Package evaluation of MCPhylo on Julia 1.12.0-rc1 (228edd6610*) started at 2025-07-15T05:38:10.014 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.09s ################################################################################ # Installation # Installing MCPhylo... Resolving package versions... Installed x265_jll ───────────────────────── v3.5.0+0 Installed GR_jll ─────────────────────────── v0.73.17+0 Installed JpegTurbo_jll ──────────────────── v3.1.1+0 Installed Libmount_jll ───────────────────── v2.41.0+0 Installed libfdk_aac_jll ─────────────────── v2.0.4+0 Installed libdecor_jll ───────────────────── v0.2.2+0 Installed HypergeometricFunctions ────────── v0.3.28 Installed OffsetArrays ───────────────────── v1.17.0 Installed LERC_jll ───────────────────────── v4.0.1+0 Installed Opus_jll ───────────────────────── v1.5.2+0 Installed FFTW ───────────────────────────── v1.9.0 Installed StatsFuns ──────────────────────── v1.5.0 Installed LoggingExtras ──────────────────── v1.1.0 Installed Accessors ──────────────────────── v0.1.42 Installed Preferences ────────────────────── v1.4.3 Installed Xorg_xkbcomp_jll ───────────────── v1.4.7+0 Installed RelocatableFolders ─────────────── v1.0.1 Installed Measures ───────────────────────── v0.3.2 Installed PDMats ─────────────────────────── v0.11.35 Installed Unitful ────────────────────────── v1.23.1 Installed Contour ────────────────────────── v0.6.3 Installed ConcurrentUtilities ────────────── v2.5.0 Installed ProgressMeter ──────────────────── v1.10.4 Installed StaticArrays ───────────────────── v1.9.13 Installed NearestNeighbors ───────────────── v0.4.22 Installed Roots ──────────────────────────── v2.2.8 Installed Xorg_xcb_util_wm_jll ───────────── v0.4.2+0 Installed Grisu ──────────────────────────── v1.0.2 Installed Xorg_xcb_util_image_jll ────────── v0.4.1+0 Installed PlotUtils ──────────────────────── v1.4.3 Installed RecipesPipeline ────────────────── v0.6.12 Installed ScopedValues ───────────────────── v1.3.0 Installed CEnum ──────────────────────────── v0.5.0 Installed OpenSSL ────────────────────────── v1.5.0 Installed DelimitedFiles ─────────────────── v1.9.1 Installed Xorg_libSM_jll ─────────────────── v1.2.6+0 Installed HTTP ───────────────────────────── v1.10.17 Installed FunctionWrappers ───────────────── v1.1.3 Installed Xorg_xcb_util_jll ──────────────── v0.4.1+0 Installed Cairo_jll ──────────────────────── v1.18.5+0 Installed Fontconfig_jll ─────────────────── v2.16.0+0 Installed Statistics ─────────────────────── v1.11.1 Installed GPUArrays ──────────────────────── v11.2.3 Installed IntelOpenMP_jll ────────────────── v2025.0.4+0 Installed Xorg_libxkbfile_jll ────────────── v1.1.3+0 Installed Xorg_libXinerama_jll ───────────── v1.1.6+0 Installed ZygoteRules ────────────────────── v0.2.7 Installed Static ─────────────────────────── v1.2.0 Installed SLEEFPirates ───────────────────── v0.6.43 Installed EpollShim_jll ──────────────────── v0.0.20230411+1 Installed Xorg_libXau_jll ────────────────── v1.0.13+0 Installed Distances ──────────────────────── v0.10.12 Installed Missings ───────────────────────── v1.2.0 Installed FiniteDiff ─────────────────────── v2.27.0 Installed FFMPEG ─────────────────────────── v0.4.2 Installed RealDot ────────────────────────── v0.1.0 Installed SIMDTypes ──────────────────────── v0.1.0 Installed Showoff ────────────────────────── v1.0.3 Installed IRTools ────────────────────────── v0.4.15 Installed IrrationalConstants ────────────── v0.2.4 Installed Functors ───────────────────────── v0.3.0 Installed ColorSchemes ───────────────────── v3.30.0 Installed ArnoldiMethod ──────────────────── v0.1.0 Installed Bijectors ──────────────────────── v0.10.8 Installed JSON ───────────────────────────── v0.21.4 Installed Pango_jll ──────────────────────── v1.56.3+0 Installed GR ─────────────────────────────── v0.73.17 Installed PtrArrays ──────────────────────── v1.3.0 Installed LLVM ───────────────────────────── v9.4.2 Installed CpuId ──────────────────────────── v0.3.1 Installed Xorg_xcb_util_keysyms_jll ──────── v0.4.1+0 Installed xkbcommon_jll ──────────────────── v1.9.2+0 Installed XZ_jll ─────────────────────────── v5.8.1+0 Installed HarfBuzz_jll ───────────────────── v8.5.1+0 Installed SpecialFunctions ───────────────── v2.5.1 Installed SimpleBufferStream ─────────────── v1.2.0 Installed SentinelArrays ─────────────────── v1.4.8 Installed Clustering ─────────────────────── v0.15.8 Installed Bzip2_jll ──────────────────────── v1.0.9+0 Installed PlotThemes ─────────────────────── v3.3.0 Installed LZO_jll ────────────────────────── v2.10.3+0 Installed StaticArraysCore ───────────────── v1.4.3 Installed IfElse ─────────────────────────── v0.1.1 Installed NaNMath ────────────────────────── v1.1.3 Installed ThreadingUtilities ─────────────── v0.5.5 Installed TranscodingStreams ─────────────── v0.11.3 Installed Zygote ─────────────────────────── v0.6.77 Installed fzf_jll ────────────────────────── v0.61.1+0 Installed FriBidi_jll ────────────────────── v1.0.17+0 Installed UnicodeFun ─────────────────────── v0.4.1 Installed ManualMemory ───────────────────── v0.1.8 Installed GLFW_jll ───────────────────────── v3.4.0+2 Installed Rmath_jll ──────────────────────── v0.5.1+0 Installed Ratios ─────────────────────────── v0.4.5 Installed MbedTLS ────────────────────────── v1.1.9 Installed x264_jll ───────────────────────── v2021.5.5+0 Installed MappedArrays ───────────────────── v0.4.2 Installed JLFzf ──────────────────────────── v0.1.11 Installed