Package evaluation of PhyNEST on Julia 1.13.0-DEV.771 (d887bd21ab*) started at 2025-06-23T03:44:08.076 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.39s ################################################################################ # Installation # Installing PhyNEST... Resolving package versions... Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Libuuid_jll ───────────────── v2.41.0+0 Installed Libtiff_jll ───────────────── v4.7.1+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed InlineStrings ─────────────── v1.4.4 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed Functors ──────────────────── v0.3.0 Installed Xorg_libXinerama_jll ──────── v1.1.6+0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed libsass_jll ───────────────── v3.6.6+0 Installed OrderedCollections ────────── v1.8.1 Installed SentinelArrays ────────────── v1.4.8 Installed Optim ─────────────────────── v1.13.2 Installed Wayland_protocols_jll ─────── v1.44.0+0 Installed Fontconfig_jll ────────────── v2.16.0+0 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed NaNMath ───────────────────── v1.1.3 Installed Graphics ──────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed Librsvg_jll ───────────────── v2.54.5+0 Installed FileIO ────────────────────── v1.17.0 Installed NLSolversBase ─────────────── v7.10.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed Preferences ───────────────── v1.4.3 Installed Tables ────────────────────── v1.12.1 Installed EnumX ─────────────────────── v1.0.5 Installed Reexport ──────────────────── v1.2.2 Installed Missings ──────────────────── v1.2.0 Installed LaTeXStrings ──────────────── v1.4.0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed Crayons ───────────────────── v4.1.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed UnPack ────────────────────── v1.0.2 Installed TableTraits ───────────────── v1.0.1 Installed SortingAlgorithms ─────────── v1.2.1 Installed ADTypes ───────────────────── v1.15.0 Installed EpollShim_jll ─────────────── v0.0.20230411+1 Installed DiffResults ───────────────── v1.1.0 Installed MacroTools ────────────────── v0.5.16 Installed AbstractTrees ─────────────── v0.4.5 Installed Xorg_libXdamage_jll ───────── v1.1.6+0 Installed DataStructures ────────────── v0.18.22 Installed OpenSSH_jll ───────────────── v9.9.2+0 Installed Gettext_jll ───────────────── v0.21.0+0 Installed Sass ──────────────────────── v0.2.0 Installed FillArrays ────────────────── v1.13.0 Installed CodecZlib ─────────────────── v0.7.8 Installed MethodAnalysis ────────────── v0.4.13 Installed ArrayInterface ────────────── v7.19.0 Installed Observables ───────────────── v0.5.5 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed RoundingIntegers ──────────── v1.1.0 Installed DelimitedFiles ────────────── v1.9.1 Installed CommonSubexpressions ──────── v0.3.1 Installed DataValueInterfaces ───────── v1.0.0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Xorg_libXfixes_jll ────────── v6.0.1+0 Installed CEnum ─────────────────────── v0.5.0 Installed StatsBase ─────────────────── v0.33.21 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Expat_jll ─────────────────── v2.6.5+0 Installed Xorg_libXcursor_jll ───────── v1.2.4+0 Installed IrrationalConstants ───────── v0.2.4 Installed Cairo ─────────────────────── v1.1.1 Installed BitFlags ──────────────────── v0.1.9 Installed libpng_jll ────────────────── v1.6.49+0 Installed LeftChildRightSiblingTrees ── v0.2.0 Installed IOCapture ─────────────────── v0.2.5 Installed GTK4_jll ──────────────────── v4.14.5+0 Installed Scratch ───────────────────── v1.3.0 Installed BenchmarkTools ────────────── v1.6.0 Installed FASTX ─────────────────────── v2.1.7 Installed Setfield ──────────────────── v1.1.2 Installed Graphene_jll ──────────────── v1.10.8+0 Installed PooledArrays ──────────────── v1.4.3 Installed WorkerUtilities ───────────── v1.6.1 Installed PDMats ────────────────────── v0.11.35 Installed ForwardDiff ───────────────── v1.0.1 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed adwaita_icon_theme_jll ────── v43.0.1+0 Installed