Package evaluation to test Diversity on Julia 1.14.0-DEV.3155 (07edee4e4c*) started at 2026-09-10T17:02:11.385 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 15.28s ################################################################################ # Installation # Installing Diversity... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [d3d5718d] + Diversity v0.6.3 Updating `~/.julia/environments/v1.14/Manifest.toml` [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.2.0 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.2 [864edb3b] + DataStructures v0.19.6 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [d3d5718d] + Diversity v0.6.3 [a58aae7d] + EcoBase v0.2.0 ⌅ [842dd82b] + InlineStrings v1.4.6 [41ab1584] + InvertedIndices v1.3.1 [82899510] + IteratorInterfaceExtensions v1.0.0 [b964fa9f] + LaTeXStrings v1.4.1 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v2.0.1 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.4 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.4.8 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [91c51154] + SentinelArrays v1.4.10 [a2af1166] + SortingAlgorithms v1.2.3 [10745b16] + Statistics v1.11.5 [82ae8749] + StatsAPI v1.8.0 [88034a9c] + StringDistances v1.0.1 ⌅ [892a3eda] + StringManipulation v0.5.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.14.0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.13.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.14.0 [d6f4376e] + Markdown v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.13.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.13.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.5.7+0 [4536629a] + OpenBLAS_jll v0.3.34+0 [8e850b90] + libblastrampoline_jll v5.15.0+0 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 To see why use `status --outdated -m` Installation completed after 3.85s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... ┌ Warning: Could not use exact versions of packages in manifest, re-resolving └ @ TestEnv ~/.julia/packages/TestEnv/sTG3E/src/julia-1.13/activate_set.jl:78 Precompiling package dependencies... Precompiling project... 2.9 s ✓ StringDistances 5.1 s ✓ ResearchSoftwareMetadata 2.5 s ✓ NamedArrays 5.4 s ✓ StatsBase 4.0 s ✓ BioSymbols 1.9 s ✓ Arpack_jll 2.0 s ✓ CommonMark → CommonMarkMarkdownASTExt [ Info: Compiling VCF parser... 13.8 s ✓ VariantCallFormat 2.1 s ✓ EcoBase 1.5 s ✓ Roots → RootsUnitfulExt 9.7 s ✓ Graphs 2.6 s ✓ TreeSitter 2.1 s ✓ CategoricalArrays → CategoricalArraysJSONExt 0.0 s ✓ Conda 1.8 s ✓ ColorVectorSpace → SpecialFunctionsExt 47.5 s ✓ Documenter 6.2 s ✓ Latexify → DataFramesExt 3.1 s ✓ Unitful → LatexifyExt 1.9 s ✓ TableMetadataTools 3.1 s ✓ RandomBooleanMatrices 3.8 s ✓ OnlineStatsBase 4.9 s ✓ CategoricalArrays → CategoricalArraysStatsBaseExt 6.1 s ✓ StatsModels 11.2 s ✓ Distributions 5.3 s ✓ Clustering 111.2 s ✓ Plots 8.7 s ✓ BioSequences 1.2 s ✓ Arpack 9.7 s ✓ PopGenCore 5.9 s ✓ Diversity 5.3 s ✓ Highlights 7.1 s ✓ DataFramesMeta 13.2 s ✓ RCall 4.4 s ✓ MultipleTesting 5.0 s ✓ Distributions → DistributionsTestExt 6.5 s ✓ OnlineStats 18.9 s ✓ Phylo 17.3 s ✓ Plots → UnitfulExt 1.4 s ✓ FASTX → BioSequencesExt 4.8 s ✓ MultivariateStats 6.5 s ✓ Diversity → DiversityAxisArraysExt 6.5 s ✓ Diversity → DiversityBioSequencesExt 63.8 s ✓ Term 7.1 s ✓ SpatialEcology 9.7 s ✓ RCall → RCallAxisArraysExt 12.3 s ✓ Phylo → PhyloRCallExt 9.0 s ✓ Diversity → DiversityPhyloExt 18.8 s ✓ PopGen 21.0 s ✓ Diversity → DiversityPopGenExt 48 dependencies successfully precompiled in 528 seconds. 300 already precompiled. 1 dependency had output during precompilation: ┌ VariantCallFormat │ [ Info: Compiling VCF parser... └ Precompilation completed after 589.26s ################################################################################ # Testing # Testing Diversity Test Could not use exact versions of packages in manifest, re-resolving. Note: if you do not check your manifest file into source control, then you can probably ignore this message. However, if you do check your manifest file into source control, then you probably want to pass the `allow_reresolve = false` kwarg when calling the `Pkg.test` function. Updating `/tmp/jl_ot2Def/Project.toml` [39de3d68] + AxisArrays v0.4.8 [7e6ae17a] + BioSequences v3.5.2 [336ed68f] + CSV v0.10.17 [d3d5718d] + Diversity v0.6.3 [e30172f5] + Documenter v1.19.0 [c2308a5c] + FASTX v2.2.0 [d7ba0133] + Git v1.5.0 [98e50ef6] + JuliaFormatter v2.14.0 [d3525ed8] + ParallelTestRunner v2.8.2 [aea672f4] + Phylo v0.5.4 [91a5bcdd] + Plots v1.41.7 [af524d12] + PopGen v0.9.5 [6f49c342] + RCall v0.14.13 [58378933] + ResearchSoftwareMetadata v0.3.1 [348f2d5d] + SpatialEcology