Package evaluation to test PhyNEST on Julia 1.14.0-DEV.1272 (5444ac0564*) started at 2025-11-21T00:33:02.090 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.07s ################################################################################ # Installation # Installing PhyNEST... Resolving package versions... Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed Libtiff_jll ───────────────── v4.7.2+0 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed InlineStrings ─────────────── v1.4.5 Installed Libuuid_jll ───────────────── v2.41.2+0 Installed Functors ──────────────────── v0.3.0 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed OrderedCollections ────────── v1.8.1 Installed Optim ─────────────────────── v1.13.2 Installed SentinelArrays ────────────── v1.4.8 Installed Xorg_libXinerama_jll ──────── v1.1.6+0 Installed Wayland_protocols_jll ─────── v1.44.0+0 Installed Fontconfig_jll ────────────── v2.17.1+0 Installed libsass_jll ───────────────── v3.6.6+0 Installed FileIO ────────────────────── v1.17.1 Installed NaNMath ───────────────────── v1.1.3 Installed QuadGK ────────────────────── v2.11.2 Installed Graphics ──────────────────── v1.1.3 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed EnumX ─────────────────────── v1.0.5 Installed Tables ────────────────────── v1.12.1 Installed NLSolversBase ─────────────── v7.10.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed Reexport ──────────────────── v1.2.2 Installed Librsvg_jll ───────────────── v2.54.7+0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed Missings ──────────────────── v1.2.0 Installed TableTraits ───────────────── v1.0.1 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed Crayons ───────────────────── v4.1.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed Preferences ───────────────── v1.5.0 Installed UnPack ────────────────────── v1.0.2 Installed SortingAlgorithms ─────────── v1.2.2 Installed ADTypes ───────────────────── v1.19.0 Installed DiffResults ───────────────── v1.1.0 Installed MacroTools ────────────────── v0.5.16 Installed EpollShim_jll ─────────────── v0.0.20230411+1 Installed DataStructures ────────────── v0.18.22 Installed OpenSSH_jll ───────────────── v10.2.1+0 Installed AbstractTrees ─────────────── v0.4.5 Installed Sass ──────────────────────── v0.2.0 Installed DelimitedFiles ────────────── v1.9.1 Installed FillArrays ────────────────── v1.15.0 Installed Xorg_libXdamage_jll ───────── v1.1.6+0 Installed CodecZlib ─────────────────── v0.7.8 Installed MethodAnalysis ────────────── v1.0.0 Installed Observables ───────────────── v0.5.5 Installed ArrayInterface ────────────── v7.22.0 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Cairo ─────────────────────── v1.1.1 Installed StatsBase ─────────────────── v0.33.21 Installed DataValueInterfaces ───────── v1.0.0 Installed RoundingIntegers ──────────── v1.1.0 Installed CEnum ─────────────────────── v0.5.0 Installed CommonSubexpressions ──────── v0.3.1 Installed Xorg_libXfixes_jll ────────── v6.0.2+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed Expat_jll ─────────────────── v2.7.3+0 Installed IrrationalConstants ───────── v0.2.6 Installed libpng_jll ────────────────── v1.6.50+0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed Xorg_libXcursor_jll ───────── v1.2.4+0 Installed BitFlags ──────────────────── v0.1.9 Installed LeftChildRightSiblingTrees ── v0.2.1 Installed Scratch ───────────────────── v1.3.0 Installed Setfield ──────────────────── v1.1.2 