FreeType2_jll ──────────────────── v2.13.4+0 Installed CommonSubexpressions ───────────── v0.3.1 Installed DataStructures ─────────────────── v0.18.22 Installed Colors ─────────────────────────── v0.13.1 Installed ChainRules ─────────────────────── v1.72.5 Installed StatsAPI ───────────────────────── v1.7.1 Installed CommonWorldInvalidations ───────── v1.0.0 Installed Compat ─────────────────────────── v4.17.0 Installed CodecZlib ──────────────────────── v0.7.8 Installed libpng_jll ─────────────────────── v1.6.50+0 Installed StaticArrayInterface ───────────── v1.8.0 Installed Xorg_libxcb_jll ────────────────── v1.17.1+0 Installed StatsBase ──────────────────────── v0.33.21 Installed ExceptionUnwrapping ────────────── v0.1.11 Installed mtdev_jll ──────────────────────── v1.1.7+0 Installed libaom_jll ─────────────────────── v3.11.0+0 Installed Dbus_jll ───────────────────────── v1.16.2+0 Installed Scratch ────────────────────────── v1.3.0 Installed StatsPlots ─────────────────────── v0.15.7 Installed ColorTypes ─────────────────────── v0.12.1 Installed oneTBB_jll ─────────────────────── v2022.0.0+0 Installed BitTwiddlingConvenienceFunctions ─ v0.1.6 Installed eudev_jll ──────────────────────── v3.2.14+0 Installed DiffRules ──────────────────────── v1.15.1 Installed MCPhylo ────────────────────────── v0.9.5 Installed Plots ──────────────────────────── v1.40.16 Installed LayoutPointers ─────────────────── v0.1.17 Installed Xorg_libXext_jll ───────────────── v1.3.7+0 Installed ArgCheck ───────────────────────── v2.5.0 Installed Zstd_jll ───────────────────────── v1.5.7+1 Installed TensorCore ─────────────────────── v0.1.1 Installed TableTraits ────────────────────── v1.0.1 Installed Xorg_xcb_util_cursor_jll ───────── v0.1.5+0 Installed Expat_jll ──────────────────────── v2.6.5+0 Installed Inflate ────────────────────────── v0.1.5 Installed HashArrayMappedTries ───────────── v0.2.0 Installed MKL_jll ────────────────────────── v2025.0.1+1 Installed Parsers ────────────────────────── v2.8.3 Installed Setfield ───────────────────────── v1.1.2 Installed Libtiff_jll ────────────────────── v4.7.1+0 Installed Format ─────────────────────────── v1.3.7 Installed LoopVectorization ──────────────── v0.12.172 Installed DiffResults ────────────────────── v1.1.0 Installed DataValueInterfaces ────────────── v1.0.0 Installed JLLWrappers ────────────────────── v1.7.0 Installed ColorVectorSpace ───────────────── v0.11.0 Installed ConstructionBase ───────────────── v1.6.0 Installed AbstractFFTs ───────────────────── v1.5.0 Installed Libffi_jll ─────────────────────── v3.4.7+0 Installed LLVMExtra_jll ──────────────────── v0.0.37+2 Installed libevdev_jll ───────────────────── v1.13.4+0 Installed Xorg_libXrender_jll ────────────── v0.9.12+0 Installed AbstractTrees ──────────────────── v0.4.5 Installed OrderedCollections ─────────────── v1.8.1 Installed libinput_jll ───────────────────── v1.28.1+0 Installed Xorg_libXi_jll ─────────────────── v1.8.3+0 Installed Ogg_jll ────────────────────────── v1.3.6+0 Installed KernelDensity ──────────────────── v0.6.10 Installed PolyesterWeave ─────────────────── v0.2.2 Installed Vulkan_Loader_jll ──────────────── v1.3.243+0 Installed ChainRulesCore ─────────────────── v1.25.2 Installed Interpolations ─────────────────── v0.15.1 Installed Qt6ShaderTools_jll ─────────────── v6.8.2+1 Installed Reexport ───────────────────────── v1.2.2 Installed Qt6Declarative_jll ─────────────── v6.8.2+1 Installed ArrayInterface ─────────────────── v7.19.0 Installed AliasTables ────────────────────── v1.1.3 Installed CloseOpenIntervals ─────────────── v0.1.13 Installed LogExpFunctions ────────────────── v0.3.29 Installed KernelAbstractions ─────────────── v0.9.37 Installed CompositionsBase ───────────────── v0.1.2 Installed MbedTLS_jll ────────────────────── v2.28.6+2 Installed FFTW_jll ───────────────────────── v3.3.11+0 Installed UnPack ─────────────────────────── v1.0.2 Installed UnsafeAtomics ──────────────────── v0.3.0 Installed MacroTools ─────────────────────── v0.5.16 Installed Xorg_libXcursor_jll ────────────── v1.2.4+0 Installed SparseInverseSubset ────────────── v0.1.2 Installed CommonSolve ────────────────────── v0.2.4 Installed InverseFunctions ───────────────── v0.1.17 Installed Libuuid_jll ────────────────────── v2.41.0+0 Installed SimpleTraits ───────────────────── v0.9.4 Installed MCPhyloTree ────────────────────── v1.1.7 Installed OpenSpecFun_jll ────────────────── v0.5.6+0 Installed Atomix ─────────────────────────── v1.1.1 Installed GPUArraysCore ──────────────────── v0.2.0 Installed Xorg_xcb_util_renderutil_jll ───── v0.3.10+0 Installed Xorg_libICE_jll ────────────────── v1.1.2+0 Installed DocStringExtensions ────────────── v0.9.5 Installed Pixman_jll ─────────────────────── v0.44.2+0 Installed Graphite2_jll ──────────────────── v1.3.15+0 Installed libass_jll ─────────────────────── v0.15.2+0 Installed StableRNGs ─────────────────────── v1.0.3 Installed Adapt ──────────────────────────── v4.3.0 Installed Widgets ────────────────────────── v0.6.7 Installed Wayland_jll ────────────────────── v1.24.0+0 Installed MultivariateStats ──────────────── v0.10.3 Installed Rmath ──────────────────────────── v0.8.0 Installed Arpack_jll ─────────────────────── v3.5.1+1 Installed Latexify ───────────────────────── v0.16.8 Installed VectorizationBase ──────────────── v0.21.71 Installed Xorg_xtrans_jll ────────────────── v1.6.0+0 Installed LightGraphs ────────────────────── v1.3.5 Installed FFMPEG_jll ─────────────────────── v4.4.4+1 