Package evaluation to test SummarizedExperiments on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-27T17:16:51.974


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

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

Set-up completed after 15.64s


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

Installing SummarizedExperiments...
   Resolving package versions...
   Installed OrderedCollections ────────── v1.8.2
   Installed SummarizedExperiments ─────── v0.2.0
   Installed IteratorInterfaceExtensions ─ v1.0.0
   Installed InvertedIndices ───────────── v1.3.1
   Installed DataAPI ───────────────────── v1.16.0
   Installed Compat ────────────────────── v4.18.1
   Installed InlineStrings ─────────────── v1.4.5
   Installed Statistics ────────────────── v1.11.1
   Installed DataStructures ────────────── v0.18.22
   Installed SentinelArrays ────────────── v1.4.10
   Installed StringManipulation ────────── v0.5.0
   Installed Tables ────────────────────── v1.14.0
   Installed DataValueInterfaces ───────── v1.0.0
   Installed Reexport ──────────────────── v1.2.2
   Installed PrecompileTools ───────────── v1.3.4
   Installed PooledArrays ──────────────── v1.4.3
   Installed Preferences ───────────────── v1.5.2
   Installed DataFrames ────────────────── v1.8.2
   Installed Missings ──────────────────── v1.2.0
   Installed PrettyTables ──────────────── v3.4.8
   Installed SortingAlgorithms ─────────── v1.2.3
   Installed LaTeXStrings ──────────────── v1.4.1
   Installed Crayons ───────────────────── v4.2.0
   Installed TableTraits ───────────────── v1.0.1
    Updating `~/.julia/environments/v1.14/Project.toml`
  [b04b66ec] + SummarizedExperiments v0.2.0
    Updating `~/.julia/environments/v1.14/Manifest.toml`
  [34da2185] + Compat v4.18.1
  [a8cc5b0e] + Crayons v4.2.0
  [9a962f9c] + DataAPI v1.16.0
  [a93c6f00] + DataFrames v1.8.2
⌅ [864edb3b] + DataStructures v0.18.22
  [e2d170a0] + DataValueInterfaces v1.0.0
  [842dd82b] + InlineStrings v1.4.5
  [41ab1584] + InvertedIndices v1.3.1
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [b964fa9f] + LaTeXStrings v1.4.1
  [e1d29d7a] + Missings v1.2.0
⌅ [bac558e1] + OrderedCollections v1.8.2
  [2dfb63ee] + PooledArrays v1.4.3
  [aea7be01] + PrecompileTools v1.3.4
  [21216c6a] + Preferences v1.5.2
  [08abe8d2] + PrettyTables v3.4.8
  [189a3867] + Reexport v1.2.2
  [91c51154] + SentinelArrays v1.4.10
  [a2af1166] + SortingAlgorithms v1.2.3
  [10745b16] + Statistics v1.11.1
  [892a3eda] + StringManipulation v0.5.0
  [b04b66ec] + SummarizedExperiments v0.2.0
  [3783bdb8] + TableTraits v1.0.1
  [bd369af6] + Tables v1.14.0
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates 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 v1.14.0
  [d6f4376e] + Markdown v1.11.0
  [de0858da] + Printf v1.11.0
  [3fa0cd96] + REPL v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v1.13.0
  [6462fe0b] + Sockets v1.11.0
  [f489334b] + StyledStrings v1.13.0
  [fa267f1f] + TOML v1.0.3
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0
  [4536629a] + OpenBLAS_jll v0.3.34+0
  [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 4.55s


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

Precompiling PkgEval dependencies...
Precompiling project...
   4.6 s  ✓ TestEnv
  1 dependency successfully precompiled in 5 seconds. 27 already precompiled.