v0.11.0 ⌅ [2913bbd2] + StatsBase v0.33.21 [56ddb016] ~ Logging ⇒ v1.11.0 [44cfe95a] ~ Pkg ⇒ v1.14.0 [8dfed614] ~ Test ⇒ v1.11.0 Updating `/tmp/jl_ot2Def/Manifest.toml` [a4c015fc] + ANSIColoredPrinters v0.0.1 [1520ce14] + AbstractTrees v0.4.5 [7d9f7c33] + Accessors v0.1.45 [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [7d9fca2a] + Arpack v0.5.4 [15f4f7f2] + AutoHashEquals v2.2.0 [67c07d97] + Automa v1.2.0 [39de3d68] + AxisArrays v0.4.8 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [7e6ae17a] + BioSequences v3.5.2 [3c28c6f8] + BioSymbols v5.2.0 [e1450e63] + BufferedStreams v1.2.2 [fa961155] + CEnum v0.5.0 [336ed68f] + CSV v0.10.17 [324d7699] + CategoricalArrays v1.1.1 [8be319e6] + Chain v1.0.0 [aaaa29a8] + Clustering v0.15.8 [da1fd8a2] + CodeTracking v3.0.2 [944b1d66] + CodecZlib v0.7.9 [35d6a980] + ColorSchemes v3.31.0 [3da002f7] + ColorTypes v0.12.1 [c3611d14] + ColorVectorSpace v0.11.0 [5ae59095] + Colors v0.13.1 [861a8166] + Combinatorics v1.1.0 [a80b9123] + CommonMark v1.0.4 [38540f10] + CommonSolve v0.2.14 [a33af91c] + CompositionsBase v0.1.2 [8f4d0f93] + Conda v1.10.3 [187b0558] + ConstructionBase v1.6.0 [d38c429a] + Contour v0.6.3 [1313f7d8] + DataFramesMeta v0.15.6 ⌅ [864edb3b] ↓ DataStructures v0.19.6 ⇒ v0.18.22 [e7dc6d0d] + DataValues v0.4.13 [8bb1440f] + DelimitedFiles v1.9.1 [31c24e10] + Distributions v0.25.131 [d3d5718d] + Diversity v0.6.3 [ffbed154] + DocStringExtensions v0.9.5 [e30172f5] + Documenter v1.19.0 [4e289a0a] + EnumX v1.0.7 [c2308a5c] + FASTX v2.2.0 [c87230d0] + FFMPEG v0.4.5 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.17.0 ⌅ [53c48c17] + FixedPointNumbers v0.8.6 [1fa38f19] + Format v1.3.7 [28b8d3ca] + GR v0.73.27 ⌃ [a0844989] + Gamma v1.1.0 [d7ba0133] + Git v1.5.0 [c27321d9] + Glob v1.5.0 ⌃ [86223c79] + Graphs v1.13.1 [cd3eb016] + HTTP v2.6.7 [eafb193a] + Highlights v0.6.2 [34004b35] + HypergeometricFunctions v0.3.30 [b5f81e59] + IOCapture v1.0.0 [d25df0c9] + Inflate v0.1.5 [8197267c] + IntervalSets v0.7.14 [3587e190] + InverseFunctions v0.1.17 [92d709cd] + IrrationalConstants v0.2.6 [c8e1da08] + IterTools v1.10.0 [1c8ee90f] + IterableTables v1.0.0 [1019f520] + JLFzf v0.1.11 [692b3bcd] + JLLWrappers v1.8.0 [682c06a0] + JSON v1.8.0 [98e50ef6] + JuliaFormatter v2.14.0 [70703baa] + JuliaSyntax v1.0.2 [23fbe1c1] + Latexify v0.16.12 [0e77f7df] + LazilyInitializedFields v1.3.0 ⌅ [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [36869731] + Malt v1.4.1 [d0879d2d] + MarkdownAST v0.1.3 [442fdcdd] + Measures v0.3.3 ⌅ [f8716d33] + MultipleTesting v0.5.1 [6f286f6a] + MultivariateStats v0.10.5 [1c23619d] + MyterialColors v0.3.0 [77ba4419] + NaNMath v1.1.4 [86f7a689] + NamedArrays v0.10.5 [b8a86587] + NearestNeighbors v0.4.29 [a15396b6] + OnlineStats v1.7.4 [925886fa] + OnlineStatsBase v1.7.3 ⌅ [bac558e1] ↓ OrderedCollections v2.0.1 ⇒ v1.8.2 ⌃ [90014a1f] + PDMats v0.11.35 [d3525ed8] + ParallelTestRunner v2.8.2 [d96e819e] + Parameters v0.13.1 [fae87a5f] + ParserCombinator v2.2.1 ⌅ [69de0a69] + Parsers v2.8.8 [aea672f4] + Phylo v0.5.4 [ccf2f8ad] + PlotThemes v3.3.0 [995b91a9] + PlotUtils v1.4.4 [91a5bcdd] + Plots v1.41.7 [af524d12] + PopGen v0.9.5 [45b36091] + PopGenCore v0.7.3 [33c8b6b6] + ProgressLogging v0.1.6 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.3 [6f49c342] + RCall v0.14.13 [9ae346a0] + RandomBooleanMatrices v0.1.2 [e6cf234a] + RandomNumbers v1.6.0 [b3c3ace0] + RangeArrays v0.3.2 [01d81517] + RecipesPipeline v0.6.12 [2792f1a3] + RegistryInstances v0.1.0 [05181044] + RelocatableFolders v1.0.1 [ae029012] + Requires v1.3.1 [58378933] + ResearchSoftwareMetadata v0.3.1 [802f3686] + Reseau v1.4.1 [79098fc4] + Rmath v0.9.0 [f2b01f46] + Roots v3.0.8 [6c6a2e73] + Scratch v1.3.0 [1277b4bf] + ShiftedArrays v2.0.0 [992d4aef] + Showoff v1.1.1 [699a6c99] + SimpleTraits v0.9.6 [348f2d5d] + SpatialEcology v0.11.0 [276daf66] + SpecialFunctions v2.9.0 [860ef19b] + StableRNGs v1.0.4 [90137ffa] + StaticArrays v1.9.20 [1e83bf80] + StaticArraysCore v1.4.4 ⌅ [2913bbd2] + StatsBase v0.33.21 [4c63d2b9] + StatsFuns v2.2.1 [3eaba693] + StatsModels v0.7.10 [69024149] + StringEncodings v0.3.7 [354b36f9] + StringViews v2.0.1 [ec057cc2] + StructUtils v2.8.5 [9ce81f87] + TableMetadataTools v0.1.0 [382cd787] + TableTraitsUtils v1.0.2 [62fd8b95] + TensorCore v0.1.1 [22787eb5] + Term v2.2.0 [0796e94c] + Tokenize v0.5.29 [3bb67fe8] + TranscodingStreams v0.11.3 ⌅ [f42328cb] + TreeSitter v0.2.3 [7200193e] + Twiddle v1.1.2 [5c2747f8] + URIs v1.7.0 [3a884ed6] + UnPack v1.0.2 [1cfade01] + UnicodeFun v0.4.1 [1986cc42] + Unitful v1.29.0 [41fe7b60] + Unzip v0.2.0 [28eba6e3] + VariantCallFormat v0.5.9 [81def892] + VersionParsing v1.3.0 [ea10d353] + WeakRefStrings v1.4.3 [1b915085] + WinReg v1.0.0 [76eceee3] + WorkerUtilities v1.6.1 [ddb6d928] + YAML v0.4.16 ⌅ [68821587] + Arpack_jll v3.5.2+0 [6e34b625] + Bzip2_jll v1.0.9+0 [83423d85] + Cairo_jll v1.18.7+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.8.4+0 ⌅ [b22a6f82] + FFMPEG_jll v8.1.2+0 [a3f928ae] + Fontconfig_jll v2.17.1+0 [d7e528f0] + FreeType2_jll v2.14.3+1 [559328eb] + FriBidi_jll v1.0.17+0 [0656b61e] + GLFW_jll v3.5.1+0 [d2c73de3] + GR_jll v0.73.27+0 ⌅ [b0724c58] + GettextRuntime_jll v0.22.4+0 [61579ee1] + Ghostscript_jll v9.55.1+0 [020c3dae] + Git_LFS_jll v3.7.1+0 [f8c6e375] + Git_jll v2.55.0+0 [7746bdde] + Glib_jll v2.88.3+0 [3b182d85] + Graphite2_jll v1.3.16+0 [2e76f6c2] + HarfBuzz_jll v100.14004.0+0 [aacddb02] + JpegTurbo_jll v3.2.0+1 [c1c5ebd0] + LAME_jll v3.100.3+0 [88015f11] + LERC_jll v4.2.0+0 [1d63c593] + LLVMOpenMP_jll v22.1.7+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 v2.42.0+0 [89763e89] + Libtiff_jll v4.7.3+0 [38a345b3] + Libuuid_jll v2.42.0+0 [e7412a2a] + Ogg_jll v1.3.6+0 [9bd350c2] + OpenSSH_jll v10.5.1+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [91d4177d] + Opus_jll v1.6.1+0 [36c8627f] + Pango_jll v1.58.2+0 [30392449] + Pixman_jll v0.46.4+0 [c0090381] + Qt6Base_jll v6.10.2+2 [629bc702] + Qt6Declarative_jll v6.10.2+2 [ce943373] + Qt6ShaderTools_jll v6.10.2+1 [6de9746b] + Qt6Svg_jll v6.10.2+0 [e99dba38] + Qt6Wayland_jll v6.10.2+1 [f50d1b31] + Rmath_jll v0.5.2+0 [a44049a8] + Vulkan_Loader_jll v1.3.243+0 [a2964d1f] + Wayland_jll v1.24.0+0 [ffd25f8a] + XZ_jll v5.8.3+0 [f67eecfb] + Xorg_libICE_jll v1.1.2+0 [c834827a] + Xorg_libSM_jll v1.2.6+0 [4f6342f7] + Xorg_libX11_jll v1.8.13+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 v1.3.8+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] + Xorg_libXi_jll v1.8.4+0 [d1454406] + Xorg_libXinerama_jll v1.1.7+0 [ec84b674] + Xorg_libXrandr_jll v1.5.6+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [a65dc6b1] + Xorg_libpciaccess_jll v0.19.0+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.2.0+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 v2.47.0+2 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [35ca27e7] + eudev_jll v3.2.14+0 ⌅ [214eeab7] + fzf_jll v0.61.1+0 [a4ae2306] + libaom_jll v3.14.1+0 [0ac62f75] + libass_jll v0.17.5+0 [1183f4f0] + libdecor_jll v0.2.2+0 [8e53e030] + libdrm_jll v2.4.134+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 v1.6.58+0 [9a156e7d] + libva_jll v2.23.0+0 [f27f6e37] + libvorbis_jll v1.3.8+0 [009596ad] + mtdev_jll v1.1.7+0 ⌅ [695101d5] + tree_sitter_jll v0.25.10+0 [52be201e] + tree_sitter_julia_jll v0.25.0+0 ⌅ [1270edf5] + x264_jll v10164.0.1+0 [dfaa095f] + x265_jll v4.1.0+0 [d8fb68d0] + xkbcommon_jll v1.13.0+0 [0dad84c5] + ArgTools v1.2.0 [8ba89e20] + Distributed v1.12.0 [f43a241f] + Downloads v1.7.0 [b27032c2] + LibCURL v1.0.0 [76f85450] + LibGit2 v1.11.0 [56ddb016] ~ Logging ⇒ v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] ~ Pkg ⇒ v1.14.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [2f01184e] + SparseArrays v1.13.0 [4607b0f0] + SuiteSparse [a4e569a6] + Tar v1.10.0 [8dfed614] ~ Test ⇒ v1.11.0 [deac9b47] + LibCURL_jll v8.22.0+0 [e37daf67] + LibGit2_jll v1.9.7+0 [29816b5a] + LibSSH2_jll v1.11.104+0 [14a3606d] + MozillaCACerts_jll v2026.8.13 [05823500] + OpenLibm_jll v0.8.8+0 [458c3c95] + OpenSSL_jll v3.5.8+0 [efcefdf7] + PCRE2_jll v10.48.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850ede] + nghttp2_jll v1.70.0+0 [3f19e933] + p7zip_jll v17.8.2+0 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Test Successfully re-resolved Status `/tmp/jl_ot2Def/Project.toml` [39de3d68] AxisArrays v0.4.8 [7e6ae17a] BioSequences v3.5.2 [336ed68f] CSV v0.10.17 [a93c6f00] DataFrames v1.8.2 [b4f34e82] Distances v0.10.12 [d3d5718d] Diversity v0.6.3 [e30172f5] Documenter v1.19.0 [a58aae7d] EcoBase v0.2.0 [c2308a5c] FASTX v2.2.0 [d7ba0133] Git v1.5.0 [98e50ef6] JuliaFormatter v2.14.0 [e1d29d7a] Missings v1.2.0 [d3525ed8] ParallelTestRunner v2.8.2 [aea672f4] Phylo v0.5.4 [91a5bcdd] Plots v1.41.7 [af524d12] PopGen v0.9.5 [6f49c342] RCall v0.14.13 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.3.1 [348f2d5d] SpatialEcology v0.11.0 [10745b16] Statistics v1.11.5 ⌅ [2913bbd2] StatsBase v0.33.21 [88034a9c] StringDistances v1.0.1 [bd369af6] Tables v1.14.