Package evaluation to test TwoBit on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T16:50:55.152


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

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

Set-up completed after 15.14s


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

Installing TwoBit...
   Resolving package versions...
   Installed Twiddle ──────────── v1.1.2
   Installed BioSymbols ───────── v5.2.0
   Installed BioSequences ─────── v3.5.1
   Installed BioGenerics ──────── v0.1.5
   Installed TranscodingStreams ─ v0.11.3
   Installed Preferences ──────── v1.5.2
   Installed TwoBit ───────────── v0.2.0
   Installed PrecompileTools ──── v1.3.4
    Updating `~/.julia/environments/v1.14/Project.toml`
  [75842c30] + TwoBit v0.2.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.1
  [3c28c6f8] + BioSymbols v5.2.0
  [aea7be01] + PrecompileTools v1.3.4
  [21216c6a] + Preferences v1.5.2
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [75842c30] + TwoBit v0.2.0
  [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 4.85s


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

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

Precompiling package dependencies...
Precompiling project...
   0.9 s  ✓ Twiddle
   1.3 s  ✓ ANSIColoredPrinters
   1.6 s  ✓ DocStringExtensions
   1.1 s  ✓ IOCapture
  58.3 s  ✓ TranscodingStreams
  32.7 s  ✓ FormatSpecimens
  33.5 s  ✓ Preferences
  40.8 s  ✓ BioGenerics
  33.4 s  ✓ PrecompileTools
 122.7 s  ✓ BioSymbols
  69.7 s  ✓ Parsers
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
  38.3 s  ✓ JSON
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(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/TwoBit/ETT9V/src/TwoBit.jl:4
 [12] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [13] 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
 [14] top-level scope
    @ stdin:5
 [15] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [17] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [18] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [19] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/TwoBit/ETT9V/src/TwoBit.jl:1
in expression starting at stdin:5
              ✗ TwoBit
 117.0 s  ✓ Documenter
  13 dependencies successfully precompiled in 635 seconds. 22 already precompiled.

Precompilation completed after 683.51s


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

     Testing TwoBit
      Status `/tmp/jl_GOnZdQ/Project.toml`
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
⌅ [e30172f5] Documenter v0.27.25
  [3372ea36] FormatSpecimens v1.4.0
  [75842c30] TwoBit v0.2.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_GOnZdQ/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
  [3c28c6f8] BioSymbols v5.2.0
  [ffbed154] DocStringExtensions v0.9.5
⌅ [e30172f5] Documenter v0.27.25
  [3372ea36] FormatSpecimens v1.4.0
⌅ [b5f81e59] IOCapture v0.2.5
⌅ [682c06a0] JSON v0.21.4
  [69de0a69] Parsers v2.8.6
  [aea7be01] PrecompileTools v1.3.4
  [21216c6a] Preferences v1.5.2
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [75842c30] TwoBit v0.2.0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [7b1f6079] FileWatching v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [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
  [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 v1.5.5+2
  [e37daf67] LibGit2_jll v1.9.4+0
  [29816b5a] LibSSH2_jll v1.11.101+0
  [458c3c95] OpenSSL_jll v3.5.7+0
  [efcefdf7] PCRE2_jll v10.47.0+0
  [83775a58] Zlib_jll v1.3.2+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
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(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base module.jl:111
 [10] eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base.JuliaLowering /source/usr/share/julia/JuliaLowering/src/runtime.jl:118
 [11] top-level scope
    @ ~/.julia/packages/TwoBit/ETT9V/src/TwoBit.jl:4
 [12] include(mod::Module, _path::String)
    @ Base Base.jl:325
 [13] 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
 [14] top-level scope
    @ stdin:5
 [15] eval(m::Module, e::Any)
    @ Core boot.jl:522
 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base loading.jl:3132
 [17] include_string(m::Module, txt::String, fname::String)
    @ Base loading.jl:3142 [inlined]
 [18] exec_options(opts::Base.JLOptions)
    @ Base client.jl:353
 [19] _start()
    @ Base client.jl:596
in expression starting at /home/pkgeval/.julia/packages/TwoBit/ETT9V/src/TwoBit.jl:1
in expression starting at stdin:5
  2 dependencies had output during precompilation:
┌ 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/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
└  
┌ TwoBit
│  [Output was shown above]
└  
ERROR: LoadError: The following 2 packages failed to precompile:

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

TwoBit 
Failed to precompile TwoBit [75842c30-9b2d-11e9-3f58-f17fe2b89951] to "/home/pkgeval/.julia/compiled/v1.14/TwoBit/jl_xdP4yA" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/TwoBit/ETT9V/test/runtests.jl:2

Testing failed after 211.86s

ERROR: LoadError: Package TwoBit 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 942.47s: package fails to precompile