Package evaluation to test MCPhylo on Julia 1.12.4 (422f456051*) started at 2026-01-29T21:12:46.986 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.12` Set-up completed after 7.33s ################################################################################ # Installation # Installing MCPhylo... Resolving package versions... 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 v0.1.43 [79e6a3ab] + Adapt v4.4.0 [66dad0bd] + AliasTables v1.1.3 [dce04be8] + ArgCheck v2.5.0 ⌅ [ec485272] + ArnoldiMethod v0.1.0 [7d9fca2a] + Arpack v0.5.4 [4fba245c] + ArrayInterface v7.22.0 [a9b6321e] + Atomix v1.1.2 [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 v0.2.7 [082447d4] + ChainRules v1.72.6 [d360d2e6] + ChainRulesCore v1.26.0 [9e997f8a] + ChangesOfVariables v0.1.10 [fb6a15b2] + CloseOpenIntervals v0.1.13 [aaaa29a8] + Clustering v0.15.8 [944b1d66] + CodecZlib v0.7.8 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [38540f10] + CommonSolve v0.2.6 [bbf7d656] + CommonSubexpressions v0.3.1 [f70d9fcc] + CommonWorldInvalidations v1.0.0 [34da2185] + Compat v4.18.1 [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 v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [460bff9d] + ExceptionUnwrapping v0.1.11 [c87230d0] + FFMPEG v0.4.5 [b86e33f2] + FFTA v0.3.1 [1a297f60] + FillArrays v1.16.0 [6a86dc24] + FiniteDiff v2.29.0 [53c48c17] + FixedPointNumbers v0.8.5 [1fa38f19] + Format v1.3.7 ⌅ [f6369f11] + ForwardDiff v0.10.39 [069b7b12] + FunctionWrappers v1.1.3 ⌅ [d9f16b24] + Functors v0.3.0 [0c68f7d7] + GPUArrays v11.3.4 [46192b85] + GPUArraysCore v0.2.0 [28b8d3ca] + GR v0.73.22 [42e2da0e] + Grisu v1.0.2 [cd3eb016] + HTTP v1.10.19 [076d061b] + HashArrayMappedTries v0.2.0 [3e5b6fbb] + HostCPUFeatures v0.1.18 [34004b35] + HypergeometricFunctions v0.3.28 [7869d1d1] + IRTools v0.4.15 [615f187c] + IfElse v0.1.1 [d25df0c9] + Inflate v0.1.5 [18e54dd8] + IntegerMathUtils v0.1.3 [a98d9a8b] + Interpolations v0.16.2 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [82899510] + IteratorInterfaceExtensions v1.0.0 [1019f520] + JLFzf v0.1.11 [692b3bcd] + JLLWrappers v1.7.1 [682c06a0] + JSON v1.4.0 [63c18a36] + KernelAbstractions v0.9.39 [5ab0869b] + KernelDensity v0.6.11 [929cbde3] + LLVM v9.4.4 [b964fa9f] + LaTeXStrings v1.4.0 [23fbe1c1] + Latexify v0.16.10 [10f19ff3] + LayoutPointers v0.1.17 [093fc24a] + LightGraphs v1.3.5 [2ab3a3ac] + LogExpFunctions v0.3.29 [e6f89c97] + LoggingExtras v1.2.0 [bdcacae8] + LoopVectorization v0.12.173 [af0ac7d2] + MCPhylo v0.9.5 [e53f0ae0] + MCPhyloTree v1.1.7 [1914dd2f] + MacroTools v0.5.16 [d125e4d3] + ManualMemory v0.1.8 [dbb5928d] + MappedArrays v0.4.3 [739be429] + MbedTLS v1.1.9 [442fdcdd] + Measures v0.3.3 [e1d29d7a] + Missings v1.2.0 [46d2c3a1] + MuladdMacro v0.2.4 [6f286f6a] + MultivariateStats v0.10.3 [77ba4419] + NaNMath v1.1.3 [b8a86587] + NearestNeighbors v0.4.26 [510215fc] + Observables v0.5.5 [6fe1bfb0] + OffsetArrays v1.17.0 [4d8831e6] + OpenSSL v1.6.1 [bac558e1] + OrderedCollections v1.8.1 ⌃ [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [ccf2f8ad] + PlotThemes v3.3.0 [995b91a9] + PlotUtils v1.4.4 [91a5bcdd] + Plots v1.41.4 [1d0040c9] + PolyesterWeave v0.2.2 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.1 [27ebfcd6] + Primes v0.5.7 [92933f4c] + ProgressMeter v1.11.0 [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 v1.16.2 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v2.2.10 [94e857df] + SIMDTypes v0.1.0 [476501e8] + SLEEFPirates v0.6.43 [431bcebd] + SciMLPublic v1.0.1 [7e506255] + ScopedValues v1.5.0 [6c6a2e73] + Scratch v1.3.0 [91c51154] + SentinelArrays v1.4.9 [efcf1570] + Setfield v1.1.2 [992d4aef] + Showoff v1.0.3 [777ac1f9] + SimpleBufferStream v1.2.0 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [dc90abb0] + SparseInverseSubset v0.1.2 [276daf66] + SpecialFunctions v2.6.1 [860ef19b] + StableRNGs v1.0.4 [aedffcd0] + Static v1.3.1 [0d7ed370] + StaticArrayInterface v1.8.0 [90137ffa] + StaticArrays v1.9.16 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v1.5.2 [f3b207a7] + StatsPlots v0.15.8 [09ab397b] + StructArrays v0.7.2 [ec057cc2] + StructUtils v2.6.2 [ab02a1b2] + TableOperations v1.2.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [62fd8b95] + TensorCore v0.1.1 [8290d209] + ThreadingUtilities v0.5.5 [3bb67fe8] + TranscodingStreams v0.11.3 [5c2747f8] + URIs v1.6.1 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [013be700] + UnsafeAtomics v0.3.0 [41fe7b60] + Unzip v0.2.0 [3d5dd08c] + VectorizationBase v0.21.72 [cc8bc4a8] + Widgets v0.6.7 [efce3f68] + WoodburyMatrices v1.1.0 ⌅ [e88e6eb3] + Zygote v0.6.77 [700de1a5] + ZygoteRules v0.2.7 ⌅ [68821587] + Arpack_jll v3.5.2+0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.5+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.7.3+0 [b22a6f82] + FFMPEG_jll v8.0.1+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [0656b61e] + GLFW_jll v3.4.1+0 [d2c73de3] + GR_jll v0.73.22+0 [b0724c58] + GettextRuntime_jll v0.22.4+0 [61579ee1] + Ghostscript_jll v9.55.1+0 [7746bdde] + Glib_jll v2.86.2+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.1+0 [aacddb02] + JpegTurbo_jll v3.1.4+0 [c1c5ebd0] + LAME_jll v3.100.3+0 [88015f11] + LERC_jll v4.0.1+0 [dad2f222] + LLVMExtra_jll v0.0.38+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 