Installed BitFlags ───────────────────────── v0.1.9 Installed CPUSummary ─────────────────────── v0.2.6 Installed Xorg_xkeyboard_config_jll ──────── v2.44.0+0 Installed LLVMOpenMP_jll ─────────────────── v18.1.8+0 Installed DataAPI ────────────────────────── v1.16.0 Installed Tables ─────────────────────────── v1.12.1 Installed FixedPointNumbers ──────────────── v0.8.5 Installed Xorg_libXrandr_jll ─────────────── v1.5.5+0 Installed RecipesBase ────────────────────── v1.3.4 Installed LAME_jll ───────────────────────── v3.100.3+0 Installed Xorg_libXfixes_jll ─────────────── v6.0.1+0 Installed Qt6Wayland_jll ─────────────────── v6.8.2+1 Installed PrecompileTools ────────────────── v1.3.2 Installed IteratorInterfaceExtensions ────── v1.0.0 Installed Libiconv_jll ───────────────────── v1.18.0+0 Installed Qt6Base_jll ────────────────────── v6.8.2+1 Installed GettextRuntime_jll ─────────────── v0.22.4+0 Installed StructArrays ───────────────────── v0.7.1 Installed HostCPUFeatures ────────────────── v0.1.17 Installed URIs ───────────────────────────── v1.6.1 Installed TableOperations ────────────────── v1.2.0 Installed ReverseDiff ────────────────────── v1.16.1 Installed LaTeXStrings ───────────────────── v1.4.0 Installed libvorbis_jll ──────────────────── v1.3.8+0 Installed Libglvnd_jll ───────────────────── v1.7.1+1 Installed Glib_jll ───────────────────────── v2.84.3+0 Installed AxisAlgorithms ─────────────────── v1.1.0 Installed FillArrays ─────────────────────── v1.13.0 Installed QuadGK ─────────────────────────── v2.11.2 Installed Arpack ─────────────────────────── v0.5.4 Installed ForwardDiff ────────────────────── v0.10.38 Installed Xorg_libXdmcp_jll ──────────────── v1.1.6+0 Installed Xorg_libX11_jll ────────────────── v1.8.12+0 Installed Unzip ──────────────────────────── v0.2.0 Installed Requires ───────────────────────── v1.3.1 Installed Observables ────────────────────── v0.5.5 Installed WoodburyMatrices ───────────────── v1.0.0 Installed UnitfulLatexify ────────────────── v1.7.0 Installed ChangesOfVariables ─────────────── v0.1.10 Installed SortingAlgorithms ──────────────── v1.2.1 Installed Distributions ──────────────────── v0.25.120 Installing 81 artifacts Installed artifact Xorg_xcb_util_renderutil 32.1 KiB Installed artifact Arpack 147.2 KiB Installed artifact Wayland 390.6 KiB Installed artifact libvorbis 271.0 KiB Installed artifact Dbus 489.8 KiB Installed artifact Xorg_xtrans 48.2 KiB Installed artifact Vulkan_Loader 177.3 KiB Installed artifact FreeType2 1.5 MiB Installed artifact Xorg_xcb_util_keysyms 17.8 KiB Installed artifact Pango 1.1 MiB Installed artifact GLFW 180.1 KiB Installed artifact LLVMOpenMP 661.6 KiB Installed artifact Cairo 2.2 MiB Installed artifact Xorg_libXext 699.9 KiB Installed artifact fzf 3.3 MiB Installed artifact Libglvnd 833.5 KiB Installed artifact Ogg 250.3 KiB Installed artifact Qt6Wayland 2.2 MiB Installed artifact mtdev 79.6 KiB Installed artifact Xorg_libXi 1.6 MiB Installed artifact Rmath 121.9 KiB Installed artifact Xorg_libXinerama 50.1 KiB Installed artifact XZ 1.5 MiB Installed artifact Xorg_libXcursor 227.1 KiB Installed artifact x265 1.1 MiB Installed artifact libevdev 117.1 KiB Installed artifact Libtiff 3.2 MiB Installed artifact Xorg_libXrender 435.9 KiB Installed artifact x264 2.0 MiB Installed artifact Libffi 44.2 KiB Installed artifact Libuuid 3.5 MiB Installed artifact Qt6ShaderTools 2.1 MiB Installed artifact Xorg_libSM 164.1 KiB Installed artifact LZO 208.9 KiB Installed artifact Xorg_xkeyboard_config 537.5 KiB Installed artifact Xorg_libxkbfile 486.7 KiB Installed artifact Xorg_libXrandr 354.5 KiB Installed artifact Xorg_libXdmcp 67.7 KiB Installed artifact libpng 328.4 KiB Installed artifact FriBidi 78.9 KiB Installed artifact Xorg_libXau 36.6 KiB Installed artifact Xorg_libxcb 2.1 MiB Installed artifact JpegTurbo 1.6 MiB Installed artifact Xorg_xkbcomp 274.8 KiB Installed artifact Expat 271.4 KiB Installed artifact Xorg_xcb_util_image 54.3 KiB Installed artifact libfdk_aac 2.8 MiB Installed artifact Xorg_libXfixes 195.9 KiB Installed artifact Bzip2 503.5 KiB Installed artifact Xorg_libICE 384.9 KiB Installed artifact Xorg_xcb_util 39.5 KiB Installed artifact FFMPEG 10.6 MiB Installed artifact Libmount 6.4 MiB Installed artifact Zstd 646.0 KiB Installed artifact Xorg_xcb_util_wm 147.9 KiB Installed artifact OpenSpecFun 194.9 KiB Installed artifact Xorg_xcb_util_cursor 56.8 KiB Installed artifact Glib 7.7 MiB Installed artifact libdecor 44.1 KiB Installed artifact MbedTLS 2.1 MiB Installed artifact HarfBuzz 1.7 MiB Installed artifact Fontconfig 522.5 KiB Installed artifact oneTBB 435.6 KiB Installed artifact GettextRuntime 543.0 KiB Installed artifact libaom 6.4 MiB Installed artifact LERC 272.9 KiB Installed artifact libass 372.4 KiB Installed artifact xkbcommon 263.7 KiB Installed artifact Opus 925.5 KiB Installed artifact eudev 3.9 MiB Installed artifact Libiconv 1.9 MiB Installed artifact Graphite2 120.2 KiB Installed artifact Pixman 372.2 KiB Installed artifact libinput 1.0 MiB Installed artifact LAME 292.5 KiB Installed artifact LLVMExtra 2.8 MiB Installed artifact FFTW 2.2 MiB Installed artifact GR 16.2 MiB Installed artifact Qt6Base 20.6 MiB Installed artifact Xorg_libX11 13.9 MiB Installed artifact Qt6Declarative 21.6 MiB Updating `~/.julia/environments/v1.12/Project.toml` [af0ac7d2] + MCPhylo v0.9.5 Updating `~/.julia/environments/v1.12/Manifest.toml` [621f4979] + AbstractFFTs v1.5.0 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.42 [79e6a3ab] + Adapt v4.3.