309 [22] 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:3000 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2846 [26] include_string @ ./loading.jl:2856 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:322 [28] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/SparseKmeansFeatureRanking/xOMjS/src/SparseKmeansFeatureRanking.jl:1 in expression starting at stdin: Loading failed after 70.67s 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 SparseKmeansFeatureRanking'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:602 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:517 [3] run(::Cmd) @ Base ./process.jl:514 [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:324 [7] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 203.46s: package fails to precompile