v2.41.2+0 [89763e89] + Libtiff_jll v4.7.2+0 [38a345b3] + Libuuid_jll v2.41.2+0 [c8ffd9c3] + MbedTLS_jll v2.28.1010+0 [e7412a2a] + Ogg_jll v1.3.6+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [91d4177d] + Opus_jll v1.6.0+0 [36c8627f] + Pango_jll v1.57.0+0 ⌅ [30392449] + Pixman_jll v0.44.2+0 [c0090381] + Qt6Base_jll v6.8.2+2 [629bc702] + Qt6Declarative_jll v6.8.2+1 [ce943373] + Qt6ShaderTools_jll v6.8.2+1 [e99dba38] + Qt6Wayland_jll v6.8.2+2 [f50d1b31] + Rmath_jll v0.5.1+0 [a44049a8] + Vulkan_Loader_jll v1.3.243+0 [a2964d1f] + Wayland_jll v1.24.0+0 [ffd25f8a] + XZ_jll v5.8.2+0 [f67eecfb] + Xorg_libICE_jll v1.1.2+0 [c834827a] + Xorg_libSM_jll v1.2.6+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] + Xorg_libXi_jll v1.8.3+0 [d1454406] + Xorg_libXinerama_jll v1.1.6+0 [ec84b674] + Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.1.3+0 [e920d4aa] + Xorg_xcb_util_cursor_jll v0.1.6+0 [12413925] + Xorg_xcb_util_image_jll v0.4.1+0 [2def613f] + Xorg_xcb_util_jll v0.4.1+0 [975044d2] + Xorg_xcb_util_keysyms_jll v0.4.1+0 [0d47668e] + Xorg_xcb_util_renderutil_jll v0.3.10+0 [c22f9ab0] + Xorg_xcb_util_wm_jll v0.4.2+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [35ca27e7] + eudev_jll v3.2.14+0 [214eeab7] + fzf_jll v0.61.1+0 [a4ae2306] + libaom_jll v3.13.1+0 [0ac62f75] + libass_jll v0.17.4+0 [1183f4f0] + libdecor_jll v0.2.2+0 [2db6ffa8] + libevdev_jll v1.13.4+0 [f638f0a6] + libfdk_aac_jll v2.0.4+0 [36db933b] + libinput_jll v1.28.1+0 [b53b4c65] + libpng_jll v1.6.54+0 [f27f6e37] + libvorbis_jll v1.3.8+0 [009596ad] + mtdev_jll v1.1.7+0 ⌅ [1270edf5] + x264_jll v10164.0.1+0 [dfaa095f] + x265_jll v4.1.0+0 [d8fb68d0] + xkbcommon_jll v1.13.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL 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 v1.12.1 [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 v8.15.0+0 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.11.4 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.7+0 [458c3c95] + OpenSSL_jll v3.5.4+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [bea87d4a] + SuiteSparse_jll v7.8.3+2 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.64.0+1 [3f19e933] + p7zip_jll v17.7.0+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 8.67s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling packages... 240312.3 ms ✓ StatsPlots 324812.7 ms ✓ MCPhylo 2 dependencies successfully precompiled in 586 seconds. 348 already precompiled. Precompilation completed after 603.13s ################################################################################ # Testing # Testing MCPhylo Status `/tmp/jl_enpC49/Project.toml` ⌅ [76274a88] Bijectors v0.10.8 ⌅ [864edb3b] DataStructures v0.18.22 [8bb1440f] DelimitedFiles v1.9.1 [163ba53b] DiffResults v1.1.0 [31c24e10] Distributions v0.25.123 [6a86dc24] FiniteDiff v2.29.0 ⌅ [f6369f11] ForwardDiff v0.10.39 [615f187c] IfElse v0.1.1 [093fc24a] LightGraphs v1.3.5 [2ab3a3ac] LogExpFunctions v0.3.29 [bdcacae8] LoopVectorization v0.12.173 [af0ac7d2] MCPhylo v0.9.5 [e53f0ae0] MCPhyloTree v1.1.7 ⌃ [90014a1f] PDMats v0.11.35 [91a5bcdd] Plots v1.41.4 [92933f4c] ProgressMeter v1.11.0 [3cdcf5f2] RecipesBase v1.3.4 [189a3867] Reexport v1.2.2 [37e2e3b7] ReverseDiff v1.16.2 [992d4aef] Showoff v1.0.3 [276daf66] SpecialFunctions v2.6.1 [10745b16] Statistics v1.11.1 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v1.5.2 [f3b207a7] StatsPlots v0.15.8 ⌅ [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_enpC49/Manifest.toml` [621f4979] AbstractFFTs v1.5.0 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.43 [79e6a3ab] Adapt v4.4.0 [66dad0bd] AliasTables v1.1.3 [dce04be8] ArgCheck v2.5.0 ⌅ [ec485272] ArnoldiMethod v0.1.0 [7d9fca2a] Arpack v0.5.4 [4fba245c] ArrayInterface v7.22.0 [a9b6321e] Atomix v1.1.2 [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 v0.2.7 [082447d4] ChainRules v1.72.6 [d360d2e6] ChainRulesCore v1.26.0 [9e997f8a] ChangesOfVariables v0.1.10 [fb6a15b2] CloseOpenIntervals v0.1.13 [aaaa29a8] Clustering v0.15.8 [944b1d66] CodecZlib v0.7.8 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Precompiling packages... 12853.0 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 17 seconds. 50 already precompiled. 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 >>> 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 >>> 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 >>> 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 ┌ 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 ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 135 running 1 of 1 signal (10): User defined signal 1 bitmix at /source/src/support/hashing.h:31 [inlined] typekeyvalue_hash at /source/src/jltypes.c:1832 [inlined] lookup_typevalue at /source/src/jltypes.c:1136 jl_inst_arg_tuple_type at /source/src/jltypes.c:2479 arg_tuple at /source/src/builtins.c:935 iterate at /home/pkgeval/.julia/packages/AbstractTrees/Ftf8W/src/iteration.jl:75 unknown function (ip: 0x7f4d24bfe956) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 getindex at /home/pkgeval/.julia/packages/MCPhyloTree/67FIA/src/Basics/Tree_Traversal.jl:13 collect_to! at ./array.jl:843 collect_to_with_first! at ./array.jl:826 unknown function (ip: 0x7f4cf55669f8) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 collect at ./array.jl:800 getindex at /home/pkgeval/.julia/packages/MCPhyloTree/67FIA/src/Basics/Tree_Traversal.jl:7 [inlined] maybeview at ./views.jl:148 [inlined] FelsensteinFunction at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:92 logpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:107 logpdf_sub at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/distributions/distributionstruct.jl:122 [inlined] logpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:564 [inlined] logpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:515 [inlined] logpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:515 unknown function (ip: 0x7f4d116864ef) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 logpdf! