Package evaluation to test PDBTools on Julia 1.14.0-DEV.3055 (7e75a8061a*) started at 2026-08-27T19:22:06.813 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.51s ################################################################################ # Installation # Installing PDBTools... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [e29189f1] + PDBTools v3.36.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [69e1c6dd] + CellListMap v0.10.5 [ae650224] + ChunkSplitters v3.2.0 [34da2185] + Compat v4.18.1 [187b0558] + ConstructionBase v1.6.0 [ffbed154] + DocStringExtensions v0.9.5 [1fa38f19] + Format v1.3.7 [842dd82b] + InlineStrings v1.4.5 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.7.1 [1914dd2f] + MacroTools v0.5.16 [aea21201] + MolSimToolkitShared v1.6.0 [bac558e1] + OrderedCollections v2.0.1 [e29189f1] + PDBTools v3.36.0 ⌅ [69de0a69] + Parsers v2.8.7 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [c298f58b] + ProteinSecondaryStructures v2.0.4 [fdea26ae] + SIMD v3.7.2 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.19 [1e83bf80] + StaticArraysCore v1.4.4 [ec057cc2] + StructUtils v2.8.5 [1c621080] + TestItems v1.1.0 [74334e00] + DSSP_jll v4.4.0+1 [850473c1] + STRIDE_jll v1.0.0+0 [0dad84c5] + ArgTools v1.2.0 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.12.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b27032c2] + LibCURL v1.0.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [56ddb016] + Logging v1.11.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [deac9b47] + LibCURL_jll v8.21.0+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [4536629a] + OpenBLAS_jll v0.3.34+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.70.0+0 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 5.24s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 10.8 s ✓ MolSimToolkitShared 2.0 s ✓ DSSP_jll 1.6 s ✓ STRIDE_jll 32.5 s ✓ CellListMap 54.0 s ✓ Documenter 1.8 s ✓ ProteinSecondaryStructures 40.5 s ✓ PDBTools 20.4 s ✓ PDBTools → Plotting 8 dependencies successfully precompiled in 165 seconds. 203 already precompiled. Precompilation completed after 188.97s ################################################################################ # Testing # Testing PDBTools Updating git-repo `https://github.com/lmiq/Documenter.jl` Status `/tmp/jl_8KQyqk/Project.toml` [4c88cf16] Aqua v0.8.16 [69e1c6dd] CellListMap v0.10.5 [0ca39b1e] Chairmarks v1.3.1 [ae650224] ChunkSplitters v3.2.0 [34da2185] Compat v4.18.1 [8bb1440f] DelimitedFiles v1.9.1 [e30172f5] Documenter v1.17.0 `https://github.com/lmiq/Documenter.jl#top_menu_from_pages` [1fa38f19] Format v1.3.7 [842dd82b] InlineStrings v1.4.5 [682c06a0] JSON v1.7.1 [aea21201] MolSimToolkitShared v1.6.0 [bac558e1] OrderedCollections v2.0.1 [e29189f1] PDBTools v3.36.0 [91a5bcdd] Plots v1.41.7 [aea7be01] PrecompileTools v1.3.4 [c298f58b] ProteinSecondaryStructures v2.0.4 [fdea26ae] SIMD v3.7.2 [aed2ae9c] ShowMethodTesting v1.3.0 [90137ffa] StaticArrays v1.9.19 [f8b46487] TestItemRunner v1.3.1 [1c621080] TestItems v1.1.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.7.0 [b77e0a4c] InteractiveUtils v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [de0858da] Printf v1.11.0 [2f01184e] SparseArrays v1.13.