Package evaluation of PEtabSelect on Julia 1.13.0-DEV.955 (13f6b3b5c0*) started at 2025-08-03T15:02:49.442 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.48s ################################################################################ # Installation # Installing PEtabSelect... Resolving package versions... Installed UnsafePointers ────────────── v1.0.0 Installed DataAPI ───────────────────── v1.16.0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed micromamba_jll ────────────── v1.5.12+0 Installed MacroTools ────────────────── v0.5.16 Installed OrderedCollections ────────── v1.8.1 Installed PrecompileTools ───────────── v1.3.2 Installed DataValueInterfaces ───────── v1.0.0 Installed MicroMamba ────────────────── v0.1.14 Installed CondaPkg ──────────────────── v0.2.29 Installed Parsers ───────────────────── v2.8.3 Installed Pidfile ───────────────────── v1.3.0 Installed Requires ──────────────────── v1.3.1 Installed PEtabSelect ───────────────── v0.1.0 Installed JSON3 ─────────────────────── v1.14.3 Installed Tables ────────────────────── v1.12.1 Installed pixi_jll ──────────────────── v0.41.3+0 Installed JLLWrappers ───────────────── v1.7.1 Installed Scratch ───────────────────── v1.3.0 Installed StructTypes ───────────────── v1.11.0 Installed TableTraits ───────────────── v1.0.1 Installed Preferences ───────────────── v1.4.3 Installed PythonCall ────────────────── v0.9.26 Updating `~/.julia/environments/v1.13/Project.toml` [6de2f99a] + PEtabSelect v0.1.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [992eb4ea] + CondaPkg v0.2.29 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.1 [0f8b85d8] + JSON3 v1.14.3 [1914dd2f] + MacroTools v0.5.16 [0b3b1443] + MicroMamba v0.1.14 [bac558e1] + OrderedCollections v1.8.1 [6de2f99a] + PEtabSelect v0.1.0 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [6099a3de] + PythonCall v0.9.26 [ae029012] + Requires v1.3.1 [6c6a2e73] + Scratch v1.3.0 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [e17b2a0c] + UnsafePointers v1.0.0 ⌅ [f8abcde7] + micromamba_jll v1.5.12+0 [4d7b5844] + pixi_jll v0.41.3+0 [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 v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap 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 [f489334b] + StyledStrings v1.11.0 [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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 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 1.63s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 3846.2 ms ✓ TestEnv 1 dependency successfully precompiled in 4 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 191.64s ################################################################################ # Testing # Testing PEtabSelect Status `/tmp/jl_Zh6Etg/Project.toml` [4c88cf16] Aqua v0.8.13 [992eb4ea] CondaPkg v0.2.29 [6de2f99a] PEtabSelect v0.1.0 [6099a3de] PythonCall v0.9.26 [1bc83da4] SafeTestsets v0.1.0 [ddb6d928] YAML v0.4.14 [8dfed614] Test v1.11.0 Status `/tmp/jl_Zh6Etg/Manifest.toml` [4c88cf16] Aqua v0.8.13 [34da2185] Compat v4.18.0 [992eb4ea] CondaPkg v0.2.29 [9a962f9c] DataAPI v1.16.0 [e2d170a0] DataValueInterfaces v1.0.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [0f8b85d8] JSON3 v1.14.3 [1914dd2f] MacroTools v0.5.16 [0b3b1443] MicroMamba v0.1.14 [bac558e1] OrderedCollections v1.8.1 [6de2f99a] PEtabSelect v0.1.0 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [6099a3de] PythonCall v0.9.26 [ae029012] Requires v1.3.1 [1bc83da4] SafeTestsets v0.1.0 [6c6a2e73] Scratch v1.3.0 [69024149] StringEncodings v0.3.7 [856f2bd8] StructTypes v1.11.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [e17b2a0c] UnsafePointers v1.0.0 [ddb6d928] YAML v0.4.14 [94ce4f54] Libiconv_jll v1.18.0+0 ⌅ [f8abcde7] micromamba_jll v1.5.12+0 [4d7b5844] pixi_jll v0.41.3+0 [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 v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap 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 [f489334b] StyledStrings v1.11.0 [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 v8.15.