Package evaluation to test BioAlignments on Julia 1.14.0-DEV.2593 (15c2b67521*) started at 2026-07-03T17:20:06.703


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

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

Set-up completed after 15.6s


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

Installing BioAlignments...
   Resolving package versions...
   Installed Twiddle ──────────── v1.1.2
   Installed BioGenerics ──────── v0.1.5
   Installed BioSymbols ───────── v5.2.0
   Installed BioSequences ─────── v3.5.1
   Installed BioAlignments ────── v3.1.0
   Installed TranscodingStreams ─ v0.11.3
   Installed Preferences ──────── v1.5.2
   Installed PrecompileTools ──── v1.3.4
   Installed IntervalTrees ────── v1.1.0
    Updating `~/.julia/environments/v1.14/Project.toml`
  [00701ae9] + BioAlignments v3.1.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [00701ae9] + BioAlignments v3.1.0
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.1
  [3c28c6f8] + BioSymbols v5.2.0
  [524e6230] + IntervalTrees v1.1.0
  [aea7be01] + PrecompileTools v1.3.4
  [21216c6a] + Preferences v1.5.2
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.14.0
  [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
  [e66e0078] + CompilerSupportLibraries_jll v1.5.5+2
  [4536629a] + OpenBLAS_jll v0.3.33+0
  [8e850b90] + libblastrampoline_jll v5.15.0+0

Installation completed after 4.86s


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

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

Precompiling package dependencies...
Precompiling project...
   1.5 s  ✓ ANSIColoredPrinters
   0.9 s  ✓ LazilyInitializedFields
   0.8 s  ✓ Twiddle
   1.5 s  ✓ DocStringExtensions
  74.1 s  ✓ AbstractTrees
  92.4 s  ✓ IntervalTrees
  56.8 s  ✓ TranscodingStreams
   1.1 s  ✓ IOCapture
  32.9 s  ✓ StructUtils
  31.8 s  ✓ Preferences
  36.5 s  ✓ RegistryInstances
  21.1 s  ✓ MarkdownAST
  37.5 s  ✓ BioGenerics
  16.9 s  ✓ CodecZlib
  28.0 s  ✓ JLLWrappers
  28.2 s  ✓ PrecompileTools
  27.9 s  ✓ Libiconv_jll
  29.0 s  ✓ Git_LFS_jll
  29.7 s  ✓ OpenSSH_jll
  31.6 s  ✓ Expat_jll
 118.9 s  ✓ BioSymbols
  66.9 s  ✓ Parsers
  30.9 s  ✓ Git_jll
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
 129.8 s  ✓ JSON
  30.4 s  ✓ Git
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/BioAlignments/I6ecx/src/BioAlignments.jl:86
 [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/BioAlignments/I6ecx/src/BioAlignments.jl:3
in expression starting at stdin:5
              ✗ BioAlignments
 213.0 s  ✓ Documenter
  26 dependencies successfully precompiled in 1253 seconds. 32 already precompiled.

Precompilation completed after 1306.43s


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

     Testing BioAlignments
      Status `/tmp/jl_xH0Sfv/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
  [3c28c6f8] BioSymbols v5.2.0
  [e30172f5] Documenter v1.17.0
  [524e6230] IntervalTrees v1.1.0
  [37e2e46d] LinearAlgebra v1.14.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_xH0Sfv/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [1520ce14] AbstractTrees v0.4.5
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.1
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [ffbed154] DocStringExtensions v0.9.5
  [e30172f5] Documenter v1.17.0
  [d7ba0133] Git v1.5.0
  [b5f81e59] IOCapture v1.0.0
  [524e6230] IntervalTrees v1.1.0
  [692b3bcd] JLLWrappers v1.8.0
  [682c06a0] JSON v1.6.1
  [0e77f7df] LazilyInitializedFields v1.3.0
  [d0879d2d] MarkdownAST v0.1.3
  [69de0a69] Parsers v2.8.6
  [aea7be01] PrecompileTools v1.3.4
  [21216c6a] Preferences v1.5.2
  [2792f1a3] RegistryInstances v0.1.0
  [ec057cc2] StructUtils v2.8.2
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [2e619515] Expat_jll v2.8.1+0
  [020c3dae] Git_LFS_jll v3.7.1+0
  [f8c6e375] Git_jll v2.54.0+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [9bd350c2] OpenSSH_jll v10.3.1+0
  [0dad84c5] ArgTools v1.2.0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [f43a241f] Downloads v1.7.0
  [7b1f6079] FileWatching v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0
  [b27032c2] LibCURL v1.0.0
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.14.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.14.0
  [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
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.5.5+2
  [deac9b47] LibCURL_jll v8.21.0+0
  [e37daf67] LibGit2_jll v1.9.4+0
  [29816b5a] LibSSH2_jll v1.11.101+0
  [14a3606d] MozillaCACerts_jll v2026.5.14
  [4536629a] OpenBLAS_jll v0.3.33+0
  [458c3c95] OpenSSL_jll v3.5.7+0
  [efcefdf7] PCRE2_jll v10.47.0+0
  [83775a58] Zlib_jll v1.3.2+0
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.15.0+0
  [8e850ede] nghttp2_jll v1.69.0+0
  [3f19e933] p7zip_jll v17.8.0+0
     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/BioAlignments/I6ecx/src/BioAlignments.jl:86
 [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/BioAlignments/I6ecx/src/BioAlignments.jl:3
in expression starting at stdin:5
  2 dependencies had output during precompilation:
┌ BioAlignments
│  [Output was shown above]
└  
┌ 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
└  
ERROR: LoadError: The following 2 packages failed to precompile:

BioAlignments 
Failed to precompile BioAlignments [00701ae9-d1dc-5365-b64a-a3a3ebf5695e] to "/home/pkgeval/.julia/compiled/v1.14/BioAlignments/jl_6l20sc" (ProcessExited(1)).

BioSequences 
Failed to precompile BioSequences [7e6ae17a-c86d-528c-b3b9-7f778a29fe59] to "/home/pkgeval/.julia/compiled/v1.14/BioSequences/jl_IcM7dZ" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/BioAlignments/I6ecx/test/runtests.jl:4

Testing failed after 366.12s

ERROR: LoadError: Package BioAlignments 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 1721.47s: package fails to precompile