Package evaluation to test Phylo on Julia 1.14.0-DEV.1808 (1cd77b505e*) started at 2026-02-27T02:13:18.596 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.75s ################################################################################ # Installation # Installing Phylo... Resolving package versions... Installed Rmath_jll ─────────────────── v0.5.1+0 Installed MacroTools ────────────────── v0.5.16 Installed FillArrays ────────────────── v1.16.0 Installed DataStructures ────────────── v0.18.22 Installed HypergeometricFunctions ───── v0.3.28 Installed AliasTables ───────────────── v1.1.3 Installed ArnoldiMethod ─────────────── v0.4.0 Installed InlineStrings ─────────────── v1.4.5 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed RecipesBase ───────────────── v1.3.4 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed StatsBase ─────────────────── v0.34.10 Installed Statistics ────────────────── v1.11.1 Installed DataValueInterfaces ───────── v1.0.0 Installed SentinelArrays ────────────── v1.4.9 Installed StatsAPI ──────────────────── v1.8.0 Installed StaticArraysCore ──────────── v1.4.4 Installed Tokenize ──────────────────── v0.5.29 Installed TableTraitsUtils ──────────── v1.0.2 Installed IrrationalConstants ───────── v0.2.6 Installed Distances ─────────────────── v0.10.12 Installed QuadGK ────────────────────── v2.11.2 Installed StaticArrays ──────────────── v1.9.17 Installed DataValues ────────────────── v0.4.13 Installed StringManipulation ────────── v0.4.4 Installed Requires ──────────────────── v1.3.1 Installed PrecompileTools ───────────── v1.3.3 Installed SimpleTraits ──────────────── v0.9.5 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed IterableTables ────────────── v1.0.0 Installed AutoHashEquals ────────────── v2.2.0 Installed Rmath ─────────────────────── v0.9.0 Installed LogExpFunctions ───────────── v0.3.29 Installed Unitful ───────────────────── v1.28.0 Installed StatsFuns ─────────────────── v1.5.2 Installed Tables ────────────────────── v1.12.1 Installed Distributions ─────────────── v0.25.123 Installed ParserCombinator ──────────── v2.2.1 Installed PtrArrays ─────────────────── v1.4.0 Installed IntervalSets ──────────────── v0.7.13 Installed SpecialFunctions ──────────── v2.7.1 Installed PrettyTables ──────────────── v3.2.3 Installed DataFrames ────────────────── v1.8.1 Installed Reexport ──────────────────── v1.2.2 Installed Phylo ─────────────────────── v0.5.4 Installed Missings ──────────────────── v1.2.0 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed LaTeXStrings ──────────────── v1.4.0 Installed PDMats ────────────────────── v0.11.37 Installed SortingAlgorithms ─────────── v1.2.2 Installed Preferences ───────────────── v1.5.2 Installed Graphs ────────────────────── v1.13.1 Installed Crayons ───────────────────── v4.1.1 Installed RangeArrays ───────────────── v0.3.2 Installed IterTools ─────────────────── v1.10.0 Installed Inflate ───────────────────── v0.1.5 Installed AxisArrays ────────────────── v0.4.8 Installed DocStringExtensions ───────── v0.9.5 Installing 2 artifacts Installed artifact OpenSpecFun 194.9 KiB Installed artifact Rmath 121.9 KiB Updating `~/.julia/environments/v1.14/Project.toml` [aea672f4] + Phylo v0.5.4 Updating `~/.julia/environments/v1.14/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [ec485272] + ArnoldiMethod v0.4.0 [15f4f7f2] + AutoHashEquals v2.2.0 [39de3d68] + AxisArrays v0.4.8 [34da2185] + Compat v4.18.