Package evaluation to test SNaQ on Julia 1.14.0-DEV.1601 (79ea5eb99c*) started at 2026-01-24T18:46:13.810 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 9.87s ################################################################################ # Installation # Installing SNaQ... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed InlineStrings ─────────────── v1.4.5 Installed FilePathsBase ─────────────── v0.9.24 Installed FillArrays ────────────────── v1.16.0 Installed DataStructures ────────────── v0.18.22 Installed StringViews ───────────────── v1.3.7 Installed HypergeometricFunctions ───── v0.3.28 Installed ConstructionBase ──────────── v1.6.0 Installed AliasTables ───────────────── v1.1.3 Installed CodecZlib ─────────────────── v0.7.8 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed Functors ──────────────────── v0.5.2 Installed StatsBase ─────────────────── v0.34.10 Installed TranscodingStreams ────────── v0.11.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed SIMD ──────────────────────── v3.7.2 Installed Combinatorics ─────────────── v1.1.0 Installed Statistics ────────────────── v1.11.1 Installed InvertedIndices ───────────── v1.3.1 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.8.0 Installed SentinelArrays ────────────── v1.4.9 Installed CEnum ─────────────────────── v0.5.0 Installed Twiddle ───────────────────── v1.1.2 Installed PrecompileTools ───────────── v1.3.3 Installed StaticArrays ──────────────── v1.9.16 Installed StaticArraysCore ──────────── v1.4.4 Installed IrrationalConstants ───────── v0.2.6 Installed BioSymbols ────────────────── v5.2.0 Installed StringManipulation ────────── v0.4.2 Installed QuadGK ────────────────────── v2.11.2 Installed SNaQ ──────────────────────── v1.1.1 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed LogExpFunctions ───────────── v0.3.29 Installed Parsers ───────────────────── v2.8.3 Installed Rmath ─────────────────────── v0.9.0 Installed PrettyTables ──────────────── v3.1.2 Installed BioGenerics ───────────────── v0.1.5 Installed StatsFuns ─────────────────── v1.5.2 Installed Tables ────────────────────── v1.12.1 Installed PhyloNetworks ─────────────── v1.3.0 Installed Distributions ─────────────── v0.25.123 Installed PtrArrays ─────────────────── v1.3.0 Installed Reexport ──────────────────── v1.2.2 Installed FASTX ─────────────────────── v2.1.7 Installed Missings ──────────────────── v1.2.0 Installed DataFrames ────────────────── v1.8.1 Installed SpecialFunctions ──────────── v2.6.1 Installed CSV ───────────────────────── v0.10.15 Installed WeakRefStrings ────────────── v1.4.2 Installed Preferences ───────────────── v1.5.1 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed PDMats ────────────────────── v0.11.37 Installed NLopt ─────────────────────── v1.2.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed WorkerUtilities ───────────── v1.6.1 Installed Automa ────────────────────── v1.1.0 Installed BioSequences ──────────────── v3.5.1 Installed DocStringExtensions ───────── v0.9.5 Installed NLopt_jll ─────────────────── v2.10.0+0 Installing 3 artifacts Installed artifact Rmath 121.9 KiB Installed artifact NLopt 322.7 KiB Installed artifact OpenSpecFun 194.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [c2bf7a07] + SNaQ v1.1.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [67c07d97] + Automa v1.1.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.1 [3c28c6f8] + BioSymbols v5.2.0 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [861a8166] + Combinatorics v1.1.0 [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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [c2308a5c] + FASTX v2.1.7 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.16.0 [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 v0.11.37 [69de0a69] + Parsers v2.8.3 [33ad39ac] + PhyloNetworks v1.3.0 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [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 v1.1.1 [91c51154] + SentinelArrays v1.4.9 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.2 [354b36f9] + StringViews v1.3.7 [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 v1.13.0 [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 v1.13.0 [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 9.59s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4864.2 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 1816.9 ms ✓ InlineStrings 813.7 ms ✓ Reexport 1187.9 ms ✓ Statistics 925.3 ms ✓ DataAPI 1176.0 ms ✓ ConstructionBase 2130.7 ms ✓ IrrationalConstants 841.0 ms ✓ DataValueInterfaces 1007.6 ms ✓ StaticArraysCore 945.3 ms ✓ StatsAPI 1274.2 ms ✓ OrderedCollections 886.2 ms ✓ InvertedIndices 937.0 ms ✓ Twiddle 1269.1 ms ✓ DocStringExtensions 884.6 ms ✓ CEnum 2173.0 ms ✓ Combinatorics 1134.6 ms ✓ StringViews 1033.2 ms ✓ WorkerUtilities 2085.2 ms ✓ FillArrays 837.1 ms ✓ PtrArrays 1328.5 ms ✓ TranscodingStreams 795.7 ms ✓ IteratorInterfaceExtensions 891.9 ms ✓ LaTeXStrings 1785.7 ms ✓ Crayons 1789.6 ms ✓ PDMats 2165.6 ms ✓ SentinelArrays 1227.3 ms ✓ Compat 1198.2 ms ✓ Preferences 1359.9 ms ✓ Statistics → SparseArraysExt 1041.2 ms ✓ Missings 1107.4 ms ✓ PooledArrays 832.3 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 1520.8 ms ✓ LogExpFunctions 1585.0 ms ✓ FillArrays → FillArraysSparseArraysExt 992.8 ms ✓ FillArrays → FillArraysStatisticsExt 993.3 ms ✓ AliasTables 939.8 ms ✓ BioGenerics 983.4 ms ✓ CodecZlib 813.9 ms ✓ TableTraits 1473.5 ms ✓ FillArrays → FillArraysPDMatsExt 844.4 ms ✓ Compat → CompatLinearAlgebraExt 1215.8 ms ✓ JLLWrappers 946.7 ms ✓ PrecompileTools 1794.1 ms ✓ Tables 2100.6 ms ✓ FilePathsBase 6860.3 ms ✓ Aqua 3807.1 ms ✓ DataStructures 1316.4 ms ✓ Functors 1435.2 ms ✓ NLopt_jll 1412.0 ms ✓ Rmath_jll 1411.8 ms ✓ OpenSpecFun_jll 2572.6 ms ✓ BioSymbols 13760.6 ms ✓ StaticArrays 3180.4 ms ✓ StringManipulation 14398.0 ms ✓ SIMD 15717.7 ms ✓ Parsers 2571.8 ms ✓ FilePathsBase → FilePathsBaseTestExt 930.3 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1525.0 ms ✓ SortingAlgorithms 2763.2 ms ✓ QuadGK 1845.3 ms ✓ NLopt 1431.4 ms ✓ Rmath 4725.6 ms ✓ SpecialFunctions 9199.4 ms ✓ BioSequences 1141.8 ms ✓ StaticArrays → StaticArraysStatisticsExt 1166.2 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1711.3 ms ✓ FillArrays → FillArraysStaticArraysExt 38011.3 ms ✓ PrettyTables 16954.8 ms ✓ Automa 1087.2 ms ✓ InlineStrings → ParsersExt 4849.4 ms ✓ StatsBase 2142.2 ms ✓ HypergeometricFunctions 79615.1 ms ✓ DataFrames 18727.0 ms ✓ FASTX 2840.0 ms ✓ WeakRefStrings 2247.6 ms ✓ PDMats → StatsBaseExt 2739.5 ms ✓ StatsFuns 2116.4 ms ✓ FASTX → BioSequencesExt 26499.2 ms ✓ CSV 7862.6 ms ✓ Distributions 2922.5 ms ✓ Distributions → DistributionsTestExt 13542.6 ms ✓ PhyloNetworks 13214.1 ms ✓ SNaQ 82 dependencies successfully precompiled in 385 seconds. 39 already precompiled. Precompilation completed after 404.99s ################################################################################ # Testing # Testing SNaQ Status `/tmp/jl_cFiuwW/Project.toml` [4c88cf16] Aqua v0.8.14 [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [33ad39ac] PhyloNetworks v1.3.0 [c2bf7a07] SNaQ v1.1.1 [8ba89e20] Distributed v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_cFiuwW/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.1 [3c28c6f8] BioSymbols v5.2.0 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [861a8166] Combinatorics v1.1.0 [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 v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [c2308a5c] FASTX v2.1.7 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.16.0 [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 v0.11.37 [69de0a69] Parsers v2.8.3 [33ad39ac] PhyloNetworks v1.3.0 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.1 [08abe8d2] PrettyTables v3.1.2 [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 v1.1.1 [91c51154] SentinelArrays v1.4.9 [a2af1166] SortingAlgorithms v1.2.2 [276daf66] SpecialFunctions v2.6.1 [90137ffa] StaticArrays v1.9.16 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.8.0 [2913bbd2] StatsBase v0.34.10 [4c63d2b9] StatsFuns v1.5.2 [892a3eda] StringManipulation v0.4.2 [354b36f9] StringViews v1.3.7 [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 v1.13.0 [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 v1.14.0 [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 v1.13.0 [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 v8.18.