Package evaluation to test PDBTools on Julia 1.14.0-DEV.2621 (b841d233e9*) started at 2026-07-09T19:17:12.847 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 16.09s ################################################################################ # Installation # Installing PDBTools... Resolving package versions... Installed OrderedCollections ───────── v2.0.1 Installed InlineStrings ────────────── v1.4.5 Installed ConstructionBase ─────────── v1.6.0 Installed ChunkSplitters ───────────── v3.2.0 Installed MacroTools ───────────────── v0.5.16 Installed Compat ───────────────────── v4.18.1 Installed SIMD ─────────────────────── v3.7.2 Installed StructUtils ──────────────── v2.8.2 Installed STRIDE_jll ───────────────── v1.0.0+0 Installed ProgressMeter ────────────── v1.11.0 Installed StaticArraysCore ─────────── v1.4.4 Installed JSON ─────────────────────── v1.6.1 Installed StaticArrays ─────────────── v1.9.18 Installed CellListMap ──────────────── v0.10.3 Installed PrecompileTools ──────────── v1.3.4 Installed Parsers ──────────────────── v2.8.6 Installed JLLWrappers ──────────────── v1.8.0 Installed Setfield ─────────────────── v1.1.2 Installed DSSP_jll ─────────────────── v4.4.0+1 Installed TestItems ────────────────── v1.0.0 Installed Format ───────────────────── v1.3.7 Installed Preferences ──────────────── v1.5.2 Installed MolSimToolkitShared ──────── v1.6.0 Installed DocStringExtensions ──────── v0.9.5 Installed ProteinSecondaryStructures ─ v2.0.3 Installed PDBTools ─────────────────── v3.33.2 Installing 2 artifacts Installed artifact STRIDE 185.5 KiB Installed artifact DSSP 2.0 MiB Updating `~/.julia/environments/v1.14/Project.toml` [e29189f1] + PDBTools v3.33.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [69e1c6dd] + CellListMap v0.10.3 [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 v1.6.1 [1914dd2f] + MacroTools v0.5.16 [aea21201] + MolSimToolkitShared v1.6.0 [bac558e1] + OrderedCollections v2.0.1 [e29189f1] + PDBTools v3.33.2 [69de0a69] + Parsers v2.8.6 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [c298f58b] + ProteinSecondaryStructures v2.0.3 [fdea26ae] + SIMD v3.7.2 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [ec057cc2] + StructUtils v2.8.2 [1c621080] + TestItems v1.0.0 [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 v1.11.0 [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 v1.5.5+2 [deac9b47] + LibCURL_jll v8.21.0+0 [29816b5a] + LibSSH2_jll v1.11.101+0 [14a3606d] + MozillaCACerts_jll v2026.5.14 [4536629a] + OpenBLAS_jll v0.3.33+0 [458c3c95] + OpenSSL_jll v3.5.7+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 v1.69.0+0 Installation completed after 9.69s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 4.4 s ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling project... 