Package evaluation of PlotRNA on Julia 1.11.4 (a71dd056e0*) started at 2025-04-08T19:37:12.126 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 11.77s ################################################################################ # Installation # Installing PlotRNA... Resolving package versions... Installed JpegTurbo_jll ───────────── v3.1.1+0 Installed libfdk_aac_jll ──────────── v2.0.3+0 Installed x265_jll ────────────────── v3.5.0+0 Installed FFMPEG ──────────────────── v0.4.2 Installed SIMD ────────────────────── v3.7.1 Installed ColorTypes ──────────────── v0.12.1 Installed Graphite2_jll ───────────── v1.3.15+0 Installed Xorg_libXext_jll ────────── v1.3.6+3 Installed Pixman_jll ──────────────── v0.44.2+0 Installed libass_jll ──────────────── v0.15.2+0 Installed XML2_jll ────────────────── v2.13.6+1 Installed Libmount_jll ────────────── v2.41.0+0 Installed gdk_pixbuf_jll ──────────── v2.42.12+0 Installed NLopt_jll ───────────────── v2.10.0+0 Installed Pango_jll ───────────────── v1.56.1+0 Installed Gettext_jll ─────────────── v0.21.0+0 Installed LERC_jll ────────────────── v4.0.1+0 Installed TensorCore ──────────────── v0.1.1 Installed Zstd_jll ────────────────── v1.5.7+1 Installed Preferences ─────────────── v1.4.3 Installed Xorg_xtrans_jll ─────────── v1.6.0+0 Installed Expat_jll ───────────────── v2.6.5+0 Installed Cairo ───────────────────── v1.1.1 Installed Opus_jll ────────────────── v1.3.3+0 Installed OpenSSL_jll ─────────────── v3.0.16+0 Installed PlotRNA ─────────────────── v0.3.2 Installed FFMPEG_jll ──────────────── v4.4.4+1 Installed Libgcrypt_jll ───────────── v1.11.1+0 Installed Bzip2_jll ───────────────── v1.0.9+0 Installed ViennaRNA ───────────────── v0.11.2 Installed XZ_jll ──────────────────── v5.8.1+0 Installed HarfBuzz_jll ────────────── v8.5.0+0 Installed Unitful ─────────────────── v1.22.0 Installed LLVMOpenMP_jll ──────────── v18.1.7+0 Installed FixedPointNumbers ───────── v0.8.5 Installed Libtiff_jll ─────────────── v4.7.1+0 Installed LAME_jll ────────────────── v3.100.2+0 Installed JLLWrappers ─────────────── v1.7.0 Installed PCRE_jll ────────────────── v8.45.0+0 Installed Libiconv_jll ────────────── v1.18.0+0 Installed NaNMath ─────────────────── v1.1.3 Installed LZO_jll ─────────────────── v2.10.3+0 Installed PrecompileTools ─────────── v1.2.1 Installed ColorVectorSpace ────────── v0.11.0 Installed Libffi_jll ──────────────── v3.2.2+2 Installed OrderedCollections ──────── v1.8.0 Installed LaTeXStrings ────────────── v1.4.0 Installed GSL_jll ─────────────────── v2.7.2+0 Installed TranscodingStreams ──────── v0.11.3 Installed Xorg_libXrender_jll ─────── v0.9.11+1 Installed Rsvg ────────────────────── v1.0.0 Installed Glib_jll ────────────────── v2.82.4+0 Installed Ogg_jll ─────────────────── v1.3.5+1 Installed FriBidi_jll ─────────────── v1.0.17+0 Installed libvorbis_jll ───────────── v1.3.7+2 Installed BioStockholm ────────────── v0.2.1 Installed R2R_jll ─────────────────── v1.0.6+0 Installed Xorg_libpthread_stubs_jll ─ v0.1.2+0 Installed XSLT_jll ────────────────── v1.1.43+0 Installed CEnum ───────────────────── v0.5.0 Installed Cairo_jll ───────────────── v1.18.4+0 Installed Fontconfig_jll ──────────── v2.16.0+0 Installed FileIO ──────────────────── v1.17.0 Installed OpenBLAS32_jll ──────────── v0.3.29+0 Installed Reexport ────────────────── v1.2.2 Installed Graphics ────────────────── v1.1.3 Installed Media ───────────────────── v0.5.0 Installed Libgpg_error_jll ────────── v1.51.1+0 Installed x264_jll ────────────────── v2021.5.5+0 Installed Statistics ──────────────── v1.11.1 Installed Requires ────────────────── v1.3.1 Installed DataStructures ──────────── v0.18.22 Installed Colors ──────────────────── v0.13.0 Installed FreeType2_jll ───────────── v2.13.4+0 Installed Xorg_libXdmcp_jll ───────── v1.1.5+0 Installed Xorg_libX11_jll ─────────── v1.8.6+3 Installed ViennaRNA_jll ───────────── v2.6.4+0 Installed Juno ────────────────────── v0.8.4 Installed MacroTools ──────────────── v0.5.15 Installed UnsafePointers ──────────── v1.0.0 Installed Xorg_libXau_jll ─────────── v1.0.12+0 Installed Compat ──────────────────── v4.16.0 Installed Libuuid_jll ─────────────── v2.41.0+0 Installed Automa ──────────────────── v1.1.0 Installed Librsvg_jll ─────────────── v2.54.5+0 