Package evaluation of MCPhyloTree on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T09:08:01.990 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.93s ################################################################################ # Installation # Installing MCPhyloTree... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [e53f0ae0] + MCPhyloTree v1.1.7 Updating `~/.julia/environments/v1.11/Manifest.toml` [1520ce14] + AbstractTrees v0.4.5 [34da2185] + Compat v4.16.0 [864edb3b] + DataStructures v0.18.22 [e53f0ae0] + MCPhyloTree v1.1.7 [bac558e1] + OrderedCollections v1.8.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [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 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0 [4536629a] + OpenBLAS_jll v0.3.27+1 [8e850b90] + libblastrampoline_jll v5.11.0+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 To see why use `status --outdated -m` Installation completed after 1.99s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 15.82s ################################################################################ # Testing # Testing MCPhyloTree Status `/tmp/jl_BUJ3Rz/Project.toml` [e53f0ae0] MCPhyloTree v1.1.7 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_BUJ3Rz/Manifest.toml` [1520ce14] AbstractTrees v0.4.5 [34da2185] Compat v4.16.0 [864edb3b] DataStructures v0.18.22 [e53f0ae0] MCPhyloTree v1.1.7 [bac558e1] OrderedCollections v1.8.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [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 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization 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 v1.1.1+0 [4536629a] OpenBLAS_jll v0.3.27+1 [8e850b90] libblastrampoline_jll v5.11.0+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 ≈ 14.3379 Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:59 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [4] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:51 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::Cmd) @ Base process.jl:716 iterate(!Matched::Cmd, !Matched::Any) @ Base process.jl:721 iterate(!Matched::Core.Compiler.InstructionStream, !Matched::Int64) @ Base show.jl:2824 ... Stacktrace: [1] _append!(a::Vector{GeneralNode{Float64, Int64}}, ::Base.HasLength, iter::GeneralNode{Float64, Int64}) @ Base ./array.jl:1337 [2] append!(a::Vector{GeneralNode{Float64, Int64}}, iter::GeneralNode{Float64, Int64}) @ Base ./array.jl:1329 [3] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:298 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [5] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/basics.jl:281 [6] include(fname::String) @ Main ./sysimg.jl:38 [7] macro expansion @ ~/.julia/packages/MCPhyloTree/67FIA/test/runtests.jl:5 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [9] top-level scope @ ~/.julia/packages/MCPhyloTree/67FIA/test/runtests.jl:5 [10] include(fname::String) @ Main ./sysimg.jl:38 [11] top-level scope @ none:6 [12] eval @ ./boot.jl:430 [inlined] [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:296 [14] _start() @ Base ./client.jl:531 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 7m27.0s Node Building | 10 10 0.2s Newick_Letters | 4 4 3.2s Newick_Numbers | 4 4 0.0s Newick_List | 3 3 0.1s LargeNewick | 2 1 3 5m36.5s add_child! | 14 14 0.5s 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 0.2s 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 0.9s internal_external | 2 2 0.2s check_binary | 3 3 0.1s insert_node! | 2 1 3 9.3s delete_node! | 3 3 0.1s find_lca | 9 9 0.5s check_leafsets | 1 1 0.6s mother | 2 2 0.0s force_ultrametric | 5 5 0.7s ascii | 3 3 1.2s childtype | 2 2 0.0s find helper | 8 8 3.2s 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 5.6s one_way_compatible | 1 1 5.7s get_leaf_ranks | 1 1 0.3s 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 6.9s count_cluster_occurences | 1 1 1.5s 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 1.7s swing | 2 2 0.3s slide | 2 2 0.3s NNI | 5 5 0.3s move | 2 2 0.0s change_edge_length | 1 1 0.7s reroot | 1 1 0.1s SPR | 1 1 0.0s NNI Matrix | 3 3 0.0s upgma | 3 3 3.9s NJ | 2 2 4.3s 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 1.4s to_df | 2 2 1.7s from_df | 1 1 0.7s leave_incidence_matrix | 3 3 2.7s cov2tree | 1 1 10.6s tree_from_leaves | 4 4 0.7s dist RF | 2 2 0.0s dist RF_weighted | 1 1 0.0s BHV_bounds | 2 2 1.8s geodesic | 2 2 16.9s geodesic helper functions | 8 8 0.3s 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 454.52s ERROR: LoadError: Package MCPhyloTree errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [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/v1.11/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/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/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 492.97s: package tests unexpectedly errored