Package evaluation to load PhyNEST on Julia 1.13.0-DEV.1276 (4ca97dc26d*) started at 2025-10-10T11:15:14.525


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# Set-up
#


Set-up completed after 0.11s


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# Installation
#

Installing PhyNEST...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [115de871] + PhyNEST v0.1.12
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [47edcb42] + ADTypes v1.18.0
  [a4c015fc] + ANSIColoredPrinters v0.0.1
  [1520ce14] + AbstractTrees v0.4.5
  [79e6a3ab] + Adapt v4.4.0
  [66dad0bd] + AliasTables v1.1.3
  [4fba245c] + ArrayInterface v7.20.0
  [67c07d97] + Automa v1.1.0
  [6e4b80f9] + BenchmarkTools v1.6.0
  [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 v1.8.0
⌅ [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 v0.7.8
  [31c24e10] + Distributions v0.25.122
⌅ [ffbed154] + DocStringExtensions v0.8.6
⌅ [e30172f5] + Documenter v0.27.25
⌃ [35a29f4d] + DocumenterTools v0.1.2
  [4e289a0a] + EnumX v1.0.5
  [c2308a5c] + FASTX v2.1.7
  [5789e2e9] + FileIO v1.17.1
  [48062228] + FilePathsBase v0.9.24
  [1a297f60] + FillArrays v1.14.0
  [6a86dc24] + FiniteDiff v2.28.1
  [53c48c17] + FixedPointNumbers v0.8.5
  [08572546] + FlameGraphs v1.1.0
  [f6369f11] + ForwardDiff v1.2.1
⌅ [d9f16b24] + Functors v0.3.0
⌃ [38e38edf] + GLM v1.8.3
  [a2bd30eb] + Graphics v1.1.3
  [9db2cae5] + Gtk4 v0.7.10
  [8710efd8] + GtkObservables v2.2.1
  [34004b35] + HypergeometricFunctions v0.3.28
  [b5f81e59] + IOCapture v0.2.5
  [9b13fd28] + IndirectArrays v1.0.0
  [842dd82b] + InlineStrings v1.4.5
  [8197267c] + IntervalSets v0.7.11
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.4
  [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 v7.4.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [1914dd2f] + MacroTools v0.5.16
  [b8f27783] + MathOptInterface v1.45.0
  [fdba3010] + MathProgBase v0.7.8
  [85b6ec6f] + MethodAnalysis v1.0.0
  [e1d29d7a] + Missings v1.2.0
  [d8a4904e] + MutableArithmetics v1.6.6
  [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 v3.1.0
  [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 v0.8.0
  [d5f540fe] + RoundingIntegers v1.1.0
  [fdea26ae] + SIMD v3.7.2
  [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 v1.4.3
  [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 v1.3.5
  [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 v2.7.1+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
  [7746bdde] + Glib_jll v2.86.0+0
  [75302f13] + Graphene_jll v1.10.8+0
  [3b182d85] + Graphite2_jll v1.3.15+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
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [36c8627f] + Pango_jll v1.56.4+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 v4.17.0+0
  [b53b4c65] + libpng_jll v1.6.50+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 v0.6.4
  [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 v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [8dfed614] + Test v1.11.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [deac9b47] + LibCURL_jll v8.16.0+0
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.9.9
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [458c3c95] + OpenSSL_jll v3.5.4+0
  [efcefdf7] + PCRE2_jll v10.46.0+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850b90] + libblastrampoline_jll v5.15.0+0
  [8e850ede] + nghttp2_jll v1.67.1+0
  [3f19e933] + p7zip_jll v17.6.0+0
        Info Packages marked with ⌃ 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 10.46s


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# Precompilation
#

Precompiling PkgEval dependencies...
     Project No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml`
    Manifest No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml`

Precompiling package dependencies...
Precompiling packages...
   1481.4 ms  ✓ Functors
   1938.3 ms  ✓ Combinatorics
   1094.8 ms  ✓ MethodAnalysis
    950.5 ms  ✓ ConstructionBase → ConstructionBaseIntervalSetsExt
    888.0 ms  ✓ BioGenerics
    825.8 ms  ✓ LeftChildRightSiblingTrees
   1361.4 ms  ✓ Graphics
   1235.6 ms  ✓ DocStringExtensions
   2748.5 ms  ✓ QuadGK
   2428.8 ms  ✓ BioSymbols
  20256.4 ms  ✓ Automa
   1366.6 ms  ✓ hicolor_icon_theme_jll
   2986.1 ms  ✓ BenchmarkTools
   1592.5 ms  ✓ GTK4_jll
   9910.4 ms  ✓ FlameGraphs
   2492.3 ms  ✓ Cairo
   1113.6 ms  ✓ LogExpFunctions
   1343.2 ms  ✓ DocumenterTools
   8356.2 ms  ✓ Documenter
   8751.1 ms  ✓ BioSequences
  21483.1 ms  ✓ FASTX
   1432.7 ms  ✓ adwaita_icon_theme_jll
   4884.6 ms  ✓ SpecialFunctions
   8898.5 ms  ✓ StatsBase
   2402.8 ms  ✓ FASTX → BioSequencesExt
  48458.1 ms  ✓ Gtk4
   2243.5 ms  ✓ HypergeometricFunctions
   6371.2 ms  ✓ ForwardDiff
  25302.4 ms  ✓ GtkObservables
   3041.9 ms  ✓ StatsFuns
   2197.1 ms  ✓ ForwardDiff → ForwardDiffStaticArraysExt
   1556.5 ms  ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt
  75953.8 ms  ✓ MathOptInterface
  16477.5 ms  ✓ ProfileView
   7486.1 ms  ✓ StatsModels
  15262.9 ms  ✓ Distributions
   2308.9 ms  ✓ NLSolversBase
   7332.8 ms  ✓ NLopt
   9190.4 ms  ✓ GLM
   4203.2 ms  ✓ Distributions → DistributionsTestExt
   4459.9 ms  ✓ LineSearches
  29459.9 ms  ✓ PhyloNetworks
  10904.2 ms  ✓ Optim
   7012.2 ms  ✓ Optim → OptimMOIExt
  23657.6 ms  ✓ PhyNEST
  45 dependencies successfully precompiled in 416 seconds. 200 already precompiled.
  2 dependencies had output during precompilation:
┌ ProfileView
│  (julia:151): Gtk-WARNING **: 11:20:30.776: 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:125): Gtk-WARNING **: 11:18:35.016: 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 421.99s


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# Loading
#

Loading PhyNEST...

Loading completed after 19.16s

PkgEval succeeded after 468.01s