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 ⌅ [ec485272] + ArnoldiMethod v0.1.0 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.19.0 [a9b6321e] + Atomix v1.1.1 [13072b0f] + AxisAlgorithms v1.1.0 ⌅ [76274a88] + Bijectors v0.10.8 [d1d4a3ce] + BitFlags v0.1.9 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] + CEnum v0.5.0 [2a0fbf3d] + CPUSummary v0.2.6 [082447d4] + ChainRules v1.72.5 [d360d2e6] + ChainRulesCore v1.25.2 [9e997f8a] + ChangesOfVariables v0.1.10 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 [35d6a980] + ColorSchemes v3.30.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.4 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.17.0 [a33af91c] + CompositionsBase v0.1.2 [f0e56b4a] + ConcurrentUtilities v2.5.0 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [adafc99b] + CpuId v0.3.1 [9a962f9c] + DataAPI v1.16.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [8bb1440f] + DelimitedFiles v1.9.1 [163ba53b] + DiffResults v1.1.0 [b552c78f] + DiffRules v1.15.1 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [c87230d0] + FFMPEG v0.4.2 [7a1cc6ca] + FFTW v1.9.0 [1a297f60] + FillArrays v1.13.0 [6a86dc24] + FiniteDiff v2.27.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 ⌅ [f6369f11] + ForwardDiff v0.10.38 [069b7b12] + FunctionWrappers v1.1.3 ⌅ [d9f16b24] + Functors v0.3.0 [0c68f7d7] + GPUArrays v11.2.3 [46192b85] + GPUArraysCore v0.2.0 [28b8d3ca] + GR v0.73.17 [42e2da0e] + Grisu v1.0.2 [cd3eb016] + HTTP v1.10.17 [076d061b] + HashArrayMappedTries v0.2.0 [3e5b6fbb] + HostCPUFeatures v0.1.17 [34004b35] + HypergeometricFunctions v0.3.28 [7869d1d1] + IRTools v0.4.15 [615f187c] + IfElse v0.1.1 [d25df0c9] + Inflate v0.1.5 ⌅ [a98d9a8b] + Interpolations v0.15.1 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [1019f520] + JLFzf v0.1.11 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [63c18a36] + KernelAbstractions v0.9.37 [5ab0869b] + KernelDensity v0.6.10 [929cbde3] + LLVM v9.4.2 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.8 [10f19ff3] + LayoutPointers v0.1.17 [093fc24a] + LightGraphs v1.3.5 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.1.0 [bdcacae8] + LoopVectorization v0.12.172 [af0ac7d2] + MCPhylo v0.9.5 [e53f0ae0] + MCPhyloTree v1.1.7 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [dbb5928d] + MappedArrays v0.4.2 [739be429] + MbedTLS v1.1.9 [442fdcdd] + Measures v0.3.2 [e1d29d7a] + Missings v1.2.0 [6f286f6a] + MultivariateStats v0.10.3 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.22 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [4d8831e6] + OpenSSL v1.5.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [ccf2f8ad] + PlotThemes v3.3.0 [995b91a9] + PlotUtils v1.4.3 [91a5bcdd] + Plots v1.40.16 [1d0040c9] + PolyesterWeave v0.2.2 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [c84ed2f1] + Ratios v0.4.5 [c1ae055f] + RealDot v0.1.0 [3cdcf5f2] + RecipesBase v1.3.4 [01d81517] + RecipesPipeline v0.6.12 [189a3867] + Reexport v1.2.2 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.1 [37e2e3b7] + ReverseDiff v1.16.1 [79098fc4] + Rmath v0.8.0 [f2b01f46] + Roots v2.2.8 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [7e506255] + ScopedValues v1.3.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.8 [efcf1570] + Setfield v1.1.2 [992d4aef] + Showoff v1.0.3 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.4 [a2af1166] + SortingAlgorithms v1.2.1 [dc90abb0] + SparseInverseSubset v0.1.2 [276daf66] + SpecialFunctions v2.5.1 [860ef19b] + StableRNGs v1.0.3 [aedffcd0] + Static v1.2.0 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.0 [f3b207a7] + StatsPlots v0.15.7 [09ab397b] + StructArrays v0.7.1 [ab02a1b2] + TableOperations 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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 ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 33.13s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 5129.8 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 25 already precompiled. Precompiling package dependencies... Precompilation completed after 1391.18s ################################################################################ # Testing # Testing MCPhylo Status `/tmp/jl_fc0xdG/Project.toml` ⌅ [76274a88] Bijectors v0.10.8 [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [31c24e10] Distributions v0.25.120 [6a86dc24] FiniteDiff v2.27.0 ⌅ [f6369f11] ForwardDiff v0.10.38 [615f187c] IfElse v0.1.1 [093fc24a] LightGraphs v1.3.5 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.172 [af0ac7d2] MCPhylo v0.9.5 [e53f0ae0] MCPhyloTree v1.1.7 [90014a1f] PDMats v0.11.35 [91a5bcdd] Plots v1.40.16 [92933f4c] ProgressMeter v1.10.4 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [37e2e3b7] ReverseDiff v1.16.1 [992d4aef] Showoff v1.0.3 [276daf66] SpecialFunctions v2.5.1 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.0 [f3b207a7] StatsPlots v0.15.7 ⌅ [e88e6eb3] Zygote v0.6.77 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [d6f4376e] Markdown v1.11.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [9e88b42a] Serialization v1.11.0 [2f01184e] SparseArrays v1.12.