Package evaluation to test Microbiome on Julia 1.13.0-DEV.1319 (9cddfda8ef*) started at 2025-10-16T17:33:19.426


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.33s


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

Installing Microbiome...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [3bd8f0ae] + Microbiome v0.10.1
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [66dad0bd] + AliasTables v1.1.3
  [7d9fca2a] + Arpack v0.5.4
  [9a962f9c] + DataAPI v1.16.0
  [864edb3b] + DataStructures v0.19.1
  [e2d170a0] + DataValueInterfaces v1.0.0
⌅ [85a47980] + Dictionaries v0.3.29
  [b4f34e82] + Distances v0.10.12
  [31c24e10] + Distributions v0.25.122
  [ffbed154] + DocStringExtensions v0.9.5
  [a58aae7d] + EcoBase v0.1.7
  [1a297f60] + FillArrays v1.14.0
  [34004b35] + HypergeometricFunctions v0.3.28
  [313cdc1a] + Indexing v1.1.1
  [bd334432] + InlineTest v0.2.0
  [92d709cd] + IrrationalConstants v0.2.6
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [2ab3a3ac] + LogExpFunctions v0.3.29
  [3bd8f0ae] + Microbiome v0.10.1
  [e1d29d7a] + Missings v1.2.0
  [6f286f6a] + MultivariateStats v0.10.3
  [bac558e1] + OrderedCollections v1.8.1
  [90014a1f] + PDMats v0.11.35
  [aea7be01] + PrecompileTools v1.3.3
  [21216c6a] + Preferences v1.5.0
  [43287f4e] + PtrArrays v1.3.0
  [1fd47b50] + QuadGK v2.11.2
  [e0db7c4e] + ReTest v0.3.4
  [3cdcf5f2] + RecipesBase v1.3.4
  [189a3867] + Reexport v1.2.2
  [79098fc4] + Rmath v0.8.0
  [a2af1166] + SortingAlgorithms v1.2.2
  [276daf66] + SpecialFunctions v2.6.1
  [10745b16] + Statistics v1.11.1
  [82ae8749] + StatsAPI v1.7.1
  [2913bbd2] + StatsBase v0.34.6
  [4c63d2b9] + StatsFuns v1.5.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.12.1
⌅ [68821587] + Arpack_jll v3.5.1+1
  [efe28fd5] + OpenSpecFun_jll v0.5.6+0
  [f50d1b31] + Rmath_jll v0.5.1+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
  [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
  [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
  [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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

Installation completed after 5.1s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 40.59s


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

     Testing Microbiome
      Status `/tmp/jl_RecyRo/Project.toml`
  [e30172f5] Documenter v1.14.1
  [3bd8f0ae] Microbiome v0.10.1
  [e0db7c4e] ReTest v0.3.4
  [2f01184e] SparseArrays v1.13.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_RecyRo/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [1520ce14] AbstractTrees v0.4.5
  [66dad0bd] AliasTables v1.1.3
  [7d9fca2a] Arpack v0.5.4
  [944b1d66] CodecZlib v0.7.8
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.19.1
  [e2d170a0] DataValueInterfaces v1.0.0
⌅ [85a47980] Dictionaries v0.3.29
  [b4f34e82] Distances v0.10.12
  [31c24e10] Distributions v0.25.122
  [ffbed154] DocStringExtensions v0.9.5
  [e30172f5] Documenter v1.14.1
  [a58aae7d] EcoBase v0.1.7
  [1a297f60] FillArrays v1.14.0
  [d7ba0133] Git v1.5.0
  [34004b35] HypergeometricFunctions v0.3.28
  [b5f81e59] IOCapture v0.2.5
  [313cdc1a] Indexing v1.1.1
  [bd334432] InlineTest v0.2.0
  [92d709cd] IrrationalConstants v0.2.6
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.7.1
  [682c06a0] JSON v1.1.0
  [0e77f7df] LazilyInitializedFields v1.3.0
  [2ab3a3ac] LogExpFunctions v0.3.29
  [d0879d2d] MarkdownAST v0.1.2
  [3bd8f0ae] Microbiome v0.10.1
  [e1d29d7a] Missings v1.2.0
  [6f286f6a] MultivariateStats v0.10.3
  [bac558e1] OrderedCollections v1.8.1
  [90014a1f] PDMats v0.11.35
  [69de0a69] Parsers v2.8.3
  [aea7be01] PrecompileTools v1.3.3
  [21216c6a] Preferences v1.5.0
  [43287f4e] PtrArrays v1.3.0
  [1fd47b50] QuadGK v2.11.2
  [e0db7c4e] ReTest v0.3.4
  [3cdcf5f2] RecipesBase v1.3.4
  [189a3867] Reexport v1.2.2
  [2792f1a3] RegistryInstances v0.1.0
  [79098fc4] Rmath v0.8.0
  [a2af1166] SortingAlgorithms v1.2.2
  [276daf66] SpecialFunctions v2.6.1
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.1
  [2913bbd2] StatsBase v0.34.6
  [4c63d2b9] StatsFuns v1.5.0
  [ec057cc2] StructUtils v2.5.1
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.12.1
  [3bb67fe8] TranscodingStreams v0.11.3
⌅ [68821587] Arpack_jll v3.5.1+1
  [2e619515] Expat_jll v2.7.1+0
  [020c3dae] Git_LFS_jll v3.7.0+0
  [f8c6e375] Git_jll v2.51.1+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [9bd350c2] OpenSSH_jll v10.2.1+0
  [efe28fd5] OpenSpecFun_jll v0.5.6+0
  [f50d1b31] Rmath_jll v0.5.1+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
  [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
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.13.0
  [de0858da] Printf 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 ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
WARNING: Imported binding Test.pop_testset was undeclared at import time during import to Testset.
WARNING: Imported binding Test.push_testset was undeclared at import time during import to Testset.
ERROR: LoadError: TaskFailedException
Stacktrace:
  [1] #wait#575
    @ ./task.jl:363 [inlined]
  [2] wait
    @ ./task.jl:360 [inlined]
  [3] retest(args::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}}; dry::Bool, stats::Bool, shuffle::Bool, group::Bool, verbose::Bool, recursive::Bool, id::Nothing, strict::Bool, dup::Bool, static::Nothing, load::Bool, seed::Bool, marks::Bool, tag::Vector{Symbol}, spin::Bool, clear::Bool)
    @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1186
  [4] retest(args::Union{Regex, AbstractString, Integer, Module, Symbol, Tuple, ReTest.Pattern, AbstractArray, Pair{Module, <:Union{Regex, AbstractString, Integer, Symbol, Tuple, ReTest.Pattern, AbstractArray}}})
    @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:750
  [5] #runtests#1
    @ ~/.julia/packages/InlineTest/NAAjm/src/InlineTest.jl:81 [inlined]
  [6] runtests()
    @ Main.MicrobiomeTests ~/.julia/packages/InlineTest/NAAjm/src/InlineTest.jl:80
  [7] top-level scope
    @ ~/.julia/packages/Microbiome/StzgY/test/runtests.jl:2
  [8] include(mapexpr::Function, mod::Module, _path::String)
    @ Base ./Base.jl:310
  [9] top-level scope
    @ none:6
 [10] eval(m::Module, e::Any)
    @ Core ./boot.jl:489
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:310
 [12] _start()
    @ Base ./client.jl:577

