Package evaluation of PlotRNA on Julia 1.13.0-DEV.888 (0e1aa6c7eb*) started at 2025-07-22T23:28:22.766 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.97s ################################################################################ # Installation # Installing PlotRNA... Resolving package versions... Installed HarfBuzz_jll ──────── v8.5.1+0 Installed Bzip2_jll ─────────── v1.0.9+0 Installed JpegTurbo_jll ─────── v3.1.1+0 Installed libaom_jll ────────── v3.12.1+0 Installed Libuuid_jll ───────── v2.41.0+0 Installed libass_jll ────────── v0.15.2+0 Installed Libmount_jll ──────── v2.41.0+0 Installed Libtiff_jll ───────── v4.7.1+0 Installed MacroTools ────────── v0.5.16 Installed DataStructures ────── v0.18.22 Installed x264_jll ──────────── v2021.5.5+0 Installed Cairo_jll ─────────── v1.18.5+0 Installed Xorg_libXau_jll ───── v1.0.13+0 Installed Xorg_libX11_jll ───── v1.8.12+0 Installed Cairo ─────────────── v1.1.1 Installed Graphite2_jll ─────── v1.3.15+0 Installed OrderedCollections ── v1.8.1 Installed TensorCore ────────── v0.1.1 Installed Compat ────────────── v4.17.0 Installed Statistics ────────── v1.11.1 Installed Colors ────────────── v0.13.1 Installed UnsafePointers ────── v1.0.0 Installed CEnum ─────────────── v0.5.0 Installed TranscodingStreams ── v0.11.3 Installed PrecompileTools ───── v1.3.2 Installed R2R_jll ───────────── v1.0.6+0 Installed SIMD ──────────────── v3.7.1 Installed ViennaRNA_jll ─────── v2.6.4+0 Installed Pixman_jll ────────── v0.44.2+0 Installed Fontconfig_jll ────── v2.16.0+0 Installed Libffi_jll ────────── v3.4.7+0 Installed Expat_jll ─────────── v2.6.5+0 Installed ColorTypes ────────── v0.12.1 Installed FileIO ────────────── v1.17.0 Installed GettextRuntime_jll ── v0.22.4+0 Installed NaNMath ───────────── v1.1.3 Installed libpng_jll ────────── v1.6.50+0 Installed PCRE_jll ──────────── v8.45.0+0 Installed ColorVectorSpace ──── v0.11.0 Installed FriBidi_jll ───────── v1.0.17+0 Installed Graphics ──────────── v1.1.3 Installed Glib_jll ──────────── v2.84.3+0 Installed Requires ──────────── v1.3.1 Installed LAME_jll ──────────── v3.100.3+0 Installed Opus_jll ──────────── v1.5.2+0 Installed Rsvg ──────────────── v1.0.0 Installed Xorg_libXrender_jll ─ v0.9.12+0 Installed libvorbis_jll ─────── v1.3.8+0 Installed Librsvg_jll ───────── v2.54.7+0 Installed libfdk_aac_jll ────── v2.0.4+0 Installed OpenBLAS32_jll ────── v0.3.29+0 Installed ViennaRNA ─────────── v0.11.2 Installed Ogg_jll ───────────── v1.3.6+0 Installed Xorg_libxcb_jll ───── v1.17.1+0 Installed XML2_jll ──────────── v2.13.6+1 Installed FFMPEG_jll ────────── v4.4.4+1 Installed Xorg_libXdmcp_jll ─── v1.1.6+0 Installed GSL_jll ───────────── v2.7.2+0 Installed LZO_jll ───────────── v2.10.3+0 Installed Unitful ───────────── v1.23.1 Installed Media ─────────────── v0.5.0 Installed gdk_pixbuf_jll ────── v2.42.13+0 Installed FFMPEG ────────────── v0.4.2 Installed FixedPointNumbers ─── v0.8.5 Installed Preferences ───────── v1.4.3 Installed JLLWrappers ───────── v1.7.0 Installed LERC_jll ──────────── v4.0.1+0 Installed Libiconv_jll ──────── v1.18.0+0 Installed FreeType2_jll ─────── v2.13.4+0 Installed LLVMOpenMP_jll ────── v18.1.8+0 Installed Reexport ──────────── v1.2.2 Installed BioStockholm ──────── v0.2.1 Installed LaTeXStrings ──────── v1.4.0 Installed XZ_jll ────────────── v5.8.1+0 Installed x265_jll ──────────── v3.5.0+0 Installed Xorg_libXext_jll ──── v1.3.7+0 Installed Pango_jll ─────────── v1.56.3+0 Installed Juno ──────────────── v0.8.4 Installed NLopt_jll ─────────── v2.10.0+0 Installed Xorg_xtrans_jll ───── v1.6.0+0 Installed Automa ────────────── v1.1.0 Installed PlotRNA ───────────── v0.3.2 Installed ColorSchemes ──────── v3.30.0 Installed Luxor ─────────────── v3.8.0 Installing 49 artifacts Installed artifact Libffi 44.2 KiB Installed artifact libvorbis 271.0 KiB Installed artifact libpng 328.4 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact FreeType2 1.5 MiB Installed artifact libfdk_aac 2.8 MiB Installed artifact Fontconfig 522.5 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact x265 1.1 MiB Installed artifact Pixman 372.2 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact JpegTurbo 1.6 MiB Installed artifact Libtiff 3.2 MiB Installed artifact Libiconv 1.9 MiB Installed artifact Opus 925.5 KiB Installed artifact gdk_pixbuf 943.6 KiB Installed artifact FFMPEG 10.6 MiB Installed artifact PCRE 1.1 MiB Installed artifact x264 2.0 MiB Installed artifact Graphite2 120.2 