Precompiling package dependencies...
Precompiling project...
   1.5 s  ✓ InlineStrings
   0.7 s  ✓ ANSIColoredPrinters
   0.5 s  ✓ Reexport
   0.8 s  ✓ Statistics
   0.6 s  ✓ DataAPI
   0.5 s  ✓ DataValueInterfaces
   0.5 s  ✓ LazilyInitializedFields
   1.0 s  ✓ OrderedCollections
   0.6 s  ✓ InvertedIndices
   0.8 s  ✓ DocStringExtensions
   0.9 s  ✓ AbstractTrees
   0.8 s  ✓ TranscodingStreams
   0.5 s  ✓ IteratorInterfaceExtensions
   0.5 s  ✓ LaTeXStrings
   2.0 s  ✓ Crayons
   0.5 s  ✓ IOCapture
   2.1 s  ✓ SentinelArrays
   1.7 s  ✓ StructUtils
   0.8 s  ✓ Compat
   1.2 s  ✓ Preferences
   0.7 s  ✓ Missings
   0.7 s  ✓ PooledArrays
   5.1 s  ✓ RegistryInstances
   1.4 s  ✓ MarkdownAST
   0.8 s  ✓ CodecZlib
   0.5 s  ✓ TableTraits
   0.6 s  ✓ Compat → CompatLinearAlgebraExt
   1.4 s  ✓ JLLWrappers
   0.9 s  ✓ PrecompileTools
   1.5 s  ✓ Tables
   2.9 s  ✓ DataStructures
   1.5 s  ✓ Libiconv_jll
   0.8 s  ✓ Git_LFS_jll
   0.9 s  ✓ OpenSSH_jll
   0.8 s  ✓ Expat_jll
   6.1 s  ✓ StringManipulation
  10.9 s  ✓ Parsers
   1.0 s  ✓ StructUtils → StructUtilsTablesExt
   1.3 s  ✓ SortingAlgorithms
   1.5 s  ✓ Git_jll
  42.3 s  ✓ PrettyTables
   9.5 s  ✓ JSON
   0.9 s  ✓ InlineStrings → ParsersExt
   1.9 s  ✓ Git
  78.8 s  ✓ DataFrames
  51.4 s  ✓ Documenter
   7.2 s  ✓ SummarizedExperiments
  47 dependencies successfully precompiled in 252 seconds. 33 already precompiled.

