Package evaluation to test PlotRNA on Julia 1.14.0-DEV.65 (b05afe0f25*) started at 2025-11-12T00:12:08.813 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.62s ################################################################################ # Installation # Installing PlotRNA... Resolving package versions... Installed libaom_jll ────────── v3.13.1+0 Installed Libuuid_jll ───────── v2.41.2+0 Installed Bzip2_jll ─────────── v1.0.9+0 Installed JpegTurbo_jll ─────── v3.1.3+0 Installed HarfBuzz_jll ──────── v8.5.1+0 Installed MacroTools ────────── v0.5.16 Installed libass_jll ────────── v0.17.4+0 Installed DataStructures ────── v0.18.22 Installed Libmount_jll ──────── v2.41.2+0 Installed Cairo_jll ─────────── v1.18.5+0 Installed Libtiff_jll ───────── v4.7.2+0 Installed x264_jll ──────────── v10164.0.1+0 Installed Xorg_libXau_jll ───── v1.0.13+0 Installed OrderedCollections ── v1.8.1 Installed TranscodingStreams ── v0.11.3 Installed Xorg_libX11_jll ───── v1.8.12+0 Installed Compat ────────────── v4.18.1 Installed Graphite2_jll ─────── v1.3.15+0 Installed SIMD ──────────────── v3.7.2 Installed TensorCore ────────── v0.1.1 Installed Statistics ────────── v1.11.1 Installed Cairo ─────────────── v1.1.1 Installed ViennaRNA_jll ─────── v2.6.4+0 Installed UnsafePointers ────── v1.0.0 Installed CEnum ─────────────── v0.5.0 Installed Libffi_jll ────────── v3.4.7+0 Installed PrecompileTools ───── v1.3.3 Installed Pixman_jll ────────── v0.44.2+0 Installed Fontconfig_jll ────── v2.17.1+0 Installed Colors ────────────── v0.13.1 Installed Expat_jll ─────────── v2.7.3+0 Installed ColorTypes ────────── v0.12.1 Installed R2R_jll ───────────── v1.0.6+0 Installed PCRE_jll ──────────── v8.45.0+0 Installed libpng_jll ────────── v1.6.50+0 Installed GettextRuntime_jll ── v0.22.4+0 Installed FileIO ────────────── v1.17.1 Installed NaNMath ───────────── v1.1.3 Installed ColorVectorSpace ──── v0.11.0 Installed FriBidi_jll ───────── v1.0.17+0 Installed Glib_jll ──────────── v2.86.0+0 Installed Graphics ──────────── v1.1.3 Installed Requires ──────────── v1.3.1 Installed Librsvg_jll ───────── v2.54.7+0 Installed LAME_jll ──────────── v3.100.3+0 Installed OpenBLAS32_jll ────── v0.3.29+0 Installed Opus_jll ──────────── v1.5.2+0 Installed Xorg_libXrender_jll ─ v0.9.12+0 Installed libvorbis_jll ─────── v1.3.8+0 Installed libfdk_aac_jll ────── v2.0.4+0 Installed Ogg_jll ───────────── v1.3.6+0 Installed ViennaRNA ─────────── v0.11.2 Installed Unitful ───────────── v1.25.1 Installed Xorg_libxcb_jll ───── v1.17.1+0 Installed XML2_jll ──────────── v2.13.9+0 Installed FFMPEG_jll ────────── v8.0.0+0 Installed Rsvg ──────────────── v1.1.0 Installed Xorg_libXdmcp_jll ─── v1.1.6+0 Installed Media ─────────────── v0.5.0 Installed GSL_jll ───────────── v2.7.2+0 Installed LZO_jll ───────────── v2.10.3+0 Installed Reexport ──────────── v1.2.2 Installed FixedPointNumbers ─── v0.8.5 Installed Preferences ───────── v1.5.0 Installed FFMPEG ────────────── v0.4.5 Installed gdk_pixbuf_jll ────── v2.42.13+0 Installed FreeType2_jll ─────── v2.13.4+0 Installed JLLWrappers ───────── v1.7.1 Installed LERC_jll ──────────── v4.0.1+0 Installed Libiconv_jll ──────── v1.18.0+0 Installed LLVMOpenMP_jll ────── v18.1.8+0 Installed XZ_jll ────────────── v5.8.1+0 Installed LaTeXStrings ──────── v1.4.0 Installed Juno ──────────────── v0.8.4 Installed Automa ────────────── v1.1.0 Installed x265_jll ──────────── v4.1.0+0 Installed BioStockholm ──────── v0.2.1 Installed Xorg_libXext_jll ──── v1.3.7+0 Installed Pango_jll ─────────── v1.56.4+0 Installed Xorg_xtrans_jll ───── v1.6.0+0 Installed NLopt_jll ─────────── v2.10.0+0 Installed PlotRNA ───────────── v0.3.2 Installed ColorSchemes ──────── v3.31.0 Installed Luxor ─────────────── v3.8.0 Installing 49 artifacts Installed artifact Libffi 44.2 KiB Installed artifact LERC 