Package evaluation to test Phylo on Julia 1.14.0-DEV.1674 (5735163b34*) started at 2026-02-04T01:27:19.919 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 11.18s ################################################################################ # Installation # Installing Phylo... Resolving package versions... Installed MacroTools ────────────────── v0.5.16 Installed FillArrays ────────────────── v1.16.0 Installed Rmath_jll ─────────────────── v0.5.1+0 Installed HypergeometricFunctions ───── v0.3.28 Installed DataStructures ────────────── v0.18.22 Installed AliasTables ───────────────── v1.1.3 Installed InlineStrings ─────────────── v1.4.5 Installed ArnoldiMethod ─────────────── v0.4.0 Installed Compat ────────────────────── v4.18.1 Installed OrderedCollections ────────── v1.8.1 Installed DataAPI ───────────────────── v1.16.0 Installed InvertedIndices ───────────── v1.3.1 Installed StatsBase ─────────────────── v0.34.10 Installed Statistics ────────────────── v1.11.1 Installed RecipesBase ───────────────── v1.3.4 Installed IteratorInterfaceExtensions ─ v1.0.0 Installed DataValueInterfaces ───────── v1.0.0 Installed StatsAPI ──────────────────── v1.8.0 Installed SentinelArrays ────────────── v1.4.9 Installed StaticArraysCore ──────────── v1.4.4 Installed Tokenize ──────────────────── v0.5.29 Installed TableTraitsUtils ──────────── v1.0.2 Installed StaticArrays ──────────────── v1.9.16 Installed PrecompileTools ───────────── v1.3.3 Installed IrrationalConstants ───────── v0.2.6 Installed Distances ─────────────────── v0.10.12 Installed OpenSpecFun_jll ───────────── v0.5.6+0 Installed QuadGK ────────────────────── v2.11.2 Installed SimpleTraits ──────────────── v0.9.5 Installed Requires ──────────────────── v1.3.1 Installed StringManipulation ────────── v0.4.2 Installed DataValues ────────────────── v0.4.13 Installed AutoHashEquals ────────────── v2.2.0 Installed IterableTables ────────────── v1.0.0 Installed Rmath ─────────────────────── v0.9.0 Installed LogExpFunctions ───────────── v0.3.29 Installed StatsFuns ─────────────────── v1.5.2 Installed Unitful ───────────────────── v1.28.0 Installed PrettyTables ──────────────── v3.1.2 Installed Distributions ─────────────── v0.25.123 Installed Tables ────────────────────── v1.12.1 Installed Reexport ──────────────────── v1.2.2 Installed PtrArrays ─────────────────── v1.3.0 Installed IntervalSets ──────────────── v0.7.13 Installed Missings ──────────────────── v1.2.0 Installed SpecialFunctions ──────────── v2.6.1 Installed DataFrames ────────────────── v1.8.1 Installed Preferences ───────────────── v1.5.1 Installed ParserCombinator ──────────── v2.2.1 Installed PooledArrays ──────────────── v1.4.3 Installed JLLWrappers ───────────────── v1.7.1 Installed TableTraits ───────────────── v1.0.1 Installed Phylo ─────────────────────── v0.5.4 Installed PDMats ────────────────────── v0.11.37 Installed LaTeXStrings ──────────────── v1.4.0 Installed Crayons ───────────────────── v4.1.1 Installed SortingAlgorithms ─────────── v1.2.2 Installed IterTools ─────────────────── v1.10.0 Installed AxisArrays ────────────────── v0.4.8 Installed RangeArrays ───────────────── v0.3.2 Installed Graphs ────────────────────── v1.13.1 Installed DocStringExtensions ───────── v0.9.5 Installed Inflate ───────────────────── v0.1.5 Installing 2 artifacts Installed artifact Rmath 121.9 KiB Installed artifact OpenSpecFun 194.9 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 v1.5.1 [08abe8d2] + PrettyTables v3.1.2 [43287f4e] + PtrArrays v1.3.0 [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 v2.6.1 [90137ffa] + StaticArrays v1.9.16 [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 v0.4.2 [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 9.16s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling packages... 4698.1 ms ✓ TestEnv 1 dependency successfully precompiled in 5 seconds. 27 already precompiled. Precompiling package dependencies... Precompiling packages... 5119.9 ms ✓ MacroTools 2119.2 ms ✓ InlineStrings 1229.8 ms ✓ Reexport 976.5 ms ✓ TensorCore 1998.7 ms ✓ IrrationalConstants 914.2 ms ✓ Measures 791.0 ms ✓ DataValueInterfaces 854.5 ms ✓ StatsAPI 2133.8 ms ✓ Format 1092.9 ms ✓ IterTools 992.0 ms ✓ IntervalSets 973.0 ms ✓ Inflate 896.3 ms ✓ Contour 1225.6 ms ✓ TranscodingStreams 1206.6 ms ✓ LaTeXStrings 989.3 ms ✓ Glob 1376.3 ms ✓ Statistics 947.6 ms ✓ StaticArraysCore 908.3 ms ✓ StableRNGs 906.8 ms ✓ AutoHashEquals 800.2 ms ✓ PtrArrays 793.9 ms ✓ SimpleBufferStream 1171.2 ms ✓ Grisu 882.9 ms ✓ DataAPI 1209.9 ms ✓ URIs 869.5 ms ✓ InvertedIndices 856.6 ms ✓ BitFlags 932.0 ms ✓ ShiftedArrays 835.7 ms ✓ WinReg 2218.9 ms ✓ FillArrays 854.2 ms ✓ RangeArrays 1276.8 ms ✓ OrderedCollections 3342.1 ms ✓ Tokenize 1098.7 ms ✓ DocStringExtensions 1057.3 ms ✓ Unzip 762.2 ms ✓ IteratorInterfaceExtensions 1863.5 ms ✓ Crayons 1004.8 ms ✓ DelimitedFiles 1012.2 ms ✓ NaNMath 1181.1 ms ✓ Requires 1440.0 ms ✓ ConcurrentUtilities 1876.7 ms ✓ PDMats 979.3 ms ✓ Scratch 33715.2 ms ✓ Unitful 2156.2 ms ✓ SentinelArrays 1131.5 ms ✓ LoggingExtras 3543.7 ms ✓ UnicodeFun 1191.1 ms ✓ Compat 1657.0 ms ✓ ExceptionUnwrapping 1249.3 ms ✓ JLLWrappers 3300.4 ms ✓ StringManipulation 2869.7 ms ✓ RecipesBase 3365.4 ms ✓ SimpleTraits 1007.0 ms ✓ InlineStrings → ParsersExt 1868.0 ms ✓ DataValues 784.9 ms ✓ IntervalSets → IntervalSetsRandomExt 978.1 ms ✓ CodecZlib 1308.0 ms ✓ Statistics → SparseArraysExt 3982.3 ms ✓ FixedPointNumbers 1509.8 ms ✓ Distances 778.1 ms ✓ IntervalSets → IntervalSetsStatisticsExt 14058.9 ms ✓ StaticArrays 5477.2 ms ✓ ParserCombinator 981.0 ms ✓ AliasTables 929.8 ms ✓ Showoff 1017.8 ms ✓ Missings 1027.8 ms ✓ PooledArrays 3948.3 ms ✓ OpenSSL 1556.5 ms ✓ FillArrays → FillArraysSparseArraysExt 1010.4 ms ✓ FillArrays → FillArraysStatisticsExt 6238.2 ms ✓ CSTParser 1386.1 ms ✓ LogExpFunctions 