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:270 logpdf! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:194 [inlined] lpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:341 [inlined] #sample!#298 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/slicesimplex.jl:82 sample! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:337 unknown function (ip: 0x7f4d116aa986) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 sample! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:328 mcmc_worker! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:231 mcmc_worker! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:194 [inlined] mcmc_or_convergence at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:219 [inlined] iterate at ./generator.jl:48 [inlined] _collect at ./array.jl:810 pmap2 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:89 unknown function (ip: 0x7f4d118fce03) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:179 [inlined] macro expansion at ./task.jl:662 [inlined] assign_mcmc_work at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:172 #mcmc_master!#48 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:166 mcmc_master! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:135 [inlined] #mcmc#47 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:123 mcmc at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:75 unknown function (ip: 0x7f4d11651fcc) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_body at /source/src/interpreter.c:581 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_61918.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/utils.jl:5 [inlined] macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:94 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:93 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] top-level scope at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:56 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_invoke at /source/src/gf.c:4021 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_61918.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_55866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7f4d2d1dd249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 wait at ./process.jl:685 wait at ./process.jl:686 jfptr_wait_46335.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2553 unknown function (ip: 0x7e9409315ec3) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #205 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2493 withenv at ./env.jl:265 #190 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2308 with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2161 #186 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2275 #mktempdir#21 at ./file.jl:936 unknown function (ip: 0x7e9409303f2c) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 mktempdir at ./file.jl:932 mktempdir at ./file.jl:932 #sandbox#182 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2222 [inlined] sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2212 unknown function (ip: 0x7e9409301769) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #test#193 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2478 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2384 [inlined] #test#170 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:538 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:515 unknown function (ip: 0x7e9409300cd1) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 #test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:169 unknown function (ip: 0x7e94092fcfc0) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:158 #test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:157 [inlined] #test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 [inlined] test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:156 unknown function (ip: 0x7e94092f6b8f) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2930 include at ./Base.jl:306 exec_options at ./client.jl:317 _start at ./client.jl:550 jfptr__start_55866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7e9411a75249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007e93f75fc010 Total snapshots: 319. Utilization: 0% ╎319 @Base/client.jl:550 _start() ╎ 319 @Base/client.jl:317 exec_options(opts::Base.JLOptions) ╎ 319 @Base/Base.jl:306 include(mod::Module, _path::String) ╎ 319 @Base/loading.jl:2930 _include(mapexpr::Function, mod::Module, _pat… ╎ 319 @Base/loading.jl:2870 include_string(mapexpr::typeof(identity), mo… ╎ 319 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 