Installed BenchmarkTools ────────────── v1.6.3 Installed PooledArrays ──────────────── v1.4.3 Installed IOCapture ─────────────────── v0.2.5 Installed Graphene_jll ──────────────── v1.10.8+0 Installed FASTX ─────────────────────── v2.1.7 Installed PDMats ────────────────────── v0.11.35 Installed GTK4_jll ──────────────────── v4.18.6+0 Installed WorkerUtilities ───────────── v1.6.1 Installed DocStringExtensions ───────── v0.9.5 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed adwaita_icon_theme_jll ────── v43.0.1+0 Installed BioSequences ──────────────── v3.5.0 Installed ForwardDiff ───────────────── v1.3.0 Installed DifferentiationInterface ──── v0.7.12 Installed MathOptInterface ──────────── v1.46.0 Installed StringViews ───────────────── v1.3.5 Installed ShiftedArrays ─────────────── v2.0.0 Installed AliasTables ───────────────── v1.1.3 Installed Combinatorics ─────────────── v1.0.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed Git_LFS_jll ───────────────── v3.7.0+0 Installed DataAPI ───────────────────── v1.16.0 Installed SIMD ──────────────────────── v3.7.2 Installed InvertedIndices ───────────── v1.3.1 Installed StatsModels ───────────────── v0.6.33 Installed Xorg_libXi_jll ────────────── v1.8.3+0 Installed Wayland_jll ───────────────── v1.24.0+0 Installed Twiddle ───────────────────── v1.1.2 Installed StaticArraysCore ──────────── v1.4.4 Installed Colors ────────────────────── v0.13.1 Installed GtkObservables ────────────── v2.2.1 Installed StaticArrays ──────────────── v1.9.15 Installed Xorg_libxkbfile_jll ───────── v1.1.3+0 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed ColorTypes ────────────────── v0.12.1 Installed StringManipulation ────────── v0.4.1 Installed Requires ──────────────────── v1.3.1 Installed Xorg_xkbcomp_jll ──────────── v1.4.7+0 Installed Glib_jll ──────────────────── v2.86.0+0 Installed DiffRules ─────────────────── v1.15.1 Installed LogExpFunctions ───────────── v0.3.29 Installed Git_jll ───────────────────── v2.51.3+0 Installed Documenter ────────────────── v0.27.25 Installed JSON ──────────────────────── v0.21.4 Installed PrettyTables ──────────────── v3.1.1 Installed Parsers ───────────────────── v2.8.3 Installed CSV ───────────────────────── v0.10.15 Installed Distributions ─────────────── v0.25.122 Installed FiniteDiff ────────────────── v2.29.0 Installed DocumenterTools ───────────── v0.1.21 Installed Rmath ─────────────────────── v0.9.0 Installed StatsFuns ─────────────────── v1.5.2 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed BioGenerics ───────────────── v0.1.5 Installed Xorg_xkeyboard_config_jll ─── v2.44.0+0 Installed MutableArithmetics ────────── v1.6.7 Installed WeakRefStrings ────────────── v1.4.2 Installed PhyloNetworks ─────────────── v0.15.3 Installed DataFrames ────────────────── v1.8.1 Installed JLLWrappers ───────────────── v1.7.1 Installed StructTypes ───────────────── v1.11.0 Installed FilePathsBase ─────────────── v0.9.24 Installed XZ_jll ────────────────────── v5.8.1+0 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed Pango_jll ─────────────────── v1.57.0+0 Installed NLopt ─────────────────────── v0.6.5 Installed JpegTurbo_jll ─────────────── v3.1.3+0 Installed GLM ───────────────────────── v1.8.3 Installed Adapt ─────────────────────── v4.4.0 Installed ConstructionBase ──────────── v1.6.0 Installed HypergeometricFunctions ───── v0.3.28 Installed Libmount_jll ──────────────── v2.41.2+0 Installed Gumbo_jll ─────────────────── v0.10.2+0 