Package evaluation to load Kmers on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T16:11:08.822 ################################################################################ # Set-up # Set-up completed after 0.16s ################################################################################ # Installation # Installing Kmers... Resolving package versions... Installed BioSymbols ────── v5.2.0 Installed Twiddle ───────── v1.1.2 Installed Kmers ─────────── v1.2.0 Installed Preferences ───── v1.5.2 Installed PrecompileTools ─ v1.3.4 Installed BioSequences ──── v3.4.2 Updating `~/.julia/environments/v1.14/Project.toml` [445028e4] + Kmers v1.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` ⌅ [7e6ae17a] + BioSequences v3.4.2 [3c28c6f8] + BioSymbols v5.2.0 [445028e4] + Kmers v1.2.0 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [7200193e] + Twiddle v1.1.2 [ade2ca70] + Dates v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 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 To see why use `status --outdated -m` Installation completed after 8.67s ################################################################################ # Precompilation # Precompiling PkgEval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 project... 0.8 s ✓ Twiddle 30.7 s ✓ Preferences 31.3 s ✓ PrecompileTools 118.5 s ✓ BioSymbols ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent. Stacktrace:  [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96  [2] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129  [3] eval(m::Module, e::Any)  @ Core boot.jl:522  [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745  [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]  [6] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129  [7] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:326  [8] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:224  [9] include(mod::Module, _path::String)  @ Base Base.jl:325  [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [11] top-level scope  @ stdin:5  [12] eval(m::Module, e::Any)  @ Core boot.jl:522  [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [14] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [15] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [16] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/counting.jl:129 in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:8 in expression starting at stdin:5 ✗ BioSequences ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base loading.jl:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base module.jl:60  [10] _eval_using(to::Module, path::Expr, flags::UInt8)  @ Base module.jl:137 [inlined]  [11] eval_using(to::Module, path::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:130  [12] top-level scope  @ ~/.julia/packages/Kmers/SM8Rg/src/Kmers.jl:97  [13] include(mod::Module, _path::String)  @ Base Base.jl:325  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:522  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [20] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Kmers/SM8Rg/src/Kmers.jl:8 in expression starting at stdin:5 ✗ Kmers ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base loading.jl:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base module.jl:60  [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base module.jl:101  [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118  [12] top-level scope  @ ~/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:5  [13] include(mod::Module, _path::String)  @ Base Base.jl:325  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:522  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [20] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:1 in expression starting at stdin:5 ✗ Kmers → RandomExt 4 dependencies successfully precompiled in 249 seconds. 4 already precompiled. Precompilation completed after 278.58s ################################################################################ # Loading # Loading Kmers... ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent. Stacktrace:  [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96  [2] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129  [3] eval(m::Module, e::Any)  @ Core boot.jl:522  [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745  [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined]  [6] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129  [7] include(mapexpr::Function, mod::Module, _path::String)  @ Base Base.jl:326  [8] top-level scope  @ ~/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:224  [9] include(mod::Module, _path::String)  @ Base Base.jl:325  [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [11] top-level scope  @ stdin:5  [12] eval(m::Module, e::Any)  @ Core boot.jl:522  [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [14] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [15] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [16] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/counting.jl:129 in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:8 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base loading.jl:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base module.jl:60  [10] _eval_using(to::Module, path::Expr, flags::UInt8)  @ Base module.jl:137 [inlined]  [11] eval_using(to::Module, path::Expr)  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:130  [12] top-level scope  @ ~/.julia/packages/Kmers/SM8Rg/src/Kmers.jl:97  [13] include(mod::Module, _path::String)  @ Base Base.jl:325  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:522  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [20] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Kmers/SM8Rg/src/Kmers.jl:8 in expression starting at stdin:5 ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace:  [1] error(s::String)  @ Base error.jl:56  [2] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base loading.jl:2837  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base loading.jl:2685  [4] macro expansion  @ loading.jl:2599 [inlined]  [5] macro expansion  @ lock.jl:376 [inlined]  [6] __require(into::Module, mod::Symbol)  @ Base loading.jl:2563  [7] require(into::Module, mod::Symbol)  @ Base loading.jl:2539 [inlined]  [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String)  @ Base module.jl:36 [inlined]  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)  @ Base module.jl:60  [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base module.jl:101  [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})  @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118  [12] top-level scope  @ ~/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:5  [13] include(mod::Module, _path::String)  @ Base Base.jl:325  [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303  [15] top-level scope  @ stdin:5  [16] eval(m::Module, e::Any)  @ Core boot.jl:522  [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base loading.jl:3132  [18] include_string(m::Module, txt::String, fname::String)  @ Base loading.jl:3142 [inlined]  [19] exec_options(opts::Base.JLOptions)  @ Base client.jl:353  [20] _start()  @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:1 in expression starting at stdin:5 3 dependencies had output during precompilation: ┌ Kmers │ [Output was shown above] └ ┌ Kmers → RandomExt │ ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("7e6ae17a-c86d-528c-b3b9-7f778a29fe59"), "BioSequences") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) │ Stacktrace: │ [1] error(s::String) │ @ Base error.jl:56 │ [2] __require_prelocked(pkg::Base.PkgId, env::String) │ @ Base loading.jl:2837 │ [3] _require_prelocked(uuidkey::Base.PkgId, env::String) │ @ Base loading.jl:2685 │ [4] macro expansion │ @ loading.jl:2599 [inlined] │ [5] macro expansion │ @ lock.jl:376 [inlined] │ [6] __require(into::Module, mod::Symbol) │ @ Base loading.jl:2563 │ [7] require(into::Module, mod::Symbol) │ @ Base loading.jl:2539 [inlined] │ [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) │ @ Base module.jl:36 [inlined] │ [9] eval_import_path_all(at::Module, path::Expr, keyword::String) │ @ Base module.jl:60 │ [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) │ @ Base module.jl:101 │ [11] eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118 │ [12] top-level scope │ @ ~/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:5 │ [13] include(mod::Module, _path::String) │ @ Base Base.jl:325 │ [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 │ [15] top-level scope │ @ stdin:5 │ [16] eval(m::Module, e::Any) │ @ Core boot.jl:522 │ [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base loading.jl:3132 │ [18] include_string(m::Module, txt::String, fname::String) │ @ Base loading.jl:3142 [inlined] │ [19] exec_options(opts::Base.JLOptions) │ @ Base client.jl:353 │ [20] _start() │ @ Base client.jl:596 │ in expression starting at /home/pkgeval/.julia/packages/Kmers/SM8Rg/ext/RandomExt.jl:1 │ in expression starting at stdin:5 └ ┌ BioSequences │ ERROR: LoadError: Creating a new global in closed module `Base` (`##->###0`) breaks incremental compilation because the side effects will not be permanent. │ Stacktrace: │ [1] eval_closure_type(mod::Module, closure_type_name::Symbol, field_names::Core.SimpleVector, field_is_box::Core.SimpleVector) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:96 │ [2] top-level scope │ @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129 │ [3] eval(m::Module, e::Any) │ @ Core boot.jl:522 │ [4] _eval(mod::Module, iter::Base.JuliaLowering.LoweringIterator{Dict{Symbol, Dict{Int64, Any}}}; soft_scope::Nothing) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:745 │ [5] eval(mod::Module, ex::Base.JuliaSyntax.SyntaxTree{Dict{Symbol, Dict{Int64, Any}}}; macro_world::UInt64, soft_scope::Nothing, opts::@Kwargs{expr_compat_mode::Bool}) │ @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/eval.jl:718 [inlined] │ [6] top-level scope │ @ ~/.julia/packages/BioSequences/tfveE/src/counting.jl:129 │ [7] include(mapexpr::Function, mod::Module, _path::String) │ @ Base Base.jl:326 │ [8] top-level scope │ @ ~/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:224 │ [9] include(mod::Module, _path::String) │ @ Base Base.jl:325 │ [10] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 │ [11] top-level scope │ @ stdin:5 │ [12] eval(m::Module, e::Any) │ @ Core boot.jl:522 │ [13] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) │ @ Base loading.jl:3132 │ [14] include_string(m::Module, txt::String, fname::String) │ @ Base loading.jl:3142 [inlined] │ [15] exec_options(opts::Base.JLOptions) │ @ Base client.jl:353 │ [16] _start() │ @ Base client.jl:596 │ in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/counting.jl:129 │ in expression starting at /home/pkgeval/.julia/packages/BioSequences/tfveE/src/BioSequences.jl:8 │ in expression starting at stdin:5 └ ERROR: The following 3 packages failed to precompile: Kmers Failed to precompile Kmers [445028e4-d31f-4f27-89ad-17affd83fc22] to "/home/pkgeval/.julia/compiled/v1.14/Kmers/jl_VXjjAw" (ProcessExited(1)). Kmers → RandomExt Failed to precompile RandomExt [6ae6c406-71c1-52f5-a304-e5a911d74ca6] to "/home/pkgeval/.julia/compiled/v1.14/RandomExt/jl_EJ3sVY" (ProcessExited(1)). BioSequences Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to "/home/pkgeval/.julia/compiled/v1.14/BioSequences/jl_pzLGCU" (ProcessExited(1)). Loading failed after 74.76s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --check-bounds=yes --pkgimages=existing -e 'using Kmers'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error(proc::Base.Process) @ Base process.jl:612 [inlined] [2] run(::Cmd; wait::Bool) @ Base process.jl:525 [3] run(::Cmd) @ Base process.jl:522 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:197 [5] include(mod::Module, _path::String) @ Base Base.jl:325 [6] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [7] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:188 PkgEval failed after 387.54s: package fails to precompile