Package evaluation to test SNaQ on Julia 1.14.0-DEV.24 (d5fb6bbb43*) started at 2025-11-02T21:27:25.510 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.61s ################################################################################ # Installation # Installing SNaQ... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed FilePathsBase ─────────────── v0.9.24 Installed InlineStrings ─────────────── v1.4.5 Installed FillArrays ────────────────── v1.14.0 Installed StringViews ───────────────── v1.3.5 Installed HypergeometricFunctions ───── v0.3.28 Installed ConstructionBase ──────────── v1.6.0 Installed DataStructures ────────────── v0.18.22 Installed AliasTables ───────────────── v1.1.3 Installed CodecZlib ─────────────────── v0.7.8 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed StatsBase ─────────────────── v0.34.7 Installed Functors ──────────────────── v0.5.2 Installed TranscodingStreams ────────── v0.11.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed SIMD ──────────────────────── v3.7.2 Installed Combinatorics ─────────────── v1.0.3 Installed Statistics ────────────────── v1.11.1 Installed InvertedIndices ───────────── v1.3.1 Installed StatsAPI ──────────────────── v1.7.1 Installed DataValueInterfaces ───────── v1.0.0 Installed CEnum ─────────────────────── v0.5.0 Installed SentinelArrays ────────────── v1.4.8 Installed PrecompileTools ───────────── v1.3.3 Installed Twiddle ───────────────────── v1.1.2 Installed BioSymbols ────────────────── v5.2.0 Installed StaticArraysCore ──────────── v1.4.4 Installed IrrationalConstants ───────── v0.2.6 Installed StaticArrays ──────────────── v1.9.15 Installed QuadGK ────────────────────── v2.11.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed StringManipulation ────────── v0.4.1 Installed Parsers ───────────────────── v2.8.3 Installed LogExpFunctions ───────────── v0.3.29 Installed Rmath ─────────────────────── v0.9.0 Installed BioGenerics ───────────────── v0.1.5 Installed StatsFuns ─────────────────── v1.5.2 Installed PrettyTables ──────────────── v3.1.0 Installed PhyloNetworks ─────────────── v1.2.0 Installed SNaQ ──────────────────────── v1.0.0 Installed Distributions ─────────────── v0.25.122 Installed Tables ────────────────────── v1.12.1 Installed PtrArrays ─────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed SpecialFunctions ──────────── v2.6.1 Installed FASTX ─────────────────────── v2.1.7 Installed Missings ──────────────────── v1.2.0 Installed DataFrames ────────────────── v1.8.1 Installed WeakRefStrings ────────────── v1.4.2 Installed Preferences ───────────────── v1.5.0 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed PDMats ────────────────────── v0.11.36 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed Automa ────────────────────── v1.1.0 Installed NLopt ─────────────────────── v1.2.1 Installed WorkerUtilities ───────────── v1.6.1 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed DocStringExtensions ───────── v0.9.5 Installed BioSequences ──────────────── v3.5.0 Installed CSV ───────────────────────── v0.10.15 Installing 3 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact NLopt 322.7 KiB Updating `~/.julia/environments/v1.14/Project.toml` [c2bf7a07] + SNaQ v1.0.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [3c28c6f8] + BioSymbols v5.2.0 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.0.3 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.14.0 [d9f16b24] + Functors v0.5.2 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.5 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [76087f3c] + NLopt v1.2.1 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.36 [69de0a69] + Parsers v2.8.3 [33ad39ac] + PhyloNetworks v1.2.