Package evaluation to test AssignTaxonomy on Julia 1.14.0-DEV.14 (ec5cf08762*) started at 2025-11-02T16:54:35.811


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 10.94s


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

Installing AssignTaxonomy...
   Resolving package versions...
   Installed CommonWorldInvalidations ───────── v1.0.0
   Installed StringViews ────────────────────── v1.3.5
   Installed Adapt ──────────────────────────── v4.4.0
   Installed ManualMemory ───────────────────── v0.1.8
   Installed ArrayInterface ─────────────────── v7.22.0
   Installed BitTwiddlingConvenienceFunctions ─ v0.1.6
   Installed SIMDTypes ──────────────────────── v0.1.0
   Installed TranscodingStreams ─────────────── v0.11.3
   Installed IteratorInterfaceExtensions ────── v1.0.0
   Installed SIMD ───────────────────────────── v3.7.2
   Installed Compat ─────────────────────────── v4.18.1
   Installed DataAPI ────────────────────────── v1.16.0
   Installed OrderedCollections ─────────────── v1.8.1
   Installed StrideArraysCore ───────────────── v0.5.8
   Installed PrecompileTools ────────────────── v1.3.3
   Installed DataValueInterfaces ────────────── v1.0.0
   Installed CpuId ──────────────────────────── v0.3.1
   Installed LayoutPointers ─────────────────── v0.1.17
   Installed Kmers ──────────────────────────── v1.2.0
   Installed StaticArrayInterface ───────────── v1.8.0
   Installed Twiddle ────────────────────────── v1.1.2
   Installed BioSymbols ─────────────────────── v5.2.0
   Installed StringManipulation ─────────────── v0.4.1
   Installed CPUSummary ─────────────────────── v0.2.7
   Installed SciMLPublic ────────────────────── v1.0.0
   Installed Requires ───────────────────────── v1.3.1
   Installed IfElse ─────────────────────────── v0.1.1
   Installed BioGenerics ────────────────────── v0.1.5
   Installed CloseOpenIntervals ─────────────── v0.1.13
   Installed Tables ─────────────────────────── v1.12.1
   Installed Polyester ──────────────────────── v0.7.18
   Installed PrettyTables ───────────────────── v2.4.0
   Installed FASTX ──────────────────────────── v2.1.7
   Installed Reexport ───────────────────────── v1.2.2
   Installed Preferences ────────────────────── v1.5.0
   Installed Static ─────────────────────────── v1.3.1
   Installed TableTraits ────────────────────── v1.0.1
   Installed LaTeXStrings ───────────────────── v1.4.0
   Installed Crayons ────────────────────────── v4.1.1
   Installed ThreadingUtilities ─────────────── v0.5.5
   Installed Automa ─────────────────────────── v1.1.0
   Installed PolyesterWeave ─────────────────── v0.2.2
   Installed AssignTaxonomy ─────────────────── v0.1.2
   Installed BioSequences ───────────────────── v3.4.2
    Updating `~/.julia/environments/v1.14/Project.toml`
  [941572e2] + AssignTaxonomy v0.1.2
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [79e6a3ab] + Adapt v4.4.0
  [4fba245c] + ArrayInterface v7.22.0
  [941572e2] + AssignTaxonomy v0.1.2
  [67c07d97] + Automa v1.1.0
  [47718e42] + BioGenerics v0.1.5
⌅ [7e6ae17a] + BioSequences v3.4.2
  [3c28c6f8] + BioSymbols v5.2.0
  [62783981] + BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] + CPUSummary v0.2.7
  [fb6a15b2] + CloseOpenIntervals v0.1.13
  [f70d9fcc] + CommonWorldInvalidations v1.0.0
  [34da2185] + Compat v4.18.1
  [adafc99b] + CpuId v0.3.1
  [a8cc5b0e] + Crayons v4.1.1
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [c2308a5c] + FASTX v2.1.7
  [615f187c] + IfElse v0.1.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [445028e4] + Kmers v1.2.0
  [b964fa9f] + LaTeXStrings v1.4.0
  [10f19ff3] + LayoutPointers v0.1.17
  [d125e4d3] + ManualMemory v0.1.8
  [bac558e1] + OrderedCollections v1.8.1
  [f517fe37] + Polyester v0.7.18
  [1d0040c9] + PolyesterWeave v0.2.2
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
⌅ [08abe8d2] + PrettyTables v2.4.0
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [fdea26ae] + SIMD v3.7.2
  [94e857df] + SIMDTypes v0.1.0
  [431bcebd] + SciMLPublic v1.0.0
  [aedffcd0] + Static v1.3.1
  [0d7ed370] + StaticArrayInterface v1.8.0
  [7792a7ef] + StrideArraysCore v0.5.8
  [892a3eda] + StringManipulation v0.4.1
  [354b36f9] + StringViews v1.3.5
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [8290d209] + ThreadingUtilities v0.5.5
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.0.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [8e850b90] + libblastrampoline_jll v5.15.0+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 5.86s


