Package evaluation of Taxonomy on Julia 1.10.9 (96dc2d8c45*) started at 2025-06-06T12:27:17.245


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 5.05s


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

Installing Taxonomy...
   Resolving package versions...
    Updating `~/.julia/environments/v1.10/Project.toml`
  [10bb16a4] + Taxonomy v0.4.4
    Updating `~/.julia/environments/v1.10/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [9a962f9c] + DataAPI v1.16.0
  [b4f34e82] + Distances v0.10.12
  [bac558e1] + OrderedCollections v1.8.1
  [82ae8749] + StatsAPI v1.7.1
  [88034a9c] + StringDistances v0.11.3
  [10bb16a4] + Taxonomy v0.4.4
  [56f22d72] + Artifacts
  [2a0f44e3] + Base64
  [b77e0a4c] + InteractiveUtils
  [8f399da3] + Libdl
  [37e2e46d] + LinearAlgebra
  [d6f4376e] + Markdown
  [9a3f8284] + Random
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization
  [2f01184e] + SparseArrays v1.10.0
  [10745b16] + Statistics v1.10.0
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [4536629a] + OpenBLAS_jll v0.3.23+4
  [bea87d4a] + SuiteSparse_jll v7.2.1+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0

Installation completed after 4.88s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 13.52s


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

     Testing Taxonomy
      Status `/tmp/jl_nXJ9GA/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 v1.6.0
  [b77e0a4c] InteractiveUtils
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
      Status `/tmp/jl_nXJ9GA/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
  [82ae8749] StatsAPI v1.7.1
  [88034a9c] StringDistances v0.11.3
  [10bb16a4] Taxonomy v0.4.4
  [3bb67fe8] TranscodingStreams v0.11.3
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [b77e0a4c] InteractiveUtils
  [b27032c2] LibCURL v0.6.4
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [ca575930] NetworkOptions v1.2.0
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [2f01184e] SparseArrays v1.10.0
  [10745b16] Statistics v1.10.0
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.4.0+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.2+1
  [14a3606d] MozillaCACerts_jll v2023.1.10
  [4536629a] OpenBLAS_jll v0.3.23+4
  [bea87d4a] SuiteSparse_jll v7.2.1+1
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.52.0+1
     Testing Running tests...
Test Summary: | Pass  Total   Time
database.jl   |    2      2  16.3s
Test Summary: | Pass  Total   Time
taxon.jl      |   22     22  10.2s
Test Summary:    | Pass  Total  Time
AbstractTrees.jl |   13     13  2.9s
Test Summary: | Pass  Total  Time
rank.jl       |    9      9  0.3s
┌ Warning: All(args...) is deprecated, use Cols(args...) instead
│   caller = macro expansion at Test.jl:669 [inlined]
└ @ Core /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669
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(h::OrderedCollections.OrderedDict{Int64, Int64}, key::Int64)
      @ OrderedCollections ~/.julia/packages/OrderedCollections/Xihhq/src/ordered_dict.jl:387
    [2] (::Taxonomy.var"#19#22"{Lineage{Taxon}})(i::Symbol)
      @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:99
    [3] iterate
      @ ./generator.jl:47 [inlined]
    [4] _collect(c::Vector{Any}, itr::Base.Generator{Vector{Any}, Taxonomy.var"#19#22"{Lineage{Taxon}}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})
      @ Base ./array.jl:854
    [5] collect_similar
      @ ./array.jl:763 [inlined]
    [6] map
      @ ./abstractarray.jl:3286 [inlined]
    [7] getindex(l::Lineage{Taxon}, idx::Cols{Tuple{Symbol, Int64, Int64}})
      @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:98
    [8] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined]
    [9] macro expansion
      @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:112 [inlined]
   [10] macro expansion
      @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
   [11] top-level scope
      @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
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(h::OrderedCollections.OrderedDict{Int64, Int64}, key::Int64)
     @ OrderedCollections ~/.julia/packages/OrderedCollections/Xihhq/src/ordered_dict.jl:387
   [2] getindex(l::Lineage{Taxon}, idx::Between{Symbol, Int64})
     @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:112
   [3] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:669 [inlined]
   [4] macro expansion
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:113 [inlined]
   [5] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
   [6] top-level scope
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
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

Stacktrace:
 [1] macro expansion
   @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123 [inlined]
 [2] macro expansion
   @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
 [3] top-level scope
   @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
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
  Stacktrace:
   [1] reformat(l::Lineage{Taxon}, ranks::Vector{Symbol})
     @ Taxonomy ~/.julia/packages/Taxonomy/05xQs/src/lineage.jl:161
   [2] macro expansion
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:130 [inlined]
   [3] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.10/Test/src/Test.jl:1577 [inlined]
   [4] top-level scope
     @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:104
   [5] include(fname::String)
     @ Base.MainInclude ./client.jl:494
   [6] top-level scope
     @ none:6
   [7] eval
     @ ./boot.jl:385 [inlined]
   [8] exec_options(opts::Base.JLOptions)
     @ Base ./client.jl:296
   [9] _start()
     @ Base ./client.jl:557
Test Summary: | Pass  Fail  Error  Total   Time
lineage.jl    |   18     1      3     22  11.6s
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 68.93s

ERROR: LoadError: Package Taxonomy errored during testing
Stacktrace:
 [1] pkgerror(msg::String)
   @ Pkg.Types /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Types.jl:70
 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.10/Pkg/src/Operations.jl:2034
 [3] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/Operations.jl:1915 [inlined]
 [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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::Base.PipeEndpoint})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:444
 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::Base.PipeEndpoint, kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:159
 [6] test
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:147 [inlined]
 [7] #test#74
   @ /opt/julia/share/julia/stdlib/v1.10/Pkg/src/API.jl:146 [inlined]
 [8] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:219
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210

PkgEval failed after 98.89s: package tests unexpectedly errored