807.2 ms ✓ TableTraits 11743.4 ms ✓ CommonMark 1090.2 ms ✓ FillArrays → FillArraysPDMatsExt 834.8 ms ✓ RelocatableFolders 1557.2 ms ✓ Unitful → PrintfExt 1703.9 ms ✓ Unitful → NaNMathExt 812.3 ms ✓ Compat → CompatLinearAlgebraExt 1286.4 ms ✓ Libffi_jll 1382.2 ms ✓ Xorg_libICE_jll 1927.2 ms ✓ LZO_jll 1430.2 ms ✓ eudev_jll 1424.1 ms ✓ mtdev_jll 1442.0 ms ✓ Bzip2_jll 1450.3 ms ✓ XZ_jll 1416.2 ms ✓ Rmath_jll 1446.4 ms ✓ OpenSpecFun_jll 1262.2 ms ✓ Xorg_xtrans_jll 1426.8 ms ✓ Opus_jll 1439.3 ms ✓ x265_jll 1495.7 ms ✓ fzf_jll 1349.6 ms ✓ libpng_jll 1137.5 ms ✓ EpollShim_jll 1323.5 ms ✓ Libmount_jll 1511.2 ms ✓ libfdk_aac_jll 1435.1 ms ✓ Libuuid_jll 1435.3 ms ✓ FriBidi_jll 1421.3 ms ✓ LERC_jll 1331.8 ms ✓ Git_LFS_jll 1199.8 ms ✓ Xorg_libXau_jll 1218.4 ms ✓ Ogg_jll 1167.4 ms ✓ libevdev_jll 1408.3 ms ✓ OpenSSH_jll 1300.3 ms ✓ LAME_jll 1543.7 ms ✓ Graphite2_jll 1967.1 ms ✓ x264_jll 1793.4 ms ✓ LLVMOpenMP_jll 1552.4 ms ✓ Libiconv_jll 1458.5 ms ✓ MbedTLS_jll 1309.7 ms ✓ libaom_jll 1468.4 ms ✓ Xorg_libXdmcp_jll 1427.4 ms ✓ Expat_jll 1498.3 ms ✓ JpegTurbo_jll 1369.0 ms ✓ IntervalSets → IntervalSetsRecipesBaseExt 1571.5 ms ✓ AxisArrays 2561.5 ms ✓ ColorTypes 1253.4 ms ✓ Distances → DistancesSparseArraysExt 4105.1 ms ✓ ArnoldiMethod 1377.3 ms ✓ StaticArrays → StaticArraysStatisticsExt 1523.5 ms ✓ FillArrays → FillArraysStaticArraysExt 1853.1 ms ✓ Tables 1242.1 ms ✓ TableTraitsUtils 3794.0 ms ✓ DataStructures 3188.1 ms ✓ CategoricalArrays 1381.0 ms ✓ Xorg_libSM_jll 1328.3 ms ✓ FreeType2_jll 1480.7 ms ✓ Rmath 4625.3 ms ✓ SpecialFunctions 2305.3 ms ✓ JLFzf 1482.0 ms ✓ libvorbis_jll 1337.7 ms ✓ libinput_jll 1413.9 ms ✓ Pixman_jll 1131.7 ms ✓ StringEncodings 1560.6 ms ✓ GettextRuntime_jll 1949.1 ms ✓ MbedTLS 1450.9 ms ✓ Xorg_libxcb_jll 1377.9 ms ✓ Dbus_jll 1431.7 ms ✓ Git_jll 1338.3 ms ✓ Wayland_jll 1426.7 ms ✓ Ghostscript_jll 1347.2 ms ✓ Libtiff_jll 1214.0 ms ✓ ColorTypes → StyledStringsExt 7520.0 ms ✓ Colors 3678.9 ms ✓ ColorVectorSpace 34283.9 ms ✓ PrettyTables 1156.4 ms ✓ IterableTables 1397.8 ms ✓ SortingAlgorithms 2499.2 ms ✓ QuadGK 39766.9 ms ✓ JuliaFormatter 9384.4 ms ✓ Graphs 1393.9 ms ✓ CategoricalArrays → CategoricalArraysRecipesBaseExt 995.1 ms ✓ CategoricalArrays → CategoricalArraysSentinelArraysExt 1193.2 ms ✓ CategoricalArrays → CategoricalArraysJSONExt 1538.4 ms ✓ Fontconfig_jll 1994.1 ms ✓ HypergeometricFunctions 2386.9 ms ✓ YAML 1429.1 ms ✓ Glib_jll 22558.1 ms ✓ HTTP 1422.4 ms ✓ Xorg_xcb_util_jll 1306.0 ms ✓ Xorg_libX11_jll 910.0 ms ✓ Git 5468.7 ms ✓ Latexify 1256.7 ms ✓ ColorVectorSpace → SpecialFunctionsExt 7967.2 ms ✓ ColorSchemes 4396.3 ms ✓ StatsBase 79578.7 ms ✓ DataFrames 2877.7 ms ✓ StatsFuns 1366.3 ms ✓ Xorg_xcb_util_renderutil_jll 1341.5 ms ✓ Xorg_xcb_util_wm_jll 1365.0 ms ✓ Xorg_xcb_util_image_jll 1253.4 ms ✓ Xorg_xcb_util_keysyms_jll 1208.5 ms ✓ Xorg_libXfixes_jll 1290.6 ms ✓ Xorg_libXrender_jll 1121.6 ms ✓ Xorg_libXext_jll 1263.5 ms ✓ Xorg_libxkbfile_jll 