Package evaluation to test BioStockholm on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T13:02:17.453 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 8.61s ################################################################################ # Installation # Installing BioStockholm... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [eeb925a3] + BioStockholm v0.2.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [67c07d97] + Automa v1.1.0 [eeb925a3] + BioStockholm v0.2.1 [bac558e1] + OrderedCollections v1.8.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [fdea26ae] + SIMD v3.7.2 [3bb67fe8] + TranscodingStreams v0.11.3 [ade2ca70] + Dates v1.11.0 [de0858da] + Printf v1.11.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 Installation completed after 1.09s ################################################################################ # 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 13.13s ################################################################################ # Testing # Testing BioStockholm Status `/tmp/jl_xWo2Tx/Project.toml` [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [eeb925a3] BioStockholm v0.2.1 [bac558e1] OrderedCollections v1.8.1 [8dfed614] Test v1.11.0 Status `/tmp/jl_xWo2Tx/Manifest.toml` [4c88cf16] Aqua v0.8.14 [67c07d97] Automa v1.1.0 [eeb925a3] BioStockholm v0.2.1 [34da2185] Compat v4.18.1 [bac558e1] OrderedCollections v1.8.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [fdea26ae] SIMD v3.7.2 [3bb67fe8] TranscodingStreams v0.11.3 [0dad84c5] ArgTools v1.1.2 [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 [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 [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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization 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 v1.3.0+1 [deac9b47] LibCURL_jll v8.17.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.12.2 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+0 Testing Running tests... testing BioStockholm testing Aqua.test_all Persistent tasks: Test Failed at /home/pkgeval/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:38 Expression: !(has_persistent_tasks(package; kwargs...)) Evaluated: !(has_persistent_tasks(Base.PkgId(Base.UUID("eeb925a3-6f9d-43e6-829e-e0ea03b76ecf"), "BioStockholm"))) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:753 [inlined] [2] test_persistent_tasks(package::Base.PkgId; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:38 [3] test_persistent_tasks @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:34 [inlined] [4] #test_persistent_tasks#57 @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:43 [inlined] [5] test_persistent_tasks @ ~/.julia/packages/Aqua/MCcFg/src/persistent_tasks.jl:42 [inlined] [6] macro expansion @ ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:109 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] test_all(testtarget::Module; ambiguities::Bool, unbound_args::Bool, undefined_exports::Bool, project_extras::Bool, stale_deps::Bool, deps_compat::Bool, piracies::Bool, persistent_tasks::Bool, undocumented_names::Bool) @ Aqua ~/.julia/packages/Aqua/MCcFg/src/Aqua.jl:109 testing constructors testing parse testing print testing write testing read Test Summary: | Pass Fail Total Time BioStockholm | 44 1 45 6m34.2s Aqua.test_all | 10 1 11 1m30.1s Method ambiguity | 1 1 7.9s Unbound type parameters | 1 1 0.1s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 4.0s Compat bounds | 4 4 0.6s Piracy | 1 1 0.2s Persistent tasks | 1 1 58.2s constructors | 4 4 4.3s parse | 12 12 4m53.3s print | 12 12 1.6s write | 4 4 0.8s read | 2 2 0.2s RNG of the outermost testset: Random.Xoshiro(0x464bd9f64fbe4045, 0xd7cd0708dde25885, 0x1055b822307f7316, 0xf69e8c5d885b6f31, 0xddb55e4a96629399) ERROR: LoadError: Some tests did not pass: 44 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioStockholm/yCcu6/test/runtests.jl:16 Testing failed after 422.52s ERROR: LoadError: Package BioStockholm 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:3067 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2916 [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 477.43s: package has test failures