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.8.1 ⌅ [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [e7dc6d0d] + DataValues v0.4.13 [b4f34e82] + Distances v0.10.12 [31c24e10] + Distributions v0.25.123 [ffbed154] + DocStringExtensions v0.9.5 [1a297f60] + FillArrays v1.16.0 ⌃ [86223c79] + Graphs v1.13.1 [34004b35] + HypergeometricFunctions v0.3.28 [d25df0c9] + Inflate v0.1.5 [842dd82b] + InlineStrings v1.4.5 [8197267c] + IntervalSets v0.7.13 [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 [692b3bcd] + JLLWrappers v1.7.1 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [1914dd2f] + MacroTools v0.5.16 [e1d29d7a] + Missings v1.2.0 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.37 [fae87a5f] + ParserCombinator v2.2.1 [aea672f4] + Phylo v0.5.4 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [08abe8d2] + PrettyTables v3.2.3 [43287f4e] + PtrArrays v1.4.0 [1fd47b50] + QuadGK v2.11.2 [b3c3ace0] + RangeArrays v0.3.2 [3cdcf5f2] + RecipesBase v1.3.4 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.9.0 [91c51154] + SentinelArrays v1.4.9 [699a6c99] + SimpleTraits v0.9.5 [a2af1166] + SortingAlgorithms v1.2.2 [276daf66] + SpecialFunctions v2.7.1 [90137ffa] + StaticArrays v1.9.17 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.8.0 [2913bbd2] + StatsBase v0.34.10 [4c63d2b9] + StatsFuns v1.5.2 [892a3eda] + StringManipulation v0.4.4 [3783bdb8] + TableTraits v1.0.1 [382cd787] + TableTraitsUtils v1.0.2 [bd369af6] + Tables v1.12.1 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.28.0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed 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 v1.13.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [de0858da] + Printf v1.11.0 [3fa0cd96] + REPL v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [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 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [4536629a] + OpenBLAS_jll v0.3.30+0 [05823500] + OpenLibm_jll v0.8.7+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [8e850b90] + libblastrampoline_jll v5.15.0+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 9.71s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4788.2 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 4587.3 ms ✓ MacroTools 1705.5 ms ✓ InlineStrings 899.4 ms ✓ Reexport 1071.2 ms ✓ TensorCore 2102.9 ms ✓ IrrationalConstants 944.1 ms ✓ Measures 861.2 ms ✓ DataValueInterfaces 945.3 ms ✓ StatsAPI 2421.8 ms ✓ Format 1303.3 ms ✓ IterTools 1179.1 ms ✓ IntervalSets 1173.1 ms ✓ Inflate 981.4 ms ✓ Contour 1364.0 ms ✓ TranscodingStreams 906.3 ms ✓ LaTeXStrings 1025.6 ms ✓ Glob 1239.7 ms ✓ Statistics 1069.5 ms ✓ StaticArraysCore 1020.8 ms ✓ StableRNGs 1031.1 ms ✓ AutoHashEquals 862.3 ms ✓ PtrArrays 868.1 ms ✓ SimpleBufferStream 1278.1 ms ✓ Grisu 918.5 ms ✓ DataAPI 1295.5 ms ✓ URIs 920.7 ms ✓ InvertedIndices 898.7 ms ✓ BitFlags 932.1 ms ✓ ShiftedArrays 946.7 ms ✓ WinReg 2316.5 ms ✓ FillArrays 900.7 ms ✓ RangeArrays 1329.0 ms ✓ OrderedCollections 3790.2 ms ✓ Tokenize 1179.2 ms ✓ DocStringExtensions 