Package evaluation to test BioSimplex on Julia 1.14.0-DEV.1372 (893635dc59*) started at 2025-12-16T13:00:48.940 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 8.99s ################################################################################ # Installation # Installing BioSimplex... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [f37aa7dd] + BioSimplex v0.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [7e6ae17a] + BioSequences v3.5.0 [f37aa7dd] + BioSimplex v0.2.0 [3c28c6f8] + BioSymbols v5.2.0 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.0 [7200193e] + Twiddle v1.1.2 [ade2ca70] + Dates v1.11.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [fa267f1f] + TOML v1.0.3 [4ec0a83e] + Unicode v1.11.0 Installation completed after 3.72s ################################################################################ # 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 12.58s ################################################################################ # Testing # Testing BioSimplex Status `/tmp/jl_v1nGhx/Project.toml` ⌃ [4c88cf16] Aqua v0.8.4 ⌃ [7e6ae17a] BioSequences v3.1.6 [f37aa7dd] BioSimplex v0.2.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_v1nGhx/Manifest.toml` ⌃ [4c88cf16] Aqua v0.8.4 ⌃ [7e6ae17a] BioSequences v3.1.6 [f37aa7dd] BioSimplex v0.2.0 ⌃ [3c28c6f8] BioSymbols v5.1.3 ⌃ [34da2185] Compat v4.12.0 ⌃ [aea7be01] PrecompileTools v1.2.0 ⌃ [21216c6a] Preferences v1.4.1 [7200193e] Twiddle v1.1.2 [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 Info Packages marked with ⌃ have new versions available and may be upgradable. Testing Running tests... WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import.  NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function Char end`.  Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. 1 dependency had output during precompilation: ┌ BioSymbols │ WARNING: Constructor for type "Char" was extended in `BioSymbols` without explicit qualification or import. │ NOTE: Assumed "Char" refers to `Base.Char`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function Char end`. │ Hint: To silence the warning, qualify `Char` as `Base.Char` in the method signature or explicitly `import Base: Char`. └ Test Summary: | Total Time biosimplex | 0 0.0s Aqua: Test Failed at /home/pkgeval/.julia/packages/Aqua/9p8ck/src/persistent_tasks.jl:29 Expression: !(has_persistent_tasks(package; kwargs...)) Evaluated: !(has_persistent_tasks(Base.PkgId(Base.UUID("f37aa7dd-fb3b-4c75-b722-300831487a5c"), "BioSimplex"))) 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/9p8ck/src/persistent_tasks.jl:29 [3] test_persistent_tasks @ ~/.julia/packages/Aqua/9p8ck/src/persistent_tasks.jl:25 [inlined] [4] #test_persistent_tasks#68 @ ~/.julia/packages/Aqua/9p8ck/src/persistent_tasks.jl:34 [inlined] [5] test_persistent_tasks(package::Module) @ Aqua ~/.julia/packages/Aqua/9p8ck/src/persistent_tasks.jl:33 [6] top-level scope @ ~/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:3 [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [8] macro expansion @ ~/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:4 [inlined] Aqua: Error During Test at /home/pkgeval/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:1 Got exception outside of a @test FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:57 [2] all_methods(mods::Module; skip_deprecated::Bool) @ Aqua.Piracy ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:55 [3] kwcall(::@NamedTuple{skip_deprecated::Bool}, ::typeof(Aqua.Piracy.all_methods), mods::Module) @ Aqua.Piracy ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:21 [4] hunt(mod::Module; skip_deprecated::Bool, kwargs::@Kwargs{}) @ Aqua.Piracy ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:193 [5] hunt(mod::Module) @ Aqua.Piracy ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:192 [6] test_piracies(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:218 [7] test_piracies(m::Module) @ Aqua ~/.julia/packages/Aqua/9p8ck/src/piracies.jl:217 [8] top-level scope @ ~/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:3 [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [10] macro expansion @ ~/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:5 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [12] top-level scope @ ~/.julia/packages/BioSimplex/IaXSI/test/runtests.jl:10 [13] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [14] top-level scope @ none:6 [15] eval(m::Module, e::Any) @ Core ./boot.jl:489 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:310 [17] _start() @ Base ./client.jl:577 Test Summary: | Pass Fail Error Total Time Aqua | 1 1 1 3 41.0s RNG of the outermost testset: Random.Xoshiro(0x7d132e52fe1efacf, 0x4dc829731a7e94f3, 0x0170f1a235925204, 0x5dc3fc7934a46ae8, 0xfdfc4a27c9f54014) ERROR: LoadError: Some tests did not pass: 1 passed, 1 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/BioSimplex/IaXSI/test/aquatests.jl:1 in expression starting at /home/pkgeval/.julia/packages/BioSimplex/IaXSI/test/runtests.jl:1 Testing failed after 69.4s ERROR: LoadError: Package BioSimplex 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 116.26s: package tests unexpectedly errored