Package evaluation of PhyNEST on Julia 1.13.0-DEV.123 (e910e6fb06*) started at 2025-03-02T01:04:14.854 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.01s ################################################################################ # Installation # Installing PhyNEST... Resolving package versions... Installed iso_codes_jll ─────────────── v4.15.1+0 Installed Libmount_jll ──────────────── v2.40.3+0 Installed JpegTurbo_jll ─────────────── v3.1.1+0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed BioGenerics ───────────────── v0.1.5 Installed HypergeometricFunctions ───── v0.3.27 Installed Preferences ───────────────── v1.4.3 Installed Xorg_xkbcomp_jll ──────────── v1.4.6+1 Installed Git_jll ───────────────────── v2.47.1+0 Installed PDMats ────────────────────── v0.11.32 Installed StatsFuns ─────────────────── v1.3.2 Installed InlineStrings ─────────────── v1.4.3 Installed MutableArithmetics ────────── v1.6.4 Installed DocumenterTools ───────────── v0.1.20 Installed StaticArrays ──────────────── v1.9.13 Installed CEnum ─────────────────────── v0.5.0 Installed Xorg_libpthread_stubs_jll ─── v0.1.2+0 Installed DelimitedFiles ────────────── v1.9.1 Installed Cairo_jll ─────────────────── v1.18.2+1 Installed InvertedIndices ───────────── v1.3.1 Installed BioSequences ──────────────── v3.4.1 Installed FileIO ────────────────────── v1.17.0 Installed Fontconfig_jll ────────────── v2.15.0+0 Installed Statistics ────────────────── v1.11.1 Installed GLM ───────────────────────── v1.8.3 Installed Libgpg_error_jll ──────────── v1.51.1+0 Installed Xorg_libXinerama_jll ──────── v1.1.5+0 Installed Xorg_libxkbfile_jll ───────── v1.1.2+1 Installed GTK4_jll ──────────────────── v4.14.5+0 Installed Xorg_libXau_jll ───────────── v1.0.12+0 Installed EpollShim_jll ─────────────── v0.0.20230411+1 Installed DataFrames ────────────────── v1.7.0 Installed Missings ──────────────────── v1.2.0 Installed Sass ──────────────────────── v0.2.0 Installed FiniteDiff ────────────────── v2.27.0 Installed SIMD ──────────────────────── v3.7.1 Installed IrrationalConstants ───────── v0.2.4 Installed Functors ──────────────────── v0.3.0 Installed hicolor_icon_theme_jll ────── v0.17.0+3 Installed Pango_jll ─────────────────── v1.56.1+0 Installed NLopt ─────────────────────── v0.6.5 Installed JSON ──────────────────────── v0.21.4 Installed PtrArrays ─────────────────── v1.3.0 Installed BenchmarkTools ────────────── v1.6.0 Installed SpecialFunctions ──────────── v2.5.0 Installed xkbcommon_jll ─────────────── v1.4.1+2 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed XZ_jll ────────────────────── v5.6.4+1 Installed CodecBzip2 ────────────────── v0.8.5 Installed SentinelArrays ────────────── v1.4.8 Installed HarfBuzz_jll ──────────────── v8.5.0+0 Installed StaticArraysCore ──────────── v1.4.3 Installed NaNMath ───────────────────── v1.1.2 Installed BioSymbols ────────────────── v5.1.3 Installed LZO_jll ───────────────────── v2.10.3+0 Installed WorkerUtilities ───────────── v1.6.1 Installed TranscodingStreams ────────── v0.11.3 Installed FriBidi_jll ───────────────── v1.0.16+0 Installed StringViews ───────────────── v1.3.4 Installed NLSolversBase ─────────────── v7.8.3 Installed MathOptInterface ──────────── v1.37.0 Installed Gumbo_jll ─────────────────── v0.10.2+0 Installed adwaita_icon_theme_jll ────── v43.0.1+0 Installed MathProgBase ──────────────── v0.7.8 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed Libepoxy_jll ──────────────── v1.5.10+0 