1107.0 ms ✓ Unzip 816.5 ms ✓ IteratorInterfaceExtensions 1953.0 ms ✓ Crayons 1012.4 ms ✓ DelimitedFiles 1074.3 ms ✓ NaNMath 1295.3 ms ✓ Requires 1549.1 ms ✓ ConcurrentUtilities 1907.7 ms ✓ PDMats 990.8 ms ✓ Scratch 33938.6 ms ✓ Unitful 2219.0 ms ✓ SentinelArrays 1173.1 ms ✓ LoggingExtras 3618.7 ms ✓ UnicodeFun 1270.0 ms ✓ Compat 1715.4 ms ✓ ExceptionUnwrapping 1426.6 ms ✓ JLLWrappers 3435.0 ms ✓ StringManipulation 2972.2 ms ✓ RecipesBase 3569.4 ms ✓ SimpleTraits 1059.4 ms ✓ InlineStrings → ParsersExt 2474.3 ms ✓ DataValues 856.4 ms ✓ IntervalSets → IntervalSetsRandomExt 1014.3 ms ✓ CodecZlib 1380.8 ms ✓ Statistics → SparseArraysExt 4044.4 ms ✓ FixedPointNumbers 1568.7 ms ✓ Distances 822.5 ms ✓ IntervalSets → IntervalSetsStatisticsExt 14329.8 ms ✓ StaticArrays 5575.4 ms ✓ ParserCombinator 1018.0 ms ✓ AliasTables 937.2 ms ✓ Showoff 1086.8 ms ✓ Missings 1078.5 ms ✓ PooledArrays 4028.6 ms ✓ OpenSSL 1593.4 ms ✓ FillArrays → FillArraysSparseArraysExt 1017.5 ms ✓ FillArrays → FillArraysStatisticsExt 6129.4 ms ✓ CSTParser 1381.3 ms ✓ LogExpFunctions 887.7 ms ✓ TableTraits 13110.8 ms ✓ CommonMark 1505.4 ms ✓ FillArrays → FillArraysPDMatsExt 1151.4 ms ✓ RelocatableFolders 2314.6 ms ✓ Unitful → PrintfExt 2143.0 ms ✓ Unitful → NaNMathExt 914.7 ms ✓ Compat → CompatLinearAlgebraExt 1556.8 ms ✓ Libffi_jll 1531.7 ms ✓ Xorg_libICE_jll 1564.3 ms ✓ LZO_jll 1567.4 ms ✓ eudev_jll 1529.7 ms ✓ mtdev_jll 1552.5 ms ✓ Bzip2_jll 1578.6 ms ✓ XZ_jll 1557.7 ms ✓ Rmath_jll 1574.2 ms ✓ OpenSpecFun_jll 1430.6 ms ✓ Xorg_xtrans_jll 1722.0 ms ✓ Opus_jll 1534.6 ms ✓ x265_jll 1592.5 ms ✓ fzf_jll 1646.2 ms ✓ libpng_jll 1244.3 ms ✓ EpollShim_jll 1623.2 ms ✓ Libmount_jll 1596.2 ms ✓ libfdk_aac_jll 1512.0 ms ✓ Libuuid_jll 1577.3 ms ✓ FriBidi_jll 1533.8 ms ✓ LERC_jll 1506.1 ms ✓ Git_LFS_jll 1514.5 ms ✓ Xorg_libXau_jll 1530.5 ms ✓ Ogg_jll 1505.8 ms ✓ libevdev_jll 1611.1 ms ✓ OpenSSH_jll 1533.1 ms ✓ LAME_jll 1511.8 ms ✓ Graphite2_jll 1535.9 ms ✓ x264_jll 1597.6 ms ✓ LLVMOpenMP_jll 1566.2 ms ✓ Libiconv_jll 1548.6 ms ✓ MbedTLS_jll 1555.3 ms ✓ libaom_jll 1628.9 ms ✓ Xorg_libXdmcp_jll 1597.9 ms ✓ Expat_jll 1508.9 ms ✓ JpegTurbo_jll 1353.7 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 1598.8 ms ✓ AxisArrays 2791.4 ms ✓ ColorTypes 1320.0 ms ✓ Distances → DistancesSparseArraysExt 4015.0 ms ✓ ArnoldiMethod 1446.0 ms ✓ StaticArrays → StaticArraysStatisticsExt 1653.9 ms ✓ FillArrays → FillArraysStaticArraysExt 1827.1 ms ✓ Tables 1696.5 ms ✓ TableTraitsUtils 3797.0 ms ✓ DataStructures 3073.6 ms ✓ CategoricalArrays 1471.8 ms ✓ Xorg_libSM_jll 1446.5 ms ✓ FreeType2_jll 1624.3 ms ✓ Rmath 4872.3 ms ✓ SpecialFunctions 2373.0 ms ✓ JLFzf 1431.2 ms ✓ libvorbis_jll 1417.2 ms ✓ libinput_jll 1419.4 ms ✓ Pixman_jll 1075.1 ms ✓ StringEncodings 1476.2 ms ✓ GettextRuntime_jll 2075.2 ms ✓ MbedTLS 1507.9 ms ✓ Xorg_libxcb_jll 1413.7 ms ✓ Dbus_jll 1448.7 ms ✓ Git_jll 1469.4 ms ✓ Wayland_jll 1525.6 ms ✓ Ghostscript_jll 1464.9 ms ✓ Libtiff_jll 1231.8 ms ✓ ColorTypes → StyledStringsExt 7657.6 ms ✓ Colors 3607.3 ms ✓ ColorVectorSpace 38454.0 ms ✓ PrettyTables 1569.4 ms ✓ IterableTables 1503.2 ms ✓ SortingAlgorithms 2689.8 ms ✓ QuadGK 39468.1 ms ✓ JuliaFormatter 9784.1 ms ✓ Graphs 1447.9 ms ✓ CategoricalArrays → CategoricalArraysRecipesBaseExt 1049.3 ms ✓ CategoricalArrays → CategoricalArraysSentinelArraysExt 1118.5 ms ✓ CategoricalArrays → CategoricalArraysJSONExt 1556.1 ms ✓ Fontconfig_jll 2167.2 ms ✓ HypergeometricFunctions 2514.3 ms ✓ YAML 1496.7 ms ✓ Glib_jll 24182.5 ms ✓ HTTP 1420.9 ms ✓ Xorg_xcb_util_jll 1430.4 ms ✓ Xorg_libX11_jll 962.0 ms ✓ Git 5959.6 ms ✓ Latexify 1495.1 ms ✓ ColorVectorSpace → SpecialFunctionsExt 8703.4 ms ✓ ColorSchemes 4893.5 ms ✓ StatsBase 77505.5 ms ✓ DataFrames 2927.3 ms ✓ StatsFuns 1393.2 ms ✓ Xorg_xcb_util_renderutil_jll 1503.5 ms ✓ Xorg_xcb_util_wm_jll 1516.5 ms ✓ Xorg_xcb_util_image_jll 1444.9 ms ✓ Xorg_xcb_util_keysyms_jll 1498.7 ms ✓ Xorg_libXfixes_jll 1461.4 ms ✓ Xorg_libXrender_jll 1489.9 ms ✓ Xorg_libXext_jll 1548.5 ms ✓ Xorg_libxkbfile_jll 3783.3 ms ✓ ResearchSoftwareMetadata 2432.6 ms ✓ Latexify → SparseArraysExt 4010.0 ms ✓ Unitful → LatexifyExt 16520.3 ms ✓ PlotUtils 1829.1 ms ✓ PDMats → StatsBaseExt 2031.3 ms ✓ CategoricalArrays → CategoricalArraysStatsBaseExt 7569.1 ms ✓ Latexify → DataFramesExt 4865.8 ms ✓ StatsModels 1470.9 ms ✓ Xorg_xcb_util_cursor_jll 1463.1 ms ✓ Xorg_libXcursor_jll 1560.8 ms ✓ Xorg_libXrandr_jll 1441.8 ms ✓ Xorg_libXinerama_jll 1391.9 ms ✓ Xorg_libXi_jll 1593.8 ms ✓ Cairo_jll 1392.7 ms ✓ Libglvnd_jll 1375.5 ms ✓ Xorg_xkbcomp_jll 9088.0 ms ✓ PlotThemes 8894.5 ms ✓ RecipesPipeline 9869.8 ms ✓ Distributions 12689.5 ms ✓ RCall 1662.7 ms ✓ HarfBuzz_jll 1379.3 ms ✓ Xorg_xkeyboard_config_jll 3696.7 ms ✓ Distributions → DistributionsTestExt 21515.1 ms ✓ Phylo 11443.3 ms ✓ RCall → RCallAxisArraysExt 1731.5 ms ✓ libass_jll 1646.1 ms ✓ Pango_jll 1581.9 ms ✓ xkbcommon_jll 16728.2 ms ✓ Phylo → PhyloRCallExt 1749.2 ms ✓ FFMPEG_jll 1571.8 ms ✓ Vulkan_Loader_jll 1665.3 ms ✓ libdecor_jll 1198.4 ms ✓ FFMPEG 1748.1 ms ✓ Qt6Base_jll 1671.6 ms ✓ GLFW_jll 1833.0 ms ✓ Qt6ShaderTools_jll 1799.8 ms ✓ GR_jll 1814.4 ms ✓ Qt6Declarative_jll 1744.3 ms ✓ Qt6Wayland_jll 6877.9 ms ✓ GR 104481.9 ms ✓ Plots 20244.3 ms ✓ Plots → UnitfulExt 218 dependencies successfully precompiled in 860 seconds. 46 already precompiled. Precompilation completed after 1017.32s ################################################################################ # Testing # Testing Phylo Status `/tmp/jl_EJMog1/Project.toml` [39de3d68] AxisArrays v0.4.8 [a93c6f00] DataFrames v1.8.1 ⌅ [864edb3b] DataStructures v0.18.22 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.123 [d7ba0133] Git v1.5.0 ⌃ [86223c79] Graphs v1.13.1 [1c8ee90f] IterableTables v1.0.0 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [e1d29d7a] Missings v1.2.0 [fae87a5f] ParserCombinator v2.2.1 [aea672f4] Phylo v0.5.4 [91a5bcdd] Plots v1.41.6 [6f49c342] RCall v0.14.12 [3cdcf5f2] RecipesBase v1.3.4 [58378933] ResearchSoftwareMetadata v0.1.5 [699a6c99] SimpleTraits v0.9.5 [10745b16] Statistics v1.11.1 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.28.0 [56ddb016] Logging v1.11.