319 @Pkg/src/API.jl:156 kwcall(::@NamedTuple{julia_args::Cmd}, ::typ… ╎ ╎ 319 @Pkg/src/API.jl:156 #test#81 ╎ ╎ 319 @Pkg/src/API.jl:157 test ╎ ╎ 319 @Pkg/src/API.jl:157 test(pkgs::Vector{String}; kwargs::Base.P… ╎ ╎ 319 @Pkg/src/API.jl:158 kwcall(::@NamedTuple{julia_args::Cmd}, :… ╎ ╎ ╎ 319 @Pkg/src/API.jl:169 test(pkgs::Vector{PackageSpec}; io::IOC… ╎ ╎ ╎ 319 @Pkg/src/API.jl:515 kwcall(::@NamedTuple{julia_args::Cmd, … ╎ ╎ ╎ 319 @Pkg/src/API.jl:538 test(ctx::Pkg.Types.Context, pkgs::Ve… ╎ ╎ ╎ 319 @Pkg/…erations.jl:2384 test ╎ ╎ ╎ 319 @Pkg/…erations.jl:2478 test(ctx::Pkg.Types.Context, pkg… ╎ ╎ ╎ ╎ 319 @Pkg/…rations.jl:2212 kwcall(::@NamedTuple{preferences… ╎ ╎ ╎ ╎ 319 @Pkg/…rations.jl:2222 #sandbox#182 ╎ ╎ ╎ ╎ 319 @Base/file.jl:932 mktempdir(fn::Function) ╎ ╎ ╎ ╎ 319 @Base/file.jl:932 mktempdir(fn::Function, parent::S… ╎ ╎ ╎ ╎ 319 @Base/file.jl:936 mktempdir(fn::Pkg.Operations.var… ╎ ╎ ╎ ╎ ╎ 319 @Pkg/…tions.jl:2275 (::Pkg.Operations.var"#186#18… ╎ ╎ ╎ ╎ ╎ 319 @Pkg/…tions.jl:2161 with_temp_env(fn::Pkg.Operat… ╎ ╎ ╎ ╎ ╎ 319 @Pkg/…tions.jl:2308 (::Pkg.Operations.var"#190#… ╎ ╎ ╎ ╎ ╎ 319 @Base/env.jl:265 withenv(::Pkg.Operations.var"… ╎ ╎ ╎ ╎ ╎ 319 @Pkg/…ions.jl:2493 (::Pkg.Operations.var"#205… ╎ ╎ ╎ ╎ ╎ ╎ 319 @Pkg/…ons.jl:2553 subprocess_handler(cmd::Cm… ╎ ╎ ╎ ╎ ╎ ╎ 319 @Base/…ss.jl:686 wait(x::Base.Process) ╎ ╎ ╎ ╎ ╎ ╎ 319 @Base/…ss.jl:685 wait(x::Base.Process, syn… ╎ ╎ ╎ ╎ ╎ ╎ 319 @Base/…on.jl:141 wait(c::Base.GenericCond… ╎ ╎ ╎ ╎ ╎ ╎ 319 @Base/…sk.jl:1228 wait() 318╎ ╎ ╎ ╎ ╎ ╎ ╎ 319 @Base/…sk.jl:1216 poptask(W::Base.Intru… ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007f4d12dfc010 Total snapshots: 209. Utilization: 100% ╎208 @Base/client.jl:550 _start() ╎ 208 @Base/client.jl:283 exec_options(opts::Base.JLOptions) ╎ 208 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 208 @Base/Base.jl:308 (::Base.IncludeInto)(fname::String) ╎ 208 @Base/Base.jl:307 include(mapexpr::Function, mod::Module, _path::St… ╎ 208 @Base/loading.jl:2930 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 208 @Base/loading.jl:2870 include_string(mapexpr::typeof(identity), m… ╎ ╎ 208 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 208 @MCPhylo/…runtests.jl:56 top-level scope ╎ ╎ 208 @Test/src/Test.jl:1776 macro expansion ╎ ╎ 208 @MCPhylo/…untests.jl:93 macro expansion ╎ ╎ ╎ 208 @Test/src/Test.jl:1776 macro expansion ╎ ╎ ╎ 208 @MCPhylo/…ntests.jl:94 macro expansion ╎ ╎ ╎ 208 @MCPhylo/…/utils.jl:5 macro expansion ╎ ╎ ╎ 208 @Base/Base.jl:308 (::Base.IncludeInto)(fname::String) ╎ ╎ ╎ 208 @Base/Base.jl:307 include(mapexpr::Function, mod::Module… ╎ ╎ ╎ ╎ 208 @Base/loading.jl:2930 _include(mapexpr::Function, mod::… ╎ ╎ ╎ ╎ 208 @Base/loading.jl:2870 include_string(mapexpr::typeof(i… ╎ ╎ ╎ ╎ 208 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ ╎ ╎ 208 @MCPhylo/…cmc.jl:75 kwcall(::@NamedTuple{burnin::Int… ╎ ╎ ╎ ╎ 208 @MCPhylo/…cmc.jl:123 mcmc(m::Model, inputs::Dict{Sy… ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…mc.jl:135 mcmc_master! ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…mc.jl:166 mcmc_master!(m::Model, window… ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…s.jl:172 assign_mcmc_work(f::Function,… ╎ ╎ ╎ ╎ ╎ 208 @Base/task.jl:662 macro expansion ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…s.jl:179 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…s.jl:89 pmap2(f::typeof(MCPhylo.mcm… ╎ ╎ ╎ ╎ ╎ ╎ 208 @Base/…ray.jl:810 _collect(c::Vector{Vector{… ╎ ╎ ╎ ╎ ╎ ╎ 208 @Base/…tor.jl:48 iterate ╎ ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…jl:219 mcmc_or_convergence ╎ ╎ ╎ ╎ ╎ ╎ 208 @MCPhylo/…jl:194 mcmc_worker! ╎ ╎ ╎ ╎ ╎ ╎ ╎ 207 @MCPhylo/…jl:231 mcmc_worker!(args::Vect… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 207 @MCPhylo/…jl:328 sample!(m::Model) ╎ ╎ ╎ ╎ ╎ ╎ ╎ 207 @MCPhylo/…jl:337 sample!(s::Sampler{MC… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @MCPhylo/…jl:92 sample!(v::Sampler{MC… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @MCPhylo/…jl:345 grlpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 24 @MCPhylo/…jl:94 logpdfgrad! ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @MCPhylo/…jl:184 logpdfgrad!(::Typ… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @MCPhylo/…jl:220 gradlogpdf(m::Mo… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @MCPhylo/…jl:548 gradlogpdf(s::S… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 23 @MCPhylo/…jl:556 gradlogpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 23 @MCPhylo/…jl:157 gradlogpdf_sub 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 23 @MCPhylo/…jl:124 gradlogpdf(d::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @MCPhylo/…jl:11 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @MCPhylo/…jl:107 FelsensteinFun… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:527 last ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @MCPhyloTree/…:13 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @AbstractTrees/…:75 iterate(ti:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @AbstractTrees/…:183 next(s::Ab… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:183 nextsiblin… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 5 @MCPhylo/…jl:28 FelsensteinFunc… 5╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 