Package evaluation to test BioAtomsCount on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-11T13:25:45.203 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.72s ################################################################################ # Installation # Installing BioAtomsCount... Resolving package versions... Installed Preferences ───── v1.5.0 Installed PrecompileTools ─ v1.3.3 Installed Twiddle ───────── v1.1.2 Installed BioSymbols ────── v5.2.0 Installed BioSequences ──── v3.5.0 Installed BioAtomsCount ─── v0.3.1 Updating `~/.julia/environments/v1.14/Project.toml` [85ca2092] + BioAtomsCount v0.3.1 Updating `~/.julia/environments/v1.14/Manifest.toml` [85ca2092] + BioAtomsCount v0.3.1 [7e6ae17a] + BioSequences v3.5.0 [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 5.2s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4630.5 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 810.5 ms ✓ Twiddle 1088.9 ms ✓ Preferences 871.6 ms ✓ PrecompileTools 2574.0 ms ✓ BioSymbols 9904.8 ms ✓ BioSequences 1098.8 ms ✓ BioAtomsCount 6 dependencies successfully precompiled in 16 seconds. 4 already precompiled. Precompilation completed after 34.34s ################################################################################ # Testing # Testing BioAtomsCount Status `/tmp/jl_bnGnRc/Project.toml` [4c88cf16] Aqua v0.8.14 [85ca2092] BioAtomsCount v0.3.1 [7e6ae17a] BioSequences v3.5.0 [c3a54625] JET v0.11.0 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_bnGnRc/Manifest.toml` [4c88cf16] Aqua v0.8.14 [85ca2092] BioAtomsCount v0.3.1 [7e6ae17a] BioSequences v3.5.0 [3c28c6f8] BioSymbols v5.2.0 [da1fd8a2] CodeTracking v2.0.1 [34da2185] Compat v4.18.1 [807dbc54] Compiler v0.1.1 [c3a54625] JET v0.11.0 [aa1ae85d] JuliaInterpreter v0.10.6 [70703baa] JuliaSyntax v1.0.2 [6f1432cf] LoweredCodeUtils v3.4.4 [1914dd2f] MacroTools v0.5.16 [bac558e1] OrderedCollections v1.8.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.0 [ae029012] Requires v1.3.1 [295af30f] Revise v3.12.1 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [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 v1.12.0 [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 v1.13.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets 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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.11.4 [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... ┌ Warning: precompile directive │ precompile(Tuple{mbody.sig.parameters[1], Symbol, Bool, Bool, Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:skip_include,), Tuple{Bool}}}, typeof(methods_by_execution!), Compiled, MI, Module, Expr}) │ failed. Please report an issue in Revise (after checking for duplicates) or remove this directive. └ @ Revise ~/.julia/packages/Revise/nLE4h/src/precompile.jl:65 WARNING: Imported binding Compiler.ConstCallInfo was undeclared at import time during import to JET. WARNING: Imported binding Compiler.WorldView was undeclared at import time during import to JET. ERROR: LoadError: UndefVarError: `WorldView` not defined in `JET` Suggestion: this global was defined as `Compiler.WorldView` but not assigned a value. Stacktrace:  [1] top-level scope  @ ~/.julia/packages/JET/E3oAN/src/abstractinterpret/typeinfer.jl:215  [2] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [3] top-level scope  @ ~/.julia/packages/JET/E3oAN/src/JETBase.jl:321  [4] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [5] top-level scope  @ ~/.julia/packages/JET/E3oAN/src/JET.jl:41  [6] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [7] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3151  [8] top-level scope  @ stdin:5  [9] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [10] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2997  [11] include_string  @ ./loading.jl:3007 [inlined]  [12] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [13] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/JET/E3oAN/src/abstractinterpret/typeinfer.jl:215 in expression starting at /home/pkgeval/.julia/packages/JET/E3oAN/src/JETBase.jl:321 in expression starting at /home/pkgeval/.julia/packages/JET/E3oAN/src/JET.jl:1 in expression starting at stdin:5 2 dependencies had output during precompilation: ┌ JET │ [Output was shown above] └ ┌ Revise │ ┌ Warning: precompile directive │ │ precompile(Tuple{mbody.sig.parameters[1], Symbol, Bool, Bool, Iterators.Pairs{Symbol, Bool, Tuple{Symbol}, NamedTuple{(:skip_include,), Tuple{Bool}}}, typeof(methods_by_execution!), Compiled, MI, Module, Expr}) │ │ failed. Please report an issue in Revise (after checking for duplicates) or remove this directive. │ └ @ Revise ~/.julia/packages/Revise/nLE4h/src/precompile.jl:65 └ ERROR: LoadError: The following 1 package failed to precompile: JET Failed to precompile JET [c3a54625-cd67-489e-a8e7-0a5a0ff4e31b] to "/home/pkgeval/.julia/compiled/v1.14/JET/jl_QbLZCC" (ProcessExited(1)). in expression starting at /home/pkgeval/.julia/packages/BioAtomsCount/YLOr1/test/runtests.jl:1 Testing failed after 175.29s ERROR: LoadError: Package BioAtomsCount 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:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [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:219 [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:210 PkgEval failed after 241.52s: package fails to precompile