272.9 KiB Installed artifact Fontconfig 984.8 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact Ogg 250.3 KiB Installed artifact libfdk_aac 2.8 MiB Installed artifact Libtiff 2.3 MiB Installed artifact FreeType2 1.5 MiB Installed artifact x265 1.4 MiB Installed artifact XZ 1.5 MiB Installed artifact HarfBuzz 1.7 MiB Installed artifact JpegTurbo 1.4 MiB Installed artifact FriBidi 78.9 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact x264 2.1 MiB Installed artifact libass 427.8 KiB Installed artifact libaom 6.4 MiB Installed artifact Expat 283.3 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Cairo 2.2 MiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact PCRE 1.1 MiB Installed artifact LAME 292.5 KiB Installed artifact Pixman 372.2 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Bzip2 503.5 KiB Installed artifact Graphite2 120.2 KiB Installed artifact FFMPEG 11.7 MiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact XML2 2.5 MiB Installed artifact libvorbis 271.0 KiB Installed artifact Librsvg 9.3 MiB Installed artifact Opus 925.5 KiB Installed artifact GSL 4.4 MiB Installed artifact Libiconv 1.9 MiB Installed artifact libpng 328.4 KiB Installed artifact Glib 7.7 MiB Installed artifact NLopt 322.7 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact gdk_pixbuf 943.6 KiB Installed artifact Libmount 6.5 MiB Installed artifact R2R 862.9 KiB Installed artifact Pango 1.1 MiB Installed artifact Libuuid 3.7 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact OpenBLAS32 10.0 MiB Installed artifact ViennaRNA 96.6 MiB Updating `~/.julia/environments/v1.14/Project.toml` [eab79ae3] + PlotRNA v0.3.2 Updating `~/.julia/environments/v1.14/Manifest.toml` [67c07d97] + Automa v1.1.0 [eeb925a3] + BioStockholm v0.2.1 [fa961155] + CEnum v0.5.0 [159f3aea] + Cairo v1.1.1 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.18.1 ⌅ [864edb3b] + DataStructures v0.18.22 [c87230d0] + FFMPEG v0.4.5 [5789e2e9] + FileIO v1.17.1 [53c48c17] + FixedPointNumbers v0.8.5 [a2bd30eb] + Graphics v1.1.3 [692b3bcd] + JLLWrappers v1.7.1 [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 v1.3.3 [21216c6a] + Preferences v1.5.0 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [c4c386cf] + Rsvg v1.1.0 [fdea26ae] + SIMD v3.7.2 [10745b16] + Statistics v1.11.1 [62fd8b95] + TensorCore v0.1.1 [3bb67fe8] + TranscodingStreams v0.11.3 [1986cc42] + Unitful v1.25.1 [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 v2.7.3+0 [b22a6f82] + FFMPEG_jll v8.0.0+0 [a3f928ae] + Fontconfig_jll v2.17.1+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 v2.86.0+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.3+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 v2.41.2+0 [925c91fb] + Librsvg_jll v2.54.7+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.41.2+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 v1.56.4+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 v2.13.9+0 [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 v3.13.1+0 [0ac62f75] + libass_jll v0.17.4+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 v10164.0.1+0 [dfaa095f] + x265_jll v4.1.0+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 v1.0.0 [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 v1.0.0 [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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [3a97d323] + MPFR_jll v4.2.2+0 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.0+1 [3f19e933] + p7zip_jll v17.7.0+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 27.11s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. 4639.0 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. 