Package evaluation of PlotRNA on Julia 1.13.0-DEV.636 (2bd37fbbab*) started at 2025-05-25T22:15:35.955 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.51s ################################################################################ # Installation # Installing PlotRNA... Resolving package versions... 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 v3.29.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [34da2185] + Compat v4.16.0 [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 v1.22.1 [e17b2a0c] + UnsafePointers v1.0.0 [05a721ad] + ViennaRNA v0.11.2 [6e34b625] + Bzip2_jll v1.0.9+0 ⌃ [83423d85] + Cairo_jll v1.18.4+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 [78b55507] + Gettext_jll v0.21.0+0 ⌃ [7746bdde] + Glib_jll v2.82.4+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [c1c5ebd0] + LAME_jll v3.100.2+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 v3.2.2+2 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [925c91fb] + Librsvg_jll v2.54.5+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 v1.3.5+1 [656ef2d0] + OpenBLAS32_jll v0.3.29+0 [91d4177d] + Opus_jll v1.3.3+0 [2f80f16e] + PCRE_jll v8.45.0+0 [36c8627f] + Pango_jll v1.56.1+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 v2.42.12+0 [a4ae2306] + libaom_jll v3.11.0+0 [0ac62f75] + libass_jll v0.15.2+0 [f638f0a6] + libfdk_aac_jll v2.0.3+0 [b53b4c65] + libpng_jll v1.6.48+0 [f27f6e37] + libvorbis_jll v1.3.7+2 ⌅ [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 v1.12.0 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [3a97d323] + MPFR_jll v4.2.2+0 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.12.0+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. To see why use `status --outdated -m` Installation completed after 5.19s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ 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... Precompilation completed after 1429.52s ################################################################################ # Testing # Testing PlotRNA Test Could not use exact versions of packages in manifest. Re-resolving dependencies Updating `/tmp/jl_QUPmZE/Project.toml` ⌅ [4c88cf16] + Aqua v0.6.7 ⌅ [13f3f980] + CairoMakie v0.10.12 [eab79ae3] + PlotRNA v0.3.2 [b8865327] + UnicodePlots v3.7.2 Updating `/tmp/jl_QUPmZE/Manifest.toml` [47edcb42] + ADTypes v1.14.0 [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 [96374032] + CRlibm v1.0.2 ⌅ [13f3f980] + CairoMakie v0.10.12 [d360d2e6] + ChainRulesCore v1.25.1 [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 v1.5.8 [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 v0.6.54 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.4 [4e289a0a] + EnumX v1.0.5 [429591f6] + ExactPredicates v2.2.8 [411431e0] + Extents v0.1.6 [7a1cc6ca] + FFTW v1.8.1 [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 v0.10.6 [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 v0.1.2 ⌅ [a98d9a8b] + Interpolations v0.15.1 [d1acc4aa] + IntervalArithmetic v0.22.35 [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 v0.6.9 [8cdb02fc] + LazyModules v0.3.1 [9c8b4983] + LightXML v0.9.1 [d3d80556] + LineSearches v7.3.0 [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 v7.9.1 [f09324ee] + Netpbm v1.1.1 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [52e1d378] + OpenEXR v0.3.3 [429524aa] + Optim v1.12.0 [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 v4.0.19 [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 v1.2.1 [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 v0.1.3 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 ⌅ [c5dd0088] + StableHashTraits v1.3.4 [860ef19b] + StableRNGs v1.0.3 [cae243ae] + StackViews v0.1.1 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [82ae8749] + StatsAPI v1.7.0 [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 v1.12.0 [731e570b] + TiffImages v0.11.3 [981d1d27] + TriplotBase v0.1.0 [9d95972d] + TupleTools v1.6.0 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [b8865327] + UnicodePlots v3.7.2 [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 v2025.0.4+0 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [856f044c] + MKL_jll v2025.0.1+1 [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 v1.5.0+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 v1.12.0 [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_QUPmZE/Project.toml` ⌅ [4c88cf16] Aqua v0.6.7 [eeb925a3] BioStockholm v0.2.1 ⌅ [13f3f980] CairoMakie v0.10.12 [35d6a980] ColorSchemes v3.29.0 ⌅ [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 v3.7.2 [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_QUPmZE/Manifest.toml` [47edcb42] ADTypes v1.14.0 [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 [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 v1.25.1 [a2cac450] ColorBrewer v0.4.1 [35d6a980] ColorSchemes