Package evaluation to test SummarizedExperiments on Julia 1.14.0-DEV.3106 (9d314127b9*) started at 2026-09-03T17:00:20.097 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.39s ################################################################################ # Installation # Installing SummarizedExperiments... Resolving package versions... 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 v1.11.5 ⌅ [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 To see why use `status --outdated -m` Installation completed after 3.91s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 2.7 s ✓ Tables 2.4 s ✓ Libiconv_jll 1.1 s ✓ Git_LFS_jll 1.1 s ✓ OpenSSH_jll 1.3 s ✓ Expat_jll 1.5 s ✓ StructUtils → StructUtilsTablesExt 41.5 s ✓ PrettyTables 1.9 s ✓ Git_jll 77.3 s ✓ DataFrames 0.6 s ✓ Git 5.6 s ✓ SummarizedExperiments 47.4 s ✓ Documenter 12 dependencies successfully precompiled in 185 seconds. 68 already precompiled. Precompilation completed after 199.47s ################################################################################ # Testing # Testing SummarizedExperiments Status `/tmp/jl_og3pvZ/Project.toml` [a93c6f00] DataFrames v1.8.2 ⌅ [864edb3b] DataStructures v0.18.22 [e30172f5] Documenter v1.19.0 [189a3867] Reexport v1.2.2 [b04b66ec] SummarizedExperiments v0.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_og3pvZ/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 v1.19.0 [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 v1.11.5 ⌅ [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 v10.48.0+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/13nbQ/src/utilities/utilities.jl:952 [ 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/13nbQ/src/builder_pipeline.jl:213 │ [3] dispatch(::Core.TypeEgal{Documenter.Builder.DocumentPipeline}, x::Documenter.Document) │ @ Documenter.Selectors ~/.julia/packages/Documenter/13nbQ/src/utilities/Selectors.jl:170 │ [4] (::Documenter.var"#101#102"{Documenter.Document})() │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/makedocs.jl:283 [inlined] │ [5] withenv(::Documenter.var"#101#102"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}}) │ @ Base env.jl:283 │ [6] (::Documenter.var"#99#100"{Documenter.Document})() │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/makedocs.jl:282 [inlined] │ [7] cd(f::Documenter.var"#99#100"{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}, meta::Dict{Symbol, Any}}) │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/makedocs.jl:281 │ [9] (::Documenter.var"#all_doctests#153"{Bool, Vector{Regex}, Vector{Documenter.Plugin}, Dict{Symbol, Any}, Vector{Module}})() │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:92 │ [10] macro expansion │ @ ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:118 [inlined] │ [11] macro expansion │ @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] │ [12] macro expansion │ @ ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:118 [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}, meta::Dict{Symbol, Any}) │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:118 │ [15] doctest(package::Module; manual::Bool, testset::Nothing, kwargs::@Kwargs{}) │ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:38 │ [16] doctest(package::Module) │ @ Documenter ~/.julia/packages/Documenter/13nbQ/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/13nbQ/src/doctest.jl:107 Doctests: SummarizedExperiments: Test Failed at /home/pkgeval/.julia/packages/Documenter/13nbQ/src/doctest.jl:118 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/13nbQ/src/doctest.jl:118 [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}, meta::Dict{Symbol, Any}) @ Documenter ~/.julia/packages/Documenter/13nbQ/src/doctest.jl:118 Test Summary: | Pass Fail Total Time SummarizedExperiments.jl | 12 1 13 1m34.8s Doctests: SummarizedExperiments | 1 1 1m17.8s Constructor tests | 12 12 0.1s RNG of the outermost testset: Random.Xoshiro(0xefecef9ebe75e80f, 0xd5152f97c3936f7a, 0xbb79e626e433979c, 0x768627b3a9454356, 0x563913121f1703e3) 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 109.64s 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:3298 [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 388.06s: package has test failures