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.14.0 [9a3f8284] Random v1.11.0 [fa267f1f] TOML v1.0.3 [8dfed614] Test v1.11.0 Status `/tmp/jl_ot2Def/Manifest.toml` [a4c015fc] ANSIColoredPrinters v0.0.1 [1520ce14] AbstractTrees v0.4.5 [7d9f7c33] Accessors v0.1.45 [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [7d9fca2a] Arpack v0.5.4 [15f4f7f2] AutoHashEquals v2.2.0 [67c07d97] Automa v1.2.0 [39de3d68] AxisArrays v0.4.8 [28d598bf] BGZFStreams v0.3.2 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.5.2 [3c28c6f8] BioSymbols v5.2.0 [e1450e63] BufferedStreams v1.2.2 [fa961155] CEnum v0.5.0 [336ed68f] CSV v0.10.17 [324d7699] CategoricalArrays v1.1.1 [8be319e6] Chain v1.0.0 [aaaa29a8] Clustering v0.15.8 [da1fd8a2] CodeTracking v3.0.2 [944b1d66] CodecZlib v0.7.9 [35d6a980] ColorSchemes v3.31.0 [3da002f7] ColorTypes v0.12.1 [c3611d14] ColorVectorSpace v0.11.0 [5ae59095] Colors v0.13.1 [861a8166] Combinatorics v1.1.0 [a80b9123] CommonMark v1.0.4 [38540f10] CommonSolve v0.2.14 [34da2185] Compat v4.18.1 [a33af91c] CompositionsBase v0.1.2 [8f4d0f93] Conda v1.10.3 [187b0558] ConstructionBase v1.6.0 [d38c429a] Contour v0.6.3 [a8cc5b0e] Crayons v4.2.0 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.2 [1313f7d8] DataFramesMeta v0.15.6 ⌅ [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [e7dc6d0d] DataValues v0.4.13 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.131 [d3d5718d] Diversity v0.6.3 [ffbed154] DocStringExtensions v0.9.5 [e30172f5] Documenter v1.19.0 [a58aae7d] EcoBase v0.2.0 [4e289a0a] EnumX v1.0.7 [c2308a5c] FASTX v2.2.0 [c87230d0] FFMPEG v0.4.5 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.17.0 ⌅ [53c48c17] FixedPointNumbers v0.8.6 [1fa38f19] Format v1.3.7 [28b8d3ca] GR v0.73.27 ⌃ [a0844989] Gamma v1.1.0 [d7ba0133] Git v1.5.0 [c27321d9] Glob v1.5.0 ⌃ [86223c79] Graphs v1.13.1 [cd3eb016] HTTP v2.6.7 [eafb193a] Highlights v0.6.2 [34004b35] HypergeometricFunctions v0.3.30 [b5f81e59] IOCapture v1.0.0 [d25df0c9] Inflate v0.1.5 ⌅ [842dd82b] InlineStrings v1.4.6 [8197267c] IntervalSets v0.7.14 [3587e190] InverseFunctions v0.1.17 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.6 [c8e1da08] IterTools v1.10.0 [1c8ee90f] IterableTables v1.0.0 [82899510] IteratorInterfaceExtensions v1.0.0 [1019f520] JLFzf v0.1.11 [692b3bcd] JLLWrappers v1.8.0 [682c06a0] JSON v1.8.0 [98e50ef6] JuliaFormatter v2.14.0 [70703baa] JuliaSyntax v1.0.2 [b964fa9f] LaTeXStrings v1.4.1 [23fbe1c1] Latexify v0.16.12 [0e77f7df] LazilyInitializedFields v1.3.0 ⌅ [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [36869731] Malt v1.4.1 [d0879d2d] MarkdownAST v0.1.3 [442fdcdd] Measures v0.3.3 [e1d29d7a] Missings v1.2.0 ⌅ [f8716d33] MultipleTesting v0.5.1 [6f286f6a] MultivariateStats v0.10.5 [1c23619d] MyterialColors v0.3.0 [77ba4419] NaNMath v1.1.4 [86f7a689] NamedArrays v0.10.5 [b8a86587] NearestNeighbors v0.4.29 [a15396b6] OnlineStats v1.7.4 [925886fa] OnlineStatsBase v1.7.3 ⌅ [bac558e1] OrderedCollections v1.8.2 ⌃ [90014a1f] PDMats v0.11.35 [d3525ed8] ParallelTestRunner v2.8.2 [d96e819e] Parameters v0.13.1 [fae87a5f] ParserCombinator v2.2.1 ⌅ [69de0a69] Parsers v2.8.8 [aea672f4] Phylo v0.5.4 [ccf2f8ad] PlotThemes v3.3.0 [995b91a9] PlotUtils v1.4.4 [91a5bcdd] Plots v1.41.7 [2dfb63ee] PooledArrays v1.4.3 [af524d12] PopGen v0.9.5 [45b36091] PopGenCore v0.7.3 [aea7be01] PrecompileTools v1.3.4 [21216c6a] Preferences v1.5.2 [08abe8d2] PrettyTables v3.4.8 [33c8b6b6] ProgressLogging v0.1.6 [43287f4e] PtrArrays v1.4.0 [1fd47b50] QuadGK v2.11.3 [6f49c342] RCall v0.14.13 [9ae346a0] RandomBooleanMatrices v0.1.2 [e6cf234a] RandomNumbers v1.6.0 [b3c3ace0] RangeArrays v0.3.2 [3cdcf5f2] RecipesBase v1.3.4 [01d81517] RecipesPipeline v0.6.12 [189a3867] Reexport v1.2.2 [2792f1a3] RegistryInstances v0.1.0 [05181044] RelocatableFolders v1.0.1 [ae029012] Requires v1.3.1 [58378933] ResearchSoftwareMetadata v0.3.1 [802f3686] Reseau v1.4.1 [79098fc4] Rmath v0.9.0 [f2b01f46] Roots v3.0.8 [6c6a2e73] Scratch v1.3.0 [91c51154] SentinelArrays v1.4.10 [1277b4bf] ShiftedArrays v2.0.0 [992d4aef] Showoff v1.1.1 [699a6c99] SimpleTraits v0.9.6 [a2af1166] SortingAlgorithms v1.2.3 [348f2d5d] SpatialEcology v0.11.0 [276daf66] SpecialFunctions v2.9.0 [860ef19b] StableRNGs v1.0.4 [90137ffa] StaticArrays v1.9.20 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.5 [82ae8749] StatsAPI v1.8.0 ⌅ [2913bbd2] StatsBase v0.33.21 [4c63d2b9] StatsFuns v2.2.1 [3eaba693] StatsModels v0.7.10 [88034a9c] StringDistances v1.0.1 [69024149] StringEncodings v0.3.7 ⌅ [892a3eda] StringManipulation v0.5.0 [354b36f9] StringViews v2.0.1 [ec057cc2] StructUtils v2.8.5 [9ce81f87] TableMetadataTools v0.1.0 [3783bdb8] TableTraits v1.0.1 [382cd787] TableTraitsUtils v1.0.2 [bd369af6] Tables v1.14.0 [62fd8b95] TensorCore v0.1.1 [22787eb5] Term v2.2.0 [0796e94c] Tokenize v0.5.29 [3bb67fe8] TranscodingStreams v0.11.3 ⌅ [f42328cb] TreeSitter v0.2.3 [7200193e] Twiddle v1.1.2 [5c2747f8] URIs v1.7.0 [3a884ed6] UnPack v1.0.2 [1cfade01] UnicodeFun v0.4.1 [1986cc42] Unitful v1.29.0 [41fe7b60] Unzip