Installed Graphics ──────────────────── v1.1.3 Installed WeakRefStrings ────────────── v1.4.2 Installed StatsModels ───────────────── v0.6.33 Installed Colors ────────────────────── v0.13.0 Installed CommonSubexpressions ──────── v0.3.1 Installed FreeType2_jll ─────────────── v2.13.3+1 Installed DataStructures ────────────── v0.18.20 Installed LeftChildRightSiblingTrees ── v0.2.0 Installed StatsAPI ──────────────────── v1.7.0 Installed Compat ────────────────────── v4.16.0 Installed RoundingIntegers ──────────── v1.1.0 Installed Xorg_libxcb_jll ───────────── v1.17.0+3 Installed libpng_jll ────────────────── v1.6.40+0 Installed CodecZlib ─────────────────── v0.7.8 Installed Automa ────────────────────── v1.1.0 Installed StatsBase ─────────────────── v0.33.21 Installed StructTypes ───────────────── v1.11.0 Installed Scratch ───────────────────── v1.2.1 Installed ANSIColoredPrinters ───────── v0.0.1 Installed gdk_pixbuf_jll ────────────── v2.42.12+0 Installed ColorTypes ────────────────── v0.12.0 Installed FlameGraphs ───────────────── v1.1.0 Installed DiffRules ─────────────────── v1.15.1 Installed Twiddle ───────────────────── v1.1.2 Installed Xorg_libXext_jll ──────────── v1.3.6+3 Installed Zstd_jll ──────────────────── v1.5.7+1 Installed JSON3 ─────────────────────── v1.14.1 Installed Expat_jll ─────────────────── v2.6.5+0 Installed TableTraits ───────────────── v1.0.1 Installed PositiveFactorizations ────── v0.2.4 Installed Parsers ───────────────────── v2.8.1 Installed DiffResults ───────────────── v1.1.0 Installed PrettyTables ──────────────── v2.4.0 Installed Libtiff_jll ───────────────── v4.7.1+0 Installed PooledArrays ──────────────── v1.4.3 Installed Setfield ──────────────────── v1.1.2 Installed JLLWrappers ───────────────── v1.7.0 Installed ConstructionBase ──────────── v1.5.8 Installed DataValueInterfaces ───────── v1.0.0 Installed Libffi_jll ────────────────── v3.2.2+2 Installed Xorg_libXrender_jll ───────── v0.9.11+1 Installed AbstractTrees ─────────────── v0.4.5 Installed OrderedCollections ────────── v1.8.0 Installed Combinatorics ─────────────── v1.0.2 Installed Xorg_libXi_jll ────────────── v1.8.2+0 Installed XSLT_jll ──────────────────── v1.1.42+0 Installed ArrayInterface ────────────── v7.18.0 Installed Reexport ──────────────────── v1.2.2 Installed LineSearches ──────────────── v7.3.0 Installed LogExpFunctions ───────────── v0.3.29 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed AliasTables ───────────────── v1.1.3 Installed MacroTools ────────────────── v0.5.15 Installed ProfileView ───────────────── v1.10.1 Installed Graphene_jll ──────────────── v1.10.6+0 Installed Xorg_libXcursor_jll ───────── v1.2.3+0 Installed UnPack ────────────────────── v1.0.2 Installed Librsvg_jll ───────────────── v2.54.5+0 Installed Git ───────────────────────── v1.3.1 Installed Libuuid_jll ───────────────── v2.40.3+0 Installed Gtk4 ──────────────────────── v0.7.6 Installed Wayland_protocols_jll ─────── v1.36.0+0 Installed Crayons ───────────────────── v4.1.1 Installed GtkObservables ────────────── v2.2.0 Installed DocStringExtensions ───────── v0.9.3 Installed FASTX ─────────────────────── v2.1.7 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed Pixman_jll ────────────────── v0.43.4+0 Installed Adapt ─────────────────────── v4.2.0 Installed Graphite2_jll ─────────────── v1.3.14+1 Installed Rmath ─────────────────────── v0.8.0 Installed Gettext_jll ───────────────── v0.21.0+0 Installed XML2_jll ──────────────────── v2.13.6+1 Installed Wayland_jll ───────────────── v1.21.0+2 Installed IntervalSets ──────────────── v0.7.10 Installed CSV ───────────────────────── v0.10.15 Installed PhyNEST ───────────────────── v0.1.12 Installed Xorg_xtrans_jll ───────────── v1.5.1+0 Installed Suppressor ────────────────── v0.2.8 Installed BitFlags ──────────────────── v0.1.9 Installed Cairo ─────────────────────── v1.1.1 Installed IndirectArrays ────────────── v1.0.0 Installed IOCapture ─────────────────── v0.2.5 Installed Libgcrypt_jll ─────────────── v1.11.0+0 Installed libsass_jll ───────────────── v3.6.6+0 Installed Documenter ────────────────── v0.27.25 Installed Tables ────────────────────── v1.12.0 Installed Xorg_xkeyboard_config_jll ─── v2.39.0+0 Installed DataAPI ───────────────────── v1.16.0 Installed LLVMOpenMP_jll ────────────── v18.1.7+0 Installed FixedPointNumbers ─────────── v0.8.5 Installed Xorg_libXfixes_jll ────────── v6.0.0+0 Installed Xorg_libXrandr_jll ────────── v1.5.4+0 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed PrecompileTools ───────────── v1.2.1 Installed Optim ─────────────────────── v1.11.0 Installed LaTeXStrings ──────────────── v1.4.0 Installed Gumbo ─────────────────────── v0.8.3 Installed Glib_jll ──────────────────── v2.82.4+0 Installed OpenSSH_jll ───────────────── v9.9.2+0 Installed Libglvnd_jll ──────────────── v1.7.0+0 Installed PhyloNetworks ─────────────── v0.15.3 Installed FilePathsBase ─────────────── v0.9.23 Installed FillArrays ────────────────── v1.13.0 Installed ForwardDiff ───────────────── v0.10.38 Installed QuadGK ────────────────────── v2.11.2 Installed ShiftedArrays ─────────────── v2.0.0 Installed Requires ──────────────────── v1.3.1 Installed Xorg_libXdmcp_jll ─────────── v1.1.5+0 Installed Xorg_libX11_jll ───────────── v1.8.6+3 Installed Observables ───────────────── v0.5.5 Installed Xorg_libXdamage_jll ───────── v1.1.5+4 Installed Parameters ────────────────── v0.12.3 Installed MethodAnalysis ────────────── v0.4.13 Installed Distributions ─────────────── v0.25.117 Installed StringManipulation ────────── v0.4.1 Installed SortingAlgorithms ─────────── v1.2.1 Installing 64 artifacts Installed artifact Fontconfig 527.0 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact LZO 208.9 KiB Installed artifact Libglvnd 833.5 KiB Installed artifact Cairo 2.2 MiB Installed artifact Libtiff 3.2 MiB Installed artifact Xorg_libXfixes 195.8 KiB Installed artifact Wayland 406.1 KiB Installed artifact Graphite2 120.2 KiB Installed artifact FriBidi 78.9 KiB Installed artifact adwaita_icon_theme 5.0 MiB Installed artifact Xorg_libXcursor 227.1 KiB Installed artifact Graphene 228.2 KiB Installed artifact JpegTurbo 1.6 MiB Installed artifact NLopt 322.7 KiB Installed artifact OpenSSH 4.2 MiB Installed artifact Pixman 373.2 KiB Installed artifact libsass 8.9 MiB Installed artifact libpng 326.4 KiB Installed artifact Pango 1.1 MiB Installed artifact XZ 1.4 MiB Installed artifact Xorg_libXrender 434.8 KiB Installed artifact Xorg_libXrandr 354.4 KiB Installed artifact Zstd 646.0 KiB Installed artifact hicolor_icon_theme 16.3 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact XML2 2.5 MiB Installed artifact Xorg_libXi 1.6 MiB Installed artifact Expat 271.4 KiB Installed artifact LERC 272.9 KiB Installed artifact Libepoxy 1.2 MiB Installed artifact GTK4 13.4 MiB Installed artifact FreeType2 1.5 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact XSLT 728.3 KiB Installed artifact iso_codes 6.4 MiB Installed artifact Xorg_xkeyboard_config 544.2 KiB Installed artifact Xorg_libXdamage 56.7 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXext 699.3 KiB Installed artifact Libgpg_error 575.5 KiB Installed artifact Gettext 4.5 MiB Installed artifact Gumbo 703.8 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Xorg_libpthread_stubs 1.0 KiB Installed artifact Glib 7.6 MiB Installed artifact Xorg_libXinerama 50.0 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_xkbcomp 275.