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_8KQyqk/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.16 [69e1c6dd] CellListMap v0.10.5 [0ca39b1e] Chairmarks v1.3.1 [ae650224] ChunkSplitters v3.2.0 [944b1d66] CodecZlib v0.7.9 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [9a962f9c] DataAPI v1.16.0 [864edb3b] DataStructures v0.19.6 [8bb1440f] DelimitedFiles v1.9.1 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.17.0 `https://github.com/lmiq/Documenter.jl#top_menu_from_pages` [c87230d0] FFMPEG v0.4.5 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [1fa38f19] Format v1.3.7 [28b8d3ca] GR v0.73.27 [d7ba0133] Git 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GLFW_jll v3.5.1+0 [d2c73de3] GR_jll v0.73.27+0 ⌅ [b0724c58] GettextRuntime_jll v0.22.4+0 [61579ee1] Ghostscript_jll v9.55.1+0 [020c3dae] Git_LFS_jll v3.7.1+0 [f8c6e375] Git_jll v2.55.0+0 [7746bdde] Glib_jll v2.88.3+0 [3b182d85] Graphite2_jll v1.3.16+0 ⌅ [2e76f6c2] HarfBuzz_jll v8.5.1+0 [aacddb02] JpegTurbo_jll v3.2.0+1 [c1c5ebd0] LAME_jll v3.100.3+0 [88015f11] LERC_jll v4.1.0+0 [1d63c593] LLVMOpenMP_jll v22.1.7+0 ⌅ [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.42.0+0 [89763e89] Libtiff_jll v4.7.3+0 [38a345b3] Libuuid_jll v2.42.0+0 [e7412a2a] Ogg_jll v1.3.6+0 [9bd350c2] OpenSSH_jll v10.5.1+0 [91d4177d] Opus_jll v1.6.1+0 [36c8627f] Pango_jll v1.58.0+0 [30392449] Pixman_jll v0.46.4+0 [c0090381] Qt6Base_jll v6.10.2+2 [629bc702] Qt6Declarative_jll v6.10.2+2 [ce943373] Qt6ShaderTools_jll v6.10.2+1 [6de9746b] Qt6Svg_jll v6.10.2+0 [e99dba38] Qt6Wayland_jll v6.10.2+1 [850473c1] STRIDE_jll v1.0.0+0 [a44049a8] Vulkan_Loader_jll v1.3.243+0 [a2964d1f] Wayland_jll v1.24.0+0 [ffd25f8a] XZ_jll v5.8.3+0 [f67eecfb] Xorg_libICE_jll v1.1.2+0 [c834827a] Xorg_libSM_jll v1.2.6+0 [4f6342f7] Xorg_libX11_jll v1.8.13+0 [0c0b7dd1] Xorg_libXau_jll v1.0.13+0 [935fb764] Xorg_libXcursor_jll v1.2.4+0 [a3789734] Xorg_libXdmcp_jll v1.1.6+0 [1082639a] Xorg_libXext_jll v1.3.8+0 [d091e8ba] Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] Xorg_libXi_jll v1.8.4+0 [d1454406] Xorg_libXinerama_jll v1.1.7+0 [ec84b674] Xorg_libXrandr_jll v1.5.6+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [a65dc6b1] Xorg_libpciaccess_jll v0.19.0+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [cc61e674] Xorg_libxkbfile_jll v1.2.0+0 [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.6+0 [12413925] Xorg_xcb_util_image_jll v0.4.1+0 [2def613f] Xorg_xcb_util_jll v0.4.1+0 [975044d2] Xorg_xcb_util_keysyms_jll v0.4.1+0 [0d47668e] Xorg_xcb_util_renderutil_jll v0.3.10+0 [c22f9ab0] Xorg_xcb_util_wm_jll v0.4.2+0 [35661453] Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] Xorg_xkeyboard_config_jll v2.47.0+2 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [35ca27e7] eudev_jll v3.2.14+0 ⌅ [214eeab7] fzf_jll v0.61.1+0 [a4ae2306] libaom_jll v3.14.1+0 [0ac62f75] libass_jll v0.17.4+0 [1183f4f0] libdecor_jll v0.2.2+0 [8e53e030] libdrm_jll v2.4.134+0 [2db6ffa8] libevdev_jll v1.13.4+0 [f638f0a6] libfdk_aac_jll v2.0.4+0 [36db933b] libinput_jll v1.28.1+0 [b53b4c65] libpng_jll v1.6.58+0 [9a156e7d] libva_jll v2.23.0+0 [f27f6e37] libvorbis_jll v1.3.8+0 [009596ad] mtdev_jll v1.1.7+0 ⌅ [1270edf5] x264_jll v10164.0.1+0 [dfaa095f] x265_jll v4.1.0+0 [d8fb68d0] xkbcommon_jll v1.13.0+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future 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 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [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 v1.5.7+0 [deac9b47] LibCURL_jll v8.21.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.8+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: │ │ The `select` function with the keyword argument `by` will be deprecated. │ Use `select(atoms, function)` instead. Or simply `filter(function, atoms)`. │ └ @ PDBTools ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, PDBTools.NucleosideResidue}, index::Int64) at ordered_dict.jl:455 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, PDBTools.NucleosideResidue}, index::Int64) at ordered_dict.jl:456 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, Tuple{DataType, Symbol}}, index::Int64) at ordered_dict.jl:455 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, Tuple{DataType, Symbol}}, index::Int64) at ordered_dict.jl:456 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 ┌ Warning: │ │ Memory limit reached. 