1 dependency had output during precompilation: ┌ TestEnv │ WARNING: Imported binding Operations.project_rel_path was undeclared at import time during import to TestEnv. └ ┌ Error: Failed to use TestEnv.jl; test dependencies will not be precompiled │ exception = │ UndefVarError: `project_rel_path` not defined in `TestEnv` │ Suggestion: this global was defined as `Pkg.Operations.project_rel_path` but not assigned a value. │ Stacktrace: │ [1] get_test_dir(ctx::Pkg.Types.Context, pkgspec::PackageSpec) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:75 │ [2] test_dir_has_project_file │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:52 [inlined] │ [3] maybe_gen_project_override! │ @ ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/common.jl:83 [inlined] │ [4] activate(pkg::String; allow_reresolve::Bool) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:12 │ [5] activate(pkg::String) │ @ TestEnv ~/.julia/packages/TestEnv/nGMfF/src/julia-1.11/activate_set.jl:9 │ [6] top-level scope │ @ /PkgEval.jl/scripts/precompile.jl:24 │ [7] include(mod::Module, _path::String) │ @ Base ./Base.jl:309 │ [8] exec_options(opts::Base.JLOptions) │ @ Base ./client.jl:344 │ [9] _start() │ @ Base ./client.jl:577 └ @ Main /PkgEval.jl/scripts/precompile.jl:26 Precompiling package dependencies... Precompiling packages... 4628.6 ms ✓ MacroTools 779.6 ms ✓ Reexport 1130.3 ms ✓ Statistics 891.8 ms ✓ TensorCore 859.5 ms ✓ UnsafePointers 1142.4 ms ✓ Requires 1269.9 ms ✓ OrderedCollections 875.1 ms ✓ CEnum 1271.2 ms ✓ TranscodingStreams 837.0 ms ✓ LaTeXStrings 1036.3 ms ✓ NaNMath 35376.3 ms ✓ Unitful 1143.4 ms ✓ Compat 1122.1 ms ✓ Preferences 1561.3 ms ✓ Media 3887.5 ms ✓ FixedPointNumbers 9745.0 ms ✓ FileIO 2427.9 ms ✓ Unitful → PrintfExt 845.1 ms ✓ Compat → CompatLinearAlgebraExt 1279.6 ms ✓ JLLWrappers 944.1 ms ✓ PrecompileTools 2894.0 ms ✓ Juno 2787.5 ms ✓ ColorTypes 3994.4 ms ✓ DataStructures 1412.8 ms ✓ Libmount_jll 1432.7 ms ✓ GSL_jll 1471.2 ms ✓ Libffi_jll 1504.2 ms ✓ libfdk_aac_jll 1549.6 ms ✓ Opus_jll 1544.0 ms ✓ LZO_jll 1443.4 ms ✓ Graphite2_jll 1509.4 ms ✓ Libuuid_jll 1472.3 ms ✓ x265_jll 1448.8 ms ✓ x264_jll 1430.1 ms ✓ FriBidi_jll 1562.8 ms ✓ libpng_jll 1324.2 ms ✓ OpenBLAS32_jll 1254.7 ms ✓ Bzip2_jll 1419.1 ms ✓ LERC_jll 1449.1 ms ✓ LLVMOpenMP_jll 1526.7 ms ✓ Libiconv_jll 1532.6 ms ✓ Xorg_libXau_jll 1627.3 ms ✓ libaom_jll 1391.9 ms ✓ Xorg_libXdmcp_jll 1696.2 ms ✓ XZ_jll 1642.0 ms ✓ Ogg_jll 1512.1 ms ✓ NLopt_jll 1535.9 ms ✓ LAME_jll 1601.0 ms ✓ Expat_jll 1314.0 ms ✓ Xorg_xtrans_jll 1377.3 ms ✓ JpegTurbo_jll 1532.8 ms ✓ PCRE_jll 16730.5 ms ✓ SIMD 1482.4 ms ✓ ColorTypes → StyledStringsExt 3612.6 ms ✓ ColorVectorSpace 7405.1 ms ✓ Colors 1487.7 ms ✓ FreeType2_jll 1476.1 ms ✓ Pixman_jll 1526.9 ms ✓ XML2_jll 1606.0 ms ✓ GettextRuntime_jll 1660.4 ms ✓ Xorg_libxcb_jll 1402.8 ms ✓ libvorbis_jll 1491.0 ms ✓ R2R_jll 1530.8 ms ✓ Libtiff_jll 1800.8 ms ✓ ViennaRNA_jll 20649.3 ms ✓ Automa 1284.8 ms ✓ Graphics 8348.8 ms ✓ ColorSchemes 1488.8 ms ✓ Fontconfig_jll 1483.4 ms ✓ Glib_jll 1528.0 ms ✓ Xorg_libX11_jll 8405.2 ms ✓ ViennaRNA 13342.6 ms ✓ BioStockholm 1097.1 ms ✓ Xorg_libXrender_jll 1100.6 ms ✓ Xorg_libXext_jll 1152.9 ms ✓ gdk_pixbuf_jll 1229.9 ms ✓ Cairo_jll 1274.4 ms ✓ HarfBuzz_jll 1411.4 ms ✓ libass_jll 1207.6 ms ✓ Pango_jll 1411.7 ms ✓ FFMPEG_jll 1157.2 ms ✓ Librsvg_jll 2076.3 ms ✓ Cairo 799.7 ms ✓ FFMPEG 1181.5 ms ✓ Rsvg 12567.0 ms ✓ Luxor 10640.7 ms ✓ PlotRNA 87 dependencies successfully precompiled in 262 seconds. 