Installed Xorg_libxcb_jll ─────────── v1.17.0+3 Installed libaom_jll ──────────────── v3.11.0+0 Installed libpng_jll ──────────────── v1.6.47+0 Installed ColorSchemes ────────────── v3.29.0 Installed Luxor ───────────────────── v3.8.0 Updating `~/.julia/environments/v1.11/Project.toml` [eab79ae3] + PlotRNA v0.3.2 Updating `~/.julia/environments/v1.11/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 v0.13.0 [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 v0.5.15 [e89f7d12] + Media v0.5.0 [77ba4419] + NaNMath v1.1.3 [bac558e1] + OrderedCollections v1.8.0 [eab79ae3] + PlotRNA v0.3.2 ⌅ [aea7be01] + PrecompileTools v1.2.1 [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 v1.22.0 [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 v18.1.7+0 [dd4b983a] + LZO_jll v2.10.3+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [d4300ac3] + Libgcrypt_jll v1.11.1+0 [7add5ba3] + Libgpg_error_jll v1.51.1+0 [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 [458c3c95] + OpenSSL_jll v3.0.16+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 [aed1982a] + XSLT_jll v1.1.43+0 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.6+3 [0c0b7dd1] + Xorg_libXau_jll v1.0.12+0 [a3789734] + Xorg_libXdmcp_jll v1.1.5+0 [1082639a] + Xorg_libXext_jll v1.3.6+3 [ea2f1a96] + Xorg_libXrender_jll v0.9.11+1 [14d82f49] + Xorg_libpthread_stubs_jll v0.1.2+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.0+3 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [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 v1.6.47+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 v1.6.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.11.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.2.0 [44cfe95a] + Pkg v1.11.0 [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 [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 v1.1.1+0 [781609d7] + GMP_jll v6.3.0+0 [deac9b47] + LibCURL_jll v8.6.0+0 [e37daf67] + LibGit2_jll v1.7.2+0 [29816b5a] + LibSSH2_jll v1.11.0+1 [3a97d323] + MPFR_jll v4.2.1+0 [c8ffd9c3] + MbedTLS_jll v2.28.6+0 [14a3606d] + MozillaCACerts_jll v2023.12.12 [4536629a] + OpenBLAS_jll v0.3.27+1 [05823500] + OpenLibm_jll v0.8.5+0 [efcefdf7] + PCRE2_jll v10.42.0+1 [83775a58] + Zlib_jll v1.2.13+1 [8e850b90] + libblastrampoline_jll v5.11.0+0 [8e850ede] + nghttp2_jll v1.59.0+0 [3f19e933] + p7zip_jll v17.4.0+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 38.8s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling project... 3074.2 ms ✓ TestEnv 1 dependency successfully precompiled in 3 seconds. 23 already precompiled. ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/tgnBf/src/julia-1.11/activate_set.jl:63 Precompiling package dependencies... Precompilation completed after 1657.01s ################################################################################ # Testing # Testing PlotRNA ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1920 Status `/tmp/jl_mz8QL4/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 v1.2.1 [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_mz8QL4/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 v7.18.0 [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 [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 v1.0.2 [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 v0.6.50 [31c24e10] Distributions v0.25.118 [ffbed154] DocStringExtensions v0.9.4 [4e289a0a] EnumX v1.0.5 [429591f6] ExactPredicates v2.2.8 [411431e0] Extents v0.1.5 [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 [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 [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 v0.1.2 [a98d9a8b] Interpolations v0.15.1 [d1acc4aa] IntervalArithmetic v0.22.28 [8197267c] IntervalSets v0.7.10 [92d709cd] IrrationalConstants v0.2.4 [f1662d9f] Isoband v0.1.