50 atoms read so far will be returned. │ Size of the atoms array: 0.008 MB │ └ @ PDBTools ┌ Warning: Failed reading ATOM line in PDB format, trying mmCIF reader. └ @ PDBTools ┌ Warning: Failed reading ATOM line in PDB format, trying mmCIF reader. └ @ PDBTools ┌ Warning: Failed reading ATOM line in PDB format, trying mmCIF reader. └ @ PDBTools Atom(1N-ALA1A)┌ Warning: Residue TIP3 not found in protein residues. Assuming residue charge = 0 └ @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/struct_and_iterators/Residue.jl:506 ┌ 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 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, PDBTools.ProteinResidue}, index::Int64) at ordered_dict.jl:455 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:455 ┌ Warning: `_unsetindex!(A, i)` is deprecated, use `Base.unsetindex!(A, i)` instead. │ caller = _delete!(h::OrderedCollections.OrderedDict{String, PDBTools.ProteinResidue}, index::Int64) at ordered_dict.jl:456 [inlined] └ @ OrderedCollections ~/.julia/packages/OrderedCollections/1sijc/src/ordered_dict.jl:456 ┌ Warning: gmx executable not available: some tests won't be run └ @ Main.var"##229" ~/.julia/packages/PDBTools/R45Ou/src/tools/mvalue/testing/testing.jl:207 ┌ Warning: Residue THR104 - chain A is missing O backbone atom. └ @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/tools/secondary_structure.jl:40 ┌ Warning: Residue THR104 - chain A is missing O backbone atom. └ @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/tools/secondary_structure.jl:40 Unbound type parameters detected: [1] _float_type(::AbstractVector{<:AbstractVector{T1}}) where T1<:Real @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/coordinates/distance.jl:110 [2] formula(atoms::AbstractVector{<:AtomType}) where AtomType<:Atom @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/properties/formula.jl:47 Unbound type parameters: Test Failed at /home/pkgeval/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 Expression: isempty(unbounds) Evaluated: isempty(Method[_float_type(::AbstractVector{<:AbstractVector{T1}}) where T1<:Real @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/coordinates/distance.jl:110, formula(atoms::AbstractVector{<:AtomType}) where AtomType<:Atom @ PDBTools ~/.julia/packages/PDBTools/R45Ou/src/properties/formula.jl:47]) Stacktrace: [1] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] [2] test_unbound_args(m::Module; broken::Bool) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:38 [3] test_unbound_args(m::Module) @ Aqua ~/.julia/packages/Aqua/h1qD0/src/unbound_args.jl:14 [inlined] [4] macro expansion @ ~/.julia/packages/Aqua/h1qD0/src/Aqua.jl:78 [inlined] [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2247 [inlined] [6] 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/h1qD0/src/Aqua.jl:78 Test Summary: | Pass Fail Total Time PDBTools | 79352 1 79353 10m36.9s ext | 6 6 1m43.7s src | 79336 79336 6m36.0s test/runtests.jl | 10 1 11 2m16.8s Aqua.test_all | 10 1 11 2m16.8s Method ambiguity | 1 1 10.5s Unbound type parameters | 1 1 17.7s Undefined exports | 1 1 0.0s Compare Project.toml and test/Project.toml | 1 1 0.0s Stale dependencies | 1 1 9.7s Compat bounds | 4 4 0.9s Piracy | 1 1 0.6s Persistent tasks | 1 1 1m08.8s ERROR: LoadError: Some tests did not pass: 79352 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PDBTools/R45Ou/test/runtests.jl:20 Testing failed after 683.24s ERROR: LoadError: Package PDBTools 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:3283 [3] 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:587 [4] 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 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 945.41s: package has test failures