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact LAME 292.5 KiB Installed artifact XML2 2.5 MiB Installed artifact NLopt 322.7 KiB Installed artifact Bzip2 503.5 KiB Installed artifact LERC 272.9 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Expat 271.4 KiB Installed artifact Ogg 250.3 KiB Installed artifact R2R 862.9 KiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Pango 1.1 MiB Installed artifact LZO 208.9 KiB Installed artifact libass 372.4 KiB Installed artifact Cairo 2.2 MiB Installed artifact GSL 4.4 MiB Installed artifact Glib 7.7 MiB Installed artifact FriBidi 78.9 KiB Installed artifact XZ 1.5 MiB Installed artifact Librsvg 9.3 MiB Installed artifact Libmount 6.4 MiB Installed artifact OpenBLAS32 10.0 MiB Installed artifact libaom 6.4 MiB Installed artifact ViennaRNA 96.6 MiB Updating `~/.julia/environments/v1.13/Project.toml` [eab79ae3] + PlotRNA v0.3.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [67c07d97] + Automa v1.1.0 [eeb925a3] + BioStockholm v0.2.1 [fa961155] + CEnum v0.5.0 [159f3aea] + Cairo v1.1.1 [35d6a980] + ColorSchemes v3.30.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.17.0 [864edb3b] + DataStructures v0.18.22 [c87230d0] + FFMPEG v0.4.2 [5789e2e9] + FileIO v1.17.0 [53c48c17] + FixedPointNumbers v0.8.5 [a2bd30eb] + Graphics v1.1.3 [692b3bcd] + JLLWrappers v1.7.0 [e5e0dc1b] + Juno v0.8.4 [b964fa9f] + LaTeXStrings v1.4.0 ⌅ [ae8d54c2] + Luxor v3.8.0 [1914dd2f] + MacroTools v0.5.16 [e89f7d12] + Media v0.5.0 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.1 [eab79ae3] + PlotRNA v0.3.2 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [c4c386cf] + Rsvg v1.0.0 [fdea26ae] + SIMD v3.7.1 [10745b16] + Statistics v1.11.1 [62fd8b95] + TensorCore v0.1.1 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.23.1 [e17b2a0c] + UnsafePointers v1.0.0 [05a721ad] + ViennaRNA v0.11.2 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [2e619515] + Expat_jll v2.6.5+0 ⌅ [b22a6f82] + FFMPEG_jll v4.4.4+1 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 ⌅ [1b77fbbe] + GSL_jll v2.7.2+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [7746bdde] + Glib_jll v2.84.3+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [c1c5ebd0] + LAME_jll v3.100.3+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [e9f186c6] + Libffi_jll v3.4.7+0 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [925c91fb] + Librsvg_jll v2.54.7+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.41.0+0 [079eb43e] + NLopt_jll v2.10.0+0 [e7412a2a] + Ogg_jll v1.3.6+0 [656ef2d0] + OpenBLAS32_jll v0.3.29+0 [91d4177d] + Opus_jll v1.5.2+0 [2f80f16e] + PCRE_jll v8.45.0+0 [36c8627f] + Pango_jll v1.56.3+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [1e27f72a] + R2R_jll v1.0.6+0 [b7a990de] + ViennaRNA_jll v2.6.4+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [da03df04] + gdk_pixbuf_jll v2.42.13+0 [a4ae2306] + libaom_jll v3.12.1+0 ⌅ [0ac62f75] + libass_jll v0.15.2+0 [f638f0a6] + libfdk_aac_jll v2.0.4+0 [b53b4c65] + libpng_jll v1.6.50+0 [f27f6e37] + libvorbis_jll v1.3.8+0 ⌅ [1270edf5] + x264_jll v2021.5.5+0 ⌅ [dfaa095f] + x265_jll v3.5.0+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 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [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 [9abbd945] + Profile 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 [781609d7] + GMP_jll v6.3.0+2 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [3a97d323] + MPFR_jll v4.2.2+0 [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 [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. To see why use `status --outdated -m` Installation completed after 24.37s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4651.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 26 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/iS95e/src/julia-1.11/activate_set.jl:75 Precompiling package dependencies... ERROR: LoadError: The following 2 direct dependencies failed to precompile: CairoMakie Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.13/CairoMakie/jl_14of4U" (ProcessExited(1)). ERROR: LoadError: 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] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:240 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:237 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:131 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/screen.jl:307 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:363 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:439 [13] colorbuffer @ ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [15] top-level scope @ ~/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [21] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:37 [22] include(mod::Module, _path::String) @ Base ./Base.jl:309 [23] 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:3002 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [27] include_string @ ./loading.jl:2858 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [29] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:4 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:1 in expression starting at stdin:5 CairoMakieExt Failed to precompile CairoMakieExt [e1efaa5d-ecc1-510b-a074-076b7c46d6a5] to "/home/pkgeval/.julia/compiled/v1.13/CairoMakieExt/jl_t9iThj" (ProcessExited(1)). ERROR: LoadError: 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] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:240 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:237 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:131 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/screen.jl:307 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:363 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:439 [13] colorbuffer @ ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [15] top-level scope @ ~/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [21] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:37 [22] include(mod::Module, _path::String) @ Base ./Base.jl:309 [23] 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::String) @ Base ./loading.jl:3002 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [27] include_string @ ./loading.jl:2858 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [29] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:4 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.13/CairoMakie/jl_6U72v3" (ProcessExited(1)). Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3289 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2654 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:94 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:89 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.13/FileWatching/src/pidfile.jl:115 [7] #invokelatest_gr#236 @ ./reflection.jl:1333 [inlined] [8] invokelatest_gr @ ./reflection.jl:1325 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3860 [10] maybe_cachefile_lock @ ./loading.jl:3857 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2640 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2468 [13] macro expansion @ ./loading.jl:2396 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2360 [16] require @ ./loading.jl:2336 [inlined] [17] eval_import_path @ ./module.jl:36 [inlined] [18] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [19] _eval_import(::Bool, ::Module, ::Expr, ::Expr, ::Vararg{Expr}) @ Base ./module.jl:101 [20] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/ext/CairoMakieExt.jl:7 [21] include(mod::Module, _path::String) @ Base ./Base.jl:309 [22] 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:3002 [23] top-level scope @ stdin:5 [24] eval(m::Module, e::Any) @ Core ./boot.jl:489 [25] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [26] include_string @ ./loading.jl:2858 [inlined] [27] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [28] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/ext/CairoMakieExt.jl:1 in expression starting at stdin:5 in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 1649.88s ################################################################################ # Testing # Testing PlotRNA Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_FZPcQH/Project.toml` ⌅ [4c88cf16] + Aqua v0.6.7 ⌅ [13f3f980] + CairoMakie v0.10.12 [eab79ae3] + PlotRNA v0.3.2 [b8865327] + UnicodePlots v3.8.1 Updating `/tmp/jl_FZPcQH/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [621f4979] + AbstractFFTs v1.5.0 [398f06c4] + AbstractLattices v0.3.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 ⌅ [4c88cf16] + Aqua v0.6.7 [4fba245c] + ArrayInterface v7.19.