Precompilation completed after 277.98s


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

     Testing SummarizedExperiments
      Status `/tmp/jl_VCY9DM/Project.toml`
  [a93c6f00] DataFrames v1.8.2
⌅ [864edb3b] DataStructures v0.18.22
  [e30172f5] Documenter v1.17.0
  [189a3867] Reexport v1.2.2
  [b04b66ec] SummarizedExperiments v0.2.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_VCY9DM/Manifest.toml`
  [a4c015fc] ANSIColoredPrinters v0.0.1
  [1520ce14] AbstractTrees v0.4.5
  [944b1d66] CodecZlib v0.7.9
  [34da2185] Compat v4.18.1
  [a8cc5b0e] Crayons v4.2.0
  [9a962f9c] DataAPI v1.16.0
  [a93c6f00] DataFrames v1.8.2
⌅ [864edb3b] DataStructures v0.18.22
  [e2d170a0] DataValueInterfaces v1.0.0
  [ffbed154] DocStringExtensions v0.9.5
  [e30172f5] Documenter v1.17.0
  [d7ba0133] Git v1.5.0
  [b5f81e59] IOCapture v1.0.0
  [842dd82b] InlineStrings v1.4.5
  [41ab1584] InvertedIndices v1.3.1
  [82899510] IteratorInterfaceExtensions v1.0.0
  [692b3bcd] JLLWrappers v1.8.0
  [682c06a0] JSON v1.7.1
  [b964fa9f] LaTeXStrings v1.4.1
  [0e77f7df] LazilyInitializedFields v1.3.0
  [d0879d2d] MarkdownAST v0.1.3
  [e1d29d7a] Missings v1.2.0
⌅ [bac558e1] OrderedCollections v1.8.2
⌅ [69de0a69] Parsers v2.8.7
  [2dfb63ee] PooledArrays v1.4.3
  [aea7be01] PrecompileTools v1.3.4
  [21216c6a] Preferences v1.5.2
  [08abe8d2] PrettyTables v3.4.8
  [189a3867] Reexport v1.2.2
  [2792f1a3] RegistryInstances v0.1.0
  [91c51154] SentinelArrays v1.4.10
  [a2af1166] SortingAlgorithms v1.2.3
  [10745b16] Statistics v1.11.1
  [892a3eda] StringManipulation v0.5.0
  [ec057cc2] StructUtils v2.8.5
  [b04b66ec] SummarizedExperiments v0.2.0
  [3783bdb8] TableTraits v1.0.1
  [bd369af6] Tables v1.14.0
  [3bb67fe8] TranscodingStreams v0.11.3
  [2e619515] Expat_jll v2.8.3+0
  [020c3dae] Git_LFS_jll v3.7.1+0
  [f8c6e375] Git_jll v2.55.0+0
  [94ce4f54] Libiconv_jll v1.18.0+0
  [9bd350c2] OpenSSH_jll v10.5.1+0
  [0dad84c5] ArgTools v1.2.0
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates 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 v1.13.0
  [b27032c2] LibCURL v1.0.0
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.14.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [ca575930] NetworkOptions v1.3.0
  [44cfe95a] Pkg v1.14.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v1.13.0
  [9e88b42a] Serialization v1.11.0
  [6462fe0b] Sockets v1.11.0
  [f489334b] StyledStrings v1.13.0
  [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 v1.5.7+0
  [deac9b47] LibCURL_jll v8.21.0+0
  [e37daf67] LibGit2_jll v1.9.7+0
  [29816b5a] LibSSH2_jll v1.11.104+0
  [14a3606d] MozillaCACerts_jll v2026.8.13
  [4536629a] OpenBLAS_jll v0.3.34+0
  [458c3c95] OpenSSL_jll v3.5.8+0
  [efcefdf7] PCRE2_jll v10.47.0+0
  [83775a58] Zlib_jll v1.3.2+0
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.15.0+0
  [8e850ede] nghttp2_jll v1.70.0+0
  [3f19e933] p7zip_jll v17.8.2+0
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master".
│ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error.
│ Unless this is due to a configuration error, the relevant variable should be set explicitly.
└ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/utilities/utilities.jl:719
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
┌ Error: doctest failure in ../src/setters.jl:174-190
│ 
│ ```jldoctest
│ julia> using SummarizedExperiments
│ 
│ julia> x = exampleobject(20, 10);
│ 
│ julia> length(assays(x))
│ 3
│ 
│ julia> refresh = copy(assays(x));
│ 
│ julia> delete!(refresh, "foo");
│ 
│ julia> setassays!(x, refresh)
│ 
│ julia> length(assays(x))
│ 2
│ ```
│ 
│ Subexpression:
│ 
│ delete!(refresh, "foo");
│ 
│ Evaluated output:
│ 
│ ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead.
│ │   caller = _delete!(h::OrderedDict{String, AbstractArray}, index::Int64) at ordered_dict.jl:441 [inlined]
│ └ @ OrderedCollections ~/.julia/packages/OrderedCollections/MglBA/src/ordered_dict.jl:441
│ ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead.
│ │   caller = _delete!(h::OrderedDict{String, AbstractArray}, index::Int64) at ordered_dict.jl:442 [inlined]
│ └ @ OrderedCollections ~/.julia/packages/OrderedCollections/MglBA/src/ordered_dict.jl:442
│ 
│ Expected output:
│ 
│ 
│ 
│   diff =
│    Warning: Diff output requires color.
│    ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead.
│    │   caller = _delete!(h::OrderedDict{String, AbstractArray}, index::Int64) at ordered_dict.jl:441 [inlined]
│    └ @ OrderedCollections ~/.julia/packages/OrderedCollections/MglBA/src/ordered_dict.jl:441
│    ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead.
│    │   caller = _delete!(h::OrderedDict{String, AbstractArray}, index::Int64) at ordered_dict.jl:442 [inlined]
│    └ @ OrderedCollections ~/.julia/packages/OrderedCollections/MglBA/src/ordered_dict.jl:442
└ @ Documenter ~/.julia/packages/SummarizedExperiments/Nxbzn/src/setters.jl:174
┌ Error: Doctesting failed
│   exception =
│    `makedocs` encountered a doctest error. Terminating build
│    Stacktrace:
│      [1] error(s::String)
│        @ Base error.jl:56
│      [2] runner(::Type{Documenter.Builder.Doctest}, doc::Documenter.Document)
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/builder_pipeline.jl:213
│      [3] dispatch(::Core.TypeEgal{Documenter.Builder.DocumentPipeline}, x::Documenter.Document)
│        @ Documenter.Selectors ~/.julia/packages/Documenter/AXNMp/src/utilities/Selectors.jl:170
│      [4] (::Documenter.var"#95#96"{Documenter.Document})()
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:283 [inlined]
│      [5] withenv(::Documenter.var"#95#96"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}})
│        @ Base env.jl:283
│      [6] (::Documenter.var"#93#94"{Documenter.Document})()
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:282 [inlined]
│      [7] cd(f::Documenter.var"#93#94"{Documenter.Document}, dir::String)
│        @ Base.Filesystem file.jl:113
│      [8] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{root::String, source::String, sitename::String, doctest::Symbol, modules::Vector{Module}, doctestfilters::Vector{Regex}, remotes::Nothing, plugins::Vector{Documenter.Plugin}})
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:281
│      [9] (::Documenter.var"#all_doctests#147"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Vector{Module}})()
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:85
│     [10] macro expansion
│        @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined]
│     [11] macro expansion
│        @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined]
│     [12] macro expansion
│        @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined]
│     [13] macro expansion
│        @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined]
│     [14] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin})
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110
│     [15] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{})
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:37
│     [16] doctest(package::Module)
│        @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:20
│     [17] top-level scope
│        @ ~/.julia/packages/SummarizedExperiments/Nxbzn/test/runtests.jl:3
│     [18] macro expansion
│        @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined]
│     [19] macro expansion
│        @ ~/.julia/packages/SummarizedExperiments/Nxbzn/test/runtests.jl:4 [inlined]
│     [20] include(mapexpr::Function, mod::Module, _path::String)
│        @ Base Base.jl:335
│     [21] top-level scope
│        @ none:6
│     [22] eval(m::Module, e::Any)
│        @ Core boot.jl:618
│     [23] __script_entry_eval(mod::Module, ex::Any)
│        @ Base client.jl:106 [inlined]
│     [24] exec_options(opts::Base.JLOptions)
│        @ Base client.jl:350
│     [25] _start()
│        @ Base client.jl:695
└ @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:99