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Compat ────────────────────── v4.18.1 Installed Suppressor ────────────────── v0.2.8 Installed TranscodingStreams ────────── v0.11.3 Installed Statistics ────────────────── v1.11.1 Installed PositiveFactorizations ────── v0.2.4 Installed StatsAPI ──────────────────── v1.7.1 Installed FlameGraphs ───────────────── v1.1.0 Installed BioSymbols ────────────────── v5.2.0 Installed PrecompileTools ───────────── v1.3.3 Installed Libepoxy_jll ──────────────── v1.5.11+0 Installed CodecBzip2 ────────────────── v0.8.5 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed JSON3 ─────────────────────── v1.14.3 Installed xkbcommon_jll ─────────────── v1.9.2+0 Installed ProfileView ───────────────── v1.10.2 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed XML2_jll ──────────────────── v2.13.9+0 Installed Parameters ────────────────── v0.12.3 Installed PtrArrays ─────────────────── v1.3.0 Installed hicolor_icon_theme_jll ────── v0.18.0+0 Installed iso_codes_jll ─────────────── v4.18.0+0 Installed Git ───────────────────────── v1.5.0 Installed SpecialFunctions ──────────── v2.6.1 Installed FixedPointNumbers ─────────── v0.8.5 Installed IntervalSets ──────────────── v0.7.13 Installed gdk_pixbuf_jll ────────────── v2.42.13+0 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed Gtk4 ──────────────────────── v0.7.11 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed Gumbo ─────────────────────── v0.8.3 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed LineSearches ──────────────── v7.4.1 Installed IndirectArrays ────────────── v1.0.0 Installed Automa ────────────────────── v1.1.0 Installed Xorg_libXrandr_jll ────────── v1.5.5+0 Installed PhyNEST ───────────────────── v0.1.12 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed MathProgBase ──────────────── v0.7.8 Installed ANSIColoredPrinters ───────── v0.0.1 Installing 60 artifacts Installed artifact Xorg_libXrender 435.9 KiB Installed artifact Xorg_libXinerama 50.1 KiB Installed artifact Xorg_libXcursor 227.1 KiB Installed artifact Xorg_libxkbfile 486.7 KiB Installed artifact NLopt 322.7 KiB Installed artifact hicolor_icon_theme 13.2 KiB Installed artifact Wayland_protocols 185.1 KiB Installed artifact Libiconv 1.9 MiB Installed artifact LERC 272.9 KiB Installed artifact Gumbo 703.8 KiB Installed artifact XML2 2.5 MiB Installed artifact Bzip2 503.5 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Pixman 372.2 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Xorg_libXfixes 59.0 KiB Installed artifact Xorg_libXi 1.6 MiB Installed artifact Pango 2.0 MiB Installed artifact Graphene 223.2 KiB Installed artifact Graphite2 120.2 KiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Fontconfig 984.8 KiB Installed artifact Expat 283.3 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Cairo 2.2 MiB Installed artifact Git_LFS 9.6 MiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Xorg_xkeyboard_config 537.5 KiB Installed artifact adwaita_icon_theme 5.0 MiB Installed artifact Xorg_xkbcomp 274.8 KiB Installed artifact libpng 328.4 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Xorg_libXdamage 50.0 KiB Installed artifact OpenSSH 4.3 MiB Installed artifact LZO 208.9 KiB Installed artifact Rmath 121.9 KiB Installed artifact Librsvg 9.3 MiB Installed artifact Libuuid 3.7 MiB Installed artifact Libffi 44.2 KiB Installed artifact Libepoxy 504.4 KiB Installed artifact gdk_pixbuf 943.6 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact JpegTurbo 1.4 MiB Installed artifact Glib 7.7 MiB Installed artifact Libmount 6.5 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact XZ 1.5 MiB Installed artifact Wayland 390.6 KiB Installed artifact xkbcommon 263.7 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_libXrandr 354.5 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact GTK4 14.1 MiB Installed artifact Libtiff 2.3 MiB Installed artifact libsass 8.9 MiB Installed artifact iso_codes 7.5 MiB Installed artifact Git 48.9 MiB Updating `~/.julia/environments/v1.14/Project.toml` [115de871] + PhyNEST v0.1.12 Updating `~/.julia/environments/v1.14/Manifest.toml` [47edcb42] + ADTypes v1.19.0 [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.22.0 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.3 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.0 [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 v4.18.1 [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 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.12 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.21 [4e289a0a] + EnumX v1.0.5 [c2308a5c] + FASTX v2.1.7 [5789e2e9] + FileIO v1.17.1 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 [53c48c17] + FixedPointNumbers v0.8.5 [08572546] + FlameGraphs v1.1.0 [f6369f11] + ForwardDiff v1.3.0 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [d7ba0133] + Git v1.5.0 [a2bd30eb] + Graphics v1.1.3 [9db2cae5] + Gtk4 v0.7.11 [8710efd8] + GtkObservables v2.2.1 [708ec375] + Gumbo v0.8.3 [34004b35] + HypergeometricFunctions v0.3.28 ⌅ [b5f81e59] + IOCapture v0.2.5 [9b13fd28] + IndirectArrays v1.0.0 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.13 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 ⌅ [682c06a0] + JSON v0.21.4 [0f8b85d8] + JSON3 v1.14.3 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.1 [d3d80556] + LineSearches v7.4.1 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [b8f27783] + MathOptInterface v1.46.0 [fdba3010] + MathProgBase v0.7.8 [85b6ec6f] + MethodAnalysis v1.0.0 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.7 [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 v1.3.3 [21216c6a] + Preferences v1.5.0 [08abe8d2] + PrettyTables v3.1.1 [c46f51b8] + ProfileView v1.10.2 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [d5f540fe] + RoundingIntegers v1.1.0 [fdea26ae] + SIMD v3.7.2 [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 v1.2.2 [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 v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [3eaba693] + StatsModels v0.6.33 [892a3eda] + StringManipulation v0.4.1 [354b36f9] + StringViews v1.3.5 [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 v2.7.3+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [6ebb71f1] + GTK4_jll v4.18.6+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [020c3dae] + Git_LFS_jll v3.7.0+0 [f8c6e375] + Git_jll v2.51.3+0 [7746bdde] + Glib_jll v2.86.0+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 v3.1.3+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 v1.5.11+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 v2.41.2+0 [925c91fb] + Librsvg_jll v2.54.7+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [079eb43e] + NLopt_jll v2.10.0+0 [9bd350c2] + OpenSSH_jll v10.2.1+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [f50d1b31] + Rmath_jll v0.5.1+0 [a2964d1f] + Wayland_jll v1.24.0+0 [2381bf8a] + Wayland_protocols_jll v1.44.