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Rmath 121.9 KiB Installed artifact Libgcrypt 1.8 MiB Installed artifact Libiconv 1.9 MiB Installed artifact Xorg_libxkbfile 486.0 KiB Installed artifact Wayland_protocols 129.5 KiB Installed artifact Git 49.0 MiB Installed artifact gdk_pixbuf 1.1 MiB Installed artifact Libffi 34.1 KiB Installed artifact Xorg_xtrans 47.7 KiB Installed artifact xkbcommon 509.6 KiB Installed artifact Libmount 6.3 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Librsvg 9.3 MiB Updating `~/.julia/environments/v1.13/Project.toml` [115de871] + PhyNEST v0.1.12 Updating `~/.julia/environments/v1.13/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.2.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.18.0 [67c07d97] + Automa v1.1.0 [6e4b80f9] + BenchmarkTools v1.6.0 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.1 [3c28c6f8] + BioSymbols v5.1.3 [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 v0.12.0 [5ae59095] + Colors v0.13.0 [861a8166] + Combinatorics v1.0.2 [bbf7d656] + CommonSubexpressions v0.3.1 [34da2185] + Compat v4.16.0 [187b0558] + ConstructionBase v1.5.8 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.20 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [31c24e10] + Distributions v0.25.117 [ffbed154] + DocStringExtensions v0.9.3 ⌅ [e30172f5] + Documenter v0.27.25 [35a29f4d] + DocumenterTools v0.1.20 [c2308a5c] + FASTX v2.1.7 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.23 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [08572546] + FlameGraphs v1.1.0 [f6369f11] + ForwardDiff v0.10.38 ⌅ [d9f16b24] + Functors v0.3.0 ⌃ [38e38edf] + GLM v1.8.3 [d7ba0133] + Git v1.3.1 [a2bd30eb] + Graphics v1.1.3 [9db2cae5] + Gtk4 v0.7.6 [8710efd8] + GtkObservables v2.2.0 [708ec375] + Gumbo v0.8.3 [34004b35] + HypergeometricFunctions v0.3.27 [b5f81e59] + IOCapture v0.2.5 [9b13fd28] + IndirectArrays v1.0.0 [842dd82b] + InlineStrings v1.4.3 [8197267c] + IntervalSets v0.7.10 [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 v1.14.1 [b964fa9f] + LaTeXStrings v1.4.0 [1d6d02ad] + LeftChildRightSiblingTrees v0.2.0 [d3d80556] + LineSearches v7.3.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.15 [b8f27783] + MathOptInterface v1.37.0 [fdba3010] + MathProgBase v0.7.8 [85b6ec6f] + MethodAnalysis v0.4.13 [e1d29d7a] + Missings v1.2.0 [d8a4904e] + MutableArithmetics v1.6.4 [d41bc354] + NLSolversBase v7.8.3 ⌅ [76087f3c] + NLopt v0.6.5 [77ba4419] + NaNMath v1.1.2 [510215fc] + Observables v0.5.5 [429524aa] + Optim v1.11.0 [bac558e1] + OrderedCollections v1.8.0 [90014a1f] + PDMats v0.11.32 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.1 [115de871] + PhyNEST v0.1.12 ⌅ [33ad39ac] + PhyloNetworks v0.15.3 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.2.1 [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 v1.2.1 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [1277b4bf] + ShiftedArrays v2.0.0 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.3.2 ⌅ [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 v1.12.0 [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 v1.18.2+1 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.15.0+0 [d7e528f0] + FreeType2_jll v2.13.3+1 [559328eb] + FriBidi_jll v1.0.16+0 [6ebb71f1] + GTK4_jll v4.14.5+0 [78b55507] + Gettext_jll v0.21.0+0 [f8c6e375] + Git_jll v2.47.1+0 [7746bdde] + Glib_jll v2.82.4+0 [75302f13] + Graphene_jll v1.10.6+0 [3b182d85] + Graphite2_jll v1.3.14+1 [528830af] + Gumbo_jll v0.10.2+0 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.7+0 [dd4b983a] + LZO_jll v2.10.3+0 [42c93a91] + Libepoxy_jll v1.5.10+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [d4300ac3] + Libgcrypt_jll v1.11.0+0 [7e76a0d4] + Libglvnd_jll v1.7.0+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.40.3+0 [925c91fb] + Librsvg_jll v2.54.5+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.40.3+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 v1.56.1+0 ⌅ [30392449] + Pixman_jll v0.43.4+0 [f50d1b31] + Rmath_jll v0.5.1+0 [a2964d1f] + Wayland_jll v1.21.0+2 [2381bf8a] + Wayland_protocols_jll v1.36.0+0 [02c8fc9c] + XML2_jll v2.13.6+1 [aed1982a] + XSLT_jll v1.1.42+0 [ffd25f8a] + XZ_jll v5.6.4+1 [4f6342f7] + Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] + Xorg_libXau_jll v1.0.12+0 [935fb764] + Xorg_libXcursor_jll v1.2.3+0 [0aeada51] + Xorg_libXdamage_jll v1.1.5+4 [a3789734] + Xorg_libXdmcp_jll v1.1.5+0 [1082639a] + Xorg_libXext_jll v1.3.6+3 [d091e8ba] + Xorg_libXfixes_jll v6.0.0+0 [a51aa0fd] + Xorg_libXi_jll v1.8.2+0 [d1454406] + Xorg_libXinerama_jll v1.1.5+0 [ec84b674] + Xorg_libXrandr_jll v1.5.4+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.11+1 [14d82f49] + Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.0+3 [cc61e674] + Xorg_libxkbfile_jll v1.1.2+1 [35661453] + Xorg_xkbcomp_jll v1.4.6+1 [33bec58e] + Xorg_xkeyboard_config_jll v2.39.0+0 [c5fb5394] + Xorg_xtrans_jll v1.5.1+0 [3161d3a3] + Zstd_jll v1.5.7+1 [b437f822] + adwaita_icon_theme_jll v43.0.1+0 [da03df04] + gdk_pixbuf_jll v2.42.12+0 [059c91fe] + hicolor_icon_theme_jll v0.17.0+3 [bf975903] + iso_codes_jll v4.15.1+0 ⌅ [b53b4c65] + libpng_jll v1.6.40+0 [47bcb7c8] + libsass_jll v3.6.6+0 [d8fb68d0] + xkbcommon_jll v1.4.1+2 [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 v1.12.0 [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 v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [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 46.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 6585.3 ms ✓ TestEnv 1 dependency successfully precompiled in 9 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 1063.96s ################################################################################ # Testing # Testing PhyNEST Status `/tmp/jl_0esUyn/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [8bb1440f] DelimitedFiles v1.9.1 [31c24e10] Distributions v0.25.117 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [d3d80556] LineSearches v7.3.0 [429524aa] Optim v1.11.0 [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_0esUyn/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.2.0 [66dad0bd] AliasTables v1.1.3 [4fba245c] ArrayInterface v7.18.0 [67c07d97] Automa v1.1.0 [6e4b80f9] BenchmarkTools v1.6.