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.7 [18cc8868] + BaseDirs v1.3.1 [96374032] + CRlibm v1.0.2 ⌅ [13f3f980] + CairoMakie v0.10.12 [d360d2e6] + ChainRulesCore v1.25.2 [a2cac450] + ColorBrewer v0.4.1 ⌅ [3da002f7] ↓ ColorTypes v0.12.1 ⇒ v0.11.5 ⌃ [c3611d14] ↓ ColorVectorSpace v0.11.0 ⇒ v0.10.0 ⌅ [5ae59095] ↓ Colors v0.13.1 ⇒ v0.12.11 [861a8166] + Combinatorics v1.0.3 [bbf7d656] + CommonSubexpressions v0.3.1 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 ⌅ [927a84f5] + DelaunayTriangulation v0.8.12 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.3 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [429591f6] + ExactPredicates v2.2.8 [411431e0] + Extents v0.1.6 [7a1cc6ca] + FFTW v1.9.0 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [59287772] + Formatting v0.4.3 [f6369f11] + ForwardDiff v1.0.1 [b38be410] + FreeType v4.1.1 [663a7486] + FreeTypeAbstraction v0.10.8 [68eda718] + GeoFormatTypes v0.4.4 ⌃ [cf35fbd7] + GeoInterface v1.4.1 ⌅ [5c1252a2] + GeometryBasics v0.4.11 ⌅ [3955a311] + GridLayoutBase v0.9.2 [42e2da0e] + Grisu v1.0.2 [34004b35] + HypergeometricFunctions v0.3.28 [2803e5a7] + ImageAxes v0.6.12 [c817782e] + ImageBase v0.1.7 [a09fc81d] + ImageCore v0.10.5 [82e4d734] + ImageIO v0.6.9 [bc367c6b] + ImageMetadata v0.9.10 [9b13fd28] + IndirectArrays v1.0.0 [d25df0c9] + Inflate v0.1.5 [18e54dd8] + IntegerMathUtils v0.1.3 [a98d9a8b] + Interpolations v0.16.1 [d1acc4aa] + IntervalArithmetic v0.22.36 [8197267c] + IntervalSets v0.7.11 [92d709cd] + IrrationalConstants v0.2.4 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [682c06a0] + JSON v0.21.4 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.10 [8cdb02fc] + LazyModules v0.3.1 [9c8b4983] + LightXML v0.9.2 [d3d80556] + LineSearches v7.4.0 [9b3f67b0] + LinearAlgebraX v0.2.10 [2ab3a3ac] + LogExpFunctions v0.3.29 ⌅ [ee78f7c6] + Makie v0.19.12 ⌅ [20f20a25] + MakieCore v0.6.9 [dbb5928d] + MappedArrays v0.4.2 [299715c1] + MarchingCubes v0.1.11 ⌅ [0a4f8689] + MathTeXEngine v0.5.7 [e1d29d7a] + Missings v1.2.0 [7475f97c] + Mods v2.2.6 [e94cdb99] + MosaicViews v0.3.4 [3b2b4ff1] + Multisets v0.4.5 [d41bc354] + NLSolversBase v7.10.0 [f09324ee] + Netpbm v1.1.1 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [52e1d378] + OpenEXR v0.3.3 [429524aa] + Optim v1.13.2 [90014a1f] + PDMats v0.11.35 [f57f5aa1] + PNGFiles v0.4.4 [19eb6ba3] + Packing v0.5.1 [5432bcbf] + PaddedViews v0.5.12 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [2ae35dd2] + Permutations v0.4.23 [3bbf5609] + PikaParser v0.6.1 [eebad327] + PkgVersion v0.3.3 [eab79ae3] + PlotRNA v0.3.2 [995b91a9] + PlotUtils v1.4.3 [647866c9] + PolygonOps v0.1.2 ⌃ [f27b6e38] + Polynomials v4.0.21 [85a6dd25] + PositiveFactorizations v0.2.4 [27ebfcd6] + Primes v0.5.7 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [4b34888f] + QOI v1.0.1 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [c84ed2f1] + Ratios v0.4.5 [3cdcf5f2] + RecipesBase v1.3.4 [05181044] + RelocatableFolders v1.0.1 [286e9d63] + RingLists v0.2.9 [79098fc4] + Rmath v0.8.0 [5eaf0fd0] + RoundingEmulator v0.2.1 [6c6a2e73] + Scratch v1.3.0 [efcf1570] + Setfield v1.1.2 ⌅ [65257c39] + ShaderAbstractions v0.4.1 [992d4aef] + Showoff v1.0.3 [73760f76] + SignedDistanceFields v0.4.0 [55797a34] + SimpleGraphs v0.8.6 [ec83eff0] + SimplePartitions v0.3.3 [cc47b68c] + SimplePolynomials v0.2.18 [a6525b86] + SimpleRandom v0.3.2 [699a6c99] + SimpleTraits v0.9.4 [45858cf5] + Sixel v0.1.5 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 ⌅ [c5dd0088] + StableHashTraits v1.3.4 [860ef19b] + StableRNGs v1.0.3 [cae243ae] + StackViews v0.1.2 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 ⌅ [09ab397b] + StructArrays v0.6.21 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [731e570b] + TiffImages v0.11.4 [981d1d27] + TriplotBase v0.1.0 [9d95972d] + TupleTools v1.6.0 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [b8865327] + UnicodePlots v3.8.1 [ecbed89c] + WeakKeyIdDicts v0.1.0 [e3aaa7dc] + WebP v0.1.3 [efce3f68] + WoodburyMatrices v1.0.0 [4e9b3aee] + CRlibm_jll v1.0.1+0 [5ae413db] + EarCut_jll v2.2.4+0 [f5851436] + FFTW_jll v3.3.11+0 [59f7168a] + Giflib_jll v5.2.3+0 [905a6f67] + Imath_jll v3.1.11+0 [1d5cc7b8] + IntelOpenMP_jll v2025.2.0+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [856f044c] + MKL_jll v2025.2.0+0 [6cdc7f73] + OpenBLASConsistentFPCSR_jll v0.3.29+0 [18a262bb] + OpenEXR_jll v3.2.4+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [9a68df92] + isoband_jll v0.2.3+0 [075b6546] + libsixel_jll v1.10.5+0 [c5f90fcd] + libwebp_jll v1.6.0+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [8bf52ea8] + CRC32c v1.11.0 [8ba89e20] + Distributed v1.11.0 [9fa8497b] + Future v1.11.0 [a63ad114] + Mmap v1.11.0 [3fa0cd96] + REPL v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [bea87d4a] + SuiteSparse_jll v7.10.1+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_FZPcQH/Project.toml` ⌅ [4c88cf16] Aqua v0.6.7 [eeb925a3] BioStockholm v0.2.1 ⌅ [13f3f980] CairoMakie v0.10.12 [35d6a980] ColorSchemes v3.30.0 ⌅ [ae8d54c2] Luxor v3.8.0 [eab79ae3] PlotRNA v0.3.2 [aea7be01] PrecompileTools v1.3.2 [ae029012] Requires v1.3.1 [10745b16] Statistics v1.11.1 [b8865327] UnicodePlots v3.8.1 [05a721ad] ViennaRNA v0.11.2 [1e27f72a] R2R_jll v1.0.6+0 [4af54fe1] LazyArtifacts v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_FZPcQH/Manifest.toml` [47edcb42] ADTypes v1.15.0 [621f4979] AbstractFFTs v1.5.0 [398f06c4] AbstractLattices v0.3.