Package evaluation of PhyloClustering on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-15T05:55:30.062 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.22s ################################################################################ # Installation # Installing PhyloClustering... Resolving package versions... Installed x265_jll ──────────────────── v4.1.0+0 Installed ScikitLearnBase ───────────── v0.5.0 Installed BioGenerics ───────────────── v0.1.5 Installed JpegTurbo_jll ─────────────── v3.1.1+0 Installed ImageIO ───────────────────── v0.6.9 Installed libfdk_aac_jll ────────────── v2.0.4+0 Installed AxisArrays ────────────────── v0.4.7 Installed OffsetArrays ──────────────── v1.17.0 Installed PhyloClustering ───────────── v0.2.0 Installed TiffImages ────────────────── v0.11.4 Installed Libmount_jll ──────────────── v2.41.0+0 Installed HypergeometricFunctions ───── v0.3.28 Installed PNGFiles ──────────────────── v0.4.4 Installed JpegTurbo ─────────────────── v0.1.6 Installed StatsFuns ─────────────────── v1.5.0 Installed FFTW ──────────────────────── v1.9.0 Installed LERC_jll ──────────────────── v4.0.1+0 Installed Preferences ───────────────── v1.4.3 Installed ParallelKMeans ────────────── v1.1.0 Installed Opus_jll ──────────────────── v1.5.2+0 Installed RelocatableFolders ────────── v1.0.1 Installed Permutations ──────────────── v0.4.23 Installed Multisets ─────────────────── v0.4.5 Installed StableHashTraits ──────────── v1.3.4 Installed StatisticalTraits ─────────── v3.5.0 Installed Sixel ─────────────────────── v0.1.5 Installed InlineStrings ─────────────── v1.4.4 Installed PDMats ────────────────────── v0.11.35 Installed Contour ───────────────────── v0.6.3 Installed ProgressMeter ─────────────── v1.10.4 Installed StaticArrays ──────────────── v1.9.13 Installed Grisu ─────────────────────── v1.0.2 Installed EarCut_jll ────────────────── v2.2.4+0 Installed Formatting ────────────────── v0.4.3 Installed NearestNeighbors ──────────── v0.4.22 Installed OpenEXR ───────────────────── v0.3.3 Installed EnumX ─────────────────────── v1.0.5 Installed PlotUtils ─────────────────── v1.4.3 Installed ScopedValues ──────────────── v1.3.0 Installed CEnum ─────────────────────── v0.5.0 Installed InvertedIndices ───────────── v1.3.1 Installed BaseDirs ──────────────────── v1.3.1 Installed DelimitedFiles ────────────── v1.9.1 Installed Cairo_jll ─────────────────── v1.18.5+0 Installed Fontconfig_jll ────────────── v2.16.0+0 Installed Statistics ────────────────── v1.11.1 Installed FileIO ────────────────────── v1.17.0 Installed GLM ───────────────────────── v1.9.0 Installed BioSequences ──────────────── v3.4.2 Installed Polynomials ───────────────── v4.0.21 Installed IntelOpenMP_jll ───────────── v2025.0.4+0 Installed Mods ──────────────────────── v2.2.6 Installed Netpbm ────────────────────── v1.1.1 Installed Xorg_libXau_jll ───────────── v1.0.13+0 Installed Distances ─────────────────── v0.10.12 Installed FilePaths ─────────────────── v0.8.3 Installed DataFrames ────────────────── v1.7.0 Installed SignedDistanceFields ──────── v0.4.0 Installed Missings ──────────────────── v1.2.0 Installed ColorSchemes ──────────────── v3.30.0 Installed FiniteDiff ────────────────── v2.27.0 Installed TupleTools ────────────────── v1.6.0 Installed RoundingEmulator ──────────── v0.2.1 Installed JLD2 ──────────────────────── v0.5.15 Installed SIMD ──────────────────────── v3.7.1 Installed IrrationalConstants ───────── v0.2.4 Installed TriplotBase ───────────────── v0.1.0 Installed JSON ──────────────────────── v0.21.4 Installed Functors ──────────────────── v0.4.12 Installed Showoff ───────────────────── v1.0.3 Installed Giflib_jll ────────────────── v5.2.3+0 Installed AbstractLattices ──────────── v0.3.1 Installed SimpleRandom ──────────────── v0.3.2 Installed Pango_jll ─────────────────── v1.56.3+0 Installed OpenBLASConsistentFPCSR_jll ─ v0.3.29+0 Installed PtrArrays ─────────────────── v1.3.0 Installed NLopt ─────────────────────── v1.2.0 Installed PolygonOps ────────────────── v0.1.2 Installed Clustering ────────────────── v0.15.8 Installed MathTeXEngine ─────────────── v0.5.7 Installed Bzip2_jll ─────────────────── v1.0.9+0 Installed ADTypes ───────────────────── v1.15.0 Installed SentinelArrays ────────────── v1.4.8 Installed XZ_jll ────────────────────── v5.8.1+0 Installed HarfBuzz_jll ──────────────── v8.5.1+0 Installed SpecialFunctions ──────────── v2.5.1 Installed SimpleGraphs ──────────────── v0.8.6 Installed PkgVersion ────────────────── v0.3.3 Installed isoband_jll ───────────────── v0.2.3+0 Installed StaticArraysCore ──────────── v1.4.3 Installed QOI ───────────────────────── v1.0.1 Installed PikaParser ────────────────── v0.6.1 Installed NaNMath ───────────────────── v1.1.3 Installed BioSymbols ────────────────── v5.2.0 Installed LZO_jll ───────────────────── v2.10.3+0 Installed WorkerUtilities ───────────── v1.6.1 Installed StringViews ───────────────── v1.3.4 Installed FriBidi_jll ───────────────── v1.0.17+0 Installed NLSolversBase ─────────────── v7.10.0 Installed Graphics ──────────────────── v1.1.3 Installed TranscodingStreams ────────── v0.11.3 Installed UnicodeFun ────────────────── v0.4.1 Installed WeakRefStrings ────────────── v1.4.2 Installed StatsModels ───────────────── v0.7.4 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed WebP ──────────────────────── v0.1.3 Installed ImageMetadata ─────────────── v0.9.10 Installed x264_jll ──────────────────── v10164.0.1+0 Installed UnsafeArrays ──────────────── v1.0.8 Installed Ratios ────────────────────── v0.4.5 Installed DataStructures ────────────── v0.18.22 Installed Colors ────────────────────── v0.12.11 Installed FreeType2_jll ─────────────── v2.13.4+0 Installed MappedArrays ──────────────── v0.4.2 Installed CommonSubexpressions ──────── v0.3.1 Installed StatsAPI ──────────────────── v1.7.1 Installed Compat ────────────────────── v4.17.0 Installed GridLayoutBase ────────────── v0.10.2 Installed CodecZlib ─────────────────── v0.7.8 Installed LinearAlgebraX ────────────── v0.2.10 Installed PaddedViews ───────────────── v0.5.12 Installed FreeType ──────────────────── v4.1.1 Installed StatsBase ─────────────────── v0.33.21 Installed libpng_jll ────────────────── v1.6.50+0 Installed Xorg_libxcb_jll ───────────── v1.17.1+0 Installed libaom_jll ────────────────── v3.11.0+0 Installed LazyModules ───────────────── v0.3.1 Installed Automa ────────────────────── v1.1.0 Installed Scratch ───────────────────── v1.3.0 Installed MosaicViews ───────────────── v0.3.4 Installed oneTBB_jll ────────────────── v2022.0.0+0 Installed DiffRules ─────────────────── v1.15.1 Installed ColorTypes ────────────────── v0.11.5 Installed StructTypes ───────────────── v1.11.0 Installed SimplePartitions ──────────── v0.3.3 Installed Twiddle ───────────────────── v1.1.2 Installed Xorg_libXext_jll ──────────── v1.3.7+0 Installed Zstd_jll ──────────────────── v1.5.7+1 Installed ImageCore ─────────────────── v0.10.5 Installed TableTraits ───────────────── v1.0.1 Installed TensorCore ────────────────── v0.1.1 Installed Expat_jll ─────────────────── v2.6.5+0 Installed Isoband ───────────────────── v0.1.1 Installed DiffResults ───────────────── v1.1.0 Installed Inflate ───────────────────── v0.1.5 Installed WeakKeyIdDicts ────────────── v0.1.0 Installed PositiveFactorizations ────── v0.2.4 Installed PrettyTables ──────────────── v2.4.0 Installed FreeTypeAbstraction ───────── v0.10.8 Installed HashArrayMappedTries ──────── v0.2.0 Installed Parsers ───────────────────── v2.8.3 Installed PooledArrays ──────────────── v1.4.3 Installed MKL_jll ───────────────────── v2025.0.1+1 Installed Setfield ──────────────────── v1.1.2 Installed Format ────────────────────── v1.3.7 Installed AbstractFFTs ──────────────── v1.5.0 Installed JLLWrappers ───────────────── v1.7.0 Installed Animations ────────────────── v0.4.2 Installed Extents ───────────────────── v0.1.6 Installed Imath_jll ─────────────────── v3.1.11+0 Installed Libtiff_jll ───────────────── v4.7.1+0 Installed ConstructionBase ──────────── v1.6.0 Installed DataValueInterfaces ───────── v1.0.0 Installed Libffi_jll ────────────────── v3.4.7+0 Installed CSV ───────────────────────── v0.10.15 Installed Xorg_libXrender_jll ───────── v0.9.12+0 Installed Packing ───────────────────── v0.5.1 Installed OrderedCollections ────────── v1.8.1 Installed ColorVectorSpace ──────────── v0.10.0 Installed AbstractTrees ─────────────── v0.4.5 Installed Ogg_jll ───────────────────── v1.3.6+0 Installed KernelDensity ─────────────── v0.6.10 Installed ArrayInterface ────────────── v7.19.0 Installed RingLists ─────────────────── v0.2.9 Installed Reexport ──────────────────── v1.2.2 Installed LineSearches ──────────────── v7.4.0 Installed LogExpFunctions ───────────── v0.3.29 Installed ExactPredicates ───────────── v2.2.8 Installed Interpolations ────────────── v0.16.1 Installed Combinatorics ─────────────── v1.0.3 Installed ChainRulesCore ────────────── v1.25.2 Installed MacroTools ────────────────── v0.5.16 Installed StackViews ────────────────── v0.1.2 Installed FFTW_jll ──────────────────── v3.3.11+0 Installed RangeArrays ───────────────── v0.3.2 Installed IntervalArithmetic ────────── v0.22.36 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed GeoFormatTypes ────────────── v0.4.4 Installed AliasTables ───────────────── v1.1.3 Installed SimpleTraits ──────────────── v0.9.4 Installed Libuuid_jll ───────────────── v2.41.0+0 Installed UnPack ────────────────────── v1.0.2 Installed MultivariateStats ─────────── v0.10.3 Installed DocStringExtensions ───────── v0.9.5 Installed DifferentiationInterface ──── v0.7.2 Installed OpenEXR_jll ───────────────── v3.2.4+0 Installed Crayons ───────────────────── v4.1.1 Installed ColorBrewer ───────────────── v0.4.1 Installed Adapt ─────────────────────── v4.3.0 Installed NLopt_jll ─────────────────── v2.10.0+0 Installed FASTX ─────────────────────── v2.1.7 Installed Graphite2_jll ─────────────── v1.3.15+0 Installed libass_jll ────────────────── v0.15.2+0 Installed Pixman_jll ────────────────── v0.44.2+0 Installed ScientificTypesBase ───────── v3.0.0 Installed XML2_jll ──────────────────── v2.14.1+0 Installed Rmath ─────────────────────── v0.8.0 Installed IntegerMathUtils ──────────── v0.1.3 Installed StableRNGs ────────────────── v1.0.3 Installed Arpack_jll ────────────────── v3.5.1+1 Installed ImageBase ─────────────────── v0.1.7 Installed IntervalSets ──────────────── v0.7.11 Installed MLJModelInterface ─────────── v1.11.1 Installed Cairo ─────────────────────── v1.1.1 Installed DelaunayTriangulation ─────── v0.8.12 Installed Xorg_xtrans_jll ───────────── v1.6.0+0 Installed FFMPEG_jll ────────────────── v7.1.0+0 Installed MakieCore ─────────────────── v0.7.3 Installed IndirectArrays ────────────── v1.0.0 Installed Tables ────────────────────── v1.12.1 Installed GeometryBasics ────────────── v0.4.11 Installed IterTools ─────────────────── v1.10.0 Installed DataAPI ───────────────────── v1.16.0 Installed LLVMOpenMP_jll ────────────── v18.1.8+0 Installed FixedPointNumbers ─────────── v0.8.5 Installed ShaderAbstractions ────────── v0.4.1 Installed Optim ─────────────────────── v1.13.2 Installed RecipesBase ───────────────── v1.3.4 Installed LAME_jll ──────────────────── v3.100.3+0 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed PrecompileTools ───────────── v1.3.2 Installed Libiconv_jll ──────────────── v1.18.0+0 Installed GettextRuntime_jll ────────── v0.22.4+0 Installed LaTeXStrings ──────────────── v1.4.0 Installed StructArrays ──────────────── v0.6.21 Installed Arpack ────────────────────── v0.5.4 Installed CairoMakie ────────────────── v0.11.9 Installed Primes ────────────────────── v0.5.7 Installed Glib_jll ──────────────────── v2.84.3+0 Installed libvorbis_jll ─────────────── v1.3.8+0 Installed Libglvnd_jll ──────────────── v1.7.1+1 Installed PhyloNetworks ─────────────── v0.16.4 Installed FilePathsBase ─────────────── v0.9.24 Installed FillArrays ────────────────── v1.13.0 Installed libsixel_jll ──────────────── v1.10.5+0 Installed AxisAlgorithms ────────────── v1.1.0 Installed ShiftedArrays ─────────────── v2.0.0 Installed Requires ──────────────────── v1.3.1 Installed ForwardDiff ───────────────── v1.0.1 Installed CRlibm ────────────────────── v1.0.2 Installed QuadGK ────────────────────── v2.11.2 Installed Xorg_libX11_jll ───────────── v1.8.12+0 Installed Xorg_libXdmcp_jll ─────────── v1.1.6+0 Installed ImageAxes ─────────────────── v0.6.12 Installed GeoInterface ──────────────── v1.4.1 Installed Observables ───────────────── v0.5.5 Installed LightXML ──────────────────── v0.9.2 Installed CRlibm_jll ────────────────── v1.0.1+0 Installed Parameters ────────────────── v0.12.3 Installed Distributions ─────────────── v0.25.120 Installed SortingAlgorithms ─────────── v1.2.1 Installed SimplePolynomials ─────────── v0.2.18 Installed StringManipulation ────────── v0.4.1 Installed libwebp_jll ───────────────── v1.6.0+0 Installed WoodburyMatrices ──────────── v1.0.0 Installed GaussianMixtures ──────────── v0.3.13 Installed Makie ─────────────────────── v0.20.8 Installing 58 artifacts Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Arpack 147.2 KiB Installed artifact LAME 292.5 KiB Installed artifact EarCut 80.5 KiB Installed artifact Pango 1.1 MiB Installed artifact Expat 271.4 KiB Installed artifact Libffi 44.2 KiB Installed artifact oneTBB 435.6 KiB Installed artifact OpenEXR 1.9 MiB Installed artifact FreeType2 1.5 MiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact libfdk_aac 2.8 MiB Installed artifact Cairo 2.2 MiB Installed artifact Zstd 646.0 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact Graphite2 120.2 KiB Installed artifact Imath 182.8 KiB Installed artifact Libiconv 1.9 MiB Installed artifact FFTW 2.2 MiB Installed artifact XZ 1.5 MiB Installed artifact LERC 272.9 KiB Installed artifact LZO 208.9 KiB Installed artifact NLopt 322.7 KiB Installed artifact Rmath 121.9 KiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact JpegTurbo 1.6 MiB Installed artifact Pixman 372.2 KiB Installed artifact XML2 2.5 MiB Installed artifact Libtiff 3.2 MiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact FriBidi 78.9 KiB Installed artifact CRlibm 169.5 KiB Installed artifact Ogg 250.3 KiB Installed artifact libaom 6.4 MiB Installed artifact libpng 328.4 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact OpenBLASConsistentFPCSR 9.9 MiB Installed artifact Opus 925.5 KiB Installed artifact isoband 25.7 KiB Installed artifact libvorbis 271.0 KiB Installed artifact Giflib 154.6 KiB Installed artifact libwebp 2.6 MiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact libass 372.4 KiB Installed artifact Libmount 6.4 MiB Installed artifact GettextRuntime 543.0 KiB Installed artifact libsixel 177.3 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Fontconfig 522.5 KiB Installed artifact Libglvnd 833.5 KiB Installed artifact x264 2.1 MiB Installed artifact x265 1.4 MiB Installed artifact FFMPEG 11.4 MiB Installed artifact Glib 7.7 MiB Installed artifact Xorg_libX11 13.9 MiB Updating `~/.julia/environments/v1.12/Project.toml` [2e4ec7c6] + PhyloClustering v0.2.0 Updating `~/.julia/environments/v1.12/Manifest.toml` [47edcb42] + ADTypes v1.15.0 [621f4979] + AbstractFFTs v1.5.0 [398f06c4] + AbstractLattices v0.3.1 [1520ce14] + AbstractTrees v0.4.5 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [27a7e980] + Animations v0.4.2 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.19.0 [67c07d97] + Automa v1.1.0 [13072b0f] + AxisAlgorithms v1.1.0 [39de3d68] + AxisArrays v0.4.7 [18cc8868] + BaseDirs v1.3.1 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.4.2 [3c28c6f8] + BioSymbols v5.2.0 [fa961155] + CEnum v0.5.0 [96374032] + CRlibm v1.0.2 [336ed68f] + CSV v0.10.15 [159f3aea] + Cairo v1.1.1 ⌅ [13f3f980] + CairoMakie v0.11.9 [d360d2e6] + ChainRulesCore v1.25.2 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 [a2cac450] + ColorBrewer v0.4.1 [35d6a980] + ColorSchemes v3.30.0 ⌅ [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 v4.17.0 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 ⌅ [927a84f5] + DelaunayTriangulation v0.8.12 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [a0c0ee7d] + DifferentiationInterface v0.7.2 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [4e289a0a] + EnumX v1.0.5 [429591f6] + ExactPredicates v2.2.8 [411431e0] + Extents v0.1.6 [c2308a5c] + FASTX v2.1.7 [7a1cc6ca] + FFTW v1.9.0 [5789e2e9] + FileIO v1.17.0 ⌅ [8fc22ac5] + FilePaths v0.8.3 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 [59287772] + Formatting v0.4.3 [f6369f11] + ForwardDiff v1.0.1 [b38be410] + FreeType v4.1.1 [663a7486] + FreeTypeAbstraction v0.10.8 ⌅ [d9f16b24] + Functors v0.4.12 [38e38edf] + GLM v1.9.0 [cc18c42c] + GaussianMixtures v0.3.13 [68eda718] + GeoFormatTypes v0.4.4 ⌃ [cf35fbd7] + GeoInterface v1.4.1 ⌅ [5c1252a2] + GeometryBasics v0.4.11 [a2bd30eb] + Graphics v1.1.3 ⌅ [3955a311] + GridLayoutBase v0.10.2 [42e2da0e] + Grisu v1.0.2 [076d061b] + HashArrayMappedTries v0.2.0 [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 [842dd82b] + InlineStrings v1.4.4 [18e54dd8] + IntegerMathUtils v0.1.3 [a98d9a8b] + Interpolations v0.16.1 [d1acc4aa] + IntervalArithmetic v0.22.36 [8197267c] + IntervalSets v0.7.11 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [f1662d9f] + Isoband v0.1.1 [c8e1da08] + IterTools v1.10.