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [3c28c6f8] BioSymbols v5.1.3 [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 v0.12.0 [5ae59095] Colors v0.13.0 [861a8166] Combinatorics v1.0.2 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [187b0558] ConstructionBase v1.5.8 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.20 [e2d170a0] DataValueInterfaces v1.0.0 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [31c24e10] Distributions v0.25.117 [ffbed154] DocStringExtensions v0.9.3 ⌅ [e30172f5] Documenter v0.27.25 [35a29f4d] DocumenterTools v0.1.20 [c2308a5c] FASTX v2.1.7 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.23 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 [08572546] FlameGraphs v1.1.0 [f6369f11] ForwardDiff v0.10.38 ⌅ [d9f16b24] Functors v0.3.0 ⌃ [38e38edf] GLM v1.8.3 [d7ba0133] Git v1.3.1 [a2bd30eb] Graphics v1.1.3 [9db2cae5] Gtk4 v0.7.6 [8710efd8] GtkObservables v2.2.0 [708ec375] Gumbo v0.8.3 [34004b35] HypergeometricFunctions v0.3.27 [b5f81e59] IOCapture v0.2.5 [9b13fd28] IndirectArrays v1.0.0 [842dd82b] InlineStrings v1.4.3 [8197267c] IntervalSets v0.7.10 [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 v1.14.1 [b964fa9f] LaTeXStrings v1.4.0 [1d6d02ad] LeftChildRightSiblingTrees v0.2.0 [d3d80556] LineSearches v7.3.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.15 [b8f27783] MathOptInterface v1.37.0 [fdba3010] MathProgBase v0.7.8 [85b6ec6f] MethodAnalysis v0.4.13 [e1d29d7a] Missings v1.2.0 [d8a4904e] MutableArithmetics v1.6.4 [d41bc354] NLSolversBase v7.8.3 ⌅ [76087f3c] NLopt v0.6.5 [77ba4419] NaNMath v1.1.2 [510215fc] Observables v0.5.5 [429524aa] Optim v1.11.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.32 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.1 [115de871] PhyNEST v0.1.12 ⌅ [33ad39ac] PhyloNetworks v0.15.3 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.2.1 [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 v1.2.1 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 [1277b4bf] ShiftedArrays v2.0.0 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.0 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.3.2 ⌅ [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 v1.12.0 [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 v1.18.2+1 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.6.5+0 [a3f928ae] Fontconfig_jll v2.15.0+0 [d7e528f0] FreeType2_jll v2.13.3+1 [559328eb] FriBidi_jll v1.0.16+0 [6ebb71f1] GTK4_jll v4.14.5+0 [78b55507] Gettext_jll v0.21.0+0 [f8c6e375] Git_jll v2.47.1+0 [7746bdde] Glib_jll v2.82.4+0 [75302f13] Graphene_jll v1.10.6+0 [3b182d85] Graphite2_jll v1.3.14+1 [528830af] Gumbo_jll v0.10.2+0 [2e76f6c2] HarfBuzz_jll v8.5.0+0 [aacddb02] JpegTurbo_jll v3.1.1+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.7+0 [dd4b983a] LZO_jll v2.10.3+0 [42c93a91] Libepoxy_jll v1.5.10+0 ⌅ [e9f186c6] Libffi_jll v3.2.2+2 [d4300ac3] Libgcrypt_jll v1.11.0+0 [7e76a0d4] Libglvnd_jll v1.7.0+0 [7add5ba3] Libgpg_error_jll v1.51.1+0 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.40.3+0 [925c91fb] Librsvg_jll v2.54.5+0 [89763e89] Libtiff_jll v4.7.1+0 [38a345b3] Libuuid_jll v2.40.3+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 v1.56.1+0 ⌅ [30392449] Pixman_jll v0.43.4+0 [f50d1b31] Rmath_jll v0.5.1+0 [a2964d1f] Wayland_jll v1.21.0+2 [2381bf8a] Wayland_protocols_jll v1.36.0+0 [02c8fc9c] XML2_jll v2.13.6+1 [aed1982a] XSLT_jll v1.1.42+0 [ffd25f8a] XZ_jll v5.6.4+1 [4f6342f7] Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] Xorg_libXau_jll v1.0.12+0 [935fb764] Xorg_libXcursor_jll v1.2.3+0 [0aeada51] Xorg_libXdamage_jll v1.1.5+4 [a3789734] Xorg_libXdmcp_jll v1.1.5+0 [1082639a] Xorg_libXext_jll v1.3.6+3 [d091e8ba] Xorg_libXfixes_jll v6.0.0+0 [a51aa0fd] Xorg_libXi_jll v1.8.2+0 [d1454406] Xorg_libXinerama_jll v1.1.5+0 [ec84b674] Xorg_libXrandr_jll v1.5.4+0 [ea2f1a96] Xorg_libXrender_jll v0.9.11+1 [14d82f49] Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] Xorg_libxcb_jll v1.17.0+3 [cc61e674] Xorg_libxkbfile_jll v1.1.2+1 [35661453] Xorg_xkbcomp_jll v1.4.6+1 [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0 [c5fb5394] Xorg_xtrans_jll v1.5.1+0 [3161d3a3] Zstd_jll v1.5.7+1 [b437f822] adwaita_icon_theme_jll v43.0.1+0 [da03df04] gdk_pixbuf_jll v2.42.12+0 [059c91fe] hicolor_icon_theme_jll v0.17.0+3 [bf975903] iso_codes_jll v4.15.1+0 ⌅ [b53b4c65] libpng_jll v1.6.40+0 [47bcb7c8] libsass_jll v3.6.6+0 [d8fb68d0] xkbcommon_jll v1.4.1+2 [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 v1.12.0 [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 v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.64.0+1 [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 2.8s Test Summary: | Pass Total Time Testing site pattern proabilities | 1000 1000 0.1s Testing Method-of-moment estimates of speciation times: Test Failed at /home/pkgeval/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:59 Expression: isapprox(est2, t2, atol = tol) Evaluated: isapprox(5.381862950337702, 5.6031; atol = 0.2) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:59 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1771 [inlined] [4] top-level scope @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:41 Testing Method-of-moment estimates of speciation times: Test Failed at /home/pkgeval/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:75 Expression: isapprox(est3, t3, atol = tol) Evaluated: isapprox(7.204033825184799, 7.4831; atol = 0.2) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:75 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1771 [inlined] [4] top-level scope @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:41 Testing Method-of-moment estimates of speciation times: Test Failed at /home/pkgeval/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:60 Expression: isapprox(est3, t3, atol = tol) Evaluated: isapprox(6.904653403267987, 6.6906; atol = 0.2) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:679 [inlined] [2] macro expansion @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:60 [inlined] [3] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1771 [inlined] [4] top-level scope @ ~/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:41 Test Summary: | Pass Fail Total Time Testing Method-of-moment estimates of speciation times | 1497 3 1500 7.3s RNG of the outermost testset: Random.Xoshiro(0x92fd7934d12d5ea1, 0x42556b2e22c7c58c, 0xaddd0cdd3c51d6df, 0xb7e557d9f78e8f2c, 0xc69462072c03cbd4) ERROR: LoadError: Some tests did not pass: 1497 passed, 3 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PhyNEST/bC6xd/test/test_check.jl:40 in expression starting at /home/pkgeval/.julia/packages/PhyNEST/bC6xd/test/runtests.jl:11 Testing failed after 63.97s ERROR: LoadError: Package PhyNEST errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.13/Pkg/src/Operations.jl:2386 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2241 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.13/Pkg/src/API.jl:486 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:307 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:328 [12] _start() @ Base ./client.jl:560 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1219.65s: package has test failures