35 already precompiled. Precompilation completed after 271.62s ################################################################################ # 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. Installed MKL_jll ───────────────────── v2025.2.0+0 Installed Formatting ────────────────── v0.4.3 Installed Extents ───────────────────── v0.1.6 Installed PolygonOps ────────────────── v0.1.2 Installed MosaicViews ───────────────── v0.3.4 Installed ImageIO ───────────────────── v0.6.9 Installed AbstractLattices ──────────── v0.3.1 Installed Optim ─────────────────────── v1.13.2 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed Giflib_jll ────────────────── v5.2.3+0 Installed WoodburyMatrices ──────────── v1.0.0 Installed Tables ────────────────────── v1.12.1 Installed EnumX ─────────────────────── v1.0.5 Installed QuadGK ────────────────────── v2.11.2 Installed SimplePolynomials ─────────── v0.2.18 Installed NLSolversBase ─────────────── v7.10.0 Installed Missings ──────────────────── v1.2.0 Installed TableTraits ───────────────── v1.0.1 Installed Imath_jll ─────────────────── v3.1.11+0 Installed MappedArrays ──────────────── v0.4.2 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed Polynomials ───────────────── v4.0.21 Installed Grisu ─────────────────────── v1.0.2 Installed RangeArrays ───────────────── v0.3.2 Installed UnPack ────────────────────── v1.0.2 Installed CRlibm ────────────────────── v1.0.2 Installed ADTypes ───────────────────── v1.18.0 Installed Inflate ───────────────────── v0.1.5 Installed Aqua ──────────────────────── v0.6.7 Installed ColorBrewer ───────────────── v0.4.2 Installed OpenEXR_jll ───────────────── v3.2.4+0 Installed Packing ───────────────────── v0.5.1 Installed DiffResults ───────────────── v1.1.0 Installed AbstractTrees ─────────────── v0.4.5 Installed FillArrays ────────────────── v1.15.0 Installed LazyModules ───────────────── v0.3.1 Installed MathTeXEngine ─────────────── v0.5.7 Installed MakieCore ─────────────────── v0.6.9 Installed oneTBB_jll ────────────────── v2022.0.0+1 Installed CairoMakie ────────────────── v0.10.12 Installed UnicodeFun ────────────────── v0.4.1 Installed Observables ───────────────── v0.5.5 Installed ArrayInterface ────────────── v7.22.0 Installed StatsBase ─────────────────── v0.34.8 Installed IntelOpenMP_jll ───────────── v2025.2.0+0 Installed DataValueInterfaces ───────── v1.0.0 Installed IrrationalConstants ───────── v0.2.6 Installed CommonSubexpressions ──────── v0.3.1 Installed StructUtils ───────────────── v2.6.0 Installed isoband_jll ───────────────── v0.2.3+0 Installed IntegerMathUtils ──────────── v0.1.3 Installed RoundingEmulator ──────────── v0.2.1 Installed SimpleTraits ──────────────── v0.9.5 Installed ColorVectorSpace ──────────── v0.10.0 Installed ImageMetadata ─────────────── v0.9.10 Installed StableRNGs ────────────────── v1.0.4 Installed Contour ───────────────────── v0.6.3 Installed libsixel_jll ──────────────── v1.10.5+0 Installed libwebp_jll ───────────────── v1.6.0+0 Installed PikaParser ────────────────── v0.6.1 Installed Scratch ───────────────────── v1.3.0 Installed Setfield ──────────────────── v1.1.2 Installed ShaderAbstractions ────────── v0.4.1 Installed Interpolations ────────────── v0.16.2 Installed CRlibm_jll ────────────────── v1.0.1+0 Installed PDMats ────────────────────── v0.11.36 Installed WeakKeyIdDicts ────────────── v0.1.0 Installed DocStringExtensions ───────── v0.9.5 Installed PNGFiles ──────────────────── v0.4.4 Installed AxisArrays ────────────────── v0.4.8 Installed ImageCore ─────────────────── v0.10.5 Installed JpegTurbo ─────────────────── v0.1.6 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed StableHashTraits ──────────── v1.3.4 Installed ForwardDiff ───────────────── v1.2.2 Installed FreeType ──────────────────── v4.1.1 Installed Multisets ─────────────────── v0.4.5 Installed OpenBLASConsistentFPCSR_jll ─ v0.3.29+0 Installed DifferentiationInterface ──── v0.7.11 Installed LightXML ──────────────────── v0.9.3 Installed PkgVersion ────────────────── v0.3.3 Installed RelocatableFolders ────────── v1.0.1 Installed StackViews ────────────────── v0.1.2 Installed KernelDensity ─────────────── v0.6.10 Installed AliasTables ───────────────── v1.1.3 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed RecipesBase ───────────────── v1.3.4 