DocStringExtensions ───────── v0.9.5 Installed BioSequences ──────────────── v3.4.1 Installed StringViews ───────────────── v1.3.4 Installed StatsModels ───────────────── v0.6.33 Installed Combinatorics ─────────────── v1.0.3 Installed ShiftedArrays ─────────────── v2.0.0 Installed AliasTables ───────────────── v1.1.3 Installed DifferentiationInterface ──── v0.7.1 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed MathOptInterface ──────────── v1.41.0 Installed SIMD ──────────────────────── v3.7.1 Installed Wayland_jll ───────────────── v1.23.1+0 Installed Twiddle ───────────────────── v1.1.2 Installed Colors ────────────────────── v0.13.1 Installed Xorg_libXi_jll ────────────── v1.8.3+0 Installed GtkObservables ────────────── v2.2.0 Installed StaticArrays ──────────────── v1.9.13 Installed Xorg_libxkbfile_jll ───────── v1.1.3+0 Installed StaticArraysCore ──────────── v1.4.3 Installed Documenter ────────────────── v0.27.25 Installed CSV ───────────────────────── v0.10.15 Installed Glib_jll ──────────────────── v2.84.0+0 Installed Requires ──────────────────── v1.3.1 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed Xorg_xkbcomp_jll ──────────── v1.4.7+0 Installed StringManipulation ────────── v0.4.1 Installed ColorTypes ────────────────── v0.12.1 Installed PrettyTables ──────────────── v2.4.0 Installed Git_jll ───────────────────── v2.49.0+0 Installed JSON ──────────────────────── v0.21.4 Installed Parsers ───────────────────── v2.8.3 Installed DiffRules ─────────────────── v1.15.1 Installed LogExpFunctions ───────────── v0.3.29 Installed Distributions ─────────────── v0.25.120 Installed DocumenterTools ───────────── v0.1.20 Installed Rmath ─────────────────────── v0.8.0 Installed StatsFuns ─────────────────── v1.5.0 Installed FiniteDiff ────────────────── v2.27.0 Installed Xorg_xkeyboard_config_jll ─── v2.44.0+0 Installed BioGenerics ───────────────── v0.1.5 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed PhyloNetworks ─────────────── v0.15.3 Installed WeakRefStrings ────────────── v1.4.2 Installed DataFrames ────────────────── v1.7.0 Installed JLLWrappers ───────────────── v1.7.0 Installed XZ_jll ────────────────────── v5.8.1+0 Installed Pango_jll ─────────────────── v1.56.3+0 Installed MutableArithmetics ────────── v1.6.4 Installed StructTypes ───────────────── v1.11.0 Installed NLopt ─────────────────────── v0.6.5 Installed FilePathsBase ─────────────── v0.9.24 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed Adapt ─────────────────────── v4.3.0 Installed ConstructionBase ──────────── v1.6.0 Installed GLM ───────────────────────── v1.8.3 Installed JpegTurbo_jll ─────────────── v3.1.1+0 Installed FlameGraphs ───────────────── v1.1.0 Installed Gumbo_jll ─────────────────── v0.10.2+0 Installed Compat ────────────────────── v4.16.0 Installed HypergeometricFunctions ───── v0.3.28 Installed Suppressor ────────────────── v0.2.8 Installed Statistics ────────────────── v1.11.1 Installed Libmount_jll ──────────────── v2.41.0+0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed TranscodingStreams ────────── v0.11.3 Installed PhyNEST ───────────────────── v0.1.12 Installed PositiveFactorizations ────── v0.2.4 Installed xkbcommon_jll ─────────────── v1.8.1+0 Installed StatsAPI ──────────────────── v1.7.1 Installed PrecompileTools ───────────── v1.3.2 Installed Libepoxy_jll ──────────────── v1.5.10+0 Installed BioSymbols ────────────────── v5.2.0 Installed hicolor_icon_theme_jll ────── v0.17.0+3 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed JSON3 ─────────────────────── v1.14.3 Installed ProfileView ───────────────── v1.10.1 Installed CodecBzip2 ────────────────── v0.8.5 Installed PtrArrays ─────────────────── v1.3.0 Installed XML2_jll ──────────────────── v2.13.6+1 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Parameters ────────────────── v0.12.3 Installed iso_codes_jll ─────────────── v4.17.0+0 Installed SpecialFunctions ──────────── v2.5.1 Installed Git ───────────────────────── v1.4.0 Installed gdk_pixbuf_jll ────────────── v2.42.13+0 Installed FixedPointNumbers ─────────── v0.8.5 