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [83775a58] Zlib_jll v1.3.1+2 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PEtabSelect/hK2Tm/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/avYrV/CondaPkg.toml CondaPkg Resolving changes + openssl + petab-select (pip) + python + uv CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ init │ --format pixi └ /tmp/jl_Zh6Etg/.CondaPkg ✔ Created /tmp/jl_Zh6Etg/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_Zh6Etg/.CondaPkg/pixi.toml │ [dependencies] │ uv = ">=0.4" │ openssl = ">=3, <3.6" │ │ [dependencies.python] │ build = "*cpython*" │ channel = "conda-forge" │ version = ">=3.8,<4" │ │ [project] │ description = "automatically generated by CondaPkg.jl" │ name = ".CondaPkg" │ channel-priority = "strict" │ platforms = ["linux-64"] │ channels = ["conda-forge"] │ │ [pypi-dependencies] └ petab-select = "*" CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ install └ --manifest-path /tmp/jl_Zh6Etg/.CondaPkg/pixi.toml ✔ The default environment has been installed. Aqua: Error During Test at /home/pkgeval/.julia/packages/PEtabSelect/hK2Tm/test/aqua.jl:3 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/1UuaV/src/piracies.jl:55 [3] all_methods @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:21 [inlined] [4] #hunt#30 @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:194 [inlined] [5] hunt @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:193 [inlined] [6] test_piracies(m::Module; broken::Bool, kwargs::@Kwargs{}) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:219 [7] test_piracies(m::Module) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:218 [8] top-level scope @ ~/.julia/packages/PEtabSelect/hK2Tm/test/aqua.jl:4 [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [10] macro expansion @ ~/.julia/packages/PEtabSelect/hK2Tm/test/aqua.jl:10 [inlined] [11] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [12] top-level scope @ ~/.julia/packages/SafeTestsets/raUNr/src/SafeTestsets.jl:4 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [14] macro expansion @ ~/.julia/packages/PEtabSelect/hK2Tm/test/runtests.jl:4 [inlined] [15] eval(m::Module, e::Any) @ Core ./boot.jl:489 [16] top-level scope @ ~/.julia/packages/PEtabSelect/hK2Tm/test/runtests.jl:28 [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [18] top-level scope @ none:6 [19] eval(m::Module, e::Any) @ Core ./boot.jl:489 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [21] _start() @ Base ./client.jl:553 Test Summary: | Pass Error Total Time Aqua Quality Check | 8 1 9 3m19.5s Aqua | 8 1 9 2m06.4s julia | 1 1 0.1s Base.PkgId(Base.UUID("6de2f99a-1d3e-11f0-2fac-936eab9aa55b"), "PEtabSelect") deps | 1 1 0.5s Base.PkgId(Base.UUID("6de2f99a-1d3e-11f0-2fac-936eab9aa55b"), "PEtabSelect") extras | 1 1 0.0s Base.PkgId(Base.UUID("6de2f99a-1d3e-11f0-2fac-936eab9aa55b"), "PEtabSelect") weakdeps | 1 1 0.0s RNG of the outermost testset: Random.Xoshiro(0x41d92d75646c496d, 0xf5c6ee68db6a7ce7, 0x0ec60eac119a020b, 0x57d423f5fe73c21f, 0xd3d93dc643d81932) ERROR: LoadError: Some tests did not pass: 8 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PEtabSelect/hK2Tm/test/runtests.jl:3 Testing failed after 201.89s ERROR: LoadError: Package PEtabSelect 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:2695 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2544 [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:538 [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:515 [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:168 [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:157 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [9] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [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:155 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:311 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [14] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 476.26s: package tests unexpectedly errored