Installed Combinatorics ─────────────── v1.0.3 Installed Netpbm ────────────────────── v1.1.1 Installed DataAPI ───────────────────── v1.16.0 Installed StaticArraysCore ──────────── v1.4.4 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed ImageAxes ─────────────────── v0.6.12 Installed AbstractFFTs ──────────────── v1.5.0 Installed Mods ──────────────────────── v2.2.6 Installed Colors ────────────────────── v0.12.11 Installed StaticArrays ──────────────── v1.9.15 Installed AxisAlgorithms ────────────── v1.1.0 Installed QOI ───────────────────────── v1.0.1 Installed BaseDirs ──────────────────── v1.3.2 Installed ColorTypes ────────────────── v0.11.5 Installed SimplePartitions ──────────── v0.3.3 Installed LogExpFunctions ───────────── v0.3.29 Installed DiffRules ─────────────────── v1.15.1 Installed Distributions ─────────────── v0.25.122 Installed FreeTypeAbstraction ───────── v0.10.8 Installed Parsers ───────────────────── v2.8.3 Installed Rmath ─────────────────────── v0.9.0 Installed JSON ──────────────────────── v1.2.1 Installed FiniteDiff ────────────────── v2.29.0 Installed GeoFormatTypes ────────────── v0.4.5 Installed StatsFuns ─────────────────── v1.5.2 Installed OpenEXR ───────────────────── v0.3.3 Installed SignedDistanceFields ──────── v0.4.0 Installed GridLayoutBase ────────────── v0.9.2 Installed Primes ────────────────────── v0.5.7 Installed GeometryBasics ────────────── v0.4.11 Installed ExactPredicates ───────────── v2.2.9 Installed PaddedViews ───────────────── v0.5.12 Installed StructTypes ───────────────── v1.11.0 Installed IterTools ─────────────────── v1.10.0 Installed TiffImages ────────────────── v0.11.6 Installed Adapt ─────────────────────── v4.4.0 Installed ConstructionBase ──────────── v1.6.0 Installed TriplotBase ───────────────── v0.1.0 Installed MarchingCubes ─────────────── v0.1.11 Installed HypergeometricFunctions ───── v0.3.28 Installed EarCut_jll ────────────────── v2.2.4+0 Installed PlotUtils ─────────────────── v1.4.4 Installed Sixel ─────────────────────── v0.1.5 Installed LinearAlgebraX ────────────── v0.2.10 Installed RingLists ─────────────────── v0.2.9 Installed PositiveFactorizations ────── v0.2.4 Installed StatsAPI ──────────────────── v1.7.1 Installed ImageBase ─────────────────── v0.1.7 Installed StructArrays ──────────────── v0.6.21 Installed ProgressMeter ─────────────── v1.11.0 Installed WebP ──────────────────────── v0.1.3 Installed OffsetArrays ──────────────── v1.17.0 Installed ChainRulesCore ────────────── v1.26.0 Installed UnicodePlots ──────────────── v3.8.1 Installed DelaunayTriangulation ─────── v0.8.12 Installed Ratios ────────────────────── v0.4.5 Installed TupleTools ────────────────── v1.6.0 Installed Isoband ───────────────────── v0.1.1 Installed PtrArrays ─────────────────── v1.3.0 Installed Animations ────────────────── v0.4.2 Installed Parameters ────────────────── v0.12.3 Installed IntervalArithmetic ────────── v1.0.1 Installed IntervalSets ──────────────── v0.7.12 Installed Showoff ───────────────────── v1.0.3 Installed SpecialFunctions ──────────── v2.6.1 Installed FFTW ──────────────────────── v1.10.0 Installed FFTW_jll ──────────────────── v3.3.11+0 Installed LineSearches ──────────────── v7.4.0 Installed Permutations ──────────────── v0.4.23 Installed IndirectArrays ────────────── v1.0.0 Installed GeoInterface ──────────────── v1.4.1 Installed SimpleRandom ──────────────── v0.3.2 Installed SimpleGraphs ──────────────── v0.8.7 Installed Makie ─────────────────────── v0.19.12 Installing 13 artifacts Installed artifact isoband 25.7 KiB Installed artifact Rmath 121.9 KiB Installed artifact EarCut 80.5 KiB Installed artifact CRlibm 169.5 KiB Installed artifact Giflib 154.6 KiB Installed artifact libsixel 177.3 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Imath 182.8 KiB Installed artifact libwebp 2.6 MiB Installed artifact OpenEXR 1.9 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact FFTW 2.2 MiB Installed artifact OpenBLASConsistentFPCSR 9.9 MiB Updating `/tmp/jl_QP4aew/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_QP4aew/Manifest.toml` [47edcb42] + ADTypes v1.18.0 [621f4979] + AbstractFFTs v1.5.0 [398f06c4] + AbstractLattices v0.3.