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_EJMog1/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [ec485272] ArnoldiMethod v0.4.0 [15f4f7f2] AutoHashEquals v2.2.0 [39de3d68] AxisArrays v0.4.8 [d1d4a3ce] BitFlags v0.1.9 [00ebfdb7] CSTParser v3.4.3 [324d7699] CategoricalArrays v1.0.2 [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 ⌅ [a80b9123] CommonMark v0.8.16 [34da2185] Compat v4.18.1 [f0e56b4a] ConcurrentUtilities v2.5.1 [8f4d0f93] Conda v1.10.3 [d38c429a] Contour v0.6.3 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.8.1 ⌅ [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 v0.25.123 [ffbed154] DocStringExtensions v0.9.5 [460bff9d] ExceptionUnwrapping v0.1.11 [c87230d0] FFMPEG v0.4.5 [1a297f60] FillArrays v1.16.0 [53c48c17] FixedPointNumbers v0.8.5 [1fa38f19] Format v1.3.7 [28b8d3ca] GR v0.73.22 [d7ba0133] Git v1.5.0 [c27321d9] Glob v1.4.0 ⌃ [86223c79] Graphs v1.13.1 [42e2da0e] Grisu v1.0.2 [cd3eb016] HTTP v1.10.19 [34004b35] HypergeometricFunctions v0.3.28 [d25df0c9] Inflate v0.1.5 [842dd82b] InlineStrings v1.4.5 [8197267c] IntervalSets v0.7.13 [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 v1.7.1 ⌅ [682c06a0] JSON v0.21.4 ⌅ [98e50ef6] JuliaFormatter v1.0.62 [b964fa9f] LaTeXStrings v1.4.0 [23fbe1c1] Latexify v0.16.10 [2ab3a3ac] LogExpFunctions v0.3.29 [e6f89c97] LoggingExtras v1.2.0 [1914dd2f] MacroTools v0.5.16 [739be429] MbedTLS v1.1.10 [442fdcdd] Measures v0.3.3 [e1d29d7a] Missings v1.2.0 [77ba4419] NaNMath v1.1.3 [4d8831e6] OpenSSL v1.6.1 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.37 [fae87a5f] ParserCombinator v2.2.1 [69de0a69] Parsers v2.8.3 [aea672f4] Phylo v0.5.4 [ccf2f8ad] PlotThemes v3.3.0 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Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... [ Info: Potentially missing tests: - Branch.jl - Node.jl [ Info: Running tests for files: = API.jl = Interface.jl = Iterators.jl = LinkTree.jl = Phylo.jl = RecursiveTree.jl = Tree.jl = TreeSet.jl = metrics.jl = newick.jl = nexus.jl = plot.jl = rand.jl = routes.jl = show.jl = trim.jl [ Info: Running tests... * Testing API.jl ... * Testing Interface.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' ┌ Warning: Wrong number of roots for OneRoot tree (7) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/LinkTree.jl:250 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/LinkTree.jl:250 ┌ Warning: Wrong number of roots for OneRoot tree (7) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:151 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:151 * Testing Iterators.jl ... * Testing LinkTree.jl ... * Testing Phylo.jl ... * Testing RecursiveTree.jl ... ┌ Warning: Mismatch between branch id 7 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:221 ┌ Warning: Mismatch between branch id 7 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between branch id 8 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between node name Node 5 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:176 ┌ Warning: Mismatch between branch id 8 and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:229 ┌ Warning: Mismatch between node name Dog and its connections └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/RecursiveTree.jl:184 * Testing Tree.jl ... ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: Wrong number of roots for OneRoot tree (2) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: LeafInfo names do not match actual leaves of tree └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:202 ┌ Warning: Wrong number of roots for OneRoot tree (3) └ @ Phylo ~/.julia/packages/Phylo/sQ0CW/src/Tree.jl:215 BinaryTree(): Test Failed at /home/pkgeval/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:115 Expression: all(a.data .