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.0 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [79098fc4] + Rmath v0.9.0 [fdea26ae] + SIMD v3.7.2 [c2bf7a07] + SNaQ v1.0.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.7 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.5 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [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 [7b1f6079] + FileWatching 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 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization 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 v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [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 9.91s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4948.5 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ 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... 1730.2 ms ✓ InlineStrings 844.0 ms ✓ Reexport 1122.4 ms ✓ Statistics 877.3 ms ✓ DataAPI 1138.7 ms ✓ ConstructionBase 1970.8 ms ✓ IrrationalConstants 757.2 ms ✓ DataValueInterfaces 973.6 ms ✓ StaticArraysCore 831.8 ms ✓ StatsAPI 1263.6 ms ✓ OrderedCollections 884.2 ms ✓ InvertedIndices 856.5 ms ✓ Twiddle 1151.0 ms ✓ DocStringExtensions 1170.6 ms ✓ CEnum 2079.4 ms ✓ Combinatorics 1074.7 ms ✓ StringViews 1024.0 ms ✓ WorkerUtilities 2204.8 ms ✓ FillArrays 825.3 ms ✓ PtrArrays 1281.2 ms ✓ TranscodingStreams 749.7 ms ✓ IteratorInterfaceExtensions 874.9 ms ✓ LaTeXStrings 1211.7 ms ✓ SuiteSparse 1847.8 ms ✓ Crayons 2848.1 ms ✓ SentinelArrays 1142.9 ms ✓ Compat 1156.7 ms ✓ Preferences 1486.8 ms ✓ Statistics → SparseArraysExt 993.2 ms ✓ Missings 1040.6 ms ✓ PooledArrays 768.7 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1450.3 ms ✓ LogExpFunctions 1508.7 ms ✓ FillArrays → FillArraysSparseArraysExt 946.9 ms ✓ FillArrays → FillArraysStatisticsExt 981.9 ms ✓ AliasTables 941.8 ms ✓ BioGenerics 935.9 ms ✓ CodecZlib 766.3 ms ✓ TableTraits 1854.4 ms ✓ PDMats 834.8 ms ✓ Compat → CompatLinearAlgebraExt 1234.6 ms ✓ JLLWrappers 941.2 ms ✓ PrecompileTools 1819.4 ms ✓ Tables 1463.9 ms ✓ FillArrays → FillArraysPDMatsExt 2062.7 ms ✓ FilePathsBase 4103.7 ms ✓ DataStructures 1328.6 ms ✓ Functors 1549.0 ms ✓ NLopt_jll 1469.2 ms ✓ Rmath_jll 1463.7 ms ✓ OpenSpecFun_jll 2716.4 ms ✓ BioSymbols 14718.9 ms ✓ StaticArrays 3285.5 ms ✓ StringManipulation 17308.6 ms ✓ SIMD 17316.8 ms ✓ Parsers 1097.0 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1672.6 ms ✓ SortingAlgorithms 2809.5 ms ✓ QuadGK 2050.9 ms ✓ NLopt 1512.7 ms ✓ Rmath 4577.3 ms ✓ SpecialFunctions 7732.7 ms ✓ BioSequences 1055.4 ms ✓ StaticArrays → StaticArraysStatisticsExt 1049.9 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 29138.7 ms ✓ PrettyTables 16702.5 ms ✓ Automa 1036.9 ms ✓ InlineStrings → ParsersExt 5009.4 ms ✓ StatsBase 2484.3 ms ✓ HypergeometricFunctions 83100.1 ms ✓ DataFrames 20862.0 ms ✓ FASTX 2972.8 ms ✓ WeakRefStrings 2439.5 ms ✓ PDMats → StatsBaseExt 2621.6 ms ✓ StatsFuns 2419.7 ms ✓ FASTX → BioSequencesExt 28548.0 ms ✓ CSV 9816.8 ms ✓ Distributions 19880.5 ms ✓ PhyloNetworks 20860.7 ms ✓ SNaQ 79 dependencies successfully precompiled in 393 seconds. 