Package evaluation to test BioSequences on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T16:11:26.119


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 15.47s


################################################################################
# Installation
#

Installing BioSequences...
   Resolving package versions...
   Installed BioSymbols ────── v5.2.0
   Installed Twiddle ───────── v1.1.2
   Installed BioSequences ──── v3.5.1
   Installed Preferences ───── v1.5.2
   Installed PrecompileTools ─ v1.3.4
    Updating `~/.julia/environments/v1.14/Project.toml`
  [7e6ae17a] + BioSequences v3.5.1
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [7e6ae17a] + BioSequences v3.5.1
  [3c28c6f8] + BioSymbols v5.2.0
  [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

Installation completed after 4.6s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...
Precompiling project...
   9.0 s  ✓ TestEnv
  1 dependency successfully precompiled in 9 seconds. 27 already precompiled.

Precompiling package dependencies...
Precompiling project...
   0.8 s  ✓ StatsAPI
   0.7 s  ✓ Twiddle
   1.5 s  ✓ DocStringExtensions
 153.3 s  ✓ OrderedCollections
   1.1 s  ✓ DataAPI
   1.4 s  ✓ Statistics
  37.7 s  ✓ PtrArrays
   2.6 s  ✓ IrrationalConstants
   1.8 s  ✓ StableRNGs
  32.1 s  ✓ Preferences
 174.6 s  ✓ DataStructures
  57.4 s  ✓ Missings
  43.1 s  ✓ Statistics → SparseArraysExt
  38.4 s  ✓ AliasTables
   1.8 s  ✓ LogExpFunctions
  32.3 s  ✓ JLLWrappers
  31.7 s  ✓ PrecompileTools
  40.9 s  ✓ SortingAlgorithms
  32.5 s  ✓ Libiconv_jll
 120.9 s  ✓ BioSymbols
ERROR: LoadError: Creating a new global in closed module `IrrationalConstants` (`#kw_body#_#48`) breaks incremental compilation because the side effects will not be permanent.
Stacktrace:
  [1] top-level scope
    @ ~/.julia/packages/StatsBase/2Znv8/src/scalarstats.jl:527
  [2] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
  [3] top-level scope
    @ ~/.julia/packages/StatsBase/2Znv8/src/StatsBase.jl:251
  [4] include(mod::Module, _path::String)
    @ Base Base.jl:325
  [5] 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
  [6] top-level scope
    @ stdin:5
  [7] eval(m::Module, e::Any)
    @ Core boot.jl:522
  [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
  [9] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [10] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [11] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/StatsBase/2Znv8/src/scalarstats.jl:527
in expression starting at /home/pkgeval/.julia/packages/StatsBase/2Znv8/src/StatsBase.jl:1
in expression starting at stdin:5
              ✗ StatsBase
  77.6 s  ✓ StringEncodings
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/31amM/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/31amM/src/counting.jl:129
  [7] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
  [8] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225
  [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/31amM/src/counting.jl:129
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8
in expression starting at stdin:5
              ✗ BioSequences
  96.4 s  ✓ YAML
  22 dependencies successfully precompiled in 1179 seconds. 14 already precompiled.

Precompilation completed after 1231.4s


################################################################################
# Testing
#

     Testing BioSequences
      Status `/tmp/jl_qD1Baj/Project.toml`
  [7e6ae17a] BioSequences v3.5.1
  [3c28c6f8] BioSymbols v5.2.0
  [aea7be01] PrecompileTools v1.3.4
  [860ef19b] StableRNGs v1.0.4
  [2913bbd2] StatsBase v0.34.12
  [7200193e] Twiddle v1.1.2
  [ddb6d928] YAML v0.4.16
  [37e2e46d] LinearAlgebra v1.14.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_qD1Baj/Manifest.toml`
  [66dad0bd] AliasTables v1.1.3
  [7e6ae17a] BioSequences v3.5.1
  [3c28c6f8] BioSymbols v5.2.0
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.5
  [ffbed154] DocStringExtensions v0.9.5
  [92d709cd] IrrationalConstants v0.2.6
  [692b3bcd] JLLWrappers v1.8.0
  [2ab3a3ac] LogExpFunctions v1.0.1
  [e1d29d7a] Missings v1.2.0
⌅ [bac558e1] OrderedCollections v1.8.2
  [aea7be01] PrecompileTools v1.3.4
  [21216c6a] Preferences v1.5.2
  [43287f4e] PtrArrays v1.4.0
  [a2af1166] SortingAlgorithms v1.2.3
  [860ef19b] StableRNGs v1.0.4
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.8.0
  [2913bbd2] StatsBase v0.34.12
  [69024149] StringEncodings v0.3.7
  [7200193e] Twiddle v1.1.2
  [ddb6d928] YAML v0.4.16
  [94ce4f54] Libiconv_jll v1.18.0+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates 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
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.13.0
  [9e88b42a] Serialization v1.11.0
  [2f01184e] SparseArrays v1.13.0
  [f489334b] StyledStrings v1.13.0
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.5.5+2
  [4536629a] OpenBLAS_jll v0.3.33+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [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...
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/31amM/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/31amM/src/counting.jl:129
  [7] include(mapexpr::Function, mod::Module, _path::String)
    @ Base Base.jl:326
  [8] top-level scope
    @ ~/.julia/packages/BioSequences/31amM/src/BioSequences.jl:225
  [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/31amM/src/counting.jl:129
in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/src/BioSequences.jl:8
in expression starting at stdin:5
  1 dependency had output during precompilation:
┌ BioSequences
│  [Output was shown above]
└  
ERROR: LoadError: The following 1 package failed to precompile:

BioSequences 
Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to "/home/pkgeval/.julia/compiled/v1.14/BioSequences/jl_QETQik" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/BioSequences/31amM/test/runtests.jl:1

Testing failed after 347.92s

ERROR: LoadError: Package BioSequences 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:3247
  [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
  [8] include(mod::Module, _path::String)
    @ Base Base.jl:325
  [9] exec_options(opts::Base.JLOptions)
    @ Base client.jl:355
 [10] _start()
    @ Base client.jl:596
in expression starting at /PkgEval.jl/scripts/evaluate.jl:214

PkgEval failed after 1627.05s: package fails to precompile