Package evaluation of Taxonomy on Julia 1.13.0-DEV.790 (77b90b9e62*) started at 2025-07-01T00:28:06.966


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 7.9s


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

Installing Taxonomy...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [10bb16a4] + Taxonomy v0.4.4
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [9a962f9c] + DataAPI v1.16.0
  [b4f34e82] + Distances v0.10.12
  [bac558e1] + OrderedCollections v1.8.1
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [88034a9c] + StringDistances v0.11.3
  [10bb16a4] + Taxonomy v0.4.4
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.12.0
  [d6f4376e] + Markdown v1.11.0
  [f489334b] + StyledStrings v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [8e850b90] + libblastrampoline_jll v5.13.1+0

Installation completed after 0.97s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 15.81s


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# Testing
#

     Testing Taxonomy
      Status `/tmp/jl_f2mIyY/Project.toml`
  [1520ce14] AbstractTrees v0.4.5
  [944b1d66] CodecZlib v0.7.8
  [9a962f9c] DataAPI v1.16.0
  [bac558e1] OrderedCollections v1.8.1
  [88034a9c] StringDistances v0.11.3
  [10bb16a4] Taxonomy v0.4.4
  [f43a241f] Downloads v1.7.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_f2mIyY/Manifest.toml`
  [1520ce14] AbstractTrees v0.4.5
  [944b1d66] CodecZlib v0.7.8
  [9a962f9c] DataAPI v1.16.0
  [b4f34e82] Distances v0.10.12
  [bac558e1] OrderedCollections v1.8.1
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [88034a9c] StringDistances v0.11.3
  [10bb16a4] Taxonomy v0.4.4
  [3bb67fe8] TranscodingStreams v0.11.3
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [f43a241f] Downloads v1.7.0
  [7b1f6079] FileWatching v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0
  [b27032c2] LibCURL v0.6.4
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.12.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [f489334b] StyledStrings v1.11.0
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [deac9b47] LibCURL_jll v8.14.1+1
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.5.20
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.0+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.65.0+0
     Testing Running tests...
Test Summary: | Pass  Total   Time
database.jl   |    2      2  14.1s
Test Summary: | Pass  Total   Time
taxon.jl      |   22     22  13.6s
Test Summary:    | Pass  Total  Time
AbstractTrees.jl |   13     13  4.1s
Test Summary: | Pass  Total  Time
rank.jl       |    9      9  0.8s
┌ Warning: All(args...) is deprecated, use Cols(args...) instead
│   caller = top-level scope at runtests.jl:104
└ @ Core ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104

lineage.jl: Error During Test at /home/pkgeval/.julia/packages/Taxonomy/05xQs/test/runtests.jl:112
  Test threw exception
  Expression: lineage[All(3, 24, 29)] == lineage[Cols(3, 24, 29)] == lineage[Cols(:superkingdom, 24, 29)] == lineage[Cols(:superkingdom, :order, :family)]
  KeyError: key 8 not found
  Stacktrace:
    [1] getindex
      @ ~/.julia/packages/OrderedCollections/Xihhq/src/ordered_dict.jl:387 [inlined]
    [2] #27
      @ ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:99 [inlined]
    [3] iterate
      @ ./generator.jl:48 [inlined]
    [4] _collect(c::Vector{Any}, itr::Base.Generator{Vector{Any}, Taxonomy.var"#27#28"{Lineage{Taxon}}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})
      @ Base ./array.jl:816
    [5] collect_similar
      @ ./array.jl:738 [inlined]
    [6] map
      @ ./abstractarray.jl:3374 [inlined]
    [7] getindex(l::Lineage{Taxon}, idx::Cols{Tuple{Symbol, Int64, Int64}})
      @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:98
    [8] top-level scope
      @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
    [9] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined]
   [10] macro expansion
      @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:112 [inlined]
   [11] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined]