v3.29.0 ⌅ [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 v4.16.0 [187b0558] ConstructionBase v1.5.8 [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 v0.6.54 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.4 [4e289a0a] EnumX v1.0.5 [429591f6] ExactPredicates v2.2.8 [411431e0] Extents v0.1.6 [c87230d0] FFMPEG v0.4.2 [7a1cc6ca] FFTW v1.8.1 [5789e2e9] FileIO v1.17.0 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 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[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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [3a97d323] MPFR_jll v4.2.2+0 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.0+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.12.0+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 Skipping Base.active_repl Skipping Base.MainInclude.Distributed Skipping Base.MainInclude.InteractiveUtils ┌ 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:727 [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:1833 [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:727 [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:1833 [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:727 [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:1833 [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:727 [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:1833 [inlined] [15] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:28 Precompiling packages... 14576.0 ms ✓ UnicodePlots → UnitfulExt 1 dependency successfully precompiled in 15 seconds. 49 already precompiled. testing uniplot Precompiling packages... 31391.1 ms ✓ ImageCore 6888.5 ms ✓ StableHashTraits 117659.6 ms ✓ TiffImages 34215.1 ms ✓ Polynomials 11976.0 ms ✓ GeometryBasics 5785.6 ms ✓ OpenEXR 8573.4 ms ✓ ForwardDiff 1251.4 ms ✓ IntervalArithmetic → IntervalArithmeticDiffRulesExt 10766.2 ms ✓ Distributions 7514.3 ms ✓ ExactPredicates 4105.4 ms ✓ ImageBase 6483.3 ms ✓ PNGFiles 10042.0 ms ✓ JpegTurbo 8105.5 ms ✓ WebP 9363.3 ms ✓ Sixel 3554.8 ms ✓ Polynomials → PolynomialsChainRulesCoreExt 3620.7 ms ✓ Polynomials → PolynomialsFFTWExt 3998.1 ms ✓ SimplePolynomials 4967.5 ms ✓ Polynomials → PolynomialsMakieCoreExt 10588.7 ms ✓ GridLayoutBase 2866.6 ms ✓ Packing 3355.3 ms ✓ ShaderAbstractions 4396.8 ms ✓ FreeTypeAbstraction 3815.6 ms ✓ ForwardDiff → ForwardDiffStaticArraysExt 1597.5 ms ✓ DifferentiationInterface → DifferentiationInterfaceForwardDiffExt 3529.4 ms ✓ IntervalArithmetic → IntervalArithmeticForwardDiffExt 5685.8 ms ✓ Distributions → DistributionsTestExt 4943.1 ms ✓ SimpleRandom 5633.2 ms ✓ Distributions → DistributionsChainRulesCoreExt 5890.8 ms ✓ ImageAxes 4107.0 ms ✓ LinearAlgebraX 24416.5 ms ✓ MathTeXEngine 4434.1 ms ✓ NLSolversBase 17951.6 ms ✓ KernelDensity 4344.5 ms ✓ ImageMetadata 6562.1 ms ✓ LineSearches 8307.5 ms ✓ Netpbm 11111.8 ms ✓ Optim 8996.3 ms ✓ SimpleGraphs 12986.0 ms ✓ DelaunayTriangulation 201840.2 ms ✓ Makie 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.  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ======================================================================================  cmd: /opt/julia/bin/julia 462 running 1 of 1  signal (10): User defined signal 1 ijl_new_structv at /source/src/datatype.c:1596 unknown function (ip: 0x7fff2f3e08ff) at (unknown file) handle_any_const_result! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1306 compute_inlining_cases at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1378 handle_call! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1410 assemble_inline_todo! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:1661 ssa_inlining_pass! at ./../usr/share/julia/Compiler/src/ssair/inlining.jl:76 run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1031 run_passes_ipo_safe at ./../usr/share/julia/Compiler/src/optimize.jl:1044 optimize at ./../usr/share/julia/Compiler/src/optimize.jl:1017 jfptr_optimize_85116.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 finish_nocycle at ./../usr/share/julia/Compiler/src/typeinfer.jl:232 jfptr_finish_nocycle_86913.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4496 const_prop_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:1354 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:904 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:874 handle1 at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:178 infercalls at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:252 abstract_call_gf_by_type at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:338 abstract_call_known at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2802 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2909 infercalls at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:1858 abstract_apply at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:1878 abstract_call_known at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2654 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2909 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2902 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3062 abstract_eval_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3080 abstract_eval_statement_expr at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3436 abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3825 [inlined] abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3782 [inlined] typeinf_local at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4331 jfptr_typeinf_local_86937.