== b.data) Evaluated: all(Bool[1, 1, 1, 1, 1, 1, 1, 1, 1, 1 … 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]) Stacktrace: [1] top-level scope @ ~/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:71 [2] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2243 [inlined] [3] macro expansion @ ~/.julia/packages/Phylo/sQ0CW/test/test_Tree.jl:115 [inlined] [4] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:781 [inlined] * Testing TreeSet.jl ... * Testing metrics.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' * Testing newick.jl ... [ Info: Created a tree called 'Tree' [ Info: Created a tree called 'Tree' * Testing nexus.jl ... [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' [ Info: Created a tree called 'TREE1' [ Info: Created a tree called 'TREE2' * Testing plot.jl ... * Testing rand.jl ... * Testing routes.jl ... * Testing show.jl ... ┌ Info: These tests only check that the show() commands └ do not give warnings or errors, not that they are correct! * Testing trim.jl ... [ Info: Running tests for extensions: = PhyloRCallExt.jl [ Info: Running extension tests... * Testing PhyloRCallExt.jl extension... ┌ 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/FKyW5/src/io.jl:166 Test Summary: | Pass Fail Total Time Phylo.jl | 1398 1 1399 6m50.1s t = API | 20 20 7.5s t = Interface | 390 390 1m43.6s t = Iterators | 74 74 11.8s t = LinkTree | 11 11 6.2s t = Phylo | 9 9 2.9s t = RecursiveTree | 71 71 11.8s t = Tree | 67 1 68 30.5s NamedBinaryTree() | 34 34 16.0s BinaryTree() | 33 1 34 14.4s t = TreeSet | 87 87 10.0s t = metrics | 6 6 1.9s t = newick | 136 136 39.4s t = nexus | 114 114 34.4s t = plot | 4 4 1m09.5s t = rand | 52 52 17.6s t = routes | 144 144 23.3s t = show | 202 202 17.5s t = trim | 10 10 12.6s t = PhyloRCallExt | 0 8.2s RNG of the outermost testset: Xoshiro(0x9951797c85a704f1, 0xb9d66be14dfba82b, 0xb170153285fd9556, 0xe90a07f7bdd1fd77, 0x9d4b5ee33e4bd661) ERROR: LoadError: Some tests did not pass: 1398 passed, 1 failed, 0 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/Phylo/sQ0CW/test/runtests.jl:10 Testing failed after 451.63s ERROR: LoadError: Package Phylo 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:3138 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3003 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:586 [5] kwcall(::@NamedTuple{julia_args::Cmd, io::IOContext{IO}}, ::typeof(Pkg.API.test), ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:562 [6] 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 [7] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:161 [8] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [9] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [inlined] [10] kwcall(::@NamedTuple{julia_args::Cmd}, ::typeof(Pkg.API.test), pkg::String) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [11] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [12] include(mod::Module, _path::String) @ Base ./Base.jl:323 [13] exec_options(opts::Base.JLOptions) @ Base ./client.jl:344 [14] _start() @ Base ./client.jl:585 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1541.82s: package has test failures