Package evaluation to test MCPhyloTree on Julia 1.14.0-DEV.24 (d5fb6bbb43*) started at 2025-11-02T13:41:10.254 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.67s ################################################################################ # Installation # Installing MCPhyloTree... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [e53f0ae0] + MCPhyloTree v1.1.7 Updating `~/.julia/environments/v1.14/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e53f0ae0] + MCPhyloTree v1.1.7 [bac558e1] + OrderedCollections v1.8.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [10745b16] + Statistics v1.11.1 [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 [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 To see why use `status --outdated -m` Installation completed after 1.22s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ 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... 3486.8 ms ✓ MCPhyloTree 1 dependency successfully precompiled in 4 seconds. 20 already precompiled. Precompilation completed after 16.29s ################################################################################ # Testing # Testing MCPhyloTree Status `/tmp/jl_TVDUWF/Project.toml` [e53f0ae0] MCPhyloTree v1.1.7 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_TVDUWF/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [34da2185] Compat v4.18.1 ⌅ [864edb3b] DataStructures v0.18.22 [e53f0ae0] MCPhyloTree v1.1.7 [bac558e1] OrderedCollections v1.8.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [10745b16] Statistics v1.11.1 [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... LargeNewick: Test Failed at /home/pkgeval/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:59 Expression: 17.9712 ≈ round(tree.height, digits = 4) Evaluated: 17.9712 ≈ 15.5461 Stacktrace: [1] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:51 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:59 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] insert_node!: Error During Test at /home/pkgeval/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:280 Got exception outside of a @test MethodError: no method matching iterate(::GeneralNode{Float64, Int64}) The function `iterate` exists, but no method is defined for this combination of argument types. Closest candidates are: iterate(!Matched::Compiler.MethodLookupResult, Any...) @ Base /opt/julia/share/julia/Compiler/src/methodtable.jl:11 iterate(!Matched::Compiler.ForwardToBackedgeIterator, !Matched::Int64) @ Base /opt/julia/share/julia/Compiler/src/typeinfer.jl:705 iterate(!Matched::Compiler.ForwardToBackedgeIterator) @ Base /opt/julia/share/julia/Compiler/src/typeinfer.jl:705 ... Stacktrace: [1] _append!(a::Vector{GeneralNode{Float64, Int64}}, ::Base.HasLength, iter::GeneralNode{Float64, Int64}) @ Base ./array.jl:1423 [2] append!(a::Vector{GeneralNode{Float64, Int64}}, iter::GeneralNode{Float64, Int64}) @ Base ./array.jl:1416 [3] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:281 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [5] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:298 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [7] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/runtests.jl:5 [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [9] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/runtests.jl:5 [inlined] [10] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [11] top-level scope @ none:6 [12] eval(m::Module, e::Any) @ Core ./boot.jl:489 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [14] _start() @ Base ./client.jl:577 Tree #2 has a different set of leaves than the first tree Tree #4 has a different set of leaves than the first tree done basics done utils done search done traversal Tree #3 has a different set of leaves than the first tree Tree #3 has a different set of leaves than the first tree done consensus done ladderize Warning: No node named "K" in treeWarning: No node named "L" in treeWarning: No node named "L" in treedone pruning done spr done moves done building done distances Test Summary: | Pass Fail Error Total Time MCPhyloTree | 259 1 1 261 6m45.8s Node Building | 10 10 0.1s Newick_Letters | 4 4 2.6s Newick_Numbers | 4 4 0.0s Newick_List | 3 3 0.0s LargeNewick | 2 1 3 5m13.3s add_child! | 14 14 0.4s remove_child! | 9 9 0.1s remove_child! by node | 9 9 0.2s tree_length | 1 1 0.1s tree_height | 1 1 0.0s node_height | 1 1 0.0s node_age | 4 4 0.0s node_depth | 3 3 0.0s get_path | 2 2 0.1s path_length | 2 2 0.0s get_sister | 2 2 0.1s set_binary! | 3 3 0.0s number_nodes! | 3 3 0.0s blv | 3 3 0.8s internal_external | 2 2 0.3s check_binary | 3 3 0.2s insert_node! | 2 1 3 3.7s delete_node! | 3 3 0.1s find_lca | 9 9 0.4s check_leafsets | 1 1 0.6s mother | 2 2 0.0s force_ultrametric | 5 5 1.0s ascii | 3 3 0.9s childtype | 2 2 0.0s find helper | 8 8 2.4s search | 7 7 0.2s traversal post_order | 6 6 0.3s traversal pre_order | 5 5 0.4s traversal level_order | 4 4 0.3s traversal leaves | 1 1 0.0s find_common_clusters | 5 5 4.7s one_way_compatible | 1 1 5.0s get_leaf_ranks | 1 1 0.2s order_tree! | 2 2 0.2s max/min_leaf_rank | 8 8 0.0s x_left_right | 10 10 0.1s majority_consensus_tree | 3 3 7.0s loose_consensus_tree | 3 3 0.2s greedy_consensus_tree | 1 1 5.8s count_cluster_occurences | 1 1 1.3s ladderize | 4 4 0.3s Pruning leaf | 4 4 1.0s Pruning root | 1 1 0.0s Pruning misc | 3 3 0.0s Pruning inplace | 1 1 0.0s spr | 14 14 1.5s swing | 2 2 0.3s slide | 2 2 0.2s NNI | 5 5 0.3s move | 2 2 0.0s change_edge_length | 1 1 0.5s reroot | 1 1 0.1s SPR | 1 1 0.0s NNI Matrix | 3 3 6.6s upgma | 3 3 2.9s NJ | 2 2 3.3s binary | 2 2 0.0s newick | 1 1 0.0s to_covariance | 1 1 1.6s ladderize | 1 1 0.0s distance matrix | 1 1 0.4s to_df | 2 2 1.6s from_df | 1 1 0.5s leave_incidence_matrix | 3 3 2.3s cov2tree | 1 1 9.0s tree_from_leaves | 4 4 0.5s dist RF | 2 2 0.0s dist RF_weighted | 1 1 0.0s BHV_bounds | 2 2 1.6s geodesic | 2 2 15.5s geodesic helper functions | 8 8 0.3s RNG of the outermost testset: Xoshiro(0x7948272387a4dfd8, 0x2339e828d81e9de3, 0xd5ed0cee1b7ec2a3, 0x11b79afede1cb76a, 0x8c9c5d3cac438a96) ERROR: LoadError: Some tests did not pass: 259 passed, 1 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MCPhyloTree/67FIA/test/runtests.jl:4 Testing failed after 415.81s ERROR: LoadError: Package MCPhyloTree 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 457.45s: package tests unexpectedly errored