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4489 const_prop_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:1354 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:904 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:874 handle1 at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:178 infercalls at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:252 abstract_call_gf_by_type at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:338 abstract_call_known at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2802 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2909 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2902 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3062 abstract_eval_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3080 abstract_eval_statement_expr at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3436 abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3825 [inlined] abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3782 [inlined] typeinf_local at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4331 jfptr_typeinf_local_86937.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4489 const_prop_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:1354 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:904 abstract_call_method_with_const_args at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:874 handle1 at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:178 infercalls at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:252 abstract_call_gf_by_type at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:338 abstract_call_known at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2802 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2909 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:2902 abstract_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3062 abstract_eval_call at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3080 abstract_eval_statement_expr at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3436 abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3825 [inlined] abstract_eval_basic_statement at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3782 [inlined] typeinf_local at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4331 jfptr_typeinf_local_86937.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4489 typeinf_ext at ./../usr/share/julia/Compiler/src/typeinfer.jl:1391 add_codeinsts_to_jit! at ./../usr/share/julia/Compiler/src/typeinfer.jl:1528 typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1561 typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1568 jfptr_typeinf_ext_toplevel_83201.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] jl_type_infer at /source/src/gf.c:444 jl_compile_method_internal at /source/src/gf.c:2991 _jl_invoke at /source/src/gf.c:3482 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] jl_f__apply_iterate at /source/src/builtins.c:864 #plot!#166 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/interfaces.jl:292 plot! at /home/pkgeval/.julia/packages/Makie/RgxaV/src/interfaces.jl:275 unknown function (ip: 0x72eb0e1230b5) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] jl_f__apply_iterate at /source/src/builtins.c:864 #plot!#164 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/interfaces.jl:259 plot! at /home/pkgeval/.julia/packages/Makie/RgxaV/src/interfaces.jl:257 unknown function (ip: 0x72eb0e122f2a) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] jl_f__apply_iterate at /source/src/builtins.c:864 #mesh!#46 at /home/pkgeval/.julia/packages/MakieCore/tAY2U/src/recipes.jl:39 mesh! at /home/pkgeval/.julia/packages/MakieCore/tAY2U/src/recipes.jl:38 [inlined] #RectangleZoom#1209 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/types.jl:674 RectangleZoom at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/types.jl:666 [inlined] #RectangleZoom#1210 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/types.jl:682 [inlined] RectangleZoom at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/types.jl:681 [inlined] register_events! at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks/axis.jl:64 #initialize_block!