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.9+0 [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 v6.0.2+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 v0.18.0+0 [bf975903] + iso_codes_jll v4.18.0+0 [b53b4c65] + libpng_jll v1.6.50+0 [47bcb7c8] + libsass_jll v3.6.6+0 [d8fb68d0] + xkbcommon_jll v1.9.2+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 [9abbd945] + Profile 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 v2025.11.4 [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 ⌃ 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 30.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4778.1 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/i9lgt/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/i9lgt/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... 4309.6 ms ✓ MacroTools 1688.9 ms ✓ InlineStrings 762.9 ms ✓ Reexport 1070.0 ms ✓ ConstructionBase 2028.4 ms ✓ IrrationalConstants 754.1 ms ✓ DataValueInterfaces 857.9 ms ✓ StatsAPI 1047.5 ms ✓ Observables 832.5 ms ✓ Twiddle 1023.0 ms ✓ IntervalSets 812.4 ms ✓ CEnum 967.0 ms ✓ Functors 2041.7 ms ✓ Combinatorics 1038.2 ms ✓ StringViews 1245.1 ms ✓ TranscodingStreams 825.1 ms ✓ LaTeXStrings 1121.9 ms ✓ Statistics 975.0 ms ✓ StaticArraysCore 794.2 ms ✓ Suppressor 794.0 ms ✓ PtrArrays 995.4 ms ✓ ANSIColoredPrinters 989.1 ms ✓ PositiveFactorizations 866.0 ms ✓ DataAPI 847.7 ms ✓ InvertedIndices 850.5 ms ✓ BitFlags 874.5 ms ✓ ShiftedArrays 1169.2 ms ✓ AbstractTrees 893.2 ms ✓ EnumX 1050.2 ms ✓ WorkerUtilities 2066.5 ms ✓ FillArrays 816.3 ms ✓ IndirectArrays 816.7 ms ✓ RoundingIntegers 789.7 ms ✓ UnPack 1238.1 ms ✓ OrderedCollections 1385.4 ms ✓ ADTypes 1087.6 ms ✓ DocStringExtensions 771.5 ms ✓ IteratorInterfaceExtensions 1743.2 ms ✓ Crayons 846.1 ms ✓ IOCapture 952.3 ms ✓ DelimitedFiles 948.3 ms ✓ NaNMath 1083.8 ms ✓ Requires 1189.8 ms ✓ SuiteSparse 1911.3 ms ✓ MathProgBase 866.2 ms ✓ Scratch 2550.5 ms ✓ SentinelArrays 1555.2 ms ✓ StructTypes 1088.3 ms ✓ Compat 1070.5 ms ✓ Preferences 10146.3 ms ✓ MutableArithmetics 1600.1 ms ✓ CommonSubexpressions 784.8 ms ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 783.1 ms ✓ IntervalSets → IntervalSetsRandomExt 759.0 ms ✓ ConstructionBase → ConstructionBaseIntervalSetsExt 908.5 ms ✓ BioGenerics 963.6 ms ✓ CodecZlib 1293.8 ms ✓ Statistics → SparseArraysExt 3706.1 ms ✓ FixedPointNumbers 831.6 ms ✓ IntervalSets → IntervalSetsStatisticsExt 862.2 ms ✓ DiffResults 930.2 ms ✓ AliasTables 931.7 ms ✓ Missings 1084.2 ms ✓ PooledArrays 869.8 ms ✓ LeftChildRightSiblingTrees 1099.5 ms ✓ MethodAnalysis 1539.3 ms ✓ FillArrays → FillArraysSparseArraysExt 968.1 ms ✓ FillArrays → FillArraysStatisticsExt 916.8 ms ✓ Parameters 797.6 ms ✓ ADTypes → ADTypesConstructionBaseExt 1827.2 ms ✓ DifferentiationInterface 1273.9 ms ✓ LogExpFunctions 760.4 ms ✓ TableTraits 905.1 ms ✓ Adapt 8982.9 ms ✓ FileIO 1746.6 ms ✓ PDMats 818.2 ms ✓ Compat → CompatLinearAlgebraExt 892.9 ms ✓ PrecompileTools 1199.7 ms ✓ JLLWrappers 2954.3 ms ✓ Setfield 2729.4 ms ✓ ColorTypes 1310.0 ms ✓ DifferentiationInterface → DifferentiationInterfaceSparseArraysExt 1742.7 ms ✓ Tables 1135.0 ms ✓ ArrayInterface 1233.8 ms ✓ Adapt → AdaptSparseArraysExt 1450.4 ms ✓ FillArrays → FillArraysPDMatsExt 2049.8 ms ✓ FilePathsBase 3896.5 ms ✓ DataStructures 2493.1 ms ✓ BioSymbols 2945.9 ms ✓ StringManipulation 16124.3 ms ✓ SIMD 12406.2 ms ✓ StaticArrays 14993.8 ms ✓ Parsers 1273.5 ms ✓ Libffi_jll 1874.0 ms ✓ LZO_jll 1614.0 ms ✓ Bzip2_jll 1792.9 ms ✓ XZ_jll 1668.8 ms ✓ NLopt_jll 1380.9 ms ✓ Rmath_jll 1391.0 ms ✓ OpenSpecFun_jll 1201.5 ms ✓ Xorg_xtrans_jll 1392.0 ms ✓ libpng_jll 1404.2 ms ✓ iso_codes_jll 1139.8 ms ✓ EpollShim_jll 1221.1 ms ✓ Wayland_protocols_jll 1399.5 ms ✓ Libmount_jll 1389.0 ms ✓ Libuuid_jll 1393.2 ms ✓ FriBidi_jll 1411.0 ms ✓ LERC_jll 1413.7 ms ✓ Git_LFS_jll 1367.0 ms ✓ libsass_jll 1382.7 ms ✓ Gumbo_jll 1402.5 ms ✓ Xorg_libXau_jll 1481.1 ms ✓ OpenSSH_jll 1392.4 ms ✓ hicolor_icon_theme_jll 1360.4 ms ✓ Graphite2_jll 1390.8 ms ✓ LLVMOpenMP_jll 1400.6 ms ✓ Libiconv_jll 1384.3 ms ✓ Xorg_libXdmcp_jll 1395.8 ms ✓ Expat_jll 1424.3 ms ✓ JpegTurbo_jll 1287.8 ms ✓ ColorTypes → StyledStringsExt 7880.7 ms ✓ Colors 738.8 ms ✓ ArrayInterface → ArrayInterfaceStaticArraysCoreExt 1245.6 ms ✓ ArrayInterface → ArrayInterfaceSparseArraysExt 2616.5 ms ✓ FilePathsBase → FilePathsBaseTestExt 938.7 ms ✓ FilePathsBase → FilePathsBaseMmapExt 1902.3 ms ✓ SortingAlgorithms 3125.8 ms ✓ QuadGK 9450.6 ms ✓ BioSequences 39210.7 ms ✓ PrettyTables 19644.7 ms ✓ Automa 1343.7 ms ✓ StaticArrays → StaticArraysStatisticsExt 1331.9 ms ✓ ConstructionBase → ConstructionBaseStaticArraysExt 1353.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceStaticArraysExt 1398.0 ms ✓ Adapt → AdaptStaticArraysExt 12700.4 ms ✓ JSON3 3487.4 ms ✓ JSON 917.3 ms ✓ InlineStrings → ParsersExt 988.4 ms ✓ CodecBzip2 1475.9 ms ✓ FreeType2_jll 1460.8 ms ✓ Rmath 4557.1 ms ✓ SpecialFunctions 2054.6 ms ✓ Sass 1278.5 ms ✓ Gumbo 1393.7 ms ✓ adwaita_icon_theme_jll 1394.8 ms ✓ Pixman_jll 1441.6 ms ✓ XML2_jll 1401.7 ms ✓ GettextRuntime_jll 1466.8 ms ✓ Xorg_libxcb_jll 1436.3 ms ✓ Git_jll 1438.0 ms ✓ Wayland_jll 1431.3 ms ✓ Libtiff_jll 1361.6 ms ✓ Graphics 10561.7 ms ✓ FlameGraphs 1311.3 ms ✓ FiniteDiff 8962.0 ms ✓ StatsBase 91906.8 ms ✓ DataFrames 22638.2 ms ✓ FASTX 9028.6 ms ✓ Documenter 3052.0 ms ✓ BenchmarkTools 2542.8 ms ✓ WeakRefStrings 1506.8 ms ✓ Fontconfig_jll 2481.2 ms ✓ HypergeometricFunctions 1268.7 ms ✓ DiffRules 1464.2 ms ✓ Glib_jll 1420.8 ms ✓ Xorg_libX11_jll 957.9 ms ✓ Git 1406.6 ms ✓ FiniteDiff → FiniteDiffStaticArraysExt 1288.8 ms ✓ FiniteDiff → FiniteDiffSparseArraysExt 986.7 ms ✓ DifferentiationInterface → DifferentiationInterfaceFiniteDiffExt 2407.6 ms ✓ FASTX → BioSequencesExt 29832.5 ms ✓ CSV 2824.5 ms ✓ StatsFuns 6262.6 ms ✓ ForwardDiff 1473.1 ms ✓ Graphene_jll 1430.5 ms ✓ Xorg_libXfixes_jll 1418.4 ms ✓ Xorg_libXrender_jll 1268.0 ms ✓ Xorg_libXext_jll 1286.1 ms ✓ Xorg_libxkbfile_jll 1204.7 ms ✓ gdk_pixbuf_jll 3338.0 ms ✓ DocumenterTools 7051.8 ms ✓ StatsModels 14310.5 ms ✓ Distributions 2129.5 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1499.1 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 76938.8 ms ✓ MathOptInterface 1495.6 ms ✓ Xorg_libXdamage_jll 1496.9 ms ✓ Xorg_libXcursor_jll 1513.8 ms ✓ Xorg_libXrandr_jll 1442.8 ms ✓ Xorg_libXinerama_jll 1410.3 ms ✓ Xorg_libXi_jll 1477.6 ms ✓ Cairo_jll 1391.1 ms ✓ Libglvnd_jll 1582.2 ms ✓ Xorg_xkbcomp_jll 9189.5 ms ✓ GLM 4155.6 ms ✓ Distributions → DistributionsTestExt 2344.8 ms ✓ NLSolversBase 7130.3 ms ✓ NLopt 1497.1 ms ✓ HarfBuzz_jll 1492.3 ms ✓ Libepoxy_jll 1231.6 ms ✓ Xorg_xkeyboard_config_jll 4307.6 ms ✓ LineSearches 30179.0 ms ✓ PhyloNetworks 1516.4 ms ✓ Pango_jll 1426.5 ms ✓ xkbcommon_jll 10793.6 ms ✓ Optim 2599.2 ms ✓ Cairo 1523.0 ms ✓ Librsvg_jll 1566.7 ms ✓ GTK4_jll 6930.2 ms ✓ Optim → OptimMOIExt 49186.5 ms ✓ Gtk4  (julia:1104): Gtk-WARNING **: 00:47:49.023: Unable to acquire session bus: Cannot spawn a message bus without a machine-id: Invalid machine ID in /workspace/destdir/var/lib/dbus/machine-id or /etc/machine-id 25198.5 ms ✓ GtkObservables  (julia:1114): Gtk-WARNING **: 00:48:23.191: Unable to acquire session bus: Cannot spawn a message bus without a machine-id: Invalid machine ID in /workspace/destdir/var/lib/dbus/machine-id or /etc/machine-id 18730.6 ms ✓ ProfileView 25363.6 ms ✓ PhyNEST 214 dependencies successfully precompiled in 887 seconds. 