Doctests: SummarizedExperiments: Test Failed at /home/pkgeval/.julia/packages/Documenter/AXNMp/src/doctest.jl:110
  Expression: all_doctests()
  Stacktrace:
   [1] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined]
   [2] macro expansion
     @ ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110 [inlined]
   [3] macro expansion
     @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined]
   [4] doctest(source::String, modules::Vector{Module}; fix::Bool, testset::String, doctestfilters::Vector{Regex}, plugins::Vector{Documenter.Plugin})
     @ Documenter ~/.julia/packages/Documenter/AXNMp/src/doctest.jl:110
Test Summary:                     | Pass  Fail  Total     Time
SummarizedExperiments.jl          |   12     1     13  1m32.7s
  Doctests: SummarizedExperiments |          1      1  1m19.8s
  Constructor tests               |   12           12     0.1s
RNG of the outermost testset: Random.Xoshiro(0xefd411d16ae80a24, 0x8138bae79ffca995, 0xcb3e913f431dc045, 0x176db0d877c5cb73, 0x0fb6eeafe0db5861)
ERROR: LoadError: Some tests did not pass: 12 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /home/pkgeval/.julia/packages/SummarizedExperiments/Nxbzn/test/runtests.jl:2

Testing failed after 107.16s

ERROR: LoadError: Package SummarizedExperiments 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:3283
 [3] 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:587
 [4] 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
 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160
 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd})
   @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined]
 [7] top-level scope
   @ /PkgEval.jl/scripts/evaluate.jl:223
in expression starting at /PkgEval.jl/scripts/evaluate.jl:214

PkgEval failed after 450.36s: package has test failures