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 ⌅ [4c88cf16] Aqua v0.6.7 [4fba245c] ArrayInterface v7.19.0 [67c07d97] Automa v1.1.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.7 [18cc8868] BaseDirs v1.3.1 [eeb925a3] BioStockholm v0.2.1 [fa961155] CEnum v0.5.0 [96374032] 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v1.6.0+0 [1317d2d5] oneTBB_jll v2022.0.0+0 ⌅ [1270edf5] x264_jll v2021.5.5+0 ⌅ [dfaa095f] x265_jll v3.5.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [8bf52ea8] CRC32c 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 [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 [37e2e46d] LinearAlgebra v1.13.0 [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 [9abbd945] Profile v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [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 [781609d7] GMP_jll v6.3.0+2 [deac9b47] LibCURL_jll v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [3a97d323] MPFR_jll v4.2.2+0 [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 ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... testing PlotRNA testing Aqua.test_all ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.var"#undefined_exports##0#undefined_exports##1"{Vector{Symbol}}, x::Module) at exports.jl:5 └ @ Core ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 ┌ Warning: `isbindingresolved(m::Module, var::Symbol)` is deprecated, use `true` instead. │ caller = walkmodules(f::Aqua.Piracy.var"#3#4"{Bool, IdSet{Any}, Vector{Method}}, x::Module) at exports.jl:5 └ @ Core ~/.julia/packages/Aqua/zpdNP/src/exports.jl:5 testing plot_structure ┌ Warning: Can't find java executable, skipping VARNA tests └ @ Main ~/.julia/packages/PlotRNA/j5Vgx/test/runtests.jl:12 testing R2R.run_r2r R2R.run_r2r: Error During Test at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 Test threw exception Expression: R2R.run_r2r(msa) isa Tres non-zero exit code running r2r to generate out.sto Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] (::PlotRNA.R2R.var"#8#9"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#8#9"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [4] mktempdir (repeats 2 times) @ ./file.jl:895 [inlined] [5] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:870 [7] mktemp @ ./file.jl:868 [inlined] [8] run_r2r(msa::MSA{Char}; GSC_weighted_consensus::Bool, identity_levels::Vector{Float64}, present_levels::Vector{Float64}, max_noncanon::Float64) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:134 [9] run_r2r(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined] [11] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [13] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:20 R2R.run_r2r: Error During Test at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 Test threw exception Expression: R2R.run_r2r(msa) isa Tres non-zero exit code running r2r to generate out.sto Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] (::PlotRNA.R2R.var"#8#9"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#8#9"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [4] mktempdir (repeats 2 times) @ ./file.jl:895 [inlined] [5] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:870 [7] mktemp @ ./file.jl:868 [inlined] [8] run_r2r(msa::MSA{Char}; GSC_weighted_consensus::Bool, identity_levels::Vector{Float64}, present_levels::Vector{Float64}, max_noncanon::Float64) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:134 [9] run_r2r(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined] [11] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [13] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:20 testing R2R.plot R2R.plot: Error During Test at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 Test threw exception Expression: R2R.plot(msa) isa Tres non-zero exit code running r2r to generate