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [033835bb] + JLD2 v0.5.15 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [b835a17e] + JpegTurbo v0.1.6 [5ab0869b] + KernelDensity v0.6.10 [b964fa9f] + LaTeXStrings v1.4.0 [8cdb02fc] + LazyModules v0.3.1 [9c8b4983] + LightXML v0.9.2 [d3d80556] + LineSearches v7.4.0 [9b3f67b0] + LinearAlgebraX v0.2.10 [2ab3a3ac] + LogExpFunctions v0.3.29 [e80e1ace] + MLJModelInterface v1.11.1 [1914dd2f] + MacroTools v0.5.16 ⌅ [ee78f7c6] + Makie v0.20.8 ⌅ [20f20a25] + MakieCore v0.7.3 [dbb5928d] + MappedArrays v0.4.2 ⌅ [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 [6f286f6a] + MultivariateStats v0.10.3 [d41bc354] + NLSolversBase v7.10.0 [76087f3c] + NLopt v1.2.0 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.22 [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 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [f57f5aa1] + PNGFiles v0.4.4 [19eb6ba3] + Packing v0.5.1 [5432bcbf] + PaddedViews v0.5.12 [42b8e9d4] + ParallelKMeans v1.1.0 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [2ae35dd2] + Permutations v0.4.23 [2e4ec7c6] + PhyloClustering v0.2.0 ⌅ [33ad39ac] + PhyloNetworks v0.16.4 [3bbf5609] + PikaParser v0.6.1 [eebad327] + PkgVersion v0.3.3 [995b91a9] + PlotUtils v1.4.3 [647866c9] + PolygonOps v0.1.2 ⌃ [f27b6e38] + Polynomials v4.0.21 [2dfb63ee] + PooledArrays v1.4.3 [85a6dd25] + PositiveFactorizations v0.2.4 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [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 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[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 [deac9b47] + LibCURL_jll v8.11.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.64.0+1 [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 28.39s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4519.9 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... ERROR: LoadError: The following 2 direct dependencies failed to precompile: PhyloClustering Failed to precompile PhyloClustering [2e4ec7c6-185f-4bfd-8419-ce336ea983f6] to "/home/pkgeval/.julia/compiled/v1.12/PhyloClustering/jl_t8UB9C". ERROR: LoadError: FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:54 [2] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:255 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:252 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:129 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/screen.jl:311 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:382 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:466 [13] colorbuffer @ ~/.julia/packages/Makie/VRavR/src/display.jl:457 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:457 [15] top-level scope @ ~/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [21] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:36 [22] include(mod::Module, _path::String) @ Base ./Base.jl:305 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:2991 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [27] include_string @ ./loading.jl:2847 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [29] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:3 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.12/CairoMakie/jl_LRn3CX". Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3278 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2647 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114 [7] #invokelatest_gr#232 @ ./reflection.jl:1282 [inlined] [8] invokelatest_gr @ ./reflection.jl:1274 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3849 [10] maybe_cachefile_lock @ ./loading.jl:3846 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2633 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2461 [13] macro expansion @ ./loading.jl:2389 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2354 [16] require(into::Module, mod::Symbol) @ Base ./loading.jl:2330 [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [18] top-level scope @ ~/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:5 [19] include(mod::Module, _path::String) @ Base ./Base.jl:305 [20] 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:2991 [21] top-level scope @ stdin:5 [22] eval(m::Module, e::Any) @ Core ./boot.jl:489 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [24] include_string @ ./loading.jl:2847 [inlined] [25] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [26] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/helper.jl:1 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:3 in expression starting at stdin:5 CairoMakie Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.12/CairoMakie/jl_j6ZLd0". ERROR: LoadError: FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:54 [2] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:255 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:252 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:129 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/screen.jl:311 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:382 