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [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 v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+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 1m06.3s ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/AATBD/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 put in blacklist edge 11 put in blacklist edge 9 30.0 gene trees per 4-taxon set put in blacklist edge 11 put in blacklist edge 6 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/AATBD/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/AATBD/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 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 1 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; 2026-01-24 19:6:6.066 seed: 66662 for run 1, 2026-01-24 19:6:6.066 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (6,4,((7)#H111:::0.9083438819930102,((#H111:::0.0916561180069898,10):1.333215271021925,8):0.09670829811845263)5:0.958937389055883)1; with -loglik 0.11023402188786652 from run number 1 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 1 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; 2026-01-24 19:7:40.679 seed: 79806 for run 1, 2026-01-24 19:7:40.682 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (6,4,((7)#H111:::1.0,((#H111:::0.0,8):2.2271423783562168e-5,10):0.052363912467201346)5:1.0005337446961264)1; with -loglik 0.8643250954488512 from run number 1 ┌ Warning: these taxa will be deleted from the starting topology, they have no quartet CF data: │ 60 └ @ SNaQ ~/.julia/packages/SNaQ/AATBD/src/snaq_optimization.jl:2073 hybrid edges for hybrid node 5 have missing gamma's, set default: 0.9,0.1 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 1 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; 2026-01-24 19:7:52.985 seed: 1234 for run 1, 2026-01-24 19:7:52.986 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (6,4,((7)#H111:::1.0,((#H111:::0.0,8):2.2271423783562168e-5,10):0.052363912467201346)5:1.0005337446961264)1; with -loglik 0.8643250954488512 from run number 1 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 2 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; 2026-01-24 19:7:55.577 seed: 123 for run 1, 2026-01-24 19:7:55.581 seed: 52121 for run 2, 2026-01-24 19:7:58.132 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (#H111:7.172595948984188::0.06267070715795212,8,(10,(7,((6,4)1:0.0)#H111:1.4328670073515855::0.9373292928420479)5:0.09631058675670329):6.249115892774974); with -loglik 0.005286911785715772 from run number 2 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 2 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; using 2 processors 2026-01-24 19:8:21.635 From worker 4: seed: 123 for run 1, 2026-01-24 19:8:35.106 From worker 4: seed: 52121 for run 2, 2026-01-24 19:9:15.456 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (6,4,((10,(#H111:::0.0,8):2.9921172118024813e-5):0.052363633369246314,(7)#H111:::1.0)5:1.0005326659090306)1; with -loglik 0.8643250955298982 from run number 2 optimization of topology, BL and inheritance probabilities in SNaQ.jl using: hmax = 1, tolerance parameters: ftolRel=0.01, ftolAbs=0.01, xtolAbs=0.01, xtolRel=0.01. max number of failed proposals = 1, liktolAbs = 1.0e-6. rootname for files: snaq BEGIN: 2 runs on starting tree (6,4,((7)#H111:::0.9,((#H111:::0.1,8):1.0,10):0.1)5:0.2)1; 2026-01-24 19:9:18.176 seed: 123 for run 1, 2026-01-24 19:9:18.189 seed: 52121 for run 2, 2026-01-24 19:9:20.507 best network and networks with different hybrid/gene flow directions printed to .networks file MaxNet is (6,4,((7)#H111:::1.0,((#H111:::0.0,8):0.0015443938702141983,10):0.05236390138676052)5:1.0005338164741053)1; with -loglik 0.8643250954488176 from run number 2 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/AATBD/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/AATBD/test/test_5taxon_readTopology.jl:6 overwritten at /home/pkgeval/.julia/packages/SNaQ/AATBD/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/AATBD/src/auxiliary.jl:9 ┌ Warning: SNaQ.CHECKNET is true: will slow snaq! down. └ @ SNaQ ~/.julia/packages/SNaQ/AATBD/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 30.0 gene trees per 4-taxon set 16.0 gene trees per 4-taxon set will use all quartets on 6 taxa calculating obsCF from 6 gene trees and for 15 quartets Reading in quartets... 