19 already precompiled. Precompilation completed after 401.8s ################################################################################ # Testing # Testing SNaQ Status `/tmp/jl_rL5cFh/Project.toml` [4c88cf16] Aqua v0.8.14 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [336ed68f] CSV v0.10.15 [861a8166] Combinatorics v1.0.3 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [31c24e10] Distributions v0.25.122 [c2308a5c] FASTX v2.1.7 [d9f16b24] Functors v0.5.2 [38e38edf] GLM v1.9.0 [76087f3c] NLopt v1.2.1 [33ad39ac] PhyloNetworks v1.2.0 [c2bf7a07] SNaQ v1.0.0 [90137ffa] StaticArrays v1.9.15 [10745b16] Statistics v1.11.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_rL5cFh/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.14.0 [d9f16b24] Functors v0.5.2 [38e38edf] GLM v1.9.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.5 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [76087f3c] NLopt v1.2.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.36 [69de0a69] Parsers v2.8.3 [33ad39ac] PhyloNetworks v1.2.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.0 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [79098fc4] Rmath v0.9.0 [fdea26ae] SIMD v3.7.2 [c2bf7a07] SNaQ v1.0.0 [91c51154] SentinelArrays v1.4.8 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.7 [4c63d2b9] StatsFuns v1.5.2 [3eaba693] StatsModels v0.7.7 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.5 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [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 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization 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 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.67.1+0 [3f19e933] p7zip_jll v17.6.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Test Summary: | Pass Total Time Code quality (Aqua.jl) | 5 5 36.1s ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 read 1/2 bootstrap tree files read 2/2 bootstrap tree files hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 between 10.0 and 20.0 gene trees per 4-taxon set hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 between 10.0 and 20.0 gene trees per 4-taxon set 1 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged (ngenes too). 15.0 gene trees per 4-taxon set descriptive stat of input data printed to file tmp.log descriptive stat of input data printed to file tmp.log found 2 4-taxon sets uninformative about between-species relationships, out of 13. These 4-taxon sets will be deleted from the data frame. 11 informative 4-taxon sets will be used. 11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged. hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1 netstring = "(((8,7:0.2):0.0,(6,(4)#H9:::0.6):0.4):0.4,10,#H9:::0.4);" outgroup defined D hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 WARNING: Method definition whichtree(String) in module Main at /home/pkgeval/.julia/packages/SNaQ/ZBOHm/test/test_5taxon_readTopology.jl:6 overwritten at /home/pkgeval/.julia/packages/SNaQ/ZBOHm/test/test_parameters.jl:10. hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 2 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/ZBOHm/src/auxiliary.jl:9 hybrid edges for hybrid node 8 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 15 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 4 have missing gamma's, set default: 0.9,0.1 Reading in trees, looking at 15 quartets in each... 0+------+100% ****** will use all quartets on 6 taxa calculating obsCF from 6 gene trees and for 15 quartets Reading in quartets... 