3.6 s ✓ MacroTools 1.4 s ✓ InlineStrings 0.5 s ✓ Reexport 0.6 s ✓ TensorCore 0.9 s ✓ ConstructionBase 2.0 s ✓ IrrationalConstants 0.6 s ✓ Measures 0.6 s ✓ StatsAPI 0.6 s ✓ LazilyInitializedFields 1.8 s ✓ Format 0.5 s ✓ ShowMethodTesting 0.6 s ✓ Contour 0.8 s ✓ TranscodingStreams 0.5 s ✓ LaTeXStrings 0.5 s ✓ TestItems 0.8 s ✓ Statistics 0.6 s ✓ StaticArraysCore 0.6 s ✓ ChunkSplitters 0.6 s ✓ StableRNGs 0.5 s ✓ PtrArrays 0.5 s ✓ SimpleBufferStream 0.8 s ✓ ANSIColoredPrinters 0.9 s ✓ Grisu 0.6 s ✓ DataAPI 0.9 s ✓ URIs 0.6 s ✓ BitFlags 0.9 s ✓ AbstractTrees 1.0 s ✓ OrderedCollections 0.8 s ✓ DocStringExtensions 0.8 s ✓ Unzip 0.5 s ✓ IOCapture ┌ Warning: DEPRECATION NOTICE │ │ Formatting.jl has been unmaintained for a while, with some serious │ correctness bugs compromising the original purpose of the package. As a result, │ it has been deprecated - consider using an alternative, such as │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ If you are not using Formatting.jl as a direct dependency, please consider │ opening an issue on any packages you are using that do use it as a dependency. │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ package originally brings it in as a dependency. └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 0.8 s ✓ Formatting 0.7 s ✓ DelimitedFiles 0.7 s ✓ NaNMath 0.8 s ✓ Requires 1.1 s ✓ ConcurrentUtilities 1.0 s ✓ Chairmarks 2.4 s ✓ ProgressMeter 1.1 s ✓ Scratch ERROR: LoadError: ParseError: # Error @ /home/pkgeval/.julia/packages/Unitful/sxiHA/src/logarithm.jl:127:5 Base. *(::MixedUnits, ::MixedUnits) = # └───────────────────────────────┘ ── extra tokens after end of expression Stacktrace: [1] top-level scope @ ~/.julia/packages/Unitful/sxiHA/src/logarithm.jl:127 [2] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [3] top-level scope @ ~/.julia/packages/Unitful/sxiHA/src/Unitful.jl:67 [4] include(mod::Module, _path::String) @ Base Base.jl:325 [5] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 [6] top-level scope @ stdin:5 [7] eval(m::Module, e::Any) @ Core boot.jl:545 [8] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base loading.jl:3132 [9] include_string(m::Module, txt::String, fname::String) @ Base loading.jl:3142 [inlined] [10] exec_options(opts::Base.JLOptions) @ Base client.jl:353 [11] _start() @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Unitful/sxiHA/src/logarithm.jl:127 in expression starting at /home/pkgeval/.julia/packages/Unitful/sxiHA/src/Unitful.jl:1 in expression starting at stdin:5 ✗ Unitful 1.3 s ✓ LoggingExtras 1.3 s ✓ StructUtils 0.8 s ✓ Compat 1.4 s ✓ Preferences 2.9 s ✓ DataStructures 1.2 s ✓ ExceptionUnwrapping 3.5 s ✓ UnicodeFun 0.5 s ✓ ConstructionBase → ConstructionBaseLinearAlgebraExt 4.5 s ✓ RegistryInstances 0.7 s ✓ CodecZlib 27.2 s ✓ TestItemRunner 1.5 s ✓ Statistics → SparseArraysExt 2.2 s ✓ FixedPointNumbers 0.7 s ✓ AliasTables 0.9 s ✓ Showoff 0.7 s ✓ Missings 4.2 s ✓ OpenSSL 1.4 s ✓ MarkdownAST 1.2 s ✓ LogExpFunctions 3.6 s ✓ Latexify 0.5 s ✓ Chairmarks → StatisticsChairmarksExt 1.2 s ✓ RelocatableFolders ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("1986cc42-f94f-5a68-af5c-568840ba703d"), "Unitful") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2837 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2685 [4] macro expansion @ loading.jl:2599 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2563 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2539 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_using(to::Module, path::Expr, flags::UInt8) @ Base module.jl:137 [inlined] [11] top-level scope @ ~/.julia/packages/Unitful/sxiHA/ext/ConstructionBaseUnitfulExt.jl:2 [12] include(mod::Module, _path::String) @ Base Base.jl:325 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 [14] top-level scope @ stdin:5 [15] eval(m::Module, e::Any) @ Core boot.jl:545 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base loading.jl:3132 [17] include_string(m::Module, txt::String, fname::String) @ Base loading.jl:3142 [inlined] [18] exec_options(opts::Base.JLOptions) @ Base client.jl:353 [19] _start() @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Unitful/sxiHA/ext/ConstructionBaseUnitfulExt.jl:1 in expression starting at stdin:5 ✗ Unitful → ConstructionBaseUnitfulExt ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("1986cc42-f94f-5a68-af5c-568840ba703d"), "Unitful") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2837 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2685 [4] macro expansion @ loading.jl:2599 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2563 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2539 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_using(to::Module, path::Expr, flags::UInt8) @ Base module.jl:137 [inlined] [11] top-level scope @ ~/.julia/packages/Unitful/sxiHA/ext/PrintfExt.jl:4 [12] include(mod::Module, _path::String) @ Base Base.jl:325 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 [14] top-level scope @ stdin:5 [15] eval(m::Module, e::Any) @ Core boot.jl:545 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base loading.jl:3132 [17] include_string(m::Module, txt::String, fname::String) @ Base loading.jl:3142 [inlined] [18] exec_options(opts::Base.JLOptions) @ Base client.jl:353 [19] _start() @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Unitful/sxiHA/ext/PrintfExt.jl:1 in expression starting at stdin:5 ✗ Unitful → PrintfExt 0.8 s ✓ StructUtils → StructUtilsStaticArraysCoreExt 0.5 s ✓ Compat → CompatLinearAlgebraExt 1.5 s ✓ PrecompileTools 1.3 s ✓ JLLWrappers 1.2 s ✓ SortingAlgorithms 1.9 s ✓ Setfield 2.6 s ✓ ColorTypes ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("1986cc42-f94f-5a68-af5c-568840ba703d"), "Unitful") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2837 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2685 [4] macro expansion @ loading.jl:2599 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2563 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2539 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) @ Base module.jl:101 [11] top-level scope @ ~/.julia/packages/UnitfulLatexify/RZL4m/src/UnitfulLatexify.jl:3 [12] include(mod::Module, _path::String) @ Base Base.jl:325 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 [14] top-level scope @ stdin:5 [15] eval(m::Module, e::Any) @ Core boot.jl:545 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base loading.jl:3132 [17] include_string(m::Module, txt::String, fname::String) @ Base loading.jl:3142 [inlined] [18] exec_options(opts::Base.JLOptions) @ Base client.jl:353 [19] _start() @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/UnitfulLatexify/RZL4m/src/UnitfulLatexify.jl:1 in expression starting at stdin:5 ✗ UnitfulLatexify 6.4 s ✓ Aqua 12.9 s ✓ SIMD 12.9 s ✓ StaticArrays 3.0 s ✓ RecipesBase 9.3 s ✓ Parsers 1.5 s ✓ Libffi_jll 1.1 s ✓ Xorg_libICE_jll 1.3 s ✓ eudev_jll 1.1 s ✓ mtdev_jll 1.2 s ✓ Bzip2_jll 1.4 s ✓ DSSP_jll 1.5 s ✓ XZ_jll 0.9 s ✓ Xorg_xtrans_jll 1.1 s ✓ Opus_jll 1.2 s ✓ STRIDE_jll 1.1 s ✓ x265_jll 1.1 s ✓ fzf_jll 1.1 s ✓ libpng_jll 1.1 s ✓ EpollShim_jll 1.1 s ✓ Libmount_jll 1.1 s ✓ libfdk_aac_jll 1.0 s ✓ Libuuid_jll 1.1 s ✓ FriBidi_jll 1.1 s ✓ LERC_jll 1.1 s ✓ Git_LFS_jll 1.1 s ✓ Xorg_libXau_jll 1.1 s ✓ Ogg_jll 1.1 s ✓ libevdev_jll 1.6 s ✓ OpenSSH_jll 1.6 s ✓ LAME_jll 1.8 s ✓ Graphite2_jll 1.3 s ✓ x264_jll 1.2 s ✓ Xorg_libpciaccess_jll 1.3 s ✓ LLVMOpenMP_jll 1.3 s ✓ Libiconv_jll 1.1 s ✓ MbedTLS_jll 1.1 s ✓ libaom_jll 1.1 s ✓ Xorg_libXdmcp_jll 1.1 s ✓ Expat_jll 1.1 s ✓ JpegTurbo_jll 4.4 s ✓ StatsBase 1.0 s ✓ ColorTypes → StyledStringsExt 4.7 s ✓ Colors 1.4 s ✓ ColorVectorSpace 1.3 s ✓ StaticArrays → StaticArraysStatisticsExt 1.3 s ✓ ConstructionBase → ConstructionBaseStaticArraysExt 8.7 s ✓ MolSimToolkitShared 5.9 s ✓ JSON 0.8 s ✓ InlineStrings → ParsersExt 1.4 s ✓ Xorg_libSM_jll 1.0 s ✓ FreeType2_jll 1.4 s ✓ ProteinSecondaryStructures 1.9 s ✓ JLFzf 1.0 s ✓ libvorbis_jll 1.0 s ✓ libinput_jll 1.8 s ✓ libdrm_jll 1.0 s ✓ Pixman_jll 1.3 s ✓ GettextRuntime_jll 1.6 s ✓ MbedTLS 1.3 s ✓ Xorg_libxcb_jll 1.1 s ✓ Dbus_jll 1.2 s ✓ Git_jll 1.1 s ✓ Wayland_jll 1.1 s ✓ Libtiff_jll 8.5 s ✓ ColorSchemes 27.6 s ✓ CellListMap 1.4 s ✓ Fontconfig_jll 1.0 s ✓ Glib_jll 24.7 s ✓ HTTP 1.2 s ✓ Xorg_xcb_util_jll 1.1 s ✓ Xorg_libX11_jll 0.8 s ✓ Git 21.4 s ✓ PlotUtils 40.4 s ✓ PDBTools 1.3 s ✓ Xorg_xcb_util_renderutil_jll 1.3 s ✓ Xorg_xcb_util_wm_jll 1.1 s ✓ Xorg_xcb_util_image_jll 1.1 s ✓ Xorg_xcb_util_keysyms_jll 1.2 s ✓ Xorg_libXfixes_jll 1.1 s ✓ Xorg_libXrender_jll 1.2 s ✓ Xorg_libXext_jll 1.2 s ✓ Xorg_libxkbfile_jll 55.9 s ✓ Documenter 8.3 s ✓ PlotThemes 6.2 s ✓ RecipesPipeline 0.9 s ✓ Xorg_xcb_util_cursor_jll 0.9 s ✓ Xorg_libXcursor_jll 0.9 s ✓ Xorg_libXrandr_jll 0.9 s ✓ Xorg_libXinerama_jll 1.8 s ✓ Xorg_libXi_jll 1.5 s ✓ Cairo_jll 1.2 s ✓ libva_jll 1.2 s ✓ Libglvnd_jll 1.3 s ✓ Xorg_xkbcomp_jll 1.6 s ✓ HarfBuzz_jll 1.3 s ✓ Xorg_xkeyboard_config_jll 1.2 s ✓ libass_jll 1.5 s ✓ Pango_jll 1.2 s ✓ xkbcommon_jll 1.3 s ✓ FFMPEG_jll 1.2 s ✓ Vulkan_Loader_jll 1.4 s ✓ libdecor_jll 0.9 s ✓ FFMPEG 1.4 s ✓ Qt6Base_jll 1.3 s ✓ GLFW_jll 1.4 s ✓ Qt6ShaderTools_jll 1.2 s ✓ Qt6Svg_jll 1.3 s ✓ GR_jll 1.5 s ✓ Qt6Declarative_jll 1.4 s ✓ Qt6Wayland_jll 5.6 s ✓ GR 112.0 s ✓ Plots ERROR: LoadError: Precompiled image Base.PkgId(Base.UUID("1986cc42-f94f-5a68-af5c-568840ba703d"), "Unitful") not available with flags CacheFlags(; use_pkgimages=false, debug_level=1, check_bounds=1, inline=true, opt_level=0) Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] __require_prelocked(pkg::Base.PkgId, env::String) @ Base loading.jl:2837 [3] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base loading.jl:2685 [4] macro expansion @ loading.jl:2599 [inlined] [5] macro expansion @ lock.jl:376 [inlined] [6] __require(into::Module, mod::Symbol) @ Base loading.jl:2563 [7] require(into::Module, mod::Symbol) @ Base loading.jl:2539 [inlined] [8] eval_import_path(at::Module, from::Nothing, path::Expr, keyword::String) @ Base module.jl:36 [inlined] [9] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base