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_fc0xdG/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.42 [79e6a3ab] Adapt v4.3.0 [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 ⌅ [ec485272] ArnoldiMethod v0.1.0 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.19.0 [a9b6321e] Atomix v1.1.1 [13072b0f] AxisAlgorithms v1.1.0 ⌅ [76274a88] Bijectors v0.10.8 [d1d4a3ce] BitFlags v0.1.9 [62783981] BitTwiddlingConvenienceFunctions v0.1.6 [fa961155] CEnum v0.5.0 [2a0fbf3d] CPUSummary v0.2.6 [082447d4] ChainRules v1.72.5 [d360d2e6] ChainRulesCore v1.25.2 [9e997f8a] ChangesOfVariables v0.1.10 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [35d6a980] ColorSchemes v3.30.0 [3da002f7] ColorTypes 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[46192b85] GPUArraysCore v0.2.0 [28b8d3ca] GR v0.73.17 [42e2da0e] Grisu v1.0.2 [cd3eb016] HTTP v1.10.17 [076d061b] HashArrayMappedTries v0.2.0 [3e5b6fbb] HostCPUFeatures v0.1.17 [34004b35] HypergeometricFunctions v0.3.28 [7869d1d1] IRTools v0.4.15 [615f187c] IfElse v0.1.1 [d25df0c9] Inflate v0.1.5 ⌅ [a98d9a8b] Interpolations v0.15.1 [3587e190] InverseFunctions v0.1.17 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [1019f520] JLFzf v0.1.11 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [63c18a36] KernelAbstractions v0.9.37 [5ab0869b] KernelDensity v0.6.10 [929cbde3] LLVM v9.4.2 [b964fa9f] LaTeXStrings v1.4.0 [23fbe1c1] Latexify v0.16.8 [10f19ff3] LayoutPointers v0.1.17 [093fc24a] LightGraphs v1.3.5 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.1.0 [bdcacae8] LoopVectorization v0.12.172 [af0ac7d2] MCPhylo v0.9.5 [e53f0ae0] MCPhyloTree v1.1.7 [1914dd2f] MacroTools v0.5.16 [d125e4d3] ManualMemory v0.1.8 [dbb5928d] MappedArrays v0.4.2 [739be429] MbedTLS v1.1.9 [442fdcdd] Measures v0.3.2 [e1d29d7a] Missings v1.2.0 [6f286f6a] MultivariateStats v0.10.3 [77ba4419] NaNMath v1.1.3 [b8a86587] NearestNeighbors v0.4.22 [510215fc] Observables v0.5.5 [6fe1bfb0] OffsetArrays v1.17.0 [4d8831e6] OpenSSL v1.5.0 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [ccf2f8ad] PlotThemes v3.3.0 [995b91a9] PlotUtils v1.4.3 [91a5bcdd] Plots v1.40.16 [1d0040c9] PolyesterWeave v0.2.2 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [92933f4c] ProgressMeter v1.10.4 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [c84ed2f1] Ratios v0.4.5 [c1ae055f] RealDot v0.1.0 [3cdcf5f2] RecipesBase v1.3.4 [01d81517] RecipesPipeline v0.6.12 [189a3867] Reexport v1.2.2 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.1 [37e2e3b7] ReverseDiff v1.16.1 [79098fc4] Rmath v0.8.0 [f2b01f46] Roots v2.2.8 [94e857df] SIMDTypes v0.1.0 [476501e8] SLEEFPirates v0.6.43 [7e506255] ScopedValues 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Testing Running tests... Running tests: >>> Testing distributions/phylodist.jl ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in FelsensteinFunction(Any, Array{R, 4}, Array{R, 4}, Array{R, N} where N, Array{R, 4}) where {R<:Real} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in by_max!(Array{F, 4}, F, Int64) where {F<:Real} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in _turbo_!(Base.Val{var"#UNROLL#"}, Base.Val{var"#OPS#"}, Base.Val{var"#ARF#"}, Base.Val{var"#AM#"}, Base.Val{var"#LPSYM#"}, Base.Val{Tuple{var"#LB#", var"#V#"}}, Vararg{Any, var"#num#vargs#"}) where {var"#UNROLL#", var"#OPS#", var"#ARF#", var"#AM#", var"#LPSYM#", var"#LB#", var"#V#", var"#num#vargs#"} at /home/pkgeval/.julia/packages/LoopVectorization/ImqiY/src/reconstruct_loopset.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in R_gemmturbo_large!(T, S, F, V, V, V) where {T, S, V, F} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in my_repeat(Array{F, N}, Int64, Array{T, 1}) where {F, N, T} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in comb_sum_product_loop!(A, A, A, Array{N, 1}, N) where {A, N} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in bymax!(A, Int64) where {A} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in R_gemmturbo_large_ptg!(T, S, F, V, V, V) where {T, S, F, V} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in gesp(LayoutPointers.AbstractStridedPointer{T, N, C, B, R, X, O} where O<:Tuple{Vararg{Union{Int16, Int32, Int64, Int8, UInt16, UInt32, UInt64, UInt8, Static.StaticInt{N} where N}, N}} where X<:Tuple{Vararg{Union{Int16, Int32, Int64, Int8, UInt16, UInt32, UInt64, UInt8, Static.StaticInt{N} where N}, N}} where R where B where C where N where T, Tuple{Vararg{Union{VectorizationBase.NullStep, Int16, Int32, Int64, Int8, UInt16, UInt32, UInt64, UInt8, Static.StaticInt{N} where N, VectorizationBase.LazyMulAdd{var"#s77", var"#s76", var"#s75"} where var"#s75"<:Union{Int16, Int32, Int64, Int8, UInt16, UInt32, UInt64, UInt8, Static.StaticInt{N} where N} where var"#s76" where var"#s77"}}}) at /home/pkgeval/.julia/packages/VectorizationBase/wHnQd/src/llvm_intrin/memory_addr.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in turbo_mul!(A, A, D, Array{D, 1}) where {A, D} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl MultiplePhyloDist: Error During Test at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:93 Test threw exception Expression: ((MCPhylo.__logpdf(mpd, mdf))[1])[1] ≈ -8677.360274116634 MethodError: objects of type Module are not callable The object of type `Module` exists, but no method is defined for this combination of argument types when trying to treat it as a callable object. Stacktrace: [1] FelsensteinFunction(tree_postorder::PostOrderDFS{GeneralNode{Float64, Int64}}, data::Array{Float64, 4}, Down::Array{Float64, 4}, pi_::Vector{Float64}, trmat::Array{Float64, 4}, ptg::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:56 [2] gradlogpdf(d::PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}, x::Array{Float64, 3}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:136 [3] __logpdf(d::MultiplePhyloDist, x::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:294 [4] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:3 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:45 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:93 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] MultiplePhyloDist: Error During Test at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:94 Test threw exception Expression: ((MCPhylo.