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed IntervalSets ──────────────── v0.7.11 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Gumbo ─────────────────────── v0.8.3 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Xorg_libXrandr_jll ────────── v1.5.5+0 Installed Gtk4 ──────────────────────── v0.7.8 Installed Automa ────────────────────── v1.1.0 Installed LineSearches ──────────────── v7.4.0 Installed IndirectArrays ────────────── v1.0.0 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed ANSIColoredPrinters ───────── v0.0.1 Installed MathProgBase ──────────────── v0.7.8 Installing 59 artifacts Installed artifact Xorg_libxkbfile 486.7 KiB Installed artifact Xorg_libXcursor 227.1 KiB Installed artifact Pango 1.1 MiB Installed artifact Xorg_xkeyboard_config 537.5 KiB Installed artifact Expat 271.4 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact FreeType2 1.5 MiB Installed artifact NLopt 322.7 KiB Installed artifact Gumbo 703.8 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Rmath 121.9 KiB Installed artifact FriBidi 78.9 KiB Installed artifact libpng 328.3 KiB Installed artifact hicolor_icon_theme 16.3 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Libffi 44.2 KiB Installed artifact Libepoxy 1.2 MiB Installed artifact Bzip2 503.5 KiB Installed artifact OpenSSH 4.2 MiB Installed artifact Libtiff 3.2 MiB Installed artifact Cairo 2.2 MiB Installed artifact libsass 8.9 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Xorg_libXfixes 195.9 KiB Installed artifact Fontconfig 522.5 KiB Installed artifact Libiconv 1.9 MiB Installed artifact Graphene 223.2 KiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Graphite2 120.2 KiB Installed artifact Xorg_libXinerama 50.1 KiB Installed artifact JpegTurbo 1.6 MiB Installed artifact Glib 7.7 MiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Wayland 434.3 KiB Installed artifact LERC 272.9 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact adwaita_icon_theme 5.0 MiB Installed artifact Xorg_libXdamage 50.0 KiB Installed artifact gdk_pixbuf 943.6 KiB Installed artifact Xorg_libXi 1.6 MiB Installed artifact iso_codes 7.0 MiB Installed artifact Xorg_libXrandr 354.5 KiB Installed artifact Pixman 372.2 KiB Installed artifact Libmount 6.4 MiB Installed artifact XML2 2.5 MiB Installed artifact Wayland_protocols 185.1 KiB Installed artifact Xorg_xkbcomp 274.8 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact GTK4 13.4 MiB Installed artifact xkbcommon 653.4 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Librsvg 9.3 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact XZ 1.5 MiB Installed artifact Gettext 4.5 MiB Installed artifact Git 49.6 MiB Updating `~/.julia/environments/v1.13/Project.toml` [115de871] + PhyNEST v0.1.12 Updating `~/.julia/environments/v1.13/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.19.0 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.2.0 [d1d4a3ce] + BitFlags v0.1.9 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 [523fee87] + CodecBzip2 v0.8.5 [944b1d66] + CodecZlib v0.7.8 [3da002f7] + ColorTypes v0.12.1 [5ae59095] + Colors v0.13.1 [861a8166] + Combinatorics v1.0.3 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [187b0558] + ConstructionBase v1.6.0 [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 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.1 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.20 [4e289a0a] + EnumX v1.0.5 [c2308a5c] + FASTX v2.1.7 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [08572546] + FlameGraphs v1.1.0 [f6369f11] + ForwardDiff v1.0.1 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [d7ba0133] + Git v1.4.0 [a2bd30eb] + Graphics v1.1.3 [9db2cae5] + Gtk4 v0.7.8 [8710efd8] + GtkObservables v2.2.0 [708ec375] + Gumbo v0.8.3 [34004b35] + HypergeometricFunctions v0.3.28 [b5f81e59] + IOCapture v0.2.5 [9b13fd28] + IndirectArrays v1.0.0 [842dd82b] + InlineStrings v1.4.4 [8197267c] + IntervalSets v0.7.11 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.0 [d3d80556] + LineSearches v7.