Package evaluation of Phylo on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-13T03:05:51.400 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.29s ################################################################################ # Installation # Installing Phylo... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [aea672f4] + Phylo v0.5.4 Updating `~/.julia/environments/v1.13/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [15f4f7f2] + AutoHashEquals v2.2.0 [39de3d68] + AxisArrays v0.4.7 [34da2185] + Compat v4.18.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [e7dc6d0d] + DataValues v0.4.13 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.13.0 [86223c79] + Graphs v1.13.0 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.4 [8197267c] + IntervalSets v0.7.11 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [c8e1da08] + IterTools v1.10.0 [1c8ee90f] + IterableTables v1.0.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [fae87a5f] + ParserCombinator v2.2.1 [aea672f4] + Phylo v0.5.4 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.6 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [382cd787] + TableTraitsUtils v1.0.2 [bd369af6] + Tables v1.12.1 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.24.0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [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 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.13.1+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 4.62s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 110.98s ################################################################################ # Testing # Testing Phylo Status `/tmp/jl_n9WEC0/Project.toml` [39de3d68] AxisArrays v0.4.7 [a93c6f00] DataFrames v1.7.0 ⌅ [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [d7ba0133] Git v1.4.0 [86223c79] Graphs v1.13.0 [1c8ee90f] IterableTables v1.0.0 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [e1d29d7a] Missings v1.2.0 [fae87a5f] ParserCombinator v2.2.1 [aea672f4] Phylo v0.5.4 [91a5bcdd] Plots v1.40.18 [6f49c342] RCall v0.14.9 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.1.5 [699a6c99] SimpleTraits v0.9.5 [10745b16] Statistics v1.11.1 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.24.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_n9WEC0/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [ec485272] 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v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... [ Info: Potentially missing tests: - Branch.jl - Node.jl [ Info: Running tests for files: = API.jl = Interface.jl = Iterators.jl = LinkTree.jl = Phylo.jl = RecursiveTree.jl = Tree.jl = TreeSet.jl = metrics.jl = newick.jl = nexus.jl = plot.jl = rand.jl = routes.jl = show.jl = trim.jl [ Info: Running tests... * Testing API.jl ... * Testing Interface.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' ┌ Warning: Wrong number of roots for OneRoot tree (7) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/LinkTree.jl:250 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/LinkTree.jl:250 ┌ Warning: Wrong number of roots for OneRoot tree (7) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:151 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:151 * Testing Iterators.jl ... * Testing LinkTree.jl ... * Testing Phylo.jl ... * Testing RecursiveTree.jl ... ┌ Warning: Mismatch between branch id 7 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:221 ┌ Warning: Mismatch between branch id 7 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between branch id 8 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between node name Node 5 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:176 ┌ Warning: Mismatch between branch id 8 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between node name Dog and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:184 * Testing Tree.jl ... ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: Wrong number of roots for OneRoot tree (3) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 BinaryTree(): Test Failed at /home/pkgeval/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:115 Expression: all(a.data .== b.data) Evaluated: all(Bool[1, 1, 1, 1, 1, 1, 1, 1, 1, 1 … 1, 1, 0, 0, 0, 0, 0, 0, 1, 1]) Stacktrace: [1] top-level scope @ ~/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:71 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [3] macro expansion @ ~/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:115 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:745 [inlined] * Testing TreeSet.jl ... * Testing metrics.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' * Testing newick.jl ... [ Info: Created a tree called 'Tree' [ Info: Created a tree called 'Tree' * Testing nexus.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' * Testing plot.jl ... Precompiling packages... 1362.6 ms ✓ EpollShim_jll 10273.3 ms ✓ PlotThemes 8861.2 ms ✓ RecipesPipeline 1973.3 ms ✓ Qt6ShaderTools_jll 2231.8 ms ✓ Qt6Declarative_jll 2040.0 ms ✓ Qt6Wayland_jll 104901.4 ms ✓ Plots 20309.8 ms ✓ Plots → UnitfulExt 8 dependencies successfully precompiled in 155 seconds. 172 already precompiled. Precompiling packages... 1920.2 ms ✓ ColorVectorSpace → SpecialFunctionsExt 1 dependency successfully precompiled in 2 seconds. 19 already precompiled. Precompiling packages... 8933.3 ms ✓ Latexify → DataFramesExt 1 dependency successfully precompiled in 10 seconds. 39 already precompiled. * Testing rand.jl ... * Testing routes.jl ... * Testing show.jl ... ┌ Info: These tests only check that the show() commands └ do not give warnings or errors, not that they are correct! * Testing trim.jl ... [ Info: Running tests for extensions: = PhyloRCallExt.jl [ Info: Running extension tests... * Testing PhyloRCallExt.jl extension... Precompiling packages... 7826.5 ms ✓ CategoricalArrays → CategoricalArraysRecipesBaseExt 1 dependency successfully precompiled in 8 seconds. 16 already precompiled. Precompiling packages... 1659.5 ms ✓ CategoricalArrays → CategoricalArraysJSONExt 1 dependency successfully precompiled in 2 seconds. 18 already precompiled. Precompiling packages... 10852.1 ms ✓ RCall → RCallAxisArraysExt 1 dependency successfully precompiled in 13 seconds. 86 already precompiled. ┌ Warning: RCall.jl: Loading required package: ape │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ there is no package called ‘ape’ └ @ RCall ~/.julia/packages/RCall/GLHIY/src/io.jl:171 Test Summary: | Pass Fail Total Time Phylo.jl | 1398 1 1399 9m46.8s t = API | 20 20 2.2s t = Interface | 390 390 1m44.9s t = Iterators | 74 74 11.5s t = LinkTree | 11 11 7.0s t = Phylo | 9 9 2.4s t = RecursiveTree | 71 71 12.8s t = Tree | 67 1 68 29.4s NamedBinaryTree() | 34 34 15.9s BinaryTree() | 33 1 34 13.4s t = TreeSet | 87 87 9.8s t = metrics | 6 6 1.9s t = newick | 136 136 39.9s t = nexus | 114 114 34.4s t = plot | 4 4 3m53.0s t = rand | 52 52 15.0s t = routes | 144 144 21.5s t = show | 202 202 13.2s t = trim | 10 10 10.6s t = PhyloRCallExt | 0 35.9s RNG of the outermost testset: Xoshiro(0x9951797c85a704f1, 0xb9d66be14dfba82b, 0xb170153285fd9556, 0xe90a07f7bdd1fd77, 0x9d4b5ee33e4bd661) ERROR: LoadError: Some tests did not pass: 1398 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Phylo/sQ0CW/test/runtests.jl:10 Testing failed after 632.35s ERROR: LoadError: Package Phylo 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:2672 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2521 [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:538 [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/v1.13/Pkg/src/API.jl:515 [6] 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:168 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 783.32s: package has test failures