out.sto Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] (::PlotRNA.R2R.var"#8#9"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#8#9"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [4] mktempdir (repeats 2 times) @ ./file.jl:895 [inlined] [5] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:870 [7] mktemp @ ./file.jl:868 [inlined] [8] run_r2r(msa::MSA{Char}; GSC_weighted_consensus::Bool, identity_levels::Vector{Float64}, present_levels::Vector{Float64}, max_noncanon::Float64) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:134 [9] run_r2r @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [inlined] [10] plot(msa::MSA{Char}; kwargs::@Kwargs{}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:109 [11] plot(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined] [13] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [15] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:28 R2R.plot: Error During Test at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 Test threw exception Expression: R2R.plot(msa) isa Tres non-zero exit code running r2r to generate out.sto Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] (::PlotRNA.R2R.var"#8#9"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#8#9"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [4] mktempdir (repeats 2 times) @ ./file.jl:895 [inlined] [5] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:870 [7] mktemp @ ./file.jl:868 [inlined] [8] run_r2r(msa::MSA{Char}; GSC_weighted_consensus::Bool, identity_levels::Vector{Float64}, present_levels::Vector{Float64}, max_noncanon::Float64) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:134 [9] run_r2r @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [inlined] [10] plot(msa::MSA{Char}; kwargs::@Kwargs{}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:109 [11] plot(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:738 [inlined] [13] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1858 [inlined] [15] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:28 testing uniplot Precompiling packages... Info Given CairoMakie was explicitly requested, output will be shown live  WARNING: importing deprecated binding Makie.MakieLayout into CairoMakie. The module `MakieLayout` has been removed and integrated into Makie, so simply replace all usage of `MakieLayout` with `Makie`. WARNING: importing deprecated binding Makie._alternative_fonts into CairoMakie. , use ALTERNATIVE_FONTS instead. WARNING: importing deprecated binding Makie._current_figure into CairoMakie. , use CURRENT_FIGURE instead. WARNING: importing deprecated binding Makie._default_font into CairoMakie. , use DEFAULT_FONT instead. WARNING: importing deprecated binding Makie.default_palettes into CairoMakie. , use DEFAULT_PALETTES instead. WARNING: importing deprecated binding Makie.minimal_default into CairoMakie. , use MAKIE_DEFAULT_THEME instead. ERROR: LoadError: 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] func2string(func::typeof(MakieCore.linesegments))  @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:9  [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}})  @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:21  [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})  @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:22  [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing)  @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:240  [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol)  @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:237  [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments})  @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/primitives.jl:6  [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})  @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:131  [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene)  @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:51  [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE})  @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/screen.jl:307  [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat)  @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:363  [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{})  @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:439  [13] colorbuffer  @ ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [inlined]  [14] colorbuffer(fig::Makie.FigureAxisPlot)  @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:434  [15] top-level scope  @ ~/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:6  [16] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [17] top-level scope  @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:11  [18] macro expansion  @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]  [19] macro expansion  @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:15 [inlined]  [20] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:310  [21] top-level scope  @ ~/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:37  [22] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [23] 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:3002  [24] top-level scope  @ stdin:5  [25] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2848  [27] include_string  @ ./loading.jl:2858 [inlined]  [28] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:318  [29] _start()  @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:4 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:1 in expression starting at stdin:5 ✗ CairoMakie 0 dependencies successfully precompiled in 99 seconds. 314 already precompiled. PlotRNA: Error During Test at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/runtests.jl:7 Got exception outside of a @test LoadError: The following 1 direct dependency failed to precompile: CairoMakie Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.13/CairoMakie/jl_UayqJ4" (ProcessExited(1)). WARNING: importing deprecated binding Makie.MakieLayout into CairoMakie. The module `MakieLayout` has been removed and integrated into Makie, so simply replace all usage of `MakieLayout` with `Makie`. WARNING: importing deprecated binding Makie._alternative_fonts into CairoMakie. , use ALTERNATIVE_FONTS instead. WARNING: importing deprecated binding Makie._current_figure into CairoMakie. , use CURRENT_FIGURE instead. WARNING: importing deprecated binding Makie._default_font into CairoMakie. , use DEFAULT_FONT instead. WARNING: importing deprecated binding Makie.default_palettes into CairoMakie. , use DEFAULT_PALETTES instead. WARNING: importing deprecated binding Makie.minimal_default into CairoMakie. , use MAKIE_DEFAULT_THEME instead. ERROR: LoadError: 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] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:240 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/tAY2U/src/attributes.jl:237 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:131 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/VqiwS/src/screen.jl:307 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:363 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:439 [13] colorbuffer @ ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/RgxaV/src/display.jl:434 [15] top-level scope @ ~/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [21] top-level scope @ ~/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:37 [22] include(mod::Module, _path::String) @ Base ./Base.jl:309 [23] 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:3002 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2848 [27] include_string @ ./loading.jl:2858 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:318 [29] _start() @ Base ./client.jl:553 in expression starting at /home/pkgeval/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:4 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:1 in expression starting at stdin: in expression starting at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/plot_structure_makie.jl:1 Test Summary: | Pass Error Total Time PlotRNA | 48 5 53 9m26.6s Aqua.test_all | 8 8 52.6s plot_structure | 39 39 14.1s R2R.run_r2r | 2 2 4.1s R2R.plot | 2 2 0.1s uniplot | 1 1 4.5s RNG of the outermost testset: Random.Xoshiro(0xd375b550d9e48f77, 0xa9e4a231eea58cb5, 0xd381396585d3cb3b, 0x7b58454fbdadc013, 0x5213a01072b86e42) ERROR: LoadError: Some tests did not pass: 48 passed, 0 failed, 5 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/runtests.jl:7 Testing failed after 582.6s ERROR: LoadError: Package PlotRNA 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:2661 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2510 [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] 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 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:156 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:155 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [12] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2312.2s: package fails to precompile