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 ⌅ [4c88cf16] + Aqua v0.6.7 [4fba245c] + ArrayInterface v7.22.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.8 [18cc8868] + BaseDirs v1.3.2 [96374032] + CRlibm v1.0.2 ⌅ [13f3f980] + CairoMakie v0.10.12 [d360d2e6] + ChainRulesCore v1.26.0 [a2cac450] + ColorBrewer v0.4.2 ⌅ [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 v0.7.11 [31c24e10] + Distributions v0.25.122 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [429591f6] + ExactPredicates v2.2.9 [411431e0] + Extents v0.1.6 [7a1cc6ca] + FFTW v1.10.0 [1a297f60] + FillArrays v1.15.0 [6a86dc24] + FiniteDiff v2.29.0 [59287772] + Formatting v0.4.3 [f6369f11] + ForwardDiff v1.2.2 [b38be410] + FreeType v4.1.1 [663a7486] + FreeTypeAbstraction v0.10.8 [68eda718] + GeoFormatTypes v0.4.5 ⌃ [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 v0.16.2 [d1acc4aa] + IntervalArithmetic v1.0.1 [8197267c] + IntervalSets v0.7.12 [92d709cd] + IrrationalConstants v0.2.6 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [682c06a0] + JSON v1.2.1 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.10 [8cdb02fc] + LazyModules v0.3.1 [9c8b4983] + LightXML v0.9.3 [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 v0.11.36 [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 v1.4.4 [647866c9] + PolygonOps v0.1.2 ⌃ [f27b6e38] + Polynomials v4.0.21 [85a6dd25] + PositiveFactorizations v0.2.4 [27ebfcd6] + Primes v0.5.7 [92933f4c] + ProgressMeter v1.11.0 [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 v0.9.0 [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 v0.8.7 [ec83eff0] + SimplePartitions v0.3.3 [cc47b68c] + SimplePolynomials v0.2.18 [a6525b86] + SimpleRandom v0.3.2 [699a6c99] + SimpleTraits v0.9.5 [45858cf5] + Sixel v0.1.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.6.1 ⌅ [c5dd0088] + StableHashTraits v1.3.4 [860ef19b] + StableRNGs v1.0.4 [cae243ae] + StackViews v0.1.2 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.4 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.8 [4c63d2b9] + StatsFuns v1.5.2 ⌅ [09ab397b] + StructArrays v0.6.21 [856f2bd8] + StructTypes v1.11.0 [ec057cc2] + StructUtils v2.6.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [731e570b] + TiffImages v0.11.6 [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+1 [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_QP4aew/Project.toml` ⌅ [4c88cf16] Aqua v0.6.7 [eeb925a3] BioStockholm v0.2.1 ⌅ [13f3f980] CairoMakie v0.10.12 [35d6a980] ColorSchemes v3.31.0 ⌅ [ae8d54c2] Luxor v3.8.0 [eab79ae3] PlotRNA v0.3.2 [aea7be01] PrecompileTools v1.3.3 [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_QP4aew/Manifest.toml` [47edcb42] ADTypes v1.18.0 [621f4979] AbstractFFTs v1.5.0 [398f06c4] AbstractLattices v0.3.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 ⌅ [4c88cf16] Aqua v0.6.7 [4fba245c] ArrayInterface v7.22.0 [67c07d97] Automa v1.1.