Package evaluation of Taxonomy on Julia 1.12.0-DEV.1805 (a080deafdd*) started at 2025-03-24T12:13:43.047 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.1s ################################################################################ # Installation # Installing Taxonomy... Resolving package versions... Updating `~/.julia/environments/v1.12/Project.toml` [10bb16a4] + Taxonomy v0.4.4 Updating `~/.julia/environments/v1.12/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [9a962f9c] + DataAPI v1.16.0 [b4f34e82] + Distances v0.10.12 [bac558e1] + OrderedCollections v1.8.0 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [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 [dc6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [d6f4376e] + Markdown v1.11.0 [f489334b] + StyledStrings v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.2.0+0 [4536629a] + OpenBLAS_jll v0.3.28+3 [8e850b90] + libblastrampoline_jll v5.11.2+0 Installation completed after 1.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 20.14s ################################################################################ # Testing # Testing Taxonomy Status `/tmp/jl_FsrtDJ/Project.toml` [1520ce14] AbstractTrees v0.4.5 [944b1d66] CodecZlib v0.7.8 [9a962f9c] DataAPI v1.16.0 [bac558e1] OrderedCollections v1.8.0 [88034a9c] StringDistances v0.11.3 [10bb16a4] Taxonomy v0.4.4 [f43a241f] Downloads v1.6.0 [b77e0a4c] InteractiveUtils v1.11.0 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FsrtDJ/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [944b1d66] CodecZlib v0.7.8 [9a962f9c] DataAPI v1.16.0 [b4f34e82] Distances v0.10.12 [bac558e1] OrderedCollections v1.8.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [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 v1.6.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [dc6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [ca575930] NetworkOptions v1.2.0 [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 v1.2.0+0 [deac9b47] LibCURL_jll v8.6.0+0 [29816b5a] LibSSH2_jll v1.11.0+1 [c8ffd9c3] MbedTLS_jll v2.28.6+1 [14a3606d] MozillaCACerts_jll v2024.11.26 [4536629a] OpenBLAS_jll v0.3.28+3 [83775a58] Zlib_jll v1.3.1+1 [8e850b90] libblastrampoline_jll v5.11.2+0 [8e850ede] nghttp2_jll v1.63.0+1 Testing Running tests... Test Summary: | Pass Total Time database.jl | 2 2 14.2s Test Summary: | Pass Total Time taxon.jl | 22 22 13.5s 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/EqSuR/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:810 [5] collect_similar @ ./array.jl:732 [inlined] [6] map @ ./abstractarray.jl:3410 [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/v1.12/Test/src/Test.jl:1724 [inlined] [10] macro expansion @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:112 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:676 [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/EqSuR/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/v1.12/Test/src/Test.jl:1724 [inlined] [5] macro expansion @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:113 [inlined] [6] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:676 [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/EqSuR/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:848 [5] collect_to_with_first! @ ./array.jl:826 [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:820 [7] collect_similar @ ./array.jl:732 [inlined] [8] map @ ./abstractarray.jl:3410 [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/v1.12/Test/src/Test.jl:1724 [inlined] [12] macro expansion @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:123 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:773 [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/v1.12/Test/src/Test.jl:1724 [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 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/v1.12/Test/src/Test.jl:1724 [inlined] [4] macro expansion @ ~/.julia/packages/Taxonomy/05xQs/test/runtests.jl:130 [inlined] [5] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:301 [6] top-level scope @ none:6 [7] eval(m::Module, e::Any) @ Core ./boot.jl:485 [8] exec_options(opts::Base.JLOptions) @ Base ./client.jl:295 [9] _start() @ Base ./client.jl:558 Test Summary: | Pass Fail Error Total Time lineage.jl | 18 1 3 22 18.5s 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 84.97s ERROR: LoadError: Package Taxonomy errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Types.jl:68 [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/v1.12/Pkg/src/Operations.jl:2359 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2214 [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::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:159 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:147 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:146 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:300 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:329 [12] _start() @ Base ./client.jl:558 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 133.11s: package tests unexpectedly errored