module.jl:60 [10] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) @ Base module.jl:101 [11] top-level scope @ ~/.julia/packages/Plots/rlpAr/ext/UnitfulExt.jl:8 [12] include(mod::Module, _path::String) @ Base Base.jl:325 [13] include_package_for_output(pkg::Base.PkgId, input::String, syntax_version::VersionNumber, 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:3303 [14] top-level scope @ stdin:5 [15] eval(m::Module, e::Any) @ Core boot.jl:545 [16] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base loading.jl:3132 [17] include_string(m::Module, txt::String, fname::String) @ Base loading.jl:3142 [inlined] [18] exec_options(opts::Base.JLOptions) @ Base client.jl:353 [19] _start() @ Base client.jl:596 in expression starting at /home/pkgeval/.julia/packages/Plots/rlpAr/ext/UnitfulExt.jl:4 in expression starting at stdin:5 ✗ Plots → UnitfulExt 16.0 s ✓ PDBTools → Plotting 181 dependencies successfully precompiled in 654 seconds. 38 already precompiled. 1 dependency had output during precompilation: ┌ Formatting │ ┌ Warning: DEPRECATION NOTICE │ │ │ │ Formatting.jl has been unmaintained for a while, with some serious │ │ correctness bugs compromising the original purpose of the package. As a result, │ │ it has been deprecated - consider using an alternative, such as │ │ `Format.jl` (https://github.com/JuliaString/Format.jl) or the `Printf` stdlib directly. │ │ │ │ If you are not using Formatting.jl as a direct dependency, please consider │ │ opening an issue on any packages you are using that do use it as a dependency. │ │ From Julia 1.9 onwards, you can query `]why Formatting` to figure out which │ │ package originally brings it in as a dependency. │ └ @ Formatting ~/.julia/packages/Formatting/3VxOt/src/Formatting.jl:12 └ Precompilation completed after 699.33s ################################################################################ # Testing # Testing PDBTools Updating git-repo `https://github.com/lmiq/Documenter.jl` Status `/tmp/jl_r1KqYI/Project.toml` [4c88cf16] Aqua v0.8.16 [69e1c6dd] CellListMap v0.10.3 [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 v1.6.1 [aea21201] MolSimToolkitShared v1.6.0 [bac558e1] OrderedCollections v2.0.1 [e29189f1] PDBTools v3.33.2 ⌃ [91a5bcdd] Plots v1.41.0 [aea7be01] PrecompileTools v1.3.4 [c298f58b] ProteinSecondaryStructures v2.0.3 [fdea26ae] SIMD v3.7.2 [aed2ae9c] ShowMethodTesting v1.3.0 [90137ffa] StaticArrays v1.9.18 [f8b46487] TestItemRunner v1.1.5 [1c621080] TestItems v1.0.0 [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_r1KqYI/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [66dad0bd] AliasTables v1.1.3 [4c88cf16] Aqua v0.8.16 [d1d4a3ce] BitFlags v0.1.10 [69e1c6dd] CellListMap v0.10.3 [0ca39b1e] Chairmarks v1.3.1 [ae650224] ChunkSplitters v3.2.0 [944b1d66] 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints 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: Residue TIP3 not found in protein residues. Assuming residue charge = 0 └ @ PDBTools ~/.julia/packages/PDBTools/Sfvly/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 Atom constructors: Test Failed at /home/pkgeval/.julia/packages/PDBTools/Sfvly/src/struct_and_iterators/Atom.jl:152 