5 @LoopVectorization/…:1179 macro… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @MCPhylo/…jl:36 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 7 @MCPhylo/…jl:39 FelsensteinFunc… 7╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 7 @LoopVectorization/…:1179 macro… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @MCPhylo/…jl:51 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Base/…ay.jl:1342 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…al.jl:956 _getindex(::In… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…al.jl:968 _unsafe_getind… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…ay.jl:822 similar ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…ay.jl:377 similar ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @Base/…ot.jl:661 Array 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Base/…ot.jl:651 Array 5╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 6 @MCPhylo/…jl:64 FelsensteinFunc… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Base/…er.jl:54 getproperty(x::… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @MCPhylo/…jl:66 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:187 logpdfgrad!(::Typ… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:551 gradlogpdf(s::St… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:113 gradlogpdf(d::T… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:46 gradlogpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 1 @Zygote/….jl:213 withgradient(f… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 1 @Zygote/….jl:91 (::Zygote.var"#… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @Zygote/….jl:110 (::Zygote.Pull… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Zygote/….jl:110 (::Zygote.Pull… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:94 sample!(v::Sampler{MC… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:29 deepcopy ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:69 deepcopy_internal(x… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @Base/…py.jl:128 deepcopy_internal… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:102 _deepcopy_memory… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:137 deepcopy_interna… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:99 deepcopy_internal ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…py.jl:115 _deepcopy_memo… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 1 @Base/…py.jl:69 deepcopy_intern… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 175 @MCPhylo/…jl:104 sample!(v::Sampler{M… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 175 @MCPhylo/…jl:22 refraction!(s::MCPhy… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 175 @MCPhylo/…jl:345 grlpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 175 @MCPhylo/…jl:94 logpdfgrad! ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:181 logpdfgrad!(::Ty… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:82 setindex!(m::Mod… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:59 setindex!(m::Mo… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 164 @MCPhylo/…jl:184 logpdfgrad!(::Ty… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 164 @MCPhylo/…jl:220 gradlogpdf(m::M… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 164 @MCPhylo/…jl:548 gradlogpdf(s::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 164 @MCPhylo/…jl:556 gradlogpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 164 @MCPhylo/…jl:157 gradlogpdf_sub ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 163 @MCPhylo/…jl:124 gradlogpdf(d::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 9 @MCPhylo/…jl:11 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 4 @MCPhylo/…jl:92 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 4 @Base/…ws.jl:148 maybeview ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 4 @MCPhyloTree/…:7 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 4 @Base/…ay.jl:800 collect(itr::B… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 4 @Base/…ay.jl:826 collect_to_wit… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 4 @Base/…ay.jl:843 collect_to!(de… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +11 4 @MCPhyloTree/…:13 getindex(n::P… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +12 3 @AbstractTrees/…:75 iterate(ti:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +13 2 @AbstractTrees/…:183 next(s::Ab… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +14 2 @AbstractTrees/…:183 nextsiblin… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 5 @MCPhylo/…jl:94 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 5 @Base/…ws.jl:148 maybeview ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 2 @MCPhyloTree/…:10 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 2 @AbstractTrees/…:74 iterate ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 2 @AbstractTrees/…:75 iterate 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 2 @AbstractTrees/…:188 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 3 @MCPhyloTree/…:13 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 3 @AbstractTrees/…:75 iterate(ti:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:183 next(s::Ab… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @AbstractTrees/…:182 