    nested task error: TaskFailedException
    
        nested task error: UndefVarError: `push_testset` not defined in `ReTest.Testset`
        Suggestion: this global was defined as `Test.push_testset` but not assigned a value.
        Stacktrace:
          [1] macro expansion
            @ ~/.julia/packages/ReTest/3Ikse/src/testset.jl:517 [inlined]
          [2] macro expansion
            @ ~/.julia/packages/Microbiome/StzgY/test/MicrobiomeTests.jl:11 [inlined]
          [3] top-level scope
            @ ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:517
          [4] eval(m::Module, e::Any)
            @ Core ./boot.jl:489
          [5] (::ReTest.var"#110#111"{ReTest.Testset.Format})(mod::Module, ts::ReTest.TestsetExpr, pat::ReTest.And, chan::@NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing})
            @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1154
          [6] #local_remotecall_thunk##0
            @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:425 [inlined]
          [7] run_work_thunk(thunk::Distributed.var"#local_remotecall_thunk##0#local_remotecall_thunk##1"{ReTest.var"#110#111"{ReTest.Testset.Format}, Tuple{Module, ReTest.TestsetExpr, ReTest.And, @NamedTuple{out::Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, compute::Channel{Nothing}, preview::Nothing}}, @Kwargs{}}, print_error::Bool)
            @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/process_messages.jl:70
          [8] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})
            @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:450
          [9] remotecall_fetch
            @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:449 [inlined]
         [10] remotecall_fetch
            @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:492 [inlined]
         [11] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()
            @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151
        Stacktrace:
         [1] remotecall_fetch(::Function, ::Distributed.LocalProcess, ::Module, ::Vararg{Any}; kwargs::@Kwargs{})
           @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:451
         [2] remotecall_fetch
           @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:449 [inlined]
         [3] remotecall_fetch
           @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/remotecall.jl:492 [inlined]
         [4] (::ReTest.var"#106#107"{Int64, ReTest.Testset.Format, Nothing, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()
           @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1151
    Stacktrace:
     [1] sync_end(c::Channel{Any})
       @ Base ./task.jl:601
     [2] macro expansion
       @ ./task.jl:634 [inlined]
     [3] (::ReTest.var"#96#97"{Bool, ReTest.Testset.Format, Bool, Base.RefValue{Int64}, Bool, ReTest.var"#take_latest!#91", Nothing, ReentrantLock, Bool, ReTest.Testset.ReTestSet, Base.Threads.Atomic{Bool}, Base.RefValue{Exception}, Channel{Nothing}, Distributed.RemoteChannel{Channel{Union{Nothing, ReTest.Testset.ReTestSet}}}, Vector{Any}, ReTest.And, Module})()
       @ ReTest ~/.julia/packages/ReTest/3Ikse/src/ReTest.jl:1104
in expression starting at /home/pkgeval/.julia/packages/Microbiome/StzgY/test/runtests.jl:2

Testing failed after 106.7s

ERROR: LoadError: Package Microbiome 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{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:2674
  [3] test
    @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2523 [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/v1.13/Pkg/src/API.jl:548
  [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/v1.13/Pkg/src/API.jl:525
  [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/API.jl:161
  [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
    @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:160
  [9] test
    @ /opt/julia/share/julia/stdlib/v1.13/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/v1.13/Pkg/src/API.jl:159
 [11] top-level scope
    @ /PkgEval.jl/scripts/evaluate.jl:219
 [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:210

PkgEval failed after 178.96s: package tests unexpectedly errored