__logpdf(mpd, mdf))[2])[1] ≈ -8677.360274116634 MethodError: objects of type Module are not callable The object of type `Module` exists, but no method is defined for this combination of argument types when trying to treat it as a callable object. Stacktrace: [1] FelsensteinFunction(tree_postorder::PostOrderDFS{GeneralNode{Float64, Int64}}, data::Array{Float64, 4}, Down::Array{Float64, 4}, pi_::Vector{Float64}, trmat::Array{Float64, 4}, ptg::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:56 [2] gradlogpdf(d::PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}, x::Array{Float64, 3}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:136 [3] __logpdf(d::MultiplePhyloDist, x::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:294 [4] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:3 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [6] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:45 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [8] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/distributions/phylodist.jl:94 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:677 [inlined] >>> Testing distributions/treeconstraints.jl ┌ Warning: Skipped line with unsupported constraint type 'AbstractString["test", ""][1]'. │ Allowed types are 'mono', 'not_mono' and 'exc' └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/TreeConstraints.jl:162 ┌ Warning: Some trivial 'mono' / 'not_mono' type constraints were removed. │ A valid 'mono' / 'not_mono' constraint needs at least 2 elements. └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/TreeConstraints.jl:31 ┌ Warning: Some trivial 'exc' type constraints were removed. │ A non-trivial 'exc' constraints needs at least 2 elements in the first, and at least 1 in the second part of the tuple └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/TreeConstraints.jl:35 >>> Testing distributions/treedists.jl >>> Testing likelihood/rates.jl >>> Testing likelihood/substitutionmodels.jl >>> Testing likelihood/felsenstein.jl ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 Felsenstein grad: Error During Test at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/likelihood/felsenstein.jl:23 Got exception outside of a @test MethodError: objects of type Module are not callable The object of type `Module` exists, but no method is defined for this combination of argument types when trying to treat it as a callable object. Stacktrace: [1] FelsensteinFunction(tree_postorder::PostOrderDFS{GeneralNode{Float64, Int64}}, data::Array{Float64, 4}, Down::Array{Float64, 4}, pi_::Vector{Float64}, trmat::Array{Float64, 4}, ptg::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:56 [2] gradlogpdf(d::PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}, x::Array{Float64, 3}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:136 [3] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/likelihood/felsenstein.jl:24 [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [5] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/likelihood/felsenstein.jl:34 [inlined] [6] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [7] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/utils.jl:5 [inlined] [8] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:64 [inlined] [9] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [10] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:63 [inlined] [11] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [12] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:56 [13] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [14] top-level scope @ none:6 [15] eval(m::Module, e::Any) @ Core ./boot.jl:489 [16] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [17] _start() @ Base ./client.jl:554 >>> Testing mcmc/discretediag.jl >>> Testing mcmc/modelbuilding.jl >>> Testing model/dependent.jl >>> Testing model/variate.jl >>> Testing output/asdsf.jl >>> Testing output/chains.jl >>> Testing output/gelman.jl WARNING: llvmcall with integer pointers is deprecated. Use actual pointers instead, replacing i32 or i64 with i8* or ptr in turbo_dot(Array{T, 1}, Array{T, 1}) where {T} at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/VectorizedFunctions.jl >>> Testing parser/csv.jl >>> Testing parser/nexus.jl ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 >>> Testing parser/parser.jl ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 >>> Testing samplers/sampler_construction.jl >>> Testing samplers/linear_model_uvp.jl >>> Testing samplers/linear_model_mvp.jl >>> Testing samplers/tree_samplers.jl ┌ Warning: Keyword datatype not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 ┌ Warning: Keyword interleave not understood, will be ignored └ @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Parser/ParseNexus.jl:92 PNUTS: Error During Test at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:46 Got exception outside of a @test MethodError: objects of type Module are not callable The object of type `Module` exists, but no method is defined for this combination of argument types when trying to treat it as a callable object. Stacktrace: [1] FelsensteinFunction(tree_postorder::PostOrderDFS{GeneralNode{Float64, Int64}}, data::Array{Float64, 4}, Down::Array{Float64, 4}, pi_::Vector{Float64}, trmat::Array{Float64, 4}, ptg::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:56 [2] gradlogpdf(d::PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}, x::Array{Float64, 3}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:136 [3] gradlogpdf_sub @ ~/.julia/packages/MCPhylo/KWPlY/src/distributions/distributionstruct.jl:157 [inlined] [4] gradlogpdf @ ~/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:556 [inlined] [5] gradlogpdf(s::Stochastic{Array{Float64, 3}, var"#311#312", PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:548 [6] gradlogpdf(m::Model, targets::Vector{Symbol}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:220 [7] logpdfgrad!