lineage.jl: Error During Test at /home/pkgeval/.julia/packages/Taxonomy/05xQs/test/runtests.jl:113
  Test threw exception
  Expression: lineage[Between(3, 29)] == lineage[Between(:superkingdom, 29)] == lineage[Between(3, :family)] == lineage[Between(:superkingdom, :family)]
  KeyError: key 8 not found
  Stacktrace:
   [1] getindex
     @ ~/.julia/packages/OrderedCollections/Xihhq/src/ordered_dict.jl:387 [inlined]
   [2] getindex(l::Lineage{Taxon}, idx::Between{Symbol, Int64})
     @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:112
   [3] top-level scope
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
   [4] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined]
   [5] macro expansion
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:113 [inlined]
   [6] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined]

lineage.jl: Test Failed at /home/pkgeval/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123
  Expression: lineage[Cols(:order, :superkingdom, :family)]
    Expected: LineageIndexError
      Thrown: KeyError
      KeyError: key 8 not found
      Stacktrace:
        [1] getindex
          @ ~/.julia/packages/OrderedCollections/Xihhq/src/ordered_dict.jl:387 [inlined]
        [2] #27
          @ ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:99 [inlined]
        [3] iterate
          @ ./generator.jl:48 [inlined]
        [4] collect_to!(dest::Vector{Int64}, itr::Base.Generator{Vector{Symbol}, Taxonomy.var"#27#28"{Lineage{Taxon}}}, offs::Int64, st::Int64)
          @ Base ./array.jl:854
        [5] collect_to_with_first!
          @ ./array.jl:832 [inlined]
        [6] _collect(c::Vector{Symbol}, itr::Base.Generator{Vector{Symbol}, Taxonomy.var"#27#28"{Lineage{Taxon}}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})
          @ Base ./array.jl:826
        [7] collect_similar
          @ ./array.jl:738 [inlined]
        [8] map
          @ ./abstractarray.jl:3374 [inlined]
        [9] getindex(l::Lineage{Taxon}, idx::Cols{Tuple{Symbol, Symbol, Symbol}})
          @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:98
       [10] top-level scope
          @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
       [11] macro expansion
          @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined]
       [12] macro expansion
          @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123 [inlined]
       [13] macro expansion
          @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:835 [inlined]
       [14] macro expansion
          @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123 [inlined]
  Stacktrace:
   [1] top-level scope
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
   [2] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined]
   [3] macro expansion
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123 [inlined]

lineage.jl: Error During Test at /home/pkgeval/.julia/packages/Taxonomy/05xQs/test/runtests.jl:103
  Got exception outside of a @test
  UndefVarError: `ut_source` not defined in local scope
  Suggestion: check for an assignment to a local variable that shadows a global of the same name.
  Stacktrace:
   [1] reformat(l::Lineage{Taxon}, ranks::Vector{Symbol})
     @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:161
   [2] top-level scope
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
   [3] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined]
   [4] macro expansion
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:130 [inlined]
   [5] include(mapexpr::Function, mod::Module, _path::String)
     @ Base ./Base.jl:310
   [6] top-level scope
     @ none:6
   [7] eval(m::Module, e::Any)
     @ Core ./boot.jl:489
   [8] exec_options(opts::Base.JLOptions)
     @ Base ./client.jl:290
   [9] _start()
     @ Base ./client.jl:557
Test Summary: | Pass  Fail  Error  Total   Time
lineage.jl    |   18     1      3     22  22.8s
RNG of the outermost testset: Random.Xoshiro(0x94c05eb668a3415e, 0x1a2139d15e070960, 0x71423e13614a91bc, 0x7d6b245b91c08cca, 0x875d410c65710fb0)
ERROR: LoadError: Some tests did not pass: 18 passed, 1 failed, 3 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/Taxonomy/05xQs/test/runtests.jl:103

Testing failed after 91.19s

ERROR: LoadError: Package Taxonomy errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/Operations.jl:2423
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2278 [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/v1.13/Pkg/src/API.jl:500
  [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164
  [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152
  [7] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined]
  [8] #test#81
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined]
  [9] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:324
 [12] _start()
    @ Base ./client.jl:557
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 132.72s: package tests unexpectedly errored