#1284 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks/axis.jl:495 initialize_block! at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks/axis.jl:160 [inlined] #_block#1090 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks.jl:374 _block at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks.jl:272 [inlined] #_#1088 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks.jl:253 [inlined] Block at /home/pkgeval/.julia/packages/Makie/RgxaV/src/makielayout/blocks.jl:252 unknown function (ip: 0x72eb103136c2) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 get_axis at /home/pkgeval/.julia/packages/Makie/RgxaV/src/figureplotting.jl:48 #plot#1768 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/figureplotting.jl:65 plot at /home/pkgeval/.julia/packages/Makie/RgxaV/src/figureplotting.jl:58 [inlined] #poly#65 at /home/pkgeval/.julia/packages/MakieCore/tAY2U/src/recipes.jl:35 [inlined] poly at /home/pkgeval/.julia/packages/MakieCore/tAY2U/src/recipes.jl:34 unknown function (ip: 0x72eb2f7c0714) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_75002.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 eval_body at /source/src/interpreter.c:557 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_75002.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_eval_module_expr at /source/src/toplevel.c:200 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:661 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _include at ./loading.jl:2906 include at ./Base.jl:309 include_package_for_output at ./loading.jl:3000 jfptr_include_package_for_output_22666.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 include_string at ./loading.jl:2856 [inlined] exec_options at ./client.jl:329 _start at ./client.jl:564 jfptr__start_20713.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] true_main at /source/src/jlapi.c:963 jl_repl_entrypoint at /source/src/jlapi.c:1130 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x72eb30b62249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file)  ============================================================== Profile collected. A report will print at the next yield point ==============================================================  ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 254 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x7c1f5be63f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 2 signal (10): User defined signal 1 unknown function (ip: 0x7c0c50c17f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x00007c0c37736c20 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007c0c3a1fc100 Total snapshots: 1. Utilization: 0% ╎1 @Base/task.jl:1150 wait_forever() ╎ 1 @Base/task.jl:1216 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 unknown function (ip: 0x7c0c50c17f14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520  [462] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/Makie/RgxaV/precompile/shared-precompile.jl:6 _ZN4llvm19SelectionDAGBuilder18visitGetElementPtrERKNS_4UserE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm19SelectionDAGBuilder5visitERKNS_11InstructionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel16SelectBasicBlockENS_21ilist_iterator_w_bitsINS_12ilist_detail12node_optionsINS_11InstructionELb1ELb0EvLb1ENS_10BasicBlockEEELb0ELb1EEES7_Rb at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20SelectAllBasicBlocksERKNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm16SelectionDAGISel20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) [254] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/plot_structure_makie.jl:1 wait at ./task.jl:1216 _ZN4llvm9MapVectorIjNS_11SmallVectorIPNS_10BasicBlockELj2EEENS_13SmallDenseMapIjjLj4ENS_12DenseMapInfoIjvEENS_6detail12DenseMapPairIjjEEEENS1_ISt4pairIjS4_ELj4EEEEixERKj at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) wait_forever at ./task.jl:1150 _ZL23simplifyFunctionCFGImplRN4llvm8FunctionERKNS_19TargetTransformInfoEPNS_13DominatorTreeERKNS_18SimplifyCFGOptionsE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 _ZL19simplifyFunctionCFGRN4llvm8FunctionERKNS_19TargetTransformInfoEPNS_13DominatorTreeERKNS_18SimplifyCFGOptionsE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm15SimplifyCFGPass3runERNS_8FunctionERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) wait_forever at ./task.jl:1150 run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_8FunctionENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm27ModuleToFunctionPassAdaptor3runERNS_6ModuleERNS_15AnalysisManagerIS1_JEEE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/usr/include/llvm/IR/PassManagerInternal.h:91 _ZN4llvm11PassManagerINS_6ModuleENS_15AnalysisManagerIS1_JEEEJEE3runERS1_RS3_ at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) run at /source/src/pipeline.cpp:791 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 26763233 (Pool: 26762620; Big: 613); GC: 33 operator() at /source/src/jitlayers.cpp:1475 withModuleDo<(anonymous namespace)::sizedOptimizerT::operator()(llvm::orc::ThreadSafeModule) [with long unsigned int N = 4]:: > at /source/usr/include/llvm/ExecutionEngine/Orc/ThreadSafeModule.h:136 [inlined] operator() at /source/src/jitlayers.cpp:1436 [inlined] operator() at /source/src/jitlayers.cpp:1588 [inlined] addModule at /source/src/jitlayers.cpp:2045 jl_compile_codeinst_now at /source/src/jitlayers.cpp:649 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:840 jl_compile_method_internal at /source/src/gf.c:3004 _jl_invoke at /source/src/gf.c:3482 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] jl_f_invokelatest at /source/src/builtins.c:877 profile_printing_listener at ./Base.jl:337 #start_profile_listener##0 at ./Base.jl:355 jfptr_YY.start_profile_listenerYY.YY.0_16767.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30703.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 43535457 (Pool: 43534629; Big: 828); GC: 41 _ZN4llvm22SelectionDAGISelLegacy20runOnMachineFunctionERNS_15MachineFunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm19MachineFunctionPass13runOnFunctionERNS_8FunctionE.part.0 at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager13runOnFunctionERNS_8FunctionE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm13FPPassManager11runOnModuleERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm6legacy15PassManagerImpl3runERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) _ZN4llvm3orc14SimpleCompilerclERNS_6ModuleE at /opt/julia/bin/../lib/julia/libLLVM.so.20.1jl (unknown line) operator() at /source/src/jitlayers.cpp:1577 addModule at /source/src/jitlayers.cpp:2058 jl_compile_codeinst_now at /source/src/jitlayers.cpp:649 jl_compile_codeinst_impl at /source/src/jitlayers.cpp:840 jl_compile_method_internal at /source/src/gf.c:3004 _jl_invoke at /source/src/gf.c:3482 [inlined] ijl_apply_generic at /source/src/gf.c:3690 draw_atomic at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/primitives.jl:311 draw_plot at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:131 unknown function (ip: 0x72eb0e1f85ad) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 cairo_draw at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/infrastructure.jl:51 colorbuffer at /home/pkgeval/.julia/packages/CairoMakie/VqiwS/src/screen.jl:307 colorbuffer at /home/pkgeval/.julia/packages/Makie/RgxaV/src/display.jl:363 unknown function (ip: 0x72eb0e18d0a8) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 #colorbuffer#1046 at /home/pkgeval/.julia/packages/Makie/RgxaV/src/display.jl:439 colorbuffer at /home/pkgeval/.julia/packages/Makie/RgxaV/src/display.jl:434 [inlined] colorbuffer at /home/pkgeval/.julia/packages/Makie/RgxaV/src/display.jl:434 unknown function (ip: 0x72eb0e171ff2) at (unknown file) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_75002.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 eval_body at /source/src/interpreter.c:557 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 include_string at ./loading.jl:2846 _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 _include at ./loading.jl:2906 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_75002.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3490 [inlined] ijl_apply_generic at /source/src/gf.c:3690 jl_apply at /source/src/julia.h:2336 [inlined] do_call at /source/src/interpreter.c:124 eval_value at /source/src/interpreter.c:242 eval_stmt_value at /source/src/interpreter.c:193 [inlined] eval_body at /source/src/interpreter.c:707 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:776 jl_eval_module_expr at /source/src/toplevel.c:200 [inlined] jl_toplevel_eval_flex at /source/src/toplevel.c:661 jl_toplevel_eval_flex at /source/src/toplevel.c:716 ijl_toplevel_eval at /source/src/toplevel.c:788 ijl_toplevel_eval_in at /source/src/toplevel.c:833 eval at ./boot.jl:489 val already in a list atexit hook threw an error: ErrorException("schedule: Task not runnable") error at ./error.jl:44 #schedule#595 at ./task.jl:1035 schedule at ./task.jl:1027 [inlined] uv_writecb_task at ./stream.jl:1200 jlcapi_YY.uv_writecb_task_21726.1 at /opt/julia/lib/julia/sys.so (unknown line) uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926 uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227 uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824 uv_run at /workspace/srcdir/libuv/src/unix/core.c:420 ijl_process_events at /source/src/jl_uv.c:393 process_events at ./libuv.jl:126 [inlined] wait at ./task.jl:1201 uv_write at ./stream.jl:1081 PkgEval terminated after 2739.88s: test duration exceeded the time limit