3711.5 ms ✓ ResearchSoftwareMetadata 2397.4 ms ✓ Latexify → SparseArraysExt 4172.0 ms ✓ Unitful → LatexifyExt 16556.4 ms ✓ PlotUtils 1825.2 ms ✓ PDMats → StatsBaseExt 1925.9 ms ✓ CategoricalArrays → CategoricalArraysStatsBaseExt 7772.4 ms ✓ Latexify → DataFramesExt 4735.9 ms ✓ StatsModels 1352.0 ms ✓ Xorg_xcb_util_cursor_jll 1411.4 ms ✓ Xorg_libXcursor_jll 1321.5 ms ✓ Xorg_libXrandr_jll 1411.1 ms ✓ Xorg_libXinerama_jll 1330.8 ms ✓ Xorg_libXi_jll 1380.9 ms ✓ Cairo_jll 1322.0 ms ✓ Libglvnd_jll 1334.3 ms ✓ Xorg_xkbcomp_jll 8879.7 ms ✓ PlotThemes 8402.9 ms ✓ RecipesPipeline 9286.2 ms ✓ Distributions 10945.5 ms ✓ RCall 1396.7 ms ✓ HarfBuzz_jll 1172.9 ms ✓ Xorg_xkeyboard_config_jll 3210.5 ms ✓ Distributions → DistributionsTestExt 18944.8 ms ✓ Phylo 10810.1 ms ✓ RCall → RCallAxisArraysExt 1506.1 ms ✓ libass_jll 1632.1 ms ✓ Pango_jll 1473.9 ms ✓ xkbcommon_jll 16153.2 ms ✓ Phylo → PhyloRCallExt 1800.2 ms ✓ FFMPEG_jll 1437.7 ms ✓ Vulkan_Loader_jll 1632.7 ms ✓ libdecor_jll 1045.6 ms ✓ FFMPEG 1712.6 ms ✓ Qt6Base_jll 1617.9 ms ✓ GLFW_jll 1566.6 ms ✓ Qt6ShaderTools_jll 1686.6 ms ✓ GR_jll 1705.0 ms ✓ Qt6Declarative_jll 1720.6 ms ✓ Qt6Wayland_jll 6386.6 ms ✓ GR 101236.4 ms ✓ Plots 20061.3 ms ✓ Plots → UnitfulExt 218 dependencies successfully precompiled in 822 seconds. 46 already precompiled. Precompilation completed after 959.41s ################################################################################ # Testing # Testing Phylo Status `/tmp/jl_MmK5fE/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 v1.41.4 [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_MmK5fE/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 v2.5.0 [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 v1.1.9 [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, 0, 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:2244 [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:782 [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 6m02.4s t = API | 20 20 5.7s t = Interface | 390 390 1m29.4s t = Iterators | 74 74 10.2s t = LinkTree | 11 11 5.3s t = Phylo | 9 9 2.5s t = RecursiveTree | 71 71 10.4s t = Tree | 67 1 68 26.8s NamedBinaryTree() | 34 34 13.8s BinaryTree() | 33 1 34 12.8s t = TreeSet | 87 87 9.4s t = metrics | 6 6 1.6s t = newick | 136 136 33.8s t = nexus | 114 114 32.7s t = plot | 4 4 1m05.2s t = rand | 52 52 14.1s t = routes | 144 144 20.9s t = show | 202 202 15.1s t = trim | 10 10 10.8s t = PhyloRCallExt | 0 7.0s 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 399.4s 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:3122 [3] test @ /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:2987 [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:572 [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:548 [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:309 [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 1454.75s: package has test failures