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.8 [18cc8868] BaseDirs v1.3.2 [eeb925a3] BioStockholm v0.2.1 [fa961155] CEnum v0.5.0 [96374032] CRlibm v1.0.2 [159f3aea] Cairo v1.1.1 ⌅ [13f3f980] CairoMakie v0.10.12 [d360d2e6] ChainRulesCore v1.26.0 [a2cac450] ColorBrewer v0.4.2 [35d6a980] ColorSchemes v3.31.0 ⌅ [3da002f7] ColorTypes v0.11.5 ⌃ [c3611d14] ColorVectorSpace v0.10.0 ⌅ [5ae59095] Colors v0.12.11 [861a8166] Combinatorics v1.0.3 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.18.1 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 ⌅ [927a84f5] DelaunayTriangulation v0.8.12 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.11 [31c24e10] Distributions v0.25.122 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [429591f6] ExactPredicates v2.2.9 [411431e0] Extents v0.1.6 [c87230d0] FFMPEG v0.4.5 [7a1cc6ca] FFTW v1.10.0 [5789e2e9] FileIO v1.17.1 [1a297f60] FillArrays v1.15.0 [6a86dc24] FiniteDiff v2.29.0 [53c48c17] FixedPointNumbers v0.8.5 [59287772] Formatting v0.4.3 [f6369f11] ForwardDiff v1.2.2 [b38be410] FreeType v4.1.1 [663a7486] FreeTypeAbstraction v0.10.8 [68eda718] GeoFormatTypes v0.4.5 ⌃ [cf35fbd7] GeoInterface v1.4.1 ⌅ [5c1252a2] GeometryBasics v0.4.11 [a2bd30eb] Graphics v1.1.3 ⌅ [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 v0.16.2 [d1acc4aa] IntervalArithmetic v1.0.1 [8197267c] IntervalSets v0.7.12 [92d709cd] IrrationalConstants v0.2.6 [f1662d9f] Isoband v0.1.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.1 [682c06a0] JSON v1.2.1 [b835a17e] JpegTurbo v0.1.6 [e5e0dc1b] Juno v0.8.4 [5ab0869b] KernelDensity v0.6.10 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[c5f90fcd] libwebp_jll v1.6.0+0 [1317d2d5] oneTBB_jll v2022.0.0+1 [1270edf5] x264_jll v10164.0.1+0 [dfaa095f] x265_jll v4.1.0+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 v1.0.0 [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 v1.0.0 [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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [3a97d323] MPFR_jll v4.2.2+0 [14a3606d] MozillaCACerts_jll v2025.11.4 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.7+0 [458c3c95] OpenSSL_jll v3.5.4+0 [efcefdf7] PCRE2_jll v10.47.0+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 v5.15.0+0 [8e850ede] nghttp2_jll v1.68.0+1 [3f19e933] p7zip_jll v17.7.0+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. 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:936 ┌ [4] mktempdir │ @ ./file.jl:932 [inlined] ╰──── repeated 2 times [6] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [7] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:907 [8] mktemp @ ./file.jl:905 [inlined] [9] 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 [10] run_r2r(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] [12] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] 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:936 ┌ [4] mktempdir │ @ ./file.jl:932 [inlined] ╰──── repeated 2 times [6] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [7] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:907 [8] mktemp @ ./file.jl:905 [inlined] [9] 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 [10] run_r2r(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] [12] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [14] 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:936 ┌ [4] mktempdir │ @ ./file.jl:932 [inlined] ╰──── repeated 2 times [6] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [7] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:907 [8] mktemp @ ./file.jl:905 [inlined] [9] 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 [10] run_r2r @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [inlined] [11] plot(msa::MSA{Char}; kwargs::@Kwargs{}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:109 [12] plot(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] [14] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [16] 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:936 ┌ [4] mktempdir │ @ ./file.jl:932 [inlined] ╰──── repeated 2 times [6] #6 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [7] mktemp(fn::PlotRNA.R2R.var"#6#7"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:907 [8] mktemp @ ./file.jl:905 [inlined] [9] 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 [10] run_r2r @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:113 [inlined] [11] plot(msa::MSA{Char}; kwargs::@Kwargs{}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:109 [12] plot(msa::MSA{Char}) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [13] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:750 [inlined] [14] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [15] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:1961 [inlined] [16] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:28 testing uniplot ┌ 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  Downloading artifact: IntelOpenMP  Downloading artifact: oneTBB ERROR: LoadError: ArgumentError: Cannot load (`using/import`) module SHA into module CairoMakie in package CairoMakie because package CairoMakie does not have SHA in its dependencies: - Note that the following manifests in the load path were resolved with a potentially  different DEV version of the current version, which may be the cause of the error.  Try to re-resolve them in the current version, or consider deleting them if that fails:  /tmp/jl_QP4aew/Manifest.toml - You may have a partially installed environment. Try `Pkg.instantiate()`  to ensure all packages in the environment are installed. - Or, if you have CairoMakie checked out for development and have  added SHA as a dependency but haven't updated your primary  environment's manifest file, try `Pkg.resolve()`. - Otherwise you may need to report an issue with CairoMakie Stacktrace:  [1] macro expansion  @ ./loading.jl:2491 [inlined]  [2] macro expansion  @ ./lock.jl:376 [inlined]  [3] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2471  [4] require  @ ./loading.jl:2447 [inlined]  [5] eval_import_path  @ ./module.jl:36 [inlined]  [6] _eval_import(imported::Bool, to::Module, from::Nothing, paths::Expr)  @ Base ./module.jl:111  [7] top-level scope  @ ~/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:5  [8] include(mod::Module, _path::String)  @ Base ./Base.jl:309  [9] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing)  @ Base ./loading.jl:3151  [10] top-level scope  @ stdin:5  [11] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [12] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2997  [13] include_string  @ ./loading.jl:3007 [inlined]  [14] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:342  [15] _start()  @ Base ./client.jl:577 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/CairoMakie.jl:1 in expression starting at stdin:5 3 dependencies had output during precompilation: ┌ MKL_jll │ Downloading artifact: IntelOpenMP │ Downloading artifact: oneTBB └ ┌ CairoMakie │ [Output was shown above] └ ┌ 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 └ 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 package failed to precompile: CairoMakie Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.14/CairoMakie/jl_y4jxnB" (ProcessExited(1)). 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 27m04.7s Aqua.test_all | 8 8 42.0s plot_structure | 39 39 13.2s R2R.run_r2r | 2 2 4.9s R2R.plot | 2 2 0.1s uniplot | 1 1 4.6s RNG of the outermost testset: Random.Xoshiro(0x3104e54aca741170, 0x6737526b44b59147, 0xc05319716c8f4864, 0xdb1b208318dcdf30, 0x26083f59656b4989) 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 1637.3s ERROR: LoadError: Package PlotRNA errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2946 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2795 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:572 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:548 [6] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [12] include(mod::Module, _path::String) @ Base ./Base.jl:309 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:577 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 1994.72s: package fails to precompile