Package evaluation to load MetaPhylo on Julia 1.13.0-DEV.1324 (c1d413cf8a*) started at 2025-10-17T18:25:23.304


################################################################################
# Set-up
#


Set-up completed after 0.15s


################################################################################
# Installation
#

Installing MetaPhylo...
   Resolving package versions...
   Installed ChunkCodecLibZstd ──── v1.0.0
   Installed AbstractTrees ──────── v0.4.5
   Installed OrderedCollections ─── v1.8.1
   Installed MacroTools ─────────── v0.5.16
   Installed ArnoldiMethod ──────── v0.4.0
   Installed DataStructures ─────── v0.18.22
   Installed JLD2 ───────────────── v0.6.2
   Installed MetaPhylo ──────────── v0.1.1
   Installed HashArrayMappedTries ─ v0.2.0
   Installed StaticArraysCore ───── v1.4.3
   Installed Requires ───────────── v1.3.1
   Installed Compat ─────────────── v4.18.1
   Installed ChunkCodecLibZlib ──── v1.0.0
   Installed Statistics ─────────── v1.11.1
   Installed SimpleTraits ───────── v0.9.5
   Installed StaticArrays ───────── v1.9.15
   Installed PrecompileTools ────── v1.3.3
   Installed FileIO ─────────────── v1.17.1
   Installed StaticGraphs ───────── v0.3.1
   Installed NamedTupleTools ────── v0.14.3
   Installed Reexport ───────────── v1.2.2
   Installed ChunkCodecCore ─────── v1.0.0
   Installed IntervalSets ───────── v0.7.11
   Installed ScopedValues ───────── v1.5.0
   Installed IterTools ──────────── v1.10.0
   Installed Preferences ────────── v1.5.0
   Installed AxisArrays ─────────── v0.4.8
   Installed RangeArrays ────────── v0.3.2
   Installed Lerche ─────────────── v0.5.7
   Installed Inflate ────────────── v0.1.5
   Installed Graphs ─────────────── v1.13.1
    Updating `~/.julia/environments/v1.13/Project.toml`
  [58946fd8] + MetaPhylo v0.1.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [1520ce14] + AbstractTrees v0.4.5
  [ec485272] + ArnoldiMethod v0.4.0
  [39de3d68] + AxisArrays v0.4.8
  [0b6fb165] + ChunkCodecCore v1.0.0
  [4c0bbee4] + ChunkCodecLibZlib v1.0.0
  [55437552] + ChunkCodecLibZstd v1.0.0
  [34da2185] + Compat v4.18.1
⌅ [864edb3b] + DataStructures v0.18.22
  [5789e2e9] + FileIO v1.17.1
  [86223c79] + Graphs v1.13.1
  [076d061b] + HashArrayMappedTries v0.2.0
  [d25df0c9] + Inflate v0.1.5
  [8197267c] + IntervalSets v0.7.11
  [c8e1da08] + IterTools v1.10.0
  [033835bb] + JLD2 v0.6.2
  [d42ef402] + Lerche v0.5.7
  [1914dd2f] + MacroTools v0.5.16
  [58946fd8] + MetaPhylo v0.1.1
  [d9ec5142] + NamedTupleTools v0.14.3
  [bac558e1] + OrderedCollections v1.8.1
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [b3c3ace0] + RangeArrays v0.3.2
  [189a3867] + Reexport v1.2.2
  [ae029012] + Requires v1.3.1
  [7e506255] + ScopedValues v1.5.0
  [699a6c99] + SimpleTraits v0.9.5
  [90137ffa] + StaticArrays v1.9.15
  [1e83bf80] + StaticArraysCore v1.4.3
  [4c8beaf5] + StaticGraphs v0.3.1
  [10745b16] + Statistics v1.11.1
  [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
  [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
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [1a1011a3] + SharedArrays v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.13.0
  [f489334b] + StyledStrings v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [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
  [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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 8.71s


################################################################################
# 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...
   4421.3 ms  ✓ MacroTools
    952.5 ms  ✓ NamedTupleTools
    788.0 ms  ✓ Reexport
   1118.3 ms  ✓ Statistics
    911.5 ms  ✓ StaticArraysCore
   1179.2 ms  ✓ Requires
    867.8 ms  ✓ RangeArrays
   1291.3 ms  ✓ OrderedCollections
    909.2 ms  ✓ HashArrayMappedTries
   1135.4 ms  ✓ IterTools
   1096.1 ms  ✓ AbstractTrees
   1032.2 ms  ✓ IntervalSets
   1018.2 ms  ✓ Inflate
    990.1 ms  ✓ ChunkCodecCore
   1129.4 ms  ✓ Compat
   1138.3 ms  ✓ Preferences
   3352.8 ms  ✓ SimpleTraits
   1556.2 ms  ✓ Statistics → SparseArraysExt
   8949.1 ms  ✓ FileIO
    848.0 ms  ✓ ScopedValues
    775.2 ms  ✓ IntervalSets → IntervalSetsStatisticsExt
    822.2 ms  ✓ IntervalSets → IntervalSetsRandomExt
   1003.3 ms  ✓ ChunkCodecLibZlib
   1152.6 ms  ✓ ChunkCodecLibZstd
    824.4 ms  ✓ Compat → CompatLinearAlgebraExt
    938.9 ms  ✓ PrecompileTools
   1603.9 ms  ✓ AxisArrays
   3930.0 ms  ✓ DataStructures
  14032.0 ms  ✓ StaticArrays
  46612.5 ms  ✓ JLD2
  20742.5 ms  ✓ Lerche
   1346.5 ms  ✓ StaticArrays → StaticArraysStatisticsExt
   3926.8 ms  ✓ ArnoldiMethod
  10019.3 ms  ✓ Graphs
   8824.1 ms  ✓ StaticGraphs

