Package evaluation to test PhyloCoalSimulations on Julia 1.14.0-DEV.1352 (749bc618c5*) started at 2025-12-09T23:49:22.442


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

Installing PkgEval dependencies (TestEnv)...
  Activating project at `~/.julia/environments/v1.14`

Set-up completed after 9.53s


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

Installing PhyloCoalSimulations...
   Resolving package versions...
    Updating `~/.julia/environments/v1.14/Project.toml`
  [53f7b83a] + PhyloCoalSimulations v1.1.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [67c07d97] + Automa v1.1.0
  [47718e42] + BioGenerics v0.1.5
  [7e6ae17a] + BioSequences v3.5.0
  [3c28c6f8] + BioSymbols v5.2.0
  [fa961155] + CEnum v0.5.0
  [336ed68f] + CSV v0.10.15
  [944b1d66] + CodecZlib v0.7.8
  [861a8166] + Combinatorics v1.0.3
  [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
  [31c24e10] + Distributions v0.25.122
  [ffbed154] + DocStringExtensions v0.9.5
  [c2308a5c] + FASTX v2.1.7
  [48062228] + FilePathsBase v0.9.24
  [1a297f60] + FillArrays v1.15.0
  [d9f16b24] + Functors v0.5.2
  [34004b35] + HypergeometricFunctions v0.3.28
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [b964fa9f] + LaTeXStrings v1.4.0
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [e1d29d7a] + Missings v1.2.0
  [76087f3c] + NLopt v1.2.1
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.36
  [69de0a69] + Parsers v2.8.3
  [53f7b83a] + PhyloCoalSimulations v1.1.0
  [33ad39ac] + PhyloNetworks v1.2.0
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [08abe8d2] + PrettyTables v3.1.2
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [189a3867] + Reexport v1.2.2
  [79098fc4] + Rmath v0.9.0
  [fdea26ae] + SIMD v3.7.2
  [91c51154] + SentinelArrays v1.4.8
  [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 v1.8.0
  [2913bbd2] + StatsBase v0.34.9
  [4c63d2b9] + StatsFuns v1.5.2
  [892a3eda] + StringManipulation v0.4.2
  [354b36f9] + StringViews v1.3.6
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
  [3bb67fe8] + TranscodingStreams v0.11.3
  [7200193e] + Twiddle v1.1.2
  [ea10d353] + WeakRefStrings v1.4.2
  [76eceee3] + WorkerUtilities v1.6.1
  [079eb43e] + NLopt_jll v2.10.0+0
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [7b1f6079] + FileWatching v1.11.0
  [9fa8497b] + Future v1.11.0
  [b77e0a4c] + InteractiveUtils v1.11.0
  [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.13.0
  [d6f4376e] + Markdown v1.11.0
  [a63ad114] + Mmap v1.11.0
  [de0858da] + Printf 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 v1.13.0
  [4607b0f0] + SuiteSparse
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] + OpenBLAS_jll v0.3.29+0
  [05823500] + OpenLibm_jll v0.8.7+0
  [bea87d4a] + SuiteSparse_jll v7.10.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850b90] + libblastrampoline_jll v5.15.0+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 4.57s


################################################################################
# Precompilation
#

ERROR: LoadError: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Nothing)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:10
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/precompile.jl:6

caused by: MethodError: no method matching setindex!(::Base.ScopedValues.ScopedValue{IO}, ::Base.DevNull)
The function `setindex!` exists, but no method is defined for this combination of argument types.
Stacktrace:
 [1] top-level scope
   @ /PkgEval.jl/scripts/precompile.jl:7
 [2] include(mod::Module, _path::String)
   @ Base ./Base.jl:309
 [3] exec_options(opts::Base.JLOptions)
   @ Base ./client.jl:344
 [4] _start()
   @ Base ./client.jl:577

Precompilation failed after 13.35s



################################################################################
# Testing
#