Expression: (#= /home/pkgeval/.julia/packages/PDBTools/Sfvly/src/struct_and_iterators/Atom.jl:152 =# @b(Atom(; index = 1, residue = 1, name = "CA"))).allocs <= 1 Evaluated: 2.0 <= 1 Stacktrace: [1] top-level scope @ ~/.julia/packages/PDBTools/Sfvly/src/struct_and_iterators/Atom.jl:560 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:784 [inlined] Atom(1N-ALA1A)┌ Warning: Residue THR104 - chain A is missing O backbone atom. └ @ PDBTools ~/.julia/packages/PDBTools/Sfvly/src/tools/secondary_structure.jl:40 ┌ Warning: Residue THR104 - chain A is missing O backbone atom. └ @ PDBTools ~/.julia/packages/PDBTools/Sfvly/src/tools/secondary_structure.jl:40 ┌ Warning: gmx executable not available: some tests won't be run └ @ Main.var"##217" ~/.julia/packages/PDBTools/Sfvly/src/tools/mvalue/testing/testing.jl:207 ┌ 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 Test Summary: | Pass Fail Total Time Package | 76361 1 76362 11m03.1s ext/plot_ramachandran.jl | 1 1 1m03.9s src/coordinates/contacts.jl | 52 52 58.6s src/struct_and_iterators/Residue.jl | 116 116 22.9s src/coordinates/maxmin.jl | 3 3 2.2s src/properties/residue_properties.jl | 43 43 4.5s src/tools/custom_types/sirah.jl | 21 21 22.2s src/struct_and_iterators/Segment.jl | 32 32 2.6s src/properties/nucleoside_residues.jl | 26 26 1.1s src/struct_and_iterators/Structure.jl | 20 20 4.7s src/tools/hydrogen_bonds.jl | 73 73 53.5s src/properties/elements.jl | 14 14 2.5s ext/plot_contacts.jl | 5 5 11.7s src/struct_and_iterators/Model.jl | 32 32 1.6s src/struct_and_iterators/Chain.jl | 29 29 2.2s src/struct_and_iterators/Atom.jl | 90 1 91 33.2s Atom constructors | 6 1 7 18.6s Atom default fields | 15 15 1.5s copy atom | 4 4 0.8s Atom custom fields | 6 6 0.5s Atom positions | 3 3 0.3s atom_line | 4 4 1.1s atom - show | 12 12 7.2s atoms in struct | 5 5 0.4s same_residue | 5 5 0.6s get element | 10 10 0.6s fetch atomic element properties | 16 16 1.1s AtomsBase interface | 4 4 0.2s src/coordinates/dihedrals.jl | 7 7 1.4s src/read_write/wget.jl | 5 5 1.6s src/tools/read_unitcell.jl | 14 14 5.1s src/properties/formula.jl | 6 6 4.9s test/runtests.jl | 11 11 2m09.8s src/select/select.jl | 88 88 13.8s src/select/select_with_vmd.jl | 0 0.0s src/tools/tools.jl | 7 7 9.5s src/tools/secondary_structure.jl | 9 9 13.6s src/tools/mvalue/testing/testing.jl | 334 334 1m32.5s src/tools/sasa/sasa.jl | 32 32 22.7s src/struct_and_iterators/iterators_base.jl | 1 1 0.2s src/coordinates/positions.jl | 7 7 3.2s src/read_write/parsers.jl | 11 11 0.4s src/properties/getseq.jl | 6 6 1.4s src/coordinates/distance.jl | 75118 75118 8.6s src/read_write/read_mmcif.jl | 43 43 18.0s src/tools/mvalue/creamer.jl | 15 15 4.0s src/read_write/write_mmcif.jl | 10 10 8.6s src/read_write/write_pdb.jl | 26 26 26.9s src/read_write/read_pdb.jl | 54 54 9.6s ERROR: LoadError: Some tests did not pass: 76361 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PDBTools/Sfvly/test/runtests.jl:20 Testing failed after 724.24s 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:3247 [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 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1599.42s: package has test failures