nextsiblin… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:185 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:188 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @AbstractTrees/…:177 descendleft ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +11 1 @AbstractTrees/…:177 descendleft ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +12 1 @Base/…ay.jl:472 first ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +13 1 @AbstractTrees/…:167 iterate ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +14 1 @AbstractTrees/…:174 iterate 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +15 1 @AbstractTrees/…:149 ImplicitCu… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @MCPhylo/…jl:25 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:728 collect ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…ay.jl:779 _collect ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…ay.jl:867 grow_to!(dest:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…ay.jl:885 grow_to!(dest:… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:75 iterate ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 45 @MCPhylo/…jl:28 FelsensteinFunc… 45╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 45 @LoopVectorization/…:1179 macro… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 50 @MCPhylo/…jl:39 FelsensteinFunc… 49╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 50 @LoopVectorization/…:1179 macro… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @LoopVectorization/…:389 gespf1 ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 4 @MCPhylo/…jl:51 FelsensteinFunc… 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 4 @Base/…ay.jl:1342 getindex ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…es.jl:359 to_indices ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…al.jl:919 to_indices 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…al.jl:919 to_indices ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…al.jl:956 _getindex(::In… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…al.jl:970 _unsafe_getind… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…al.jl:989 _unsafe_getind… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @Base/…al.jl:979 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Base/…an.jl:64 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +11 1 @Base/…al.jl:981 macro expansion ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +12 1 @Base/…ay.jl:928 getindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +13 1 @Base/…ay.jl:699 checkbounds ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 3 @MCPhylo/…jl:56 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 3 @Base/…st.jl:1250 dotview 2╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 3 @Base/…ws.jl:149 maybeview 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…ay.jl:211 view(::Array{F… 29╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 48 @MCPhylo/…jl:64 FelsensteinFunc… 15╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 15 @Base/…er.jl:54 getproperty(x::… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:926 getindex(::Arr… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:928 getindex(::Arr… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…ay.jl:699 checkbounds ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…ay.jl:681 checkbounds ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…ay.jl:725 checkbounds_in… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @Base/…ay.jl:754 checkindex 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Base/int.jl:86 - 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:929 getindex(::Arr… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…at.jl:495 +(x::Float64, … 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 2 @MCPhylo/…jl:66 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @MCPhylo/…jl:74 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:901 iterate(A::Vec… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/int.jl:519 < ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @MCPhylo/…jl:130 gradlogpdf(d::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Base/…py.jl:29 deepcopy ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…py.jl:128 deepcopy_inter… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…py.jl:137 deepcopy_inter… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Base/…py.jl:99 deepcopy_intern… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…py.jl:104 _deepcopy_memo… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @Base/…ry.jl:180 copy(a::Memory… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Base/…ry.jl:143 unsafe_copyto! ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +11 1 @Base/…ry.jl:125 unsafe_copyto! 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +12 1 @Base/…em.jl:28 memmove ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 10 @MCPhylo/…jl:187 logpdfgrad!