(::Type{provided}, m::Model, x::GeneralNode{Float64, Int64}, params::Vector{Symbol}, target::Vector{Symbol}, transform::Bool) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:184 [8] logpdfgrad! @ ~/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:94 [inlined] [9] grlpdf @ ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:345 [inlined] [10] nutsepsilon(x::GeneralNode{Float64, Int64}, logfgrad::MCPhylo.var"#grlpdf#sample!##1"{Sampler{MCPhylo.PNUTSTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, Model}, logf::Function, delta::Float64, target::Float64) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/samplers/tree_hamiltonian/auxilliary.jl:20 [11] sample!(v::Sampler{MCPhylo.PNUTSTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, logfun::Function; grlpdf::Function, adapt::Bool, args::@Kwargs{gen::Int64, model::Model}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/samplers/pnuts.jl:114 [12] sample! @ ~/.julia/packages/MCPhylo/KWPlY/src/samplers/pnuts.jl:103 [inlined] [13] sample!(s::Sampler{MCPhylo.PNUTSTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, m::Model) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:347 [14] sample!(m::Model) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:328 [15] mcmc_worker!(args::Vector{Any}, ASDSF_step::Int64, rc::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:231 [16] mcmc_worker! @ ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:194 [inlined] [17] mcmc_or_convergence @ ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:219 [inlined] [18] iterate @ ./generator.jl:48 [inlined] [19] _collect(c::Vector{Vector{Any}}, itr::Base.Generator{Vector{Vector{Any}}, typeof(MCPhylo.mcmc_or_convergence)}, ::Base.EltypeUnknown, isz::Base.HasShape{1}) @ Base ./array.jl:810 [20] collect_similar @ ./array.jl:732 [inlined] [21] map @ ./abstractarray.jl:3372 [inlined] [22] pmap2(f::typeof(MCPhylo.mcmc_or_convergence), lsts::Vector{Vector{Any}}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:93 [23] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:179 [inlined] [24] macro expansion @ ./task.jl:633 [inlined] [25] assign_mcmc_work(f::Function, lsts::Vector{Vector{Any}}, sp::SimulationParameters, conv_storage::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:172 [26] mcmc_master!(m::Model, window::UnitRange{Int64}, sp::SimulationParameters; burnin::Int64, conv_storage::Nothing, samplers::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:166 [27] mcmc_master! @ ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:135 [inlined] [28] mcmc(m::Model, inputs::Dict{Symbol, Any}, inits::Vector{Dict{Symbol, Any}}, iters::Int64; burnin::Int64, thin::Int64, chains::Int64, verbose::Bool, trees::Bool, params::SimulationParameters) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:123 [29] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:47 [30] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [31] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:52 [inlined] [32] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [33] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/utils.jl:5 [inlined] [34] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:94 [inlined] [35] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [36] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:93 [inlined] [37] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [38] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:56 [39] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [40] top-level scope @ none:6 [41] eval(m::Module, e::Any) @ Core ./boot.jl:489 [42] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [43] _start() @ Base ./client.jl:554 ┌ Warning: `Progress(n::Integer, desc::AbstractString, offset::Integer = 0; kwargs...)` is deprecated, use `Progress(n; desc = desc, offset = offset, kwargs...)` instead. │ caller = ip:0x0 └ @ Core :-1 PPHMC: Error During Test at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:132 Got exception outside of a @test MethodError: objects of type Module are not callable The object of type `Module` exists, but no method is defined for this combination of argument types when trying to treat it as a callable object. Stacktrace: [1] FelsensteinFunction(tree_postorder::PostOrderDFS{GeneralNode{Float64, Int64}}, data::Array{Float64, 4}, Down::Array{Float64, 4}, pi_::Vector{Float64}, trmat::Array{Float64, 4}, ptg::Array{Float64, 4}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:56 [2] gradlogpdf(d::PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}, x::Array{Float64, 3}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:136 [3] gradlogpdf_sub @ ~/.julia/packages/MCPhylo/KWPlY/src/distributions/distributionstruct.jl:157 [inlined] [4] gradlogpdf @ ~/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:556 [inlined] [5] gradlogpdf(s::Stochastic{Array{Float64, 3}, var"#311#312", PhyloDist{GeneralNode{Float64, Int64}, typeof(JC)}}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:548 [6] gradlogpdf(m::Model, targets::Vector{Symbol}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:220 [7] logpdfgrad!