39 already precompiled. 2 dependencies had output during precompilation: ┌ ProfileView │ (julia:1114): Gtk-WARNING **: 00:48:23.191: Unable to acquire session bus: Cannot spawn a message bus without a machine-id: Invalid machine ID in /workspace/destdir/var/lib/dbus/machine-id or /etc/machine-id └ ┌ GtkObservables │ (julia:1104): Gtk-WARNING **: 00:47:49.023: Unable to acquire session bus: Cannot spawn a message bus without a machine-id: Invalid machine ID in /workspace/destdir/var/lib/dbus/machine-id or /etc/machine-id └ Precompilation completed after 897.69s ################################################################################ # Testing # Testing PhyNEST Status `/tmp/jl_q5Ypu9/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.8.1 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.122 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.21 [d3d80556] LineSearches v7.4.1 [429524aa] Optim v1.13.2 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [c46f51b8] ProfileView v1.10.2 ⌅ [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_q5Ypu9/Manifest.toml` [47edcb42] ADTypes v1.19.0 [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.3 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.0 [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 v4.18.1 [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 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.12 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.21 [4e289a0a] EnumX v1.0.5 [c2308a5c] FASTX v2.1.7 [5789e2e9] FileIO v1.17.1 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 [53c48c17] FixedPointNumbers v0.8.5 [08572546] FlameGraphs v1.1.0 [f6369f11] ForwardDiff v1.3.0 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [d7ba0133] Git v1.5.0 [a2bd30eb] Graphics v1.1.3 [9db2cae5] Gtk4 v0.7.11 [8710efd8] GtkObservables v2.2.1 [708ec375] Gumbo v0.8.3 [34004b35] HypergeometricFunctions v0.3.28 ⌅ [b5f81e59] IOCapture v0.2.5 [9b13fd28] IndirectArrays v1.0.0 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 ⌅ [682c06a0] JSON v0.21.4 [0f8b85d8] JSON3 v1.14.3 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.1 [d3d80556] LineSearches v7.4.1 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [b8f27783] MathOptInterface v1.46.0 [fdba3010] MathProgBase v0.7.8 [85b6ec6f] MethodAnalysis v1.0.0 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.7 [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 v1.3.3 [21216c6a] Preferences v1.5.0 [08abe8d2] PrettyTables v3.1.1 [c46f51b8] ProfileView v1.10.2 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.9.0 [d5f540fe] RoundingIntegers v1.1.0 [fdea26ae] SIMD v3.7.2 [322a6be2] Sass v0.2.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield 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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 ⌃ 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 1.5s Test Summary: | Pass Total Time Testing site pattern proabilities | 1000 1000 0.1s Test Summary: | Pass Total Time Testing Method-of-moment estimates of speciation times | 1500 1500 0.0s Testing PhyNEST tests passed Testing completed after 45.8s PkgEval succeeded after 1003.12s