Package evaluation of PhyloNetworks on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T17:21:13.224 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.45s ################################################################################ # Installation # Installing PhyloNetworks... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [33ad39ac] + PhyloNetworks v1.0.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.1.3 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.2 [34da2185] + Compat v4.16.0 [187b0558] + ConstructionBase v1.5.8 [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 [31c24e10] + Distributions v0.25.118 [ffbed154] + DocStringExtensions v0.9.4 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [d9f16b24] + Functors v0.5.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [76087f3c] + NLopt v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.33 [69de0a69] + Parsers v2.8.1 [33ad39ac] + PhyloNetworks v1.0.0 [2dfb63ee] + PooledArrays v1.4.3 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.8.0 [fdea26ae] + SIMD v3.7.1 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 [2913bbd2] + StatsBase v0.34.4 [4c63d2b9] + StatsFuns v1.4.0 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.4 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.0 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [079eb43e] + NLopt_jll v2.10.0+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 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [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 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.11.0 [4607b0f0] + SuiteSparse [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 [05823500] + OpenLibm_jll v0.8.5+0 [bea87d4a] + SuiteSparse_jll v7.7.0+0 [83775a58] + Zlib_jll v1.2.13+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 4.61s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 69.03s ################################################################################ # Testing # Testing PhyloNetworks Status `/tmp/jl_KcShEk/Project.toml` [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.1.3 [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.0.2 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.118 [c2308a5c] FASTX v2.1.7 [d9f16b24] Functors v0.5.2 [76087f3c] NLopt v1.1.3 [33ad39ac] PhyloNetworks v1.0.0 [860ef19b] StableRNGs v1.0.2 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.4 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_KcShEk/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.1.3 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.2 [34da2185] Compat v4.16.0 [187b0558] ConstructionBase v1.5.8 [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 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [d9f16b24] Functors v0.5.2 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [76087f3c] NLopt v1.1.3 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 [69de0a69] Parsers v2.8.1 [33ad39ac] PhyloNetworks v1.0.0 [2dfb63ee] PooledArrays v1.4.3 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.8.0 [fdea26ae] SIMD v3.7.1 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [860ef19b] StableRNGs v1.0.2 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 [2913bbd2] StatsBase v0.34.4 [4c63d2b9] StatsFuns v1.4.0 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.0 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [079eb43e] NLopt_jll v2.10.0+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 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.11.0 [56ddb016] Logging v1.11.0 [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 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.11.0 [4607b0f0] SuiteSparse [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 [05823500] OpenLibm_jll v0.8.5+0 [bea87d4a] SuiteSparse_jll v7.7.0+0 [83775a58] Zlib_jll v1.2.13+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... [ Info: starting test_deprecated.jl Test Summary: | Pass Total Time deprecated | 1 1 0.5s PASSED: test_deprecated.jl [ Info: starting test_quartet.jl Test Summary: | Pass Total Time QuartetT basic tests | 1 1 1.6s Test Summary: | Pass Total Time convert QuartetT vector to table | 6 6 6.5s Reading in trees, looking at 15 quartets in each... 0+------+100% ****** Test Summary: | Pass Total Time countquartetsintrees | 9 9 25.0s PASSED: test_quartet.jl [ Info: starting test_auxiliary.jl Test Summary: | Pass Total Time auxiliary | 82 82 25.6s PASSED: test_auxiliary.jl [ Info: starting test_generatetopology.jl Test Summary: | Pass Total Time deterministic topologies | 5 5 0.5s PASSED: test_generatetopology.jl [ Info: starting test_addHybrid.jl Test Summary: | Pass Total Time addhybridedge! top function | 11 11 5.5s Test Summary: | Pass Total Time addhybridedge! helper function | 14 14 0.0s Test Summary: | Pass Total Time edge checking functions | 11 11 0.0s PASSED: test_addHybrid.jl [ Info: starting test_graph_components.jl Test Summary: | Pass Total Time Tarjan's biconnected components | 38 38 4.7s Test Summary: | Pass Total Time tree component | 18 18 3.7s PASSED: test_graph_components.jl [ Info: starting test_manipulateNet.jl Test Summary: | Pass Total Time manipulateNet | 99 99 25.7s PASSED: test_manipulateNet.jl [ Info: starting test_compareNetworks.jl Test Summary: | Pass Total Time test sets: compareNetworks | 114 114 5.0s PASSED: test_compareNetworks.jl [ Info: starting test_bootstrap.jl using seed 56056 for bootstrap trees Test Summary: | Pass Total Time testing hybridclades_support | 24 24 53.4s PASSED: test_bootstrap.jl [ Info: starting test_moves_semidirected.jl Test Summary: | Pass Total Time unconstrained NNI moves | 190 190 4.6s Test Summary: | Pass Total Time constrained NNI moves | 48 48 45.9s Test Summary: | Pass Total Time test fliphybrid! | 33 33 0.9s Test Summary: | Pass Total Time test fliphybrid! randomly choose node function | 5 5 0.1s PASSED: test_moves_semidirected.jl [ Info: starting test_parsimony.jl Test Summary: | Pass Total Time Testing parsimony score & reconstruction | 27 27 15.3s Test Summary: | Broken Total Time data from CSV, parsimony search | 1 1 2.0s PASSED: test_parsimony.jl [ Info: starting test_recursion_matrices.jl Test Summary: | Pass Total Time traits: shared path, vcv, descendence matrix | 8 8 16.6s PASSED: test_recursion_matrices.jl [ Info: starting test_calibratePairwise.jl Test Summary: | Pass Total Time calibrate with distances: 3-cycle, non-identifiable example | 8 8 14.1s Test Summary: | Pass Total Time calibrate with distances: 5-cycle example (when unrooted) | 8 8 2.0s Test Summary: | Pass Total Time starting BL by fitting data-estimated distances | 1 1 6.9s PASSED: test_calibratePairwise.jl [ Info: starting test_relaxed_reading.jl Test Summary: | Pass Total Time test: newick parsing | 35 35 4.1s PASSED: test_relaxed_reading.jl [ Info: starting test_isMajor.jl Test Summary: | Pass Total Time readnewick Hybrid Node ismajor Tests | 11 11 0.4s Test Summary: | Pass Total Time parsing extended newick | 6 6 0.1s PASSED: test_isMajor.jl [ Info: starting test_interop.jl Test Summary: | Pass Total Time testing interoperability, matrix-based net | 21 21 2.7s PASSED: test_interop.jl [ Info: starting test_nj.jl Test Summary: | Pass Total Time neighbour joining tree | 6 6 9.3s PASSED: test_nj.jl ------------------------------------- Tests passed Testing PhyloNetworks tests passed Testing completed after 338.5s PkgEval succeeded after 436.36s