     Testing PhyloCoalSimulations
      Status `/tmp/jl_T1IsKn/Project.toml`
  [31c24e10] Distributions v0.25.122
  [09f84164] HypothesisTests v0.11.6
  [53f7b83a] PhyloCoalSimulations v1.1.0
  [33ad39ac] PhyloNetworks v1.2.0
  [860ef19b] StableRNGs v1.0.4
  [10745b16] Statistics v1.11.1
  [37e2e46d] LinearAlgebra v1.13.0
  [9a3f8284] Random v1.11.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_T1IsKn/Manifest.toml`
  [7d9f7c33] Accessors v0.1.43
  [66dad0bd] AliasTables v1.1.3
  [67c07d97] Automa v1.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.0
  [3c28c6f8] BioSymbols v5.2.0
  [fa961155] CEnum v0.5.0
  [336ed68f] CSV v0.10.15
  [944b1d66] CodecZlib v0.7.8
  [861a8166] Combinatorics v1.0.3
  [38540f10] CommonSolve v0.2.4
  [34da2185] Compat v4.18.1
  [a33af91c] CompositionsBase v0.1.2
  [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
  [31c24e10] Distributions v0.25.122
  [ffbed154] DocStringExtensions v0.9.5
  [c2308a5c] FASTX v2.1.7
  [48062228] FilePathsBase v0.9.24
  [1a297f60] FillArrays v1.15.0
  [d9f16b24] Functors v0.5.2
  [34004b35] HypergeometricFunctions v0.3.28
  [09f84164] HypothesisTests v0.11.6
  [842dd82b] InlineStrings v1.4.5
  [3587e190] InverseFunctions v0.1.17
  [41ab1584] InvertedIndices v1.3.1
  [92d709cd] IrrationalConstants v0.2.6
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [b964fa9f] LaTeXStrings v1.4.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [1914dd2f] MacroTools v0.5.16
  [e1d29d7a] Missings v1.2.0
  [76087f3c] NLopt v1.2.1
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.36
  [69de0a69] Parsers v2.8.3
  [53f7b83a] PhyloCoalSimulations v1.1.0
  [33ad39ac] PhyloNetworks v1.2.0
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [08abe8d2] PrettyTables v3.1.2
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [189a3867] Reexport v1.2.2
  [79098fc4] Rmath v0.9.0
  [f2b01f46] Roots v2.2.10
  [fdea26ae] SIMD v3.7.2
  [91c51154] SentinelArrays v1.4.8
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.6.1
  [860ef19b] StableRNGs v1.0.4
  [90137ffa] StaticArrays v1.9.15
  [1e83bf80] StaticArraysCore v1.4.4
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.8.0
  [2913bbd2] StatsBase v0.34.9
  [4c63d2b9] StatsFuns v1.5.2
  [892a3eda] StringManipulation v0.4.2
  [354b36f9] StringViews v1.3.6
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [7200193e] Twiddle v1.1.2
  [ea10d353] WeakRefStrings v1.4.2
  [76eceee3] WorkerUtilities v1.6.1
  [079eb43e] NLopt_jll v2.10.0+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0
  [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
  [de0858da] Printf 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 v1.13.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.3.0+1
  [4536629a] OpenBLAS_jll v0.3.29+0
  [05823500] OpenLibm_jll v0.8.7+0
  [bea87d4a] SuiteSparse_jll v7.10.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.15.0+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("a93c6f00-e57d-5684-b7b6-d8193f3e46c0"), "DataFrames") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2813
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
  [4] macro expansion
    @ ./loading.jl:2593 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2557
  [7] require
    @ ./loading.jl:2533 [inlined]
  [8] eval_import_path
    @ ./module.jl:36 [inlined]
  [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
    @ Base ./module.jl:60
 [10] _eval_using
    @ ./module.jl:137 [inlined]
 [11] _eval_using(to::Module, path::Expr)
    @ Base ./module.jl:137
 [12] top-level scope
    @ ~/.julia/packages/PhyloNetworks/7zhDI/src/PhyloNetworks.jl:22
 [13] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3250
 [15] top-level scope
    @ stdin:5
 [16] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3092
 [18] include_string
    @ ./loading.jl:3102 [inlined]
 [19] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [20] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/PhyloNetworks/7zhDI/src/PhyloNetworks.jl:3
in expression starting at stdin:5
ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("33ad39ac-ed31-50eb-9b15-43d0656eaa72"), "PhyloNetworks") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0)
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] __require_prelocked(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2813
  [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2665
  [4] macro expansion
    @ ./loading.jl:2593 [inlined]
  [5] macro expansion
    @ ./lock.jl:376 [inlined]
  [6] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2557
  [7] require
    @ ./loading.jl:2533 [inlined]
  [8] eval_import_path
    @ ./module.jl:36 [inlined]
  [9] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)
    @ Base ./module.jl:111
 [10] top-level scope
    @ ~/.julia/packages/PhyloCoalSimulations/qWHqH/src/PhyloCoalSimulations.jl:4
 [11] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [12] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
    @ Base ./loading.jl:3250
 [13] top-level scope
    @ stdin:5
 [14] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [15] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
    @ Base ./loading.jl:3092
 [16] include_string
    @ ./loading.jl:3102 [inlined]
 [17] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:342
 [18] _start()
    @ Base ./client.jl:577
in expression starting at /home/pkgeval/.julia/packages/PhyloCoalSimulations/qWHqH/src/PhyloCoalSimulations.jl:1
in expression starting at stdin:5