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.41.0 [fdba3010] + MathProgBase v0.7.8 [85b6ec6f] + MethodAnalysis v0.4.13 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.4 [d41bc354] + NLSolversBase v7.10.0 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.3 [510215fc] + Observables v0.5.5 [429524aa] + Optim v1.13.2 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [115de871] + PhyNEST v0.1.12 ⌅ [33ad39ac] + PhyloNetworks v0.15.3 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [c46f51b8] + ProfileView v1.10.1 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [d5f540fe] + RoundingIntegers v1.1.0 [fdea26ae] + SIMD v3.7.1 [322a6be2] + Sass v0.2.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [3eaba693] + StatsModels v0.6.33 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.4 [856f2bd8] + StructTypes v1.11.0 [fd094767] + Suppressor v0.2.8 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [7200193e] + Twiddle v1.1.2 [3a884ed6] + UnPack v1.0.2 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [6ebb71f1] + GTK4_jll v4.14.5+0 [78b55507] + Gettext_jll v0.21.0+0 [f8c6e375] + Git_jll v2.49.0+0 [7746bdde] + Glib_jll v2.84.0+0 [75302f13] + Graphene_jll v1.10.8+0 [3b182d85] + Graphite2_jll v1.3.15+0 [528830af] + Gumbo_jll v0.10.2+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [42c93a91] + Libepoxy_jll v1.5.10+0 [e9f186c6] + Libffi_jll v3.4.7+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [925c91fb] + Librsvg_jll v2.54.5+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.41.0+0 [079eb43e] + NLopt_jll v2.10.0+0 ⌅ [9bd350c2] + OpenSSH_jll v9.9.2+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [36c8627f] + Pango_jll v1.56.3+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [a2964d1f] + Wayland_jll v1.23.1+0 [2381bf8a] + Wayland_protocols_jll v1.44.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [0aeada51] + Xorg_libXdamage_jll v1.1.6+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.1+0 [a51aa0fd] + Xorg_libXi_jll v1.8.3+0 [d1454406] + Xorg_libXinerama_jll v1.1.6+0 [ec84b674] + Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.1.3+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [b437f822] + adwaita_icon_theme_jll v43.0.1+0 [da03df04] + gdk_pixbuf_jll v2.42.13+0 ⌅ [059c91fe] + hicolor_icon_theme_jll v0.17.0+3 [bf975903] + iso_codes_jll v4.17.0+0 [b53b4c65] + libpng_jll v1.6.49+0 [47bcb7c8] + libsass_jll v3.6.6+0 [d8fb68d0] + xkbcommon_jll v1.8.1+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 v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [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 [9abbd945] + Profile v1.11.0 [3fa0cd96] + REPL 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 v1.12.0 [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 v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [efcefdf7] + PCRE2_jll v10.45.0+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 v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 31.05s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5052.0 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 918.16s ################################################################################ # Testing # Testing PhyNEST Status `/tmp/jl_DZY1AY/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.120 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [d3d80556] LineSearches v7.4.0 [429524aa] Optim v1.13.2 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [c46f51b8] ProfileView v1.10.1 ⌅ [2913bbd2] StatsBase v0.33.21 [fd094767] Suppressor v0.2.8 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [56ddb016] Logging v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_DZY1AY/Manifest.toml` [47edcb42] ADTypes v1.15.