0+---------------+100% *************** ┌ Warning: not specified numQ with whichQ=rand, so 10% of quartets will be sampled └ @ SNaQ ~/.julia/packages/SNaQ/AATBD/src/readquartetdata.jl:653 list of randomly selected quartets in file rand2Quartets.txt calculating obsCF from 6 gene trees and for 2 quartets Reading in quartets... 0+--+100% ** will use a random sample of 1 4-taxon sets (6.67 percent) on 6 taxa list of randomly selected quartets in file rand1Quartets.txt calculating obsCF from 6 gene trees and for 1 quartets Reading in quartets... 0+-+100% * will use a random sample of 3 4-taxon sets (20.0 percent) on 6 taxa list of randomly selected quartets in file rand3Quartets.txt calculating obsCF from 6 gene trees and for 3 quartets Reading in quartets... 0+---+100% *** will use a random sample of 7 4-taxon sets (46.67 percent) on 6 taxa list of randomly selected quartets in file rand7Quartets.txt calculating obsCF from 6 gene trees and for 7 quartets Reading in quartets... 0+-------+100% ******* will use a random sample of 12 4-taxon sets (80.0 percent) on 6 taxa list of randomly selected quartets in file rand12Quartets.txt calculating obsCF from 6 gene trees and for 12 quartets Reading in quartets... 0+------------+100% ************ will use all quartets on 6 taxa calculating obsCF from 6 gene trees and for 15 quartets Reading in quartets... 0+---------------+100% *************** table of obsCF printed to file tableCF.txt descriptive stat of input data printed to file summaryTreesQuartets.txt data consists of 6 gene trees and 15 4-taxon subsets same taxa in gene trees and quartets: ["A", "B", "C", "D", "E", "O"] Taxon A appears in 5 input trees (83.33 %) Taxon B appears in 6 input trees (100.0 %) Taxon C appears in 6 input trees (100.0 %) Taxon D appears in 6 input trees (100.0 %) Taxon E appears in 6 input trees (100.0 %) Taxon O appears in 6 input trees (100.0 %) ---------------------------- will print below only the 4-taxon subsets with data from <= 70.0% genes ---------------------------- 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/AATBD/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/AATBD/test/test_readInputData.jl:55 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/SNaQ/AATBD/test/test_readInputData.jl:77 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [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 | 240 1 241 8m59.2s read level 1: hyb edge at root then 2-cycle | 1 1 0.6s moveTargetUpdate! reject 2-cycle proposal | 1 1 9.2s test: bad diamond, max pseudo lik | 23 23 21.5s bootsnaq from quartet CF intervals | 1 1 43.5s bootsnaq from bootstrap gene trees, multiple procs | 18 18 1m52.4s correct pseudo likelihood and snaq | 43 43 3m32.5s test: delete hybridization | 20 20 1.6s multiple alleles | 26 26 16.2s test: level-1 partitions | 53 53 1.7s Read CF data | 6 6 1.5s test: reading nexus file | 7 7 1.7s test: calculate quartet CF from input gene trees | 2 1 3 13.8s test: move hybrid around cycle | 2 2 0.2s RNG of the outermost testset: Xoshiro(0xc9a352c16d4ca1a7, 0xd021b563ec5981ee, 0x4e5f67f7c627c019, 0x483b7a7332d437b0, 0xbb85d3ea74ed6dbe) ERROR: LoadError: Some tests did not pass: 240 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/SNaQ/AATBD/test/runtests.jl:54 Testing failed after 1008.28s 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:3122 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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:237 [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:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:228 PkgEval failed after 1461.32s: package has test failures