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

Precompiling PkgEval dependencies...
Precompiling packages...
   4950.4 ms  ✓ TestEnv
  1 dependency successfully precompiled in 5 seconds. 27 already precompiled.
  1 dependency had output during precompilation:
┌ TestEnv
│  WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv.
└  

┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled
│   exception =
│    UndefVarError: `project_rel_path` not defined in `TestEnv`
│    Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value.
│    Stacktrace:
│     [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75
│     [2] test_dir_has_project_file
│       @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined]
│     [3] maybe_gen_project_override!
│       @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined]
│     [4] activate(pkg::String; allow_reresolve::Bool)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12
│     [5] activate(pkg::String)
│       @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9
│     [6] top-level scope
│       @ /PkgEval.jl/scripts/precompile.jl:24
│     [7] include(mod::Module, _path::String)
│       @ Base ./Base.jl:309
│     [8] exec_options(opts::Base.JLOptions)
│       @ Base ./client.jl:344
│     [9] _start()
│       @ Base ./client.jl:577
└ @ Main /PkgEval.jl/scripts/precompile.jl:26
Precompiling package dependencies...
Precompiling packages...
    978.2 ms  ✓ ManualMemory
    801.8 ms  ✓ Reexport
    876.3 ms  ✓ DataAPI
    898.6 ms  ✓ SciMLPublic
    790.8 ms  ✓ CommonWorldInvalidations
    796.0 ms  ✓ DataValueInterfaces
   1211.6 ms  ✓ Requires
   1673.6 ms  ✓ OrderedCollections
   1165.3 ms  ✓ Twiddle
   1592.9 ms  ✓ StringViews
   1042.2 ms  ✓ IfElse
    757.9 ms  ✓ SIMDTypes
   1296.3 ms  ✓ TranscodingStreams
    763.1 ms  ✓ IteratorInterfaceExtensions
    867.6 ms  ✓ LaTeXStrings
   1943.1 ms  ✓ Crayons
   1936.1 ms  ✓ CpuId
   1228.7 ms  ✓ Compat
   1155.1 ms  ✓ Preferences
   1802.5 ms  ✓ ThreadingUtilities
    934.5 ms  ✓ Adapt
    936.4 ms  ✓ BioGenerics
    761.4 ms  ✓ TableTraits
   1321.2 ms  ✓ Compat → CompatLinearAlgebraExt
   1299.2 ms  ✓ PrecompileTools
   1331.8 ms  ✓ ArrayInterface
   1912.9 ms  ✓ Tables
   2604.5 ms  ✓ BioSymbols
   3127.4 ms  ✓ StringManipulation