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b835a17e] JpegTurbo v0.1.6 [e5e0dc1b] Juno v0.8.4 [5ab0869b] KernelDensity v0.6.9 [b964fa9f] LaTeXStrings v1.4.0 [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 ⌅ [ae8d54c2] Luxor v3.8.0 [1914dd2f] MacroTools v0.5.15 ⌅ [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 [e89f7d12] Media v0.5.0 [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 [77ba4419] NaNMath v1.1.3 [f09324ee] Netpbm v1.1.1 [510215fc] Observables v0.5.5 [6fe1bfb0] OffsetArrays v1.16.0 [52e1d378] OpenEXR v0.3.3 [429524aa] Optim v1.12.0 [bac558e1] OrderedCollections v1.8.0 [90014a1f] PDMats v0.11.33 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[8e850ede] nghttp2_jll v1.59.0+0 [3f19e933] p7zip_jll v17.4.0+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.active_repl_backend Skipping Base.cwstring 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:35 [2] (::PlotRNA.R2R.var"#4#7"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#4#7"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:819 [4] mktempdir (repeats 2 times) @ ./file.jl:815 [inlined] [5] #3 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#3#6"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:790 [7] mktemp @ ./file.jl:788 [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] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [11] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [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:35 [2] (::PlotRNA.R2R.var"#4#7"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#4#7"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:819 [4] mktempdir (repeats 2 times) @ ./file.jl:815 [inlined] [5] #3 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#3#6"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:790 [7] mktemp @ ./file.jl:788 [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] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [11] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:23 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [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:35 [2] (::PlotRNA.R2R.var"#4#7"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#4#7"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:819 [4] mktempdir (repeats 2 times) @ ./file.jl:815 [inlined] [5] #3 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#3#6"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:790 [7] mktemp @ ./file.jl:788 [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 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [13] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [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:35 [2] (::PlotRNA.R2R.var"#4#7"{String, Bool, Float64})(output_dir::String) @ PlotRNA.R2R ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:147 [3] mktempdir(fn::PlotRNA.R2R.var"#4#7"{String, Bool, Float64}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:819 [4] mktempdir (repeats 2 times) @ ./file.jl:815 [inlined] [5] #3 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:136 [inlined] [6] mktemp(fn::PlotRNA.R2R.var"#3#6"{Bool, Float64, MSA{Char}}, parent::String) @ Base.Filesystem ./file.jl:790 [7] mktemp @ ./file.jl:788 [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 @ ~/.julia/packages/PlotRNA/j5Vgx/src/r2r.jl:108 [inlined] [12] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined] [13] macro expansion @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:31 [inlined] [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.11/Test/src/Test.jl:1704 [inlined] [15] top-level scope @ ~/.julia/packages/PlotRNA/j5Vgx/test/r2r.jl:28 testing uniplot testing plot_structure_makie Test Summary: | Pass Error Total Time PlotRNA | 49 4 53 9m48.5s Aqua.test_all | 8 8 43.5s plot_structure | 39 39 7.8s R2R.run_r2r | 2 2 4.1s R2R.plot | 2 2 0.5s uniplot | 1 1 5.3s plot_structure_makie | 1 1 1m49.2s ERROR: LoadError: Some tests did not pass: 49 passed, 0 failed, 4 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/PlotRNA/j5Vgx/test/runtests.jl:7 Testing failed after 608.03s ERROR: LoadError: Package PlotRNA errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/Operations.jl:2124 [3] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2007 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{Pkg.Types.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/v1.11/Pkg/src/API.jl:481 [5] test(pkgs::Vector{Pkg.Types.PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:159 [6] test @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined] [7] #test#74 @ /opt/julia/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined] [8] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2347.96s: package tests unexpectedly errored