  1 dependency had output during precompilation:
┌ Lerche
│  WARNING: Constructor for type "String" was extended in `Lerche` without explicit qualification or import.
│    NOTE: Assumed "String" refers to `Base.String`. This behavior is deprecated and may differ in future versions.
│    NOTE: This behavior may have differed in Julia versions prior to 1.12.
│    Hint: If you intended to create a new generic function of the same name, use `function String end`.
│    Hint: To silence the warning, qualify `String` as `Base.String` in the method signature or explicitly `import Base: String`.
└  

Precompilation completed after 184.69s


################################################################################
# Loading
#

Loading MetaPhylo...
ERROR: LoadError: MethodError: Cannot `convert` an object of type SubString{String} to an object of type Set{Char}
The function `convert` exists, but no method is defined for this combination of argument types.

Closest candidates are:
  Set{T}(::Any) where T
   @ Base set.jl:47
  convert(::Type{T}, !Matched::T) where T<:AbstractSet
   @ Base set.jl:679
  convert(::Type{T}, !Matched::AbstractSet) where T<:AbstractSet
   @ Base set.jl:680
  ...

Stacktrace:
  [1] Lerche.PatternStr(value::String, flags::SubString{String})
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/lexer.jl:41
  [2] _literal_to_pattern(literal::Lerche.Token)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/load_grammar.jl:490
  [3] transformer_func(pl::Lerche.PrepareLiterals, ::Val{:literal}, literal::Lerche.Token)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/load_grammar.jl:500
  [4] transformer_func(x::Lerche.PrepareLiterals, y::Val{:literal}, meta::Lerche.Meta, z::Vector{Any})
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/utils.jl:234
  [5] _call_userfunc(t::Lerche.PrepareLiterals, tr::Lerche.Tree; new_children::Nothing)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:124
  [6] _call_userfunc
    @ ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:118 [inlined]
  [7] _transform_tree
    @ ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:201 [inlined]
  [8] (::Lerche.var"#_transform_children##0#_transform_children##1"{Lerche.PrepareLiterals})(c::Lerche.Tree)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:138
  [9] iterate
    @ ./generator.jl:48 [inlined]
 [10] _collect(c::Vector{Any}, itr::Base.Generator{Vector{Any}, Lerche.var"#_transform_children##0#_transform_children##1"{Lerche.PrepareLiterals}}, ::Base.EltypeUnknown, isz::Base.HasShape{1})
    @ Base ./array.jl:848
 [11] collect_similar
    @ ./array.jl:763 [inlined]
 [12] map
    @ ./abstractarray.jl:3390 [inlined]
 [13] _transform_children(t::Lerche.PrepareLiterals, children::Vector{Any})
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:135
 [14] transform(tip::Lerche.PrepareLiterals, tree::Lerche.Tree)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:212
 [15] transform(tc::Lerche.TransformerChain, tree::Lerche.Tree)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/visitors.jl:195
 [16] compile(g::Lerche.Grammar, start::Vector{String}, terminals_to_keep::Set{Any})
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/load_grammar.jl:642
 [17] Lerche.Lark(grammar::String, loptions::Dict{String, Any}, source::String, cache_file::String)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/lark.jl:190
 [18] Lerche.Lark(grammar::String; options::@Kwargs{parser::String, lexer::String, transformer::MetaPhylo.Newick.TreeToNewick})
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/lark.jl:123
 [19] kwcall(::@NamedTuple{parser::String, lexer::String, transformer::MetaPhylo.Newick.TreeToNewick}, ::Type{Lerche.Lark}, grammar::String)
    @ Lerche ~/.julia/packages/Lerche/xNSsO/src/lark.jl:120
 [20] top-level scope
    @ ~/.julia/packages/MetaPhylo/2I5Mk/src/newick/newick.jl:42
 [21] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
 [22] top-level scope
    @ ~/.julia/packages/MetaPhylo/2I5Mk/src/MetaPhylo.jl:32
 [23] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [24] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2777
 [25] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2536
 [26] macro expansion
    @ ./loading.jl:2464 [inlined]
 [27] macro expansion
    @ ./lock.jl:376 [inlined]
 [28] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2428
 [29] require
    @ ./loading.jl:2404 [inlined]
 [30] eval_import_path
    @ ./module.jl:36 [inlined]
 [31] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [32] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [33] top-level scope
    @ none:1
 [34] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [35] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:310
 [36] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/MetaPhylo/2I5Mk/src/newick/newick.jl:1
in expression starting at /home/pkgeval/.julia/packages/MetaPhylo/2I5Mk/src/MetaPhylo.jl:1

Loading failed after 67.59s

ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using MetaPhylo'`, ProcessExited(1)) [1]

Stacktrace:
 [1] pipeline_error
   @ ./process.jl:611 [inlined]
 [2] run(::Cmd; wait::Bool)
   @ Base ./process.jl:526
 [3] run(::Cmd)
   @ Base ./process.jl:523
 [4] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:193
 [5] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [6] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [7] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:184

PkgEval failed after 280.79s: there were unidentified errors