Precompilation completed after 69.91s


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

     Testing AssignTaxonomy
      Status `/tmp/jl_5RqoOG/Project.toml`
  [941572e2] AssignTaxonomy v0.1.2
⌅ [7e6ae17a] BioSequences v3.4.2
  [c2308a5c] FASTX v2.1.7
  [445028e4] Kmers v1.2.0
  [f517fe37] Polyester v0.7.18
⌅ [08abe8d2] PrettyTables v2.4.0
  [bd369af6] Tables v1.12.1
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_5RqoOG/Manifest.toml`
  [79e6a3ab] Adapt v4.4.0
  [4fba245c] ArrayInterface v7.22.0
  [941572e2] AssignTaxonomy v0.1.2
  [67c07d97] Automa v1.1.0
  [47718e42] BioGenerics v0.1.5
⌅ [7e6ae17a] BioSequences v3.4.2
  [3c28c6f8] BioSymbols v5.2.0
  [62783981] BitTwiddlingConvenienceFunctions v0.1.6
  [2a0fbf3d] CPUSummary v0.2.7
  [fb6a15b2] CloseOpenIntervals v0.1.13
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.18.1
  [adafc99b] CpuId v0.3.1
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [e2d170a0] DataValueInterfaces v1.0.0
  [c2308a5c] FASTX v2.1.7
  [615f187c] IfElse v0.1.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [445028e4] Kmers v1.2.0
  [b964fa9f] LaTeXStrings v1.4.0
  [10f19ff3] LayoutPointers v0.1.17
  [d125e4d3] ManualMemory v0.1.8
  [bac558e1] OrderedCollections v1.8.1
  [f517fe37] Polyester v0.7.18
  [1d0040c9] PolyesterWeave v0.2.2
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
⌅ [08abe8d2] PrettyTables v2.4.0
  [189a3867] Reexport v1.2.2
  [ae029012] Requires v1.3.1
  [fdea26ae] SIMD v3.7.2
  [94e857df] SIMDTypes v0.1.0
  [431bcebd] SciMLPublic v1.0.0
  [aedffcd0] Static v1.3.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [7792a7ef] StrideArraysCore v0.5.8
  [892a3eda] StringManipulation v0.4.1
  [354b36f9] StringViews v1.3.5
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [8290d209] ThreadingUtilities v0.5.5
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.13.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [de0858da] Printf v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.0.0
  [9e88b42a] Serialization v1.11.0
  [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
  [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: UndefVarError: `T` not defined in `SIMD`
Suggestion: check for spelling errors or missing imports.
Stacktrace:
   [1] top-level scope
     @ ~/.julia/packages/SIMD/UiGbs/src/arrayops.jl:4
   [2] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
   [3] top-level scope
     @ ~/.julia/packages/SIMD/UiGbs/src/SIMD.jl:25
   [4] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
   [5] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
   [6] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
   [7] macro expansion
     @ ./loading.jl:2504 [inlined]
   [8] macro expansion
     @ ./lock.jl:376 [inlined]
   [9] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [10] require
     @ ./loading.jl:2444 [inlined]
  [11] eval_import_path
     @ ./module.jl:36 [inlined]
  [12] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [13] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
     @ Base ./module.jl:101
  [14] top-level scope
     @ ~/.julia/packages/Automa/EyNRt/src/Automa.jl:4
  [15] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [16] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [17] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [18] macro expansion
     @ ./loading.jl:2504 [inlined]
  [19] macro expansion
     @ ./lock.jl:376 [inlined]
  [20] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [21] require
     @ ./loading.jl:2444 [inlined]
  [22] eval_import_path
     @ ./module.jl:36 [inlined]
  [23] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [24] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr})
     @ Base ./module.jl:101
  [25] top-level scope
     @ ~/.julia/packages/FASTX/KGKFv/src/FASTX.jl:4
  [26] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [27] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [28] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [29] macro expansion
     @ ./loading.jl:2504 [inlined]
  [30] macro expansion
     @ ./lock.jl:376 [inlined]
  [31] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [32] require
     @ ./loading.jl:2444 [inlined]
  [33] eval_import_path
     @ ./module.jl:36 [inlined]
  [34] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [35] _eval_using(to::Module, path::Expr)
     @ Base ./module.jl:137
  [36] top-level scope
     @ ~/.julia/packages/AssignTaxonomy/eplhI/src/AssignTaxonomy.jl:3
  [37] include(mod::Module, _path::String)
     @ Base ./Base.jl:309
  [38] __require_prelocked(pkg::Base.PkgId, env::String)
     @ Base ./loading.jl:2817
  [39] _require_prelocked(uuidkey::Base.PkgId, env::String)
     @ Base ./loading.jl:2576
  [40] macro expansion
     @ ./loading.jl:2504 [inlined]
  [41] macro expansion
     @ ./lock.jl:376 [inlined]
  [42] __require(into::Module, mod::Symbol)
     @ Base ./loading.jl:2468
  [43] require
     @ ./loading.jl:2444 [inlined]
  [44] eval_import_path
     @ ./module.jl:36 [inlined]
  [45] eval_import_path_all(at::Module, path::Expr, keyword::String)
     @ Base ./module.jl:60
  [46] _eval_using(to::Module, path::Expr)
     @ Base ./module.jl:137
  [47] top-level scope
     @ ~/.julia/packages/AssignTaxonomy/eplhI/test/runtests.jl:1
  [48] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
  [49] top-level scope
     @ none:6
  [50] eval(m::Module, e::Any)
     @ Core ./boot.jl:489
  [51] exec_options(opts::Base.JLOptions)
     @ Base ./client.jl:310
  [52] _start()
     @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/SIMD/UiGbs/src/arrayops.jl:4
in expression starting at /home/pkgeval/.julia/packages/SIMD/UiGbs/src/SIMD.jl:1
in expression starting at /home/pkgeval/.julia/packages/Automa/EyNRt/src/Automa.jl:1
in expression starting at /home/pkgeval/.julia/packages/FASTX/KGKFv/src/FASTX.jl:1
in expression starting at /home/pkgeval/.julia/packages/AssignTaxonomy/eplhI/src/AssignTaxonomy.jl:1
in expression starting at /home/pkgeval/.julia/packages/AssignTaxonomy/eplhI/test/runtests.jl:1

Testing failed after 101.41s

ERROR: LoadError: Package AssignTaxonomy 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:2936
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2785 [inlined]
  [4] 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:572
  [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548
  [6] 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
  [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined]
 [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [14] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 208.82s: package tests unexpectedly errored