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.19.0 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.2.0 [d1d4a3ce] BitFlags v0.1.9 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 [523fee87] CodecBzip2 v0.8.5 [944b1d66] CodecZlib v0.7.8 [3da002f7] ColorTypes v0.12.1 [5ae59095] Colors v0.13.1 [861a8166] Combinatorics v1.0.3 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [187b0558] ConstructionBase v1.6.0 [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 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.1 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [4e289a0a] EnumX v1.0.5 [c2308a5c] FASTX v2.1.7 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 [08572546] FlameGraphs v1.1.0 [f6369f11] ForwardDiff v1.0.1 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [d7ba0133] Git v1.4.0 [a2bd30eb] Graphics v1.1.3 [9db2cae5] Gtk4 v0.7.8 [8710efd8] GtkObservables v2.2.0 [708ec375] Gumbo v0.8.3 [34004b35] HypergeometricFunctions v0.3.28 [b5f81e59] IOCapture v0.2.5 [9b13fd28] IndirectArrays v1.0.0 [842dd82b] InlineStrings v1.4.4 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [d3d80556] LineSearches v7.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.41.0 [fdba3010] MathProgBase v0.7.8 [85b6ec6f] MethodAnalysis v0.4.13 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.4 [d41bc354] NLSolversBase v7.10.0 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.3 [510215fc] Observables v0.5.5 [429524aa] Optim v1.13.2 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [c46f51b8] ProfileView v1.10.1 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [d5f540fe] RoundingIntegers v1.1.0 [fdea26ae] SIMD v3.7.1 [322a6be2] Sass v0.2.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 ⌅ [3eaba693] StatsModels v0.6.33 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [3a884ed6] UnPack v1.0.2 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.5+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.6.5+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [6ebb71f1] GTK4_jll v4.14.5+0 [78b55507] Gettext_jll v0.21.0+0 [f8c6e375] Git_jll v2.49.0+0 [7746bdde] Glib_jll v2.84.0+0 [75302f13] Graphene_jll v1.10.8+0 [3b182d85] Graphite2_jll v1.3.15+0 [528830af] Gumbo_jll v0.10.2+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [aacddb02] JpegTurbo_jll v3.1.1+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [42c93a91] Libepoxy_jll v1.5.10+0 [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [925c91fb] Librsvg_jll v2.54.5+0 [89763e89] Libtiff_jll v4.7.1+0 [38a345b3] Libuuid_jll v2.41.0+0 [079eb43e] NLopt_jll v2.10.0+0 ⌅ [9bd350c2] OpenSSH_jll v9.9.2+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [36c8627f] Pango_jll v1.56.3+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [a2964d1f] Wayland_jll v1.23.1+0 [2381bf8a] Wayland_protocols_jll v1.44.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [ffd25f8a] XZ_jll v5.8.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [935fb764] Xorg_libXcursor_jll v1.2.4+0 [0aeada51] Xorg_libXdamage_jll v1.1.6+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.7+0 [d091e8ba] Xorg_libXfixes_jll v6.0.1+0 [a51aa0fd] Xorg_libXi_jll v1.8.3+0 [d1454406] Xorg_libXinerama_jll v1.1.6+0 [ec84b674] Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [cc61e674] Xorg_libxkbfile_jll v1.1.3+0 [35661453] Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [b437f822] adwaita_icon_theme_jll v43.0.1+0 [da03df04] gdk_pixbuf_jll v2.42.13+0 ⌅ [059c91fe] hicolor_icon_theme_jll v0.17.0+3 [bf975903] iso_codes_jll v4.17.0+0 [b53b4c65] libpng_jll v1.6.49+0 [47bcb7c8] libsass_jll v3.6.6+0 [d8fb68d0] xkbcommon_jll v1.8.1+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 v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [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 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL 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 v1.12.0 [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 v8.14.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [efcefdf7] PCRE2_jll v10.45.0+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 v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Test Summary: | Pass Total Time Testing misc.function get_average | 100 100 2.4s Test Summary: | Pass Total Time Testing site pattern proabilities | 1000 1000 0.2s Test Summary: | Pass Total Time Testing Method-of-moment estimates of speciation times | 1500 1500 0.0s Testing PhyNEST tests passed Testing completed after 47.87s PkgEval succeeded after 1027.05s