(::Type{provided}, m::Model, x::GeneralNode{Float64, Int64}, params::Vector{Symbol}, target::Vector{Symbol}, transform::Bool) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:184 [8] logpdfgrad! @ ~/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:94 [inlined] [9] grlpdf @ ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:345 [inlined] [10] sample!(v::Sampler{MCPhylo.PPHMCTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, logfun::Function; grlpdf::MCPhylo.var"#grlpdf#sample!##1"{Sampler{MCPhylo.PPHMCTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, Model}, adapt::Bool, model::Model, kwargs::@Kwargs{gen::Int64}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/samplers/pphmc.jl:92 [11] sample! @ ~/.julia/packages/MCPhylo/KWPlY/src/samplers/pphmc.jl:75 [inlined] [12] sample!(s::Sampler{MCPhylo.PPHMCTune{typeof(logpdf!), typeof(MCPhylo.logpdfgrad!), provided}, Vector{GeneralNode{Float64, Int64}}}, m::Model) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:347 [13] sample!(m::Model) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:328 [14] mcmc_worker!(args::Vector{Any}, ASDSF_step::Int64, rc::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:231 [15] mcmc_worker! @ ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:194 [inlined] [16] mcmc_or_convergence @ ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:219 [inlined] [17] iterate @ ./generator.jl:48 [inlined] [18] _collect(c::Vector{Vector{Any}}, itr::Base.Generator{Vector{Vector{Any}}, typeof(MCPhylo.mcmc_or_convergence)}, ::Base.EltypeUnknown, isz::Base.HasShape{1}) @ Base ./array.jl:810 [19] collect_similar @ ./array.jl:732 [inlined] [20] map @ ./abstractarray.jl:3372 [inlined] [21] pmap2(f::typeof(MCPhylo.mcmc_or_convergence), lsts::Vector{Vector{Any}}) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:93 [22] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:179 [inlined] [23] macro expansion @ ./task.jl:633 [inlined] [24] assign_mcmc_work(f::Function, lsts::Vector{Vector{Any}}, sp::SimulationParameters, conv_storage::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/utils.jl:172 [25] mcmc_master!(m::Model, window::UnitRange{Int64}, sp::SimulationParameters; burnin::Int64, conv_storage::Nothing, samplers::Nothing) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:166 [26] mcmc_master! @ ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:135 [inlined] [27] mcmc(m::Model, inputs::Dict{Symbol, Any}, inits::Vector{Dict{Symbol, Any}}, iters::Int64; burnin::Int64, thin::Int64, chains::Int64, verbose::Bool, trees::Bool, params::SimulationParameters) @ MCPhylo ~/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:123 [28] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:133 [29] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [30] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:138 [inlined] [31] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [32] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/utils.jl:5 [inlined] [33] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:94 [inlined] [34] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [35] macro expansion @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:93 [inlined] [36] macro expansion @ /opt/julia/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] [37] top-level scope @ ~/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:56 [38] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:304 [39] top-level scope @ none:6 [40] eval(m::Module, e::Any) @ Core ./boot.jl:489 [41] exec_options(opts::Base.JLOptions) @ Base ./client.jl:287 [42] _start() @ Base ./client.jl:554 Test Summary: | Pass Error Total Time All tests | 253 5 258 12m09.6s distributions tests | 63 2 65 4m27.8s PhyloDist.jl | 22 2 24 2m36.6s PhyloDist | 7 7 20.1s MultiplePhyloDist | 15 2 17 2m10.1s TreeConstraints.jl | 8 8 5.5s UniformBranchLength | 3 3 0.5s exponentialBL | 6 6 1m24.5s CompoundDirichlet | 12 12 19.7s TreeDistribution | 12 12 0.5s likelihood tests | 31 1 32 23.3s Rates.jl | 4 4 3.3s SubstitutionModels.jl | 26 26 19.4s Felsenstein | 1 1 0.0s Felsenstein grad | 1 1 0.4s mcmc tests | 13 13 29.0s model tests | 50 50 6.1s output tests | 43 43 1m53.1s parser tests | 16 16 3.9s sampler tests | 37 2 39 4m46.5s Sampler Construction | 5 5 0.4s Slice Multivariate | 2 2 9.1s Slice Univariate | 2 2 4.6s RWM | 2 2 2.5s NUTS_Classic | 2 2 11.4s NUTS_Riemann | 2 2 10.0s HMC | 2 2 4.6s HMC Sigma | 2 2 4.7s Slice Multivariate | 2 2 4.2s Slice Univariate | 2 2 3.2s RWM | 2 2 1.4s NUTS_Classic | 2 2 8.9s NUTS_Riemann | 2 2 10.0s HMC | 2 2 4.5s HMC Sigma | 2 2 4.4s PNUTS | 1 1 11.4s RWM_Univariate | 3 3 2m04.8s RWM_Multivariate | 1 1 59.7s PPHMC | 1 1 1.2s RNG of the outermost testset: Xoshiro(0x44630ad555db81dc, 0x5740ed9eafb990ed, 0x82966a623d1b0bc4, 0xbd014b943d5d8c0f, 0x021ef8aa441e43e0) ERROR: LoadError: Some tests did not pass: 253 passed, 0 failed, 5 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:54 Testing failed after 817.4s ERROR: LoadError: Package MCPhylo 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:303 [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 2287.42s: package tests unexpectedly errored