(::Ty… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 10 @MCPhylo/…jl:551 gradlogpdf(s::S… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 10 @MCPhylo/…jl:113 gradlogpdf(d::… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 10 @MCPhylo/…jl:46 gradlogpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 10 @Zygote/….jl:213 withgradient(f… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 10 @Zygote/….jl:91 (::Zygote.var"#… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 10 @Zygote/….jl:110 (::Zygote.Pull… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 9 @Zygote/….jl:0 (::Zygote.Pullba… 4╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 9 @MCPhylo/…jl:35 internal_logpdf 3╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 4 @Zygote/….jl:110 (::Zygote.Pull… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Base/…le.jl:33 getindex(t::Tup… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +11 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +12 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +13 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +14 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +15 1 @Zygote/….jl:22 accum(::@NamedT… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +16 1 @Zygote/….jl:22 accum(::@NamedT… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +17 1 @Zygote/….jl:22 accum(::@NamedT… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Zygote/….jl:110 (::Zygote.Pull… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:82 sample!(v::Sampler{MC… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:341 lpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:194 logpdf! ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:270 logpdf!(m::Model,… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:515 logpdf(s::Stocha… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:515 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 2 @MCPhylo/…jl:564 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 2 @MCPhylo/…jl:122 logpdf_sub ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 2 @MCPhylo/…jl:107 logpdf(d::Phyl… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 2 @MCPhylo/…jl:94 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 2 @Base/…ws.jl:148 maybeview ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 2 @MCPhyloTree/…:13 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 2 @AbstractTrees/…:75 iterate(ti:… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 2 @AbstractTrees/…:188 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @AbstractTrees/…:177 descendleft ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:177 descendleft 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @AbstractTrees/…:0 descendleft(… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @MCPhylo/…jl:89 sample!(v::Sampler{MC… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @MCPhylo/…jl:341 lpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 4 @MCPhylo/…jl:194 logpdf! ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:258 logpdf!(m::Model,… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:479 relist(m::Model,… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @MCPhylo/…jl:270 logpdf!(m::Model,… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @MCPhylo/…jl:515 logpdf(s::Stocha… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @MCPhylo/…jl:515 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 3 @MCPhylo/…jl:564 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 3 @MCPhylo/…jl:122 logpdf_sub ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 2 @MCPhylo/…jl:107 logpdf(d::Phyl… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 2 @MCPhylo/…jl:94 FelsensteinFunc… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 2 @Base/…ws.jl:148 maybeview ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 2 @MCPhyloTree/…:13 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 2 @AbstractTrees/…:75 iterate(ti:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @AbstractTrees/…:183 next(s::Ab… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @AbstractTrees/…:183 nextsiblin… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @AbstractTrees/…:185 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 1 @MCPhylo/…jl:116 logpdf(d::Phyl… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +3 1 @Base/…ay.jl:787 collect(itr::B… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +4 1 @Base/…ay.jl:867 grow_to!(dest:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +5 1 @Base/…ay.jl:894 grow_to!(dest:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +6 1 @Base/…or.jl:45 iterate ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +7 1 @AbstractTrees/…:75 iterate(ti:… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +8 1 @AbstractTrees/…:238 next(s::Ab… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +9 1 @AbstractTrees/…:81 parent 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +10 1 @Base/…er.jl:54 getproperty ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:233 mcmc_worker!