v0.2.0 [28eba6e3] VariantCallFormat v0.5.9 [81def892] VersionParsing v1.3.0 [ea10d353] WeakRefStrings v1.4.3 [1b915085] WinReg v1.0.0 [76eceee3] WorkerUtilities v1.6.1 [ddb6d928] YAML v0.4.16 ⌅ [68821587] Arpack_jll v3.5.2+0 [6e34b625] Bzip2_jll v1.0.9+0 [83423d85] Cairo_jll v1.18.7+0 [ee1fde0b] Dbus_jll v1.16.2+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.8.4+0 ⌅ [b22a6f82] FFMPEG_jll v8.1.2+0 [a3f928ae] Fontconfig_jll v2.17.1+0 [d7e528f0] FreeType2_jll v2.14.3+1 [559328eb] FriBidi_jll v1.0.17+0 [0656b61e] GLFW_jll v3.5.1+0 [d2c73de3] GR_jll v0.73.27+0 ⌅ [b0724c58] GettextRuntime_jll v0.22.4+0 [61579ee1] Ghostscript_jll v9.55.1+0 [020c3dae] Git_LFS_jll v3.7.1+0 [f8c6e375] Git_jll v2.55.0+0 [7746bdde] Glib_jll v2.88.3+0 [3b182d85] Graphite2_jll v1.3.16+0 [2e76f6c2] HarfBuzz_jll v100.14004.0+0 [aacddb02] JpegTurbo_jll v3.2.0+1 [c1c5ebd0] LAME_jll v3.100.3+0 [88015f11] LERC_jll v4.2.0+0 [1d63c593] LLVMOpenMP_jll v22.1.7+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 v2.42.0+0 [89763e89] Libtiff_jll v4.7.3+0 [38a345b3] Libuuid_jll v2.42.0+0 [e7412a2a] Ogg_jll v1.3.6+0 [9bd350c2] OpenSSH_jll v10.5.1+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [91d4177d] Opus_jll v1.6.1+0 [36c8627f] Pango_jll v1.58.2+0 [30392449] Pixman_jll v0.46.4+0 [c0090381] Qt6Base_jll v6.10.2+2 [629bc702] Qt6Declarative_jll v6.10.2+2 [ce943373] Qt6ShaderTools_jll v6.10.2+1 [6de9746b] Qt6Svg_jll v6.10.2+0 [e99dba38] Qt6Wayland_jll v6.10.2+1 [f50d1b31] Rmath_jll v0.5.2+0 [a44049a8] Vulkan_Loader_jll v1.3.243+0 [a2964d1f] Wayland_jll v1.24.0+0 [ffd25f8a] XZ_jll v5.8.3+0 [f67eecfb] Xorg_libICE_jll v1.1.2+0 [c834827a] Xorg_libSM_jll v1.2.6+0 [4f6342f7] Xorg_libX11_jll v1.8.13+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 v1.3.8+0 [d091e8ba] Xorg_libXfixes_jll v6.0.2+0 [a51aa0fd] Xorg_libXi_jll v1.8.4+0 [d1454406] Xorg_libXinerama_jll v1.1.7+0 [ec84b674] Xorg_libXrandr_jll v1.5.6+0 [ea2f1a96] Xorg_libXrender_jll v0.9.12+0 [a65dc6b1] Xorg_libpciaccess_jll v0.19.0+0 [c7cfdc94] Xorg_libxcb_jll v1.17.1+0 [cc61e674] Xorg_libxkbfile_jll v1.2.0+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 v2.47.0+2 [c5fb5394] Xorg_xtrans_jll v1.6.0+0 [35ca27e7] eudev_jll v3.2.14+0 ⌅ [214eeab7] fzf_jll v0.61.1+0 [a4ae2306] libaom_jll v3.14.1+0 [0ac62f75] libass_jll v0.17.5+0 [1183f4f0] libdecor_jll v0.2.2+0 [8e53e030] libdrm_jll v2.4.134+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 v1.6.58+0 [9a156e7d] libva_jll v2.23.0+0 [f27f6e37] libvorbis_jll v1.3.8+0 [009596ad] mtdev_jll v1.1.7+0 ⌅ [695101d5] tree_sitter_jll v0.25.10+0 [52be201e] tree_sitter_julia_jll v0.25.0+0 ⌅ [1270edf5] x264_jll v10164.0.1+0 [dfaa095f] x265_jll v4.1.0+0 [d8fb68d0] xkbcommon_jll v1.13.0+0 [0dad84c5] ArgTools v1.2.0 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.12.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.13.0 [b27032c2] LibCURL v1.0.0 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.14.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [3fa0cd96] REPL v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.13.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v1.5.7+0 [deac9b47] LibCURL_jll v8.22.0+0 [e37daf67] LibGit2_jll v1.9.7+0 [29816b5a] LibSSH2_jll v1.11.104+0 [14a3606d] MozillaCACerts_jll v2026.8.13 [4536629a] OpenBLAS_jll v0.3.34+0 [05823500] OpenLibm_jll v0.8.8+0 [458c3c95] OpenSSL_jll v3.5.8+0 [efcefdf7] PCRE2_jll v10.48.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.70.0+0 [3f19e933] p7zip_jll v17.8.2+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. Testing Running tests... [ Info: Running the core test sets: = core_ext.jl = core_test.jl * Running core_ext.jl ... [ Info: Running tests for extensions: = DiversityAxisArraysExt.jl = DiversityBioSequencesExt.jl = DiversityPhyloExt.jl = DiversityPopGenExt.jl [ Info: Running extension tests... * Testing DiversityAxisArraysExt.jl extension... * Testing DiversityBioSequencesExt.jl extension... * Testing DiversityPhyloExt.jl extension... * Testing DiversityPopGenExt.jl extension... * Running core_test.jl ... [ Info: Running tests for files: = API.jl = Diversity.jl = DiversityMeasure.jl = EcoBase.jl = Ecology.jl = EffectiveNumbers.jl = GeneralisedDiversities.jl = Hill.jl = Interface.jl = Iterators.jl = Jost.jl = Metacommunity.jl = Partition.jl = Types.jl Running 14 tests using 1 parallel jobs. If this is too many concurrent jobs, specify the `--jobs=N` argument to the tests, or set the `JULIA_CPU_THREADS` environment variable. │ Test │ ──────────────── CPU ──────────────── │ Test (Worker) │ time (s) │ GC (s) │ GC % │ Alloc (MB) │ RSS (MB) │ test_DiversityMeasure (1) │ 125.42 │ 1.76 │ 1.4 │ 3672.79 │ 1057.34 │ test_Iterators (1) │ 4.43 │ 0.00 │ 0.0 │ 117.85 │ 1057.34 │ test_Metacommunity (1) │ 10.53 │ 0.00 │ 0.0 │ 215.78 │ 1057.34 │ test_API (1) │ 4.47 │ 0.00 │ 0.0 │ 111.93 │ 1057.34 │ test_Hill (1) │ 8.40 │ 0.10 │ 1.2 │ 407.58 │ 1057.34 │ test_Ecology (1) │ 13.93 │ 0.00 │ 0.0 │ 309.87 │ 1057.34 │ test_EcoBase (1) │ 118.77 │ 1.47 │ 1.2 │ 3113.59 │ 1119.66 │ test_Diversity (1) │ 3.42 │ 0.00 │ 0.0 │ 84.46 │ 1119.66 │ test_Interface (1) │ 1.47 │ 0.00 │ 0.0 │ 21.33 │ 1120.66 │ test_Jost (1) │ 33.14 │ 0.14 │ 0.4 │ 837.72 │ 1322.22 │ test_Types (1) │ 5.14 │ 0.00 │ 0.0 │ 102.93 │ 1322.22 │ test_Partition (1) │ 1.09 │ 0.00 │ 0.0 │ 9.49 │ 1322.22 │ test_GeneralisedDiversities (1) │ 1.71 │ 0.00 │ 0.0 │ 30.04 │ 1322.22 │ test_EffectiveNumbers (1) │ 7.38 │ 0.00 │ 0.0 │ 149.84 │ 1322.22 │ Output generated during execution of 'test_DiversityMeasure': ┌ ┌ Warning: Abundances not normalised to 1, correcting... └ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 Output generated during execution of 'test_Metacommunity': ┌ ┌ Warning: Abundances not normalised to 1, correcting... └ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:86 Output generated during execution of 'test_API': ┌ ┌ Warning: Abundances not normalised to 1, correcting... │ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 │ ┌ Warning: Abundances not normalised to 1, correcting... │ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 │ ┌ Warning: Abundances not normalised to 1, correcting... └ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 Output generated during execution of 'test_Hill': ┌ ┌ Warning: Abundances not normalised to 1, correcting... └ └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 Output generated during execution of 'test_EcoBase': ┌ [ Info: Matrix data assumed to be presence-absence └ [ Info: Matrix data assumed to be presence-absence Test Summary: | Pass Broken Total Time Overall | 1174 2 1176 6m17.1s SUCCESS Test Summary: | Pass Total Time Diversity.jl | 112 112 8m26.4s [ Info: Running the extra test suites, in this order: = extras_canonical.jl = extras_pkg.jl = extras_docs.jl (concurrently) = extras_clean.jl (last) * Running extras_canonical.jl ... [ Info: Running canonical tests * test_measures.jl ... ┌ Warning: Abundances not normalised to 1, correcting... └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 ┌ Warning: Abundances not normalised to 1, correcting... └ @ Diversity ~/.julia/packages/Diversity/CB9lk/src/Metacommunity.jl:136 * test_paper.jl ... * test_types.jl ... * Running extras_pkg.jl ... [ Info: Cross validation packages: = Distances = RCall = StatsBase Running 3 tests using 1 parallel jobs. If this is too many concurrent jobs, specify the `--jobs=N` argument to the tests, or set the `JULIA_CPU_THREADS` environment variable. │ Test │ ──────────────── CPU ──────────────── │ Test (Worker) │ time (s) │ GC (s) │ GC % │ Alloc (MB) │ RSS (MB) │ pkg_StatsBase (2) │ 22.28 │ 0.42 │ 1.9 │ 546.02 │ 1074.25 │ pkg_Distances (2) │ 10.35 │ 0.28 │ 2.7 │ 509.09 │ 1074.25 │ pkg_RCall (2) │ 57.41 │ 0.50 │ 0.9 │ 789.11 │ 1074.25 │ Output generated during execution of 'pkg_RCall': ┌ ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. │ │ caller = tryEval(expr::Ptr{RCall.LangSxp}, env::Ptr{RCall.EnvSxp}, status::Base.RefValue{Int32}) at eval.jl:92 [inlined] │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/eval.jl:92 │ ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. │ │ caller = tryEval(expr::Ptr{RCall.LangSxp}, env::Ptr{RCall.EnvSxp}, status::Base.RefValue{Int32}) at eval.jl:92 [inlined] │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/eval.jl:92 │ ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. │ │ caller = tryEval(expr::Ptr{RCall.LangSxp}, env::Ptr{RCall.EnvSxp}, status::Base.RefValue{Int32}) at eval.jl:92 [inlined] │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/eval.jl:92 │ ┌ Warning: `disable_sigint` no longer defers Ctrl-C: SIGINT is delivered as a cancellation of the current ^C scope and observed at cancellation points regardless of the sigatomic region this establishes. Shield a region from cancellation by scoping `Base.CANCEL_TOKEN => nothing` over it instead. │ │ caller = tryEval(expr::Ptr{RCall.LangSxp}, env::Ptr{RCall.EnvSxp}, status::Base.RefValue{Int32}) at eval.jl:92 [inlined] │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/eval.jl:92 │ ┌ Warning: RCall.jl: Loading required package: ape │ │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ │ there is no package called ‘ape’ │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/io.jl:166 │ * installing *source* package ‘lattice’ ... │ ** this is package ‘lattice’ version ‘0.23-1’ │ ** package ‘lattice’ successfully unpacked and MD5 sums checked │ ** using staged installation │ ** libs │ sh: 1: x86_64-conda-linux-gnu-cc: not found │ x86_64-conda-linux-gnu-cc -std=gnu23 -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -fno-merge-constants -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1782736072827/work=/usr/local/src/conda/r-base-4.6.1 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c init.c -o init.o │ /bin/sh: 1: x86_64-conda-linux-gnu-cc: not found │ make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:192: init.o] Error 127 │ ERROR: compilation failed for package ‘lattice’ │ * removing ‘/tmp/jl_wM2GQL/lattice’ │ * installing *source* package ‘Rcpp’ ... │ ** this is package ‘Rcpp’ version ‘1.1.2’ │ ** package ‘Rcpp’ successfully unpacked and MD5 sums checked │ ** using staged installation │ ** libs │ sh: 1: x86_64-conda-linux-gnu-c++: not found │ x86_64-conda-linux-gnu-c++ -std=gnu++20 -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -I../inst/include/ -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -fno-merge-constants -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1782736072827/work=/usr/local/src/conda/r-base-4.6.1 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c api.cpp -o api.o │ /bin/sh: 1: x86_64-conda-linux-gnu-c++: not found │ make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:199: api.o] Error 127 │ ERROR: compilation failed for package ‘Rcpp’ │ * removing ‘/tmp/jl_wM2GQL/Rcpp’ │ * installing *source* package ‘digest’ ... │ ** this is package ‘digest’ version ‘0.6.39’ │ ** package ‘digest’ successfully unpacked and MD5 sums checked │ ** using staged installation │ ** libs │ sh: 1: x86_64-conda-linux-gnu-cc: not found │ sh: 1: x86_64-conda-linux-gnu-c++: not found │ x86_64-conda-linux-gnu-c++ -std=gnu++20 -I"/home/pkgeval/.julia/conda/3/x86_64/lib/R/include" -DNDEBUG -I. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/pkgeval/.julia/conda/3/x86_64/include -I/home/pkgeval/.julia/conda/3/x86_64/include -Wl,-rpath-link,/home/pkgeval/.julia/conda/3/x86_64/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -fno-merge-constants -isystem /home/pkgeval/.julia/conda/3/x86_64/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1782736072827/work=/usr/local/src/conda/r-base-4.6.1 -fdebug-prefix-map=/home/pkgeval/.julia/conda/3/x86_64=/usr/local/src/conda-prefix -c SpookyV2.cpp -o SpookyV2.o │ /bin/sh: 1: x86_64-conda-linux-gnu-c++: not found │ make: *** [/home/pkgeval/.julia/conda/3/x86_64/lib/R/etc/Makeconf:199: SpookyV2.o] Error 127 │ ERROR: compilation failed for package ‘digest’ │ * removing ‘/tmp/jl_wM2GQL/digest’ │ ERROR: dependency ‘lattice’ is not available for package ‘nlme’ │ Perhaps try a variation of: │ install.packages('lattice') │ * removing ‘/tmp/jl_wM2GQL/nlme’ │ ERROR: dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ are not available for package ‘ape’ │ Perhaps try a variation of: │ install.packages(c('nlme', 'lattice', 'Rcpp', 'digest')) │ * removing ‘/tmp/jl_wM2GQL/ape’ │ ┌ Warning: RCall.jl: also installing the dependencies ‘nlme’, ‘lattice’, ‘Rcpp’, ‘digest’ │ │ │ │ trying URL 'http://cran.r-project.org/src/contrib/nlme_3.1-171.tar.gz' │ │ trying URL 'http://cran.r-project.org/src/contrib/lattice_0.23-1.tar.gz' │ │ trying URL 'http://cran.r-project.org/src/contrib/Rcpp_1.1.2.tar.gz' │ │ trying URL 'http://cran.r-project.org/src/contrib/digest_0.6.39.tar.gz' │ │ trying URL 'http://cran.r-project.org/src/contrib/ape_5.8-1.tar.gz' │ │ Warning in install.packages("ape", lib = "/tmp/jl_wM2GQL", repos = "http://cran.r-project.org") : │ │ installation of package ‘lattice’ had non-zero exit status │ │ Warning in install.packages("ape", lib = "/tmp/jl_wM2GQL", repos = "http://cran.r-project.org") : │ │ installation of package ‘Rcpp’ had non-zero exit status │ │ Warning in install.packages("ape", lib = "/tmp/jl_wM2GQL", repos = "http://cran.r-project.org") : │ │ installation of package ‘digest’ had non-zero exit status │ │ Warning in install.packages("ape", lib = "/tmp/jl_wM2GQL", repos = "http://cran.r-project.org") : │ │ installation of package ‘nlme’ had non-zero exit status │ │ Warning in install.packages("ape", lib = "/tmp/jl_wM2GQL", repos = "http://cran.r-project.org") : │ │ installation of package ‘ape’ had non-zero exit status │ │ │ │ The downloaded source packages are in │ │ ‘/tmp/RtmpGujpOs/downloaded_packages’ │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/io.jl:166 │ ┌ Warning: RCall.jl: Loading required package: ape │ │ Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : │ │ there is no package called ‘ape’ │ └ @ RCall ~/.julia/packages/RCall/fTLHT/src/io.jl:166 │ ┌ Warning: ape R package not installed and would not install, skipping R crossvalidation └ └ @ Main.var"##pkg_RCall#148".ValidateRCall.ValidateRCall_rdiversity ~/.julia/packages/Diversity/CB9lk/test/run_rcall.jl:53 Test Summary: | Pass Total Time Overall | 900 900 1m43.8s SUCCESS Test Summary: | Pass Total Time Serial extras... | 459 459 2m14.7s [ Info: Running these concurrently: extras_docs Running 1 tests using 1 parallel jobs. If this is too many concurrent jobs, specify the `--jobs=N` argument to the tests, or set the `JULIA_CPU_THREADS` environment variable. │ Test │ ──────────────── CPU ──────────────── │ Test (Worker) │ time (s) │ GC (s) │ GC % │ Alloc (MB) │ RSS (MB) │ extras_docs (3) │ 280.78 │ failed at 2026-09-10T17:29:27.788 Output generated during execution of 'extras_docs': ┌ │ [ Info: Running the executable code in docs/src ... │ * api.md - 1 executable block group(s) ... │ * ecology.md - 1 executable block group(s) ... │ * framework.md - 2 executable block group(s) ... │ * genetics.md - 2 executable block group(s) ... │ * hill.md - 1 executable block group(s) ... │ * index.md - 1 executable block group(s) ... │ * jost.md - 1 executable block group(s) ... │ * largescale.md - 1 executable block group(s) ... │ * metacommunities.md - 2 executable block group(s) ... │ * phylogenetics.md - 1 executable block group(s) ... │ * vegan.md - 1 executable block group(s) ... │ │ [ Info: Building the manual to check its cross-references ... │ ┌ Warning: Unable to determine HTML(edit_link = ...) from remote HEAD branch, defaulting to "master". │ │ Calling `git remote` failed with an exception. Set JULIA_DEBUG=Documenter to see the error. │ │ Unless this is due to a configuration error, the relevant variable should be set explicitly. └ └ @ Documenter ~/.julia/packages/Documenter/13nbQ/src/utilities/utilities.jl:952 Test Summary: | Pass Error Total Time Overall | 29 1 30 4m49.5s extras_docs | 29 1 30 4m40.8s Documentation code | 29 29 4m01.1s Documentation build | 1 1 19.9s FAILURE Error in testset Documentation build: Error During Test at /home/pkgeval/.julia/packages/Diversity/CB9lk/test/extras_docs.jl:191 Test threw exception Expression: isnothing(makedocs(root = docsdir, modules = DOCS_MODULES, sitename = DOCS_SITENAME, pages = DOCS_PAGES, build = mktempdir())) ArgumentError: Unable to automatically determine remote for main repo. > `repo` is not set, and makedocs is not in a Git repository. Configure `repo` and/or `remotes` appropriately, or set `remotes = nothing` to disable remote source links altogether (e.g. if not working in a Git repository). repo: nothing Stacktrace: [1] interpret_repo_and_remotes(; root::String, repo::String, remotes::Dict{Any, Any}) @ Documenter ~/.julia/packages/Documenter/13nbQ/src/documents.jl:711 [2] Documenter.Document(; root::String, source::String, build::String, workdir::Symbol, format::Documenter.HTMLWriter.HTML, clean::Bool, doctest::Bool, linkcheck::Bool, linkcheck_ignore::Vector{Any}, linkcheck_timeout::Int64, linkcheck_useragent::String, checkdocs::Symbol, checkdocs_ignored_modules::Vector{Module}, doctestfilters::Vector{Regex}, warnonly::Vector{Symbol}, modules::Vector{Module}, pages::Vector{Pair{String, String}}, pagesonly::Bool, expandfirst::Vector{String}, plugins::Vector{Documenter.Plugin}, repo::String, remotes::Dict{Any, Any}, sitename::String, authors::String, version::String, highlightsig::Bool, draft::Bool, meta::Dict{Symbol, Any}, treat_markdown_warnings_as_error::Bool, others::@Kwargs{}) @ Documenter ~/.julia/packages/Documenter/13nbQ/src/documents.jl:474 [3] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{root::String, modules::Vector{Module}, sitename::String, pages::Vector{Pair{String, String}}, build::String}) @ Documenter ~/.julia/packages/Documenter/13nbQ/src/makedocs.jl:275 [4] top-level scope @ ~/.julia/packages/Diversity/CB9lk/test/extras_docs.jl:181 [5] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2252 [inlined] [6] macro expansion @ ~/.julia/packages/Diversity/CB9lk/test/extras_docs.jl:191 [inlined] [7] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:786 [inlined] ERROR: LoadError: Test run finished with errors in expression starting at /home/pkgeval/.julia/packages/Diversity/CB9lk/test/runtests.jl:45 Testing failed after 933.03s ERROR: LoadError: Package Diversity errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/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/v1.14/Pkg/src/Operations.jl:3298 [3] 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/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1671.14s: package tests unexpectedly errored