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:466 [13] colorbuffer @ ~/.julia/packages/Makie/VRavR/src/display.jl:457 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:457 [15] top-level scope @ ~/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [21] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:36 [22] include(mod::Module, _path::String) @ Base ./Base.jl:305 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:2991 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [27] include_string @ ./loading.jl:2847 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [29] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:3 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:1 in expression starting at stdin:5 in expression starting at /PkgEval.jl/scripts/precompile.jl:37 Precompilation failed after 1754.39s ################################################################################ # Testing # Testing PhyloClustering Status `/tmp/jl_YkBpYC/Project.toml` ⌅ [13f3f980] CairoMakie v0.11.9 [aaaa29a8] Clustering v0.15.8 [861a8166] Combinatorics v1.0.3 [b4f34e82] Distances v0.10.12 [59287772] Formatting v0.4.3 [cc18c42c] GaussianMixtures v0.3.13 [6f286f6a] MultivariateStats v0.10.3 [42b8e9d4] ParallelKMeans v1.1.0 [2e4ec7c6] PhyloClustering v0.2.0 ⌅ [33ad39ac] PhyloNetworks v0.16.4 [295af30f] Revise v3.8.0 [860ef19b] StableRNGs v1.0.3 ⌅ [2913bbd2] StatsBase v0.33.21 [fd094767] Suppressor v0.2.8 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_YkBpYC/Manifest.toml` [47edcb42] ADTypes v1.15.0 [621f4979] AbstractFFTs v1.5.0 [398f06c4] AbstractLattices v0.3.1 [1520ce14] AbstractTrees v0.4.5 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [27a7e980] Animations v0.4.2 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.19.0 [67c07d97] Automa v1.1.0 [13072b0f] AxisAlgorithms v1.1.0 [39de3d68] AxisArrays v0.4.7 [18cc8868] BaseDirs v1.3.1 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.2 [3c28c6f8] BioSymbols v5.2.0 [fa961155] CEnum v0.5.0 [96374032] CRlibm v1.0.2 [336ed68f] CSV v0.10.15 [159f3aea] Cairo v1.1.1 ⌅ [13f3f980] CairoMakie v0.11.9 [d360d2e6] ChainRulesCore v1.25.2 [aaaa29a8] Clustering v0.15.8 [da1fd8a2] CodeTracking v1.3.9 [944b1d66] CodecZlib v0.7.8 [a2cac450] ColorBrewer v0.4.1 [35d6a980] ColorSchemes v3.30.0 ⌅ [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 v4.17.0 [807dbc54] Compiler v0.1.1 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 ⌅ [927a84f5] DelaunayTriangulation v0.8.12 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [a0c0ee7d] DifferentiationInterface v0.7.2 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [4e289a0a] EnumX v1.0.5 [429591f6] ExactPredicates v2.2.8 [411431e0] Extents v0.1.6 [c2308a5c] FASTX v2.1.7 [7a1cc6ca] FFTW v1.9.0 [5789e2e9] FileIO v1.17.0 ⌅ [8fc22ac5] FilePaths v0.8.3 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [6a86dc24] FiniteDiff v2.27.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [59287772] Formatting v0.4.3 [f6369f11] ForwardDiff v1.0.1 [b38be410] FreeType v4.1.1 [663a7486] FreeTypeAbstraction v0.10.8 ⌅ [d9f16b24] Functors v0.4.12 [38e38edf] GLM v1.9.0 [cc18c42c] GaussianMixtures v0.3.13 [68eda718] GeoFormatTypes v0.4.4 ⌃ [cf35fbd7] GeoInterface v1.4.1 ⌅ [5c1252a2] GeometryBasics v0.4.11 [a2bd30eb] Graphics v1.1.3 ⌅ [3955a311] GridLayoutBase v0.10.2 [42e2da0e] Grisu v1.0.2 [076d061b] HashArrayMappedTries v0.2.0 [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 [842dd82b] InlineStrings v1.4.4 [18e54dd8] IntegerMathUtils v0.1.3 [a98d9a8b] Interpolations v0.16.1 [d1acc4aa] IntervalArithmetic v0.22.36 [8197267c] IntervalSets v0.7.11 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [f1662d9f] Isoband v0.1.1 [c8e1da08] IterTools v1.10.0 [82899510] IteratorInterfaceExtensions v1.0.0 [033835bb] JLD2 v0.5.15 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b835a17e] JpegTurbo v0.1.6 [aa1ae85d] JuliaInterpreter v0.10.3 [5ab0869b] KernelDensity v0.6.10 [b964fa9f] LaTeXStrings v1.4.0 [8cdb02fc] LazyModules v0.3.1 [9c8b4983] LightXML v0.9.2 [d3d80556] LineSearches v7.4.0 [9b3f67b0] LinearAlgebraX v0.2.10 [2ab3a3ac] LogExpFunctions v0.3.29 [6f1432cf] LoweredCodeUtils v3.4.1 [e80e1ace] MLJModelInterface v1.11.1 [1914dd2f] MacroTools v0.5.16 ⌅ [ee78f7c6] Makie v0.20.8 ⌅ [20f20a25] MakieCore v0.7.3 [dbb5928d] MappedArrays v0.4.2 ⌅ [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 [6f286f6a] MultivariateStats v0.10.3 [d41bc354] NLSolversBase v7.10.0 [76087f3c] NLopt v1.2.0 [77ba4419] NaNMath v1.1.3 [b8a86587] NearestNeighbors v0.4.22 [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 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [f57f5aa1] PNGFiles v0.4.4 [19eb6ba3] Packing v0.5.1 [5432bcbf] PaddedViews v0.5.12 [42b8e9d4] ParallelKMeans v1.1.0 [d96e819e] Parameters v0.12.3 [69de0a69] Parsers v2.8.3 [2ae35dd2] Permutations v0.4.23 [2e4ec7c6] PhyloClustering v0.2.0 ⌅ [33ad39ac] PhyloNetworks v0.16.4 [3bbf5609] PikaParser v0.6.1 [eebad327] PkgVersion v0.3.3 [995b91a9] PlotUtils v1.4.3 [647866c9] PolygonOps v0.1.2 ⌃ [f27b6e38] Polynomials v4.0.21 [2dfb63ee] PooledArrays v1.4.3 [85a6dd25] PositiveFactorizations v0.2.4 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [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 [189a3867] Reexport v1.2.2 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.1 [295af30f] Revise v3.8.0 [286e9d63] RingLists v0.2.9 [79098fc4] Rmath v0.8.0 [5eaf0fd0] RoundingEmulator v0.2.1 [fdea26ae] SIMD v3.7.1 [30f210dd] ScientificTypesBase v3.0.0 [6e75b9c4] ScikitLearnBase v0.5.0 [7e506255] ScopedValues v1.3.0 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.8 [efcf1570] Setfield v1.1.2 ⌅ [65257c39] ShaderAbstractions v0.4.1 [1277b4bf] ShiftedArrays v2.0.0 [992d4aef] Showoff v1.0.3 [73760f76] SignedDistanceFields v0.4.0 [55797a34] SimpleGraphs v0.8.6 [ec83eff0] SimplePartitions v0.3.3 [cc47b68c] SimplePolynomials v0.2.18 [a6525b86] SimpleRandom v0.3.2 [699a6c99] SimpleTraits v0.9.4 [45858cf5] Sixel v0.1.5 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 ⌅ [c5dd0088] StableHashTraits v1.3.4 [860ef19b] StableRNGs v1.0.3 [cae243ae] StackViews v0.1.2 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [64bff920] StatisticalTraits v3.5.0 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 [3eaba693] StatsModels v0.7.4 [892a3eda] StringManipulation v0.4.1 [354b36f9] StringViews v1.3.4 ⌅ [09ab397b] StructArrays v0.6.21 [856f2bd8] StructTypes v1.11.0 [fd094767] Suppressor v0.2.8 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [62fd8b95] TensorCore v0.1.1 [731e570b] TiffImages v0.11.4 [3bb67fe8] TranscodingStreams v0.11.3 [981d1d27] TriplotBase v0.1.0 [9d95972d] TupleTools v1.6.0 [7200193e] Twiddle v1.1.2 [3a884ed6] UnPack v1.0.2 [1cfade01] UnicodeFun v0.4.1 [c4a57d5a] UnsafeArrays v1.0.8 [ecbed89c] WeakKeyIdDicts v0.1.0 [ea10d353] WeakRefStrings v1.4.2 [e3aaa7dc] WebP v0.1.3 [efce3f68] WoodburyMatrices v1.0.0 [76eceee3] WorkerUtilities v1.6.1 ⌅ [68821587] Arpack_jll v3.5.1+1 [6e34b625] Bzip2_jll v1.0.9+0 [4e9b3aee] CRlibm_jll v1.0.1+0 [83423d85] Cairo_jll v1.18.5+0 [5ae413db] EarCut_jll v2.2.4+0 [2e619515] Expat_jll v2.6.5+0 [b22a6f82] FFMPEG_jll v7.1.0+0 [f5851436] FFTW_jll v3.3.11+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [b0724c58] GettextRuntime_jll v0.22.4+0 [59f7168a] Giflib_jll v5.2.3+0 [7746bdde] Glib_jll v2.84.3+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.1+0 [905a6f67] Imath_jll v3.1.11+0 [1d5cc7b8] IntelOpenMP_jll v2025.0.4+0 [aacddb02] JpegTurbo_jll v3.1.1+0 [c1c5ebd0] LAME_jll v3.100.3+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [e9f186c6] Libffi_jll v3.4.7+0 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [89763e89] Libtiff_jll v4.7.1+0 [38a345b3] Libuuid_jll v2.41.0+0 [856f044c] MKL_jll v2025.0.1+1 [079eb43e] NLopt_jll v2.10.0+0 [e7412a2a] Ogg_jll v1.3.6+0 [6cdc7f73] OpenBLASConsistentFPCSR_jll v0.3.29+0 [18a262bb] OpenEXR_jll v3.2.4+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [91d4177d] Opus_jll v1.5.2+0 [36c8627f] Pango_jll v1.56.3+0 ⌅ [30392449] Pixman_jll v0.44.2+0 [f50d1b31] Rmath_jll v0.5.1+0 [02c8fc9c] XML2_jll v2.14.1+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 [3161d3a3] Zstd_jll v1.5.7+1 [9a68df92] isoband_jll v0.2.3+0 [a4ae2306] libaom_jll v3.11.0+0 ⌅ [0ac62f75] libass_jll v0.15.2+0 [f638f0a6] libfdk_aac_jll v2.0.4+0 [b53b4c65] libpng_jll v1.6.50+0 [075b6546] libsixel_jll v1.10.5+0 [f27f6e37] libvorbis_jll v1.3.8+0 [c5f90fcd] libwebp_jll v1.6.0+0 [1317d2d5] oneTBB_jll v2022.0.0+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 [8bf52ea8] CRC32c v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [4af54fe1] LazyArtifacts v1.11.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [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 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [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 [deac9b47] LibCURL_jll v8.11.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.8.3+2 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.64.0+1 [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... Precompiling packages... ✗ CairoMakie Info Given PhyloClustering was explicitly requested, output will be shown live  WARNING: importing deprecated binding Makie.Combined into CairoMakie. , use Plot instead. WARNING: importing deprecated binding Makie.ContinuousSurface into CairoMakie. , use VertexGrid instead. WARNING: importing deprecated binding Makie.DiscreteSurface into CairoMakie. , use CellGrid instead. ERROR: LoadError: FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace:  [1] getproperty(x::Core.TypeName, f::Symbol)  @ Base ./Base_compiler.jl:54  [2] func2string(func::typeof(MakieCore.linesegments))  @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:9  [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}})  @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:21  [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})  @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:22  [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing)  @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:255  [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol)  @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:252  [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments})  @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/primitives.jl:6  [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}})  @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:129  [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene)  @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:51  [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE})  @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/screen.jl:311  [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat)  @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:382  [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{})  @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:466  [13] colorbuffer  @ ~/.julia/packages/Makie/VRavR/src/display.jl:457 [inlined]  [14] colorbuffer(fig::Makie.FigureAxisPlot)  @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:457  [15] top-level scope  @ ~/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:6  [16] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:306  [17] top-level scope  @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:11  [18] macro expansion  @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined]  [19] macro expansion  @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:15 [inlined]  [20] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:306  [21] top-level scope  @ ~/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:36  [22] include(mod::Module, _path::String)  @ Base ./Base.jl:305  [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)  @ Base ./loading.jl:2991  [24] top-level scope  @ stdin:5  [25] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2837  [27] include_string  @ ./loading.jl:2847 [inlined]  [28] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:319  [29] _start()  @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:3 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.12/CairoMakie/jl_oPaFgS". Stacktrace:  [1] error(s::String)  @ Base ./error.jl:44  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing)  @ Base ./loading.jl:3278  [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})()  @ Base ./loading.jl:2647  [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93  [5] #mkpidlock#7  @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined]  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})  @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114  [7] #invokelatest_gr#232  @ ./reflection.jl:1282 [inlined]  [8] invokelatest_gr  @ ./reflection.jl:1274 [inlined]  [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)  @ Base ./loading.jl:3849  [10] maybe_cachefile_lock  @ ./loading.jl:3846 [inlined]  [11] __require_prelocked(pkg::Base.PkgId, env::String)  @ Base ./loading.jl:2633  [12] _require_prelocked(uuidkey::Base.PkgId, env::String)  @ Base ./loading.jl:2461  [13] macro expansion  @ ./loading.jl:2389 [inlined]  [14] macro expansion  @ ./lock.jl:376 [inlined]  [15] __require(into::Module, mod::Symbol)  @ Base ./loading.jl:2354  [16] require(into::Module, mod::Symbol)  @ Base ./loading.jl:2330  [17] include(mapexpr::Function, mod::Module, _path::String)  @ Base ./Base.jl:306  [18] top-level scope  @ ~/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:5  [19] include(mod::Module, _path::String)  @ Base ./Base.jl:305  [20] 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:2991  [21] top-level scope  @ stdin:5  [22] eval(m::Module, e::Any)  @ Core ./boot.jl:489  [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String)  @ Base ./loading.jl:2837  [24] include_string  @ ./loading.jl:2847 [inlined]  [25] exec_options(opts::Base.JLOptions)  @ Base ./client.jl:319  [26] _start()  @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/helper.jl:1 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:3 in expression starting at stdin:5 ✗ PhyloClustering 0 dependencies successfully precompiled in 203 seconds. 367 already precompiled. ERROR: LoadError: The following 2 direct dependencies failed to precompile: PhyloClustering Failed to precompile PhyloClustering [2e4ec7c6-185f-4bfd-8419-ce336ea983f6] to "/home/pkgeval/.julia/compiled/v1.12/PhyloClustering/jl_ro737l". WARNING: importing deprecated binding Makie.Combined into CairoMakie. , use Plot instead. WARNING: importing deprecated binding Makie.ContinuousSurface into CairoMakie. , use VertexGrid instead. WARNING: importing deprecated binding Makie.DiscreteSurface into CairoMakie. , use CellGrid instead. ERROR: LoadError: FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:54 [2] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:255 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:252 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:129 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/screen.jl:311 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:382 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:466 [13] colorbuffer @ ~/.julia/packages/Makie/VRavR/src/display.jl:457 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:457 [15] top-level scope @ ~/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [21] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:36 [22] include(mod::Module, _path::String) @ Base ./Base.jl:305 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String) @ Base ./loading.jl:2991 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [27] include_string @ ./loading.jl:2847 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [29] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:3 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:1 in expression starting at stdin:5 ERROR: LoadError: Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.12/CairoMakie/jl_oPaFgS". Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, loadable_exts::Nothing) @ Base ./loading.jl:3278 [3] (::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId})() @ Base ./loading.jl:2647 [4] mkpidlock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:93 [5] #mkpidlock#7 @ /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:88 [inlined] [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64}) @ FileWatching.Pidfile /opt/julia/share/julia/stdlib/v1.12/FileWatching/src/pidfile.jl:114 [7] #invokelatest_gr#232 @ ./reflection.jl:1282 [inlined] [8] invokelatest_gr @ ./reflection.jl:1274 [inlined] [9] maybe_cachefile_lock(f::Base.var"#__require_prelocked##0#__require_prelocked##1"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64) @ Base ./loading.jl:3849 [10] maybe_cachefile_lock @ ./loading.jl:3846 [inlined] [11] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2633 [12] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2461 [13] macro expansion @ ./loading.jl:2389 [inlined] [14] macro expansion @ ./lock.jl:376 [inlined] [15] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2354 [16] require(into::Module, mod::Symbol) @ Base ./loading.jl:2330 [17] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [18] top-level scope @ ~/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:5 [19] include(mod::Module, _path::String) @ Base ./Base.jl:305 [20] 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:2991 [21] top-level scope @ stdin:5 [22] eval(m::Module, e::Any) @ Core ./boot.jl:489 [23] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [24] include_string @ ./loading.jl:2847 [inlined] [25] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [26] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/helper.jl:1 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/src/PhyloClustering.jl:3 in expression starting at stdin:5 CairoMakie Failed to precompile CairoMakie [13f3f980-e62b-5c42-98c6-ff1f3baf88f0] to "/home/pkgeval/.julia/compiled/v1.12/CairoMakie/jl_b9ZCia". WARNING: importing deprecated binding Makie.Combined into CairoMakie. , use Plot instead. WARNING: importing deprecated binding Makie.ContinuousSurface into CairoMakie. , use VertexGrid instead. WARNING: importing deprecated binding Makie.DiscreteSurface into CairoMakie. , use CellGrid instead. ERROR: LoadError: FieldError: type Core.TypeName has no field `mt`, available fields: `name`, `module`, `singletonname`, `names`, `atomicfields`, `constfields`, `wrapper`, `Typeofwrapper`, `cache`, `linearcache`, `partial`, `hash`, `max_args`, `n_uninitialized`, `flags`, `cache_entry_count`, `max_methods`, `constprop_heuristic` Stacktrace: [1] getproperty(x::Core.TypeName, f::Symbol) @ Base ./Base_compiler.jl:54 [2] func2string(func::typeof(MakieCore.linesegments)) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:9 [3] plotkey(::Type{MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:21 [4] plotkey(::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/recipes.jl:22 [5] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol, default::Nothing) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:255 [6] get_attribute(dict::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}, key::Symbol) @ MakieCore ~/.julia/packages/MakieCore/UAwps/src/attributes.jl:252 [7] draw_atomic(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::Union{MakieCore.Lines, MakieCore.LineSegments}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/primitives.jl:6 [8] draw_plot(scene::Makie.Scene, screen::CairoMakie.Screen{CairoMakie.IMAGE}, primitive::MakieCore.LineSegments{Tuple{Vector{GeometryBasics.Point{2, Float32}}}}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:129 [9] cairo_draw(screen::CairoMakie.Screen{CairoMakie.IMAGE}, scene::Makie.Scene) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/infrastructure.jl:51 [10] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}) @ CairoMakie ~/.julia/packages/CairoMakie/W0SZK/src/screen.jl:311 [11] colorbuffer(screen::CairoMakie.Screen{CairoMakie.IMAGE}, format::Makie.ImageStorageFormat) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:382 [12] colorbuffer(fig::Makie.FigureAxisPlot, format::Makie.ImageStorageFormat; update::Bool, backend::Module, screen_config::@Kwargs{}) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:466 [13] colorbuffer @ ~/.julia/packages/Makie/VRavR/src/display.jl:457 [inlined] [14] colorbuffer(fig::Makie.FigureAxisPlot) @ Makie ~/.julia/packages/Makie/VRavR/src/display.jl:457 [15] top-level scope @ ~/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:6 [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [17] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:11 [18] macro expansion @ ~/.julia/packages/PrecompileTools/Z8SWe/src/workloads.jl:73 [inlined] [19] macro expansion @ ~/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:15 [inlined] [20] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:306 [21] top-level scope @ ~/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:36 [22] include(mod::Module, _path::String) @ Base ./Base.jl:305 [23] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::Nothing) @ Base ./loading.jl:2991 [24] top-level scope @ stdin:5 [25] eval(m::Module, e::Any) @ Core ./boot.jl:489 [26] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2837 [27] include_string @ ./loading.jl:2847 [inlined] [28] exec_options(opts::Base.JLOptions) @ Base ./client.jl:319 [29] _start() @ Base ./client.jl:554 in expression starting at /home/pkgeval/.julia/packages/Makie/VRavR/precompile/shared-precompile.jl:3 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/precompiles.jl:10 in expression starting at /home/pkgeval/.julia/packages/CairoMakie/W0SZK/src/CairoMakie.jl:1 in expression starting at stdin:5 in expression starting at /home/pkgeval/.julia/packages/PhyloClustering/7nfrG/test/runtests.jl:1 Testing failed after 213.34s ERROR: LoadError: Package PhyloClustering errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.12/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/v1.12/Pkg/src/Operations.jl:2458 [3] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [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/v1.12/Pkg/src/API.jl:511 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:305 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:321 [12] _start() @ Base ./client.jl:554 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 2046.56s: package fails to precompile