Package evaluation of PDBTools on Julia 1.13.0-DEV.955 (13f6b3b5c0*) started at 2025-08-03T15:22:26.618 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.03s ################################################################################ # Installation # Installing PDBTools... Resolving package versions... Installed StaticArraysCore ──── v1.4.3 Installed TestItems ─────────── v1.0.0 Installed Compat ────────────── v4.18.0 Installed InlineStrings ─────── v1.4.4 Installed Preferences ───────── v1.4.3 Installed PrecompileTools ───── v1.3.2 Installed Format ────────────── v1.3.7 Installed StaticArrays ──────── v1.9.14 Installed OrderedCollections ── v1.8.1 Installed PDBTools ──────────── v3.2.0 Installed MolSimToolkitShared ─ v1.1.3 Updating `~/.julia/environments/v1.13/Project.toml` [e29189f1] + PDBTools v3.2.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [34da2185] + Compat v4.18.0 [1fa38f19] + Format v1.3.7 [842dd82b] + InlineStrings v1.4.4 [aea21201] + MolSimToolkitShared v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [e29189f1] + PDBTools v3.2.0 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [1c621080] + TestItems v1.0.0 [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 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.7.15 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 Installation completed after 3.92s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4516.3 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. Precompiling package dependencies... Precompilation completed after 660.84s ################################################################################ # Testing # Testing PDBTools Status `/tmp/jl_bClojd/Project.toml` [4c88cf16] Aqua v0.8.13 [6e4b80f9] BenchmarkTools v1.6.0 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.14.1 [1fa38f19] Format v1.3.7 [842dd82b] InlineStrings v1.4.4 [aea21201] MolSimToolkitShared v1.1.3 [bac558e1] OrderedCollections v1.8.1 [e29189f1] PDBTools v3.2.0 [91a5bcdd] Plots v1.40.17 [aea7be01] PrecompileTools v1.3.2 [aed2ae9c] ShowMethodTesting v1.2.0 [90137ffa] StaticArrays v1.9.14 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [de0858da] Printf v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_bClojd/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.13 [6e4b80f9] 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[29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.7.15 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [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... Atom(1N-ALA1A)┌ Warning: │ │ Residue `sX` will be interpreted as bridged Cysteine. │ └ @ PDBTools ┌ Warning: │ │ The element masses are not the coarse-grained ones. This must be fixed in the future. │ └ @ PDBTools ┌ Warning: │ │ Memory limit reached. 50 atoms read so far will be returned. │ Size of the atoms array: 0.006 MB │ └ @ PDBTools Piracy: Error During Test at /home/pkgeval/.julia/packages/Aqua/1UuaV/src/Aqua.jl:103 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 @ ~/.julia/packages/Aqua/1UuaV/src/piracies.jl:218 [inlined] [8] macro expansion @ ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:104 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1929 [inlined] [10] 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/1UuaV/src/Aqua.jl:104 [11] test_all(testtarget::Module) @ Aqua ~/.julia/packages/Aqua/1UuaV/src/Aqua.jl:59 [12] top-level scope @ ~/.julia/packages/PDBTools/7iXmR/test/runtests.jl:24 [13] eval(m::Module, e::Any) @ Core ./boot.jl:489 [14] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2847 [15] include_string(m::Module, txt::String, fname::String) @ Base ./loading.jl:2857 [16] #run_testitem##6 @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:118 [inlined] [17] withpath(f::TestItemRunner.var"#run_testitem##6#run_testitem##7"{String, String, Module}, path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/vendored_code.jl:7 [18] #run_testitem##4 @ ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:117 [inlined] [19] cd(f::TestItemRunner.var"#run_testitem##4#run_testitem##5"{String, String, Module}, dir::String) @ Base.Filesystem ./file.jl:112 [20] run_testitem(filepath::String, use_default_usings::Bool, setups::Vector{Symbol}, package_name::String, original_code::String, line::Int64, column::Int64, test_setup_module_set::TestItemRunner.TestSetupModuleSet, testsetups::Dict{Symbol, Any}) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:116 [21] run_tests(path::String; filter::Nothing, verbose::Bool) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:221 [22] run_tests(path::String) @ TestItemRunner ~/.julia/packages/TestItemRunner/Q6zqe/src/TestItemRunner.jl:133 [23] top-level scope @ ~/.julia/packages/PDBTools/7iXmR/test/runtests.jl:20 [24] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:312 [25] top-level scope @ none:6 [26] eval(m::Module, e::Any) @ Core ./boot.jl:489 [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [28] _start() @ Base ./client.jl:553 ┌ Warning: Residue TIP3 not found in protein residues. Assuming residue charge = 0 └ @ PDBTools ~/.julia/packages/PDBTools/7iXmR/src/struct_and_iterators/Residue.jl:108 ┌ Warning: │ │ Residue numbers are not unique and/or are not sorted. Using serial indexing (1:1:6) to define x-tick positions. │ └ @ PDBTools ┌ Warning: │ │ Residue numbers are not unique and/or are not sorted. Using serial indexing (1:3:6) to define x-tick positions. │ └ @ PDBTools ┌ Warning: │ │ Residue numbers are not unique and/or are not sorted. Using serial indexing (1:1:6) to define x-tick positions. │ └ @ PDBTools ┌ Warning: │ │ Residue numbers are not unique and/or are not sorted. Using serial indexing (1:1:6) to define x-tick positions. │ └ @ PDBTools ┌ Warning: │ │ Residue numbers are not unique and/or are not sorted. Using serial indexing (1:1:3) to define x-tick positions. │ └ @ PDBTools Test Summary: | Pass Error Total Time Package | 598 1 599 5m36.4s src/read_write/write_mmcif.jl | 9 9 28.1s src/struct_and_iterators/Atom.jl | 83 83 26.2s src/struct_and_iterators/Model.jl | 19 19 3.7s src/tools/tools.jl | 7 7 8.4s src/coordinates/distance.jl | 40 40 3.5s src/properties/elements.jl | 13 13 5.2s src/coordinates/coor.jl | 7 7 2.7s src/read_write/read_pdb.jl | 48 48 2.9s src/struct_and_iterators/iterators_base.jl | 1 1 0.1s src/tools/custom_types.jl | 4 4 2.5s src/struct_and_iterators/Segment.jl | 22 22 1.7s ext/plot_contacts.jl | 4 4 1m06.0s src/select/select.jl | 74 74 23.3s src/read_write/write_pdb.jl | 26 26 15.6s src/properties/getseq.jl | 6 6 1.4s src/properties/formula.jl | 6 6 4.0s src/select/select_with_vmd.jl | 0 0.0s src/read_write/read_mmcif.jl | 32 32 15.4s src/properties/protein_residues.jl | 33 33 0.6s src/read_write/parsers.jl | 11 11 0.3s test/runtests.jl | 10 1 11 1m48.9s Aqua.test_all | 10 1 11 1m48.9s Method ambiguity | 1 1 8.0s 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 5.6s Compat bounds | 4 4 0.7s Piracy | 1 1 6.5s Persistent tasks | 1 1 1m06.4s src/struct_and_iterators/Residue.jl | 106 106 9.5s src/coordinates/contacts.jl | 9 9 2.0s src/coordinates/maxmin.jl | 3 3 0.6s src/read_write/wget.jl | 5 5 1.0s src/struct_and_iterators/Chain.jl | 20 20 2.6s ERROR: LoadError: Some tests did not pass: 598 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PDBTools/7iXmR/test/runtests.jl:20 Testing failed after 391.33s ERROR: LoadError: Package PDBTools 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 1244.4s: package tests unexpectedly errored