(args::Vect… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:286 track(i::Int64, burnin… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:391 final_likelihood(mode… ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:117 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:119 logpdf(m::Model, no… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:515 logpdf(s::Stochast… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:564 logpdf ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:122 logpdf_sub ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhylo/…jl:107 logpdf(d::Phylo… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ 1 @MCPhyloTree/…:13 getindex(n::P… ╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +1 1 @AbstractTrees/…:75 iterate(ti:… 1╎ ╎ ╎ ╎ ╎ ╎ ╎ ╎ +2 1 @AbstractTrees/…:185 next(s::Ab… [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 poptask at ./task.jl:1216 wait at ./task.jl:1228 #wait#398 at ./condition.jl:141 _trywait at ./asyncevent.jl:163 profile_printing_listener at ./Base.jl:332 #start_profile_listener##0 at ./Base.jl:352 jfptr_YY.start_profile_listenerYY.YY.0_18905.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] start_task at /source/src/task.c:1252 unknown function (ip: (nil)) at (unknown file) Allocations: 26282048 (Pool: 26281309; Big: 739); GC: 22 [135] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/samplers/tree_samplers.jl:132 jl_gc_small_alloc_inner at /source/src/gc-stock.c:727 ijl_gc_small_alloc at /source/src/gc-stock.c:775 unknown function (ip: 0x7f4cf55f447e) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 FelsensteinFunction at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/Likelihood/LikelihoodCalculator_Node.jl:64 gradlogpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/distributions/Phylodist.jl:124 gradlogpdf_sub at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/distributions/distributionstruct.jl:157 [inlined] gradlogpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:556 [inlined] gradlogpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/dependent.jl:548 unknown function (ip: 0x7f4d1167ba9c) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 gradlogpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:220 logpdfgrad! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:184 logpdfgrad! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/sampler.jl:94 [inlined] grlpdf at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:345 [inlined] refraction! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/tree_hamiltonian/refraction.jl:22 #sample!#278 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/samplers/pphmc.jl:104 sample! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:337 unknown function (ip: 0x7f4d1151c466) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 sample! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/simulation.jl:328 mcmc_worker! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:231 mcmc_worker! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:194 [inlined] mcmc_or_convergence at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:219 [inlined] iterate at ./generator.jl:48 [inlined] _collect at ./array.jl:810 pmap2 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:89 unknown function (ip: 0x7f4d118fce03) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:179 [inlined] macro expansion at ./task.jl:662 [inlined] assign_mcmc_work at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/utils.jl:172 #mcmc_master!#48 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:166 mcmc_master! at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:135 [inlined] #mcmc#47 at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:123 mcmc at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/src/model/mcmc.jl:75 unknown function (ip: 0x7f4d11651fcc) at (unknown file) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_body at /source/src/interpreter.c:581 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_61918.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/utils.jl:5 [inlined] macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:94 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] macro expansion at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:93 [inlined] macro expansion at /source/usr/share/julia/stdlib/v1.12/Test/src/Test.jl:1776 [inlined] top-level scope at /home/pkgeval/.julia/packages/MCPhylo/KWPlY/test/runtests.jl:56 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_invoke at /source/src/gf.c:4021 jl_toplevel_eval_flex at /source/src/toplevel.c:1024 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 include_string at ./loading.jl:2870 _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 _include at ./loading.jl:2930 include at ./Base.jl:307 IncludeInto at ./Base.jl:308 jfptr_IncludeInto_61918.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:689 jl_interpret_toplevel_thunk at /source/src/interpreter.c:898 jl_toplevel_eval_flex at /source/src/toplevel.c:1035 jl_toplevel_eval_flex at /source/src/toplevel.c:975 ijl_toplevel_eval at /source/src/toplevel.c:1047 ijl_toplevel_eval_in at /source/src/toplevel.c:1092 eval at ./boot.jl:489 exec_options at ./client.jl:283 _start at ./client.jl:550 jfptr__start_55866.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4014 [inlined] ijl_apply_generic at /source/src/gf.c:4214 jl_apply at /source/src/julia.h:2391 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1139 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7f4d2d1dd249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 6499809898 (Pool: 6499804211; Big: 5687); GC: 4289 PkgEval terminated after 2723.42s: test duration exceeded the time limit