  2 dependencies had output during precompilation:
┌ PhyloNetworks
│  ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("a93c6f00-e57d-5684-b7b6-d8193f3e46c0"), "DataFrames") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=0, inline=true, opt_level=0)
│  Stacktrace:
│    [1] error(s::String)
│      @ Base ./error.jl:44
│    [2] __require_prelocked(pkg::Base.PkgId, env::String)
│      @ Base ./loading.jl:2813
│    [3] _require_prelocked(uuidkey::Base.PkgId, env::String)
│      @ Base ./loading.jl:2665
│    [4] macro expansion
│      @ ./loading.jl:2593 [inlined]
│    [5] macro expansion
│      @ ./lock.jl:376 [inlined]
│    [6] __require(into::Module, mod::Symbol)
│      @ Base ./loading.jl:2557
│    [7] require
│      @ ./loading.jl:2533 [inlined]
│    [8] eval_import_path
│      @ ./module.jl:36 [inlined]
│    [9] eval_import_path_all(at::Module, path::Expr, keyword::String)
│      @ Base ./module.jl:60
│   [10] _eval_using
│      @ ./module.jl:137 [inlined]
│   [11] _eval_using(to::Module, path::Expr)
│      @ Base ./module.jl:137
│   [12] top-level scope
│      @ ~/.julia/packages/PhyloNetworks/7zhDI/src/PhyloNetworks.jl:22
│   [13] include(mod::Module, _path::String)
│      @ Base ./Base.jl:309
│   [14] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)
│      @ Base ./loading.jl:3250
│   [15] top-level scope
│      @ stdin:5
│   [16] eval(m::Module, e::Any)
│      @ Core ./boot.jl:489
│   [17] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)
│      @ Base ./loading.jl:3092
│   [18] include_string
│      @ ./loading.jl:3102 [inlined]
│   [19] exec_options(opts::Base.JLOptions)
│      @ Base ./client.jl:342
│   [20] _start()
│      @ Base ./client.jl:577
│  in expression starting at /home/pkgeval/.julia/packages/PhyloNetworks/7zhDI/src/PhyloNetworks.jl:3
│  in expression starting at stdin:5
└  
┌ PhyloCoalSimulations
│  [Output was shown above]
└  
ERROR: LoadError: The following 2 packages failed to precompile:

PhyloNetworks 
Failed to precompile PhyloNetworks [33ad39ac-ed31-50eb-9b15-43d0656eaa72] to "/home/pkgeval/.julia/compiled/v1.14/PhyloNetworks/jl_J1nzGH" (ProcessExited(1)).

PhyloCoalSimulations 
Failed to precompile PhyloCoalSimulations [53f7b83a-06b5-4910-9a21-1896bf762ade] to "/home/pkgeval/.julia/compiled/v1.14/PhyloCoalSimulations/jl_MGlmCg" (ProcessExited(1)).

in expression starting at /home/pkgeval/.julia/packages/PhyloCoalSimulations/qWHqH/test/runtests.jl:1

Testing failed after 97.3s

ERROR: LoadError: Package PhyloCoalSimulations errored during testing
Stacktrace:
  [1] pkgerror(msg::String)
    @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68
  [2] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/Operations.jl:3053
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2902 [inlined]
  [4] test(ctx::Pkg.Types.Context, pkgs::Vector{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/v1.14/Pkg/src/API.jl:572
  [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548
  [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172
  [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined]
 [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String)
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:237
 [12] include(mod::Module, _path::String)
    @ Base ./Base.jl:309
 [13] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:344
 [14] _start()
    @ Base ./client.jl:577
in expression starting at /PkgEval.jl/scripts/evaluate.jl:228

PkgEval failed after 143.71s: package fails to precompile