0+---------------+100% *************** 11 unique 4-taxon sets were found. CF values of repeated 4-taxon sets will be averaged (ngenes too). between 4.0 and 6.0 gene trees per 4-taxon set test: calculate quartet CF from input gene trees: Test Failed at /home/pkgeval/.julia/packages/SNaQ/ZBOHm/test/test_readInputData.jl:77 Expression: df2 == (t1 = ["AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "C"], t2 = ["AB__2", "AB__2", "AB__2", "AB__2", "AB__2", "AB__2", "C", "C", "C", "D", "D"], t3 = ["C", "C", "C", "D", "D", "E", "D", "D", "E", "E", "E"], t4 = ["D", "E", "O", "E", "O", "O", "E", "O", "O", "O", "O"], CF12_34 = [1.0, 0.75, 1.0, 0.75, 1.0, 0.75, 0.0, 0.0, (3 / 5 + 4 / 6) / 2, (3 / 5 + 4 / 6) / 2, 1.0], CF13_24 = [0, 0.25, 0, 0.25, 0, 0, 0, 0, (2 / 5 + 2 / 6) / 2, (2 / 5 + 2 / 6) / 2, 0.0], CF14_23 = [0, 0, 0, 0, 0, 0.25, 1, 1, 0, 0, 0], ngenes = Union{Missing, Float64}[5, 4, 5, 4, 5, 4, 5.5, 5.5, 5.5, 5.5, 6]) Evaluated: (t1 = ["\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "\x02\0BA", "C"], t2 = ["\x02\0BA__2", "\x02\0BA__2", "\x02\0BA__2", "\x02\0BA__2", "\x02\0BA__2", "\x02\0BA__2", "C", "C", "C", "D", "D"], t3 = ["C", "C", "C", "D", "D", "E", "D", "D", "E", "E", "E"], t4 = ["D", "E", "O", "E", "O", "O", "E", "O", "O", "O", "O"], CF12_34 = [1.0, 0.75, 1.0, 0.75, 1.0, 0.75, 0.0, 0.0, 0.6333333333333333, 0.6333333333333333, 1.0], CF13_24 = [0.0, 0.25, 0.0, 0.25, 0.0, 0.0, 0.0, 0.0, 0.3666666666666667, 0.3666666666666667, 0.0], CF14_23 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.25, 1.0, 1.0, 0.0, 0.0, 0.0], ngenes = Union{Missing, Float64}[5.0, 4.0, 5.0, 4.0, 5.0, 4.0, 5.5, 5.5, 5.5, 5.5, 6.0]) == (t1 = ["AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "AB", "C"], t2 = ["AB__2", "AB__2", "AB__2", "AB__2", "AB__2", "AB__2", "C", "C", "C", "D", "D"], t3 = ["C", "C", "C", "D", "D", "E", "D", "D", "E", "E", "E"], t4 = ["D", "E", "O", "E", "O", "O", "E", "O", "O", "O", "O"], CF12_34 = [1.0, 0.75, 1.0, 0.75, 1.0, 0.75, 0.0, 0.0, 0.6333333333333333, 0.6333333333333333, 1.0], CF13_24 = [0.0, 0.25, 0.0, 0.25, 0.0, 0.0, 0.0, 0.0, 0.3666666666666667, 0.3666666666666667, 0.0], CF14_23 = [0.0, 0.0, 0.0, 0.0, 0.0, 0.25, 1.0, 1.0, 0.0, 0.0, 0.0], ngenes = Union{Missing, Float64}[5.0, 4.0, 5.0, 4.0, 5.0, 4.0, 5.5, 5.5, 5.5, 5.5, 6.0]) Stacktrace: [1] top-level scope @ ~/.julia/packages/SNaQ/ZBOHm/test/test_readInputData.jl:55 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [3] macro expansion @ ~/.julia/packages/SNaQ/ZBOHm/test/test_readInputData.jl:77 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 hybrid edges for hybrid node 3 have missing gamma's, set default: 0.9,0.1 Test Summary: | Pass Fail Total Time SNaQ.jl | 212 1 213 8m19.6s read level 1: hyb edge at root then 2-cycle | 1 1 0.6s moveTargetUpdate! reject 2-cycle proposal | 1 1 11.2s test: bad diamond, max pseudo lik | 23 23 56.0s bootsnaq from quartet CF intervals | 2 2 1m31.3s bootsnaq from bootstrap gene trees, multiple procs | 18 18 2m12.9s correct pseudo likelihood and snaq | 22 22 1m48.7s test: delete hybridization | 20 20 2.3s multiple alleles | 26 26 21.5s test: level-1 partitions | 53 53 3.2s test: reading nexus file | 7 7 2.2s test: calculate quartet CF from input gene trees | 2 1 3 19.0s test: move hybrid around cycle | 2 2 0.3s RNG of the outermost testset: Xoshiro(0x4982f340e8b24210, 0x41a786552d2d58b6, 0x509dc04f01256ec3, 0x31a191fbc59066fe, 0xfcf945addce846f3) ERROR: LoadError: Some tests did not pass: 212 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